The mtDNA variation of 321 individuals from 17 Native American populations was examined by high-resolution restriction endonuclease analysis. All mtDNAs were amplified from a variety of sources by using PCR. The mtDNA of a subset of 38 of these individuals was also analyzed by D-loop sequencing. The resulting data were combined with previous mtDNA data from five other Native American tribes, as well as with data from a variety of Asian populations, and were used to deduce the phylogenetic relationships between mtDNAs and to estimate sequence divergences. This analysis revealed the presence of four haplotype groups (haplogroups A, B, C, and D) in the Amerind, but only one haplogroup (A) in the Na-Dene, and confirmed the independent origins of the Amerinds and the Na-Dene. Further, each haplogroup appeared to have been founded by a single mtDNA haplotype, a result which is consistent with a hypothesized founder effect. Most of the variation within haplogroups was tribal specific, that is, it occurred as tribal private polymorphisms. These observations suggest that the process of tribalization began early in the history of the Amerinds, with relatively little intertribal genetic exchange occurring subsequently. The sequencing of 341 nucleotides in the mtDNA D-loop revealed that the D-loop sequence variation correlated strongly with the four haplogroups defined by restriction analysis, and it indicated that the D-loop variation, like the haplotype variation, arose predominantly after the migration of the ancestral Amerinds across the Bering land bridge.
We analyzed mRNA expression of the flt3 gene in 30 patients with acute myeloid leukemia (AML) and 50 with acute lymphoblastic leukemia (ALL). Using reverse transcriptase-polymerase chain reaction (RT-PCR), expression of flt3 was observed in 61 patients; 22 (73%) with AML and 39 (78%) with ALL. Among these, five patients with AML (one M2, two M4, and two M5) showed unexpected longer transcripts with a primer combination which could amplify the transmembrane (TM) domain through the juxtamembrane (JM) domain. For those patients who expressed flt3 mRNA, the extracellular domain of the flt3 gene was also examined by RT-PCR, but no length abnormality was seen in this region. We further analyzed the TM domain through the second tyrosine kinase domain by genomic amplifications. The five patients who showed aberrant flt3 transcripts exhibited abnormal longer PCR products in addition to the germline products at a region corresponding to the JM through the first TK (TK1) domains. Sequence analyses of the abnormal RT-PCR products demonstrated that partial sequences were tandemly duplicated. Because all these altered transcripts were in-frame, deduced protein products could be expected. Sequence analyses of the genomic DNA revealed that three of the five patients showed a simple internal duplication within exon 11; one had an internal duplication (26 bp) with a 4-bp insertion; and in the fifth patient, a 136-bp sequence from the 3' part of exon 11 to intron 11 and the first 16-bp sequence of exon 12 were each duplicated with 1-bp insertion. In order to confirm the tumor specificity of these alterations, DNA samples obtained at complete remission were also analyzed in the three patients harboring an flt3 duplication, but no abnormal PCR product other than germline was detected in any of the samples. Our results suggest that an internal tandem duplication at the JM/TK1 domains of the flt3 gene is a somatic change detected preferentially in AML, possibly containing a monocytic component.
König's lemma is a fundamental result about trees with countless applications in mathematics and computer science. In contrapositive form, it states that if a tree is finitely branching and well-founded (i.e. has no infinite paths), then it is finite. We present a coalgebraic version of König's lemma featuring two dimensions of generalization: from finitely branching trees to coalgebras for a finitary endofunctor H, and from the base category of sets to a locally finitely presentable category C, such as the category of posets, nominal sets, or convex sets. Our coalgebraic König's lemma states that, under mild assumptions on C and H, every well-founded coalgebra for H is the directed join of its well-founded subcoalgebras with finitely generated state space -- in particular, the category of well-founded coalgebras is locally presentable. As applications, we derive versions of König's lemma for graphs in a topos as well as for nominal and convex transition systems. Additionally, we show that the key construction underlying the proof gives rise to two simple constructions of the initial algebra (equivalently, the final recursive coalgebra) for the functor H: The initial algebra is bot
Logic programs with aggregates (LPA) are one of the major linguistic extensions to Logic Programming (LP). In this work, we propose a generalization of the notions of unfounded set and well-founded semantics for programs with monotone and antimonotone aggregates (LPAma programs). In particular, we present a new notion of unfounded set for LPAma programs, which is a sound generalization of the original definition for standard (aggregate-free) LP. On this basis, we define a well-founded operator for LPAma programs, the fixpoint of which is called well-founded model (or well-founded semantics) for LPAma programs. The most important properties of unfounded sets and the well-founded semantics for standard LP are retained by this generalization, notably existence and uniqueness of the well-founded model, together with a strong relationship to the answer set semantics for LPAma programs. We show that one of the D-well-founded semantics, defined by Pelov, Denecker, and Bruynooghe for a broader class of aggregates using approximating operators, coincides with the well-founded model as defined in this work on LPAma programs. We also discuss some complexity issues, most importantly we give a
Runaway stars with peculiar high velocities can generate stellar bow shocks. Only a few bow shocks show clear radio emission. Our goal is to identify and characterize new stellar bow shocks around O and Be runaway stars in the infrared (IR), and to study their possible radio emission and nature. Our input data is a catalog of O and Be runaways compiled using Gaia DR3. We used WISE IR images to search for bow shocks around these runaways, Gaia DR3 data to determine the actual motion of the runaway stars corrected for interstellar medium (ISM) motion caused by Galactic rotation, and archival radio data to search for emission signatures. We finally explored the radio detectability of these sources under thermal and nonthermal scenarios. We found 9 new stellar bow shock candidates, 3 new bubble candidates, and 1 intermediate structure candidate. One of them is an in situ bow shock candidate. We also found 17 already known bow shocks in our sample, though we discarded one, and 62 miscellaneous sources showing some IR emission around the runaways. We geometrically characterized the sources in IR using the WISE-4 band and estimated the ISM density at the bow shock positions, obtaining med
The gravity model is a mathematical model that applies Newton's universal law of gravitation to socio-economic transport phenomena and has been widely used to describe world trade, intercity traffic flows, and business transactions for more than several decades. However, its strong nonlinearity and diverse network topology make a theoretical analysis difficult, and only a short history of studies on its stability exist. In this study, the stability of gravity models defined on networks with few nodes is analyzed in detail using numerical simulations. It was found that, other than the previously known transition of stationary solutions from a unique diffusion solution to multiple localized solutions, parameter regions exist where periodic solutions with the same repeated motions and chaotic solutions with no periods are realized. The smallest network with chaotic solutions was found to be a ring with seven nodes, which produced a new type of chaotic solution in the form of a mixture of right and left periodic solutions.
In this paper, a generalized version of the von Neumann universe known as the total universe is proposed to formally introduce non-well-founded sets that include infinitons, semi-infinitons and quasi-infinitons in Russell's paradox. All three infinitons are part of infinitely generated sets that are generators of non-well-founded sets. Combining the well-founded sets with the non-well-founded sets, the total universe is a model of ZF minus the axiom of regularity and free of Russell's paradox. The axiom of regularity can not define the well-founded sets and is invalid in any system consistent with ZF set theory.
The fraction of white dwarfs found in wide binaries is estimated by cross referencing a catalogue of wide binaries with catalogues photometrically determined white-dwarf candidates and spectroscopically confirmed white dwarf stars. The wide-binary fraction of white dwarfs with hydrogen-dominated atmospheres is about 5%, but the fraction of white dwarfs with helium or carbon-dominated atmospheres is significantly larger. Using spectroscopic classifications, the binary fraction of DA white dwarfs is determined to be $0.063\pm0.002$ and for non-DA white dwarfs is larger at $0.080\pm0.004$.
Strongly regular graphs (SRGs) are highly symmetric combinatorial objects, with connections to many areas of mathematics including finite fields, finite geometries, and number theory. One can construct an SRG via the Cayley Graph of a regular partial difference set (PDS). Local search is a common class of search algorithm that iteratively adjusts a state to (locally) minimize an error function. In this work, we use local search to find PDSs. We found PDSs with 62 different parameter values in 1254 nonisomorphic groups of orders at most 147. Many of these PDSs replicate known results. In two cases, (144,52,16,20) and (147,66,25,33), the PDSs found give the first known construction of SRGs with these parameters. In some other cases, the SRG was already known but a PDS in that group was unknown. This work also corroborates the existence of (64,18,2,6) PDSs in precisely 73 groups of order 64.
We characterize well-founded algebraic lattices by means of forbidden subsemilattices of the join-semilattice made of their compact elements. More specifically, we show that an algebraic lattice $L$ is well-founded if and only if $K(L)$, the join-semilattice of compact elements of $L$, is well-founded and contains neither $[ω]^{<ω}$, nor $\underlineΩ(ω^*)$ as a join-subsemilattice. As an immediate corollary, we get that an algebraic modular lattice $L$ is well-founded if and only if $K(L)$ is well-founded and contains no infinite independent set. If $K(L)$ is a join-subsemilattice of $I_{<ω}(Q)$, the set of finitely generated initial segments of a well-founded poset $Q$, then $L$ is well-founded if and only if $K(L)$ is well-quasi-ordered.
Much work has been done on extending the well-founded semantics to general disjunctive logic programs and various approaches have been proposed. However, these semantics are different from each other and no consensus is reached about which semantics is the most intended. In this paper we look at disjunctive well-founded reasoning from different angles. We show that there is an intuitive form of the well-founded reasoning in disjunctive logic programming which can be characterized by slightly modifying some exisitng approaches to defining disjunctive well-founded semantics, including program transformations, argumentation, unfounded sets (and resolution-like procedure). We also provide a bottom-up procedure for this semantics. The significance of our work is not only in clarifying the relationship among different approaches, but also shed some light on what is an intended well-founded semantics for disjunctive logic programs.
This paper studies fundamental questions concerning category-theoretic models of induction and recursion. We are concerned with the relationship between well-founded and recursive coalgebras for an endofunctor. For monomorphism preserving endofunctors on complete and well-powered categories every coalgebra has a well-founded part, and we provide a new, shorter proof that this is the coreflection in the category of all well-founded coalgebras. We present a new more general proof of Taylor's General Recursion Theorem that every well-founded coalgebra is recursive, and we study under which hypothesis the converse holds. In addition, we present a new equivalent characterization of well-foundedness: a coalgebra is well-founded iff it admits a coalgebra-to-algebra morphism to the initial algebra.
A relevant fraction of massive stars are runaway stars. These stars move with a significant peculiar velocity with respect to their environment. We aim to discover and characterize the population of massive and early-type runaway stars in the GOSC and BeSS catalogs using Gaia DR3 astrometric data. We present a 2-dimensional method in the velocity space to discover runaway stars as those that deviate significantly from the velocity distribution of field stars, which are considered to follow the Galactic rotation curve. We found 106 O runaway stars, 42 of which were not previously identified as runaways. We found 69 Be runaway stars, 47 of which were not previously identified as runaways. The dispersion of runaway stars is a few times higher in Z and b than that of field stars. This is explained by the ejections they underwent when they became runaways. The percentage of runaways is 25.4% for O-type stars, and it is 5.2% for Be-type stars. In addition, we conducted simulations in 3 dimensions for our catalogs. They revealed that these percentages could increase to ~30% and ~6.7%, respectively. Our runaway stars include seven X-ray binaries and one gamma-ray binary. Moreover, we obtai
The shift from outcrossing to self-fertilization is among the most common transitions in plants. Until recently, however, a genome-wide view of this transition has been obscured by a dearth of appropriate data and the lack of appropriate population genomic methods to interpret such data. Here, we present novel analyses detailing the origin of the selfing species, Capsella rubella, which recently split from its outcrossing sister, Capsella grandiflora. Due to the recency of the split, most variation within C. rubella is found within C. grandiflora. We can therefore identify genomic regions where two C. rubella individuals have inherited the same or different segments of ancestral diversity (i.e. founding haplotypes) present in C. rubella's founder(s). Based on this analysis, we show that C. rubella was founded by multiple individuals drawn from a diverse ancestral population closely related to extant C. grandiflora, that drift and selection have rapidly homogenized most of this ancestral variation since C. rubella's founding, and that little novel variation has accumulated within this time. Despite the extensive loss of ancestral variation, the approximately 25% of the genome for wh
In this note we show through infinitary derivations that each provably well-founded strict partial order in ${\rm ACA}_{0}$ admits an embedding to an ordinal$<\varepsilon_{0}$.
Defined by Gelfond in 1991 (G91), epistemic specifications (or programs) are an extension of logic programming under stable models semantics that introducessubjective literals. A subjective literal al-lows checking whether some regular literal is true in all (or in some of) the stable models of the program, being those models collected in a setcalledworld view. One epistemic program may yield several world views but, under the original G91 semantics, some of them resulted from self-supported derivations. During the last eight years, several alternative approaches have been proposed to get rid of these self-supported worldviews. Unfortunately, their success could only be measured by studying their behaviour on a set of common examples in the literature, since no formal property of "self-supportedness" had been defined. To fill this gap, we extend in this paper the idea of unfounded set from standard logic programming to the epistemic case. We define when a world view is founded with respect to some program and propose the foundedness property for any semantics whose world views are always founded. Using counterexamples, we explain that the previous approaches violate foundedness, an
In this note, we use Kunen's notion of a signing to establish two theorems about the well-founded semantics of logic programs, in the case where we are interested in only (say) the positive literals of a predicate $p$ that are consequences of the program. The first theorem identifies a class of programs for which the well-founded and Fitting semantics coincide for the positive part of $p$. The second theorem shows that if a program has a signing then computing the positive part of $p$ under the well-founded semantics requires the computation of only one part of each predicate. This theorem suggests an analysis for query-answering under the well-founded semantics. In the process of proving these results, we use an alternative formulation of the well-founded semantics of logic programs, which might be of independent interest. Under consideration in Theory and Practice of Logic Programming (TPLP)
We investigate tree-automatic well-founded trees. Using Delhomme's decomposition technique for tree-automatic structures, we show that the (ordinal) rank of a tree-automatic well-founded tree is strictly below omega^omega. Moreover, we make a step towards proving that the ranks of tree-automatic well-founded partial orders are bounded by omega^omega^omega: we prove this bound for what we call upwards linear partial orders. As an application of our result, we show that the isomorphism problem for tree-automatic well-founded trees is complete for level Delta^0_{omega^omega} of the hyperarithmetical hierarchy with respect to Turing-reductions.
Many native ASP solvers exploit unfounded sets to compute consequences of a logic program via some form of well-founded negation, but disregard its contrapositive, well-founded justification (WFJ), due to computational cost. However, we demonstrate that this can hinder propagation of many relevant conditions such as reachability. In order to perform WFJ with low computational cost, we devise a method that approximates its consequences by computing dominators in a flowgraph, a problem for which linear-time algorithms exist. Furthermore, our method allows for additional unfounded set inference, called well-founded domination (WFD). We show that the effect of WFJ and WFD can be simulated for a important classes of logic programs that include reachability. This paper is a corrected and extended version of a paper published at the 12th International Conference on Logic Programming and Nonmonotonic Reasoning (LPNMR 2013). It has been adapted to exclude Theorem 10 and its consequences, but provides all missing proofs.
Despite much recent interest in compiler randomized testing (fuzzing), the practical impact of fuzzer-found compiler bugs on real-world applications has barely been assessed. We present the first quantitative and qualitative study of the tangible impact of miscompilation bugs in a mature compiler. We follow a rigorous methodology where the bug impact over the compiled application is evaluated based on (1) whether the bug appears to trigger during compilation; (2) the extent to which generated assembly code changes syntactically due to triggering of the bug; and (3) how much such changes do cause regression test suite failures and could be used to manually trigger divergences during execution. The study is conducted with respect to the compilation of more than 10 million lines of C/C++ code from 309 Debian packages, using 12% of the historical and now fixed miscompilation bugs found by four state-of-the-art fuzzers in the Clang/LLVM compiler, as well as 18 bugs found by human users compiling real code or by formal verification. The results show that almost half of the fuzzer-found bugs propagate to the generated binaries for some packages, but rarely affect their syntax and cause tw