A Binary Integer Program to Maximize the Agreement Between Partitions

This research note focuses on a problem where the cluster sizes for two partitions of the same object set are assumed known; however, the actual assignments of objects to clusters are unknown for one or both partitions. The objective is to find a contingency table that produces maximum possible agreement between the two partitions, subject to constraints that the row and column marginal frequencies for the table correspond exactly to the cluster sizes for the partitions. This problem was described by H. Messatfa (Journal of Classification, 1992, pp. 5–15), who provided a heuristic procedure based on the linear transportation problem. We present an exact solution procedure using binary integer programming. We demonstrate that our proposed method efficiently obtains optimal solutions for problems of practical size. We would like to thank the Editor, Willem Heiser, and an anonymous reviewer for helpful comments that resulted in improvements of this article.     

Loss of the SKI proto-oncogene in individuals affected with 1p36 deletion syndrome is predicted by strain-dependent defects in Ski-/- mice.

Experiments involving overexpression of Ski have suggested that this gene is involved in neural tube development and muscle differentiation. In agreement with these findings, Ski-/- mice display a cranial neural tube defect that results in exencephaly and a marked reduction in skeletal muscle mass. Here we show that the penetrance and expressivity of the phenotype changes when the null mutation is backcrossed into the C57BL6/J background, with the principal change involving a switch from a neural tube defect to midline facial clefting. Other defects, including depressed nasal bridge, eye abnormalities, skeletal muscle defects and digit abnormalities, show increased penetrance in the C57BL6/J background. These phenotypes are interesting because they resemble some of the features observed in individuals diagnosed with 1p36 deletion syndrome, a disorder caused by monosomy of the short arm of human chromosome 1p (refs. 6-9). These similarities prompted us to re-examine the chromosomal location of human SKI and to determine whether SKI is included in the deletions of 1p36. We found that human SKI is located at distal 1p36.3 and is deleted in all of the individuals tested so far who have this syndrome. Thus, SKI may contribute to some of the phenotypes common in 1p36 deletion syndrome, and particularly to facial clefting.     

Integer Programming Methods for Seriation and Unidemensional Scaling of Proximity Matrices: A Review and Some Extensions

L ₁-norm are also presented. I conclude that the computational scaling problems depends largely on the criterion of interest, with unidimensional scaling problems depends largely on the criterion of interest, with unidimensional scaling in the L ₁-norm being especially challenging.     

犹大·福克曼(1933～2008)——记科学家、外科医生和血管生成领域的开拓者

犹大·福克曼(Judah Folkman)常说:"科学在于你如何想象它"(Science goes where you imagine it).确实,很少有人能像福克曼那样在科学领域如此大胆想象.     

The material theory of induction and the epistemology of thought experiments

John D. Norton is responsible for a number of influential views in contemporary philosophy of science. This paper will discuss two of them. The material theory of induction claims that inductive arguments are ultimately justified by their material features, not their formal features. Thus, while a deductive argument can be valid irrespective of the content of the propositions that make up the argument, an inductive argument about, say, apples, will be justified (or not) depending on facts about apples. The argument view of thought experiments claims that thought experiments are arguments, and that they function epistemically however arguments do. These two views have generated a great deal of discussion, although there hasn't been much written about their combination. I argue that despite some interesting harmonies, there is a serious tension between them. I consider several options for easing this tension, before suggesting a set of changes to the argument view that I take to be consistent with Norton's fundamental philosophical commitments, and which retain what seems intuitively correct about the argument view. These changes require that we move away from a unitary epistemology of thought experiments and towards a more pluralist position.     

Huxley's defence of Darwin

This article ventures a reappraisal of Huxley's role in the Darwinian debates. First, the views on life-history held by Huxley before 1859 are identified. Next, the disharmony between these views and the view put forward by Darwin in the Origin of species (1859) is discussed. Huxley's defence of the Origin is then reviewed in an effort to show that, despite his fervour on Darwin's behalf, his advocacy of the case for natural selection was not particularly compelling, and that his own scientific work took no revolutionary new direction after 1859.     

A kinesin-mediated mechanism that couples centrosomes to nuclei

The M-type kinesin isoform, Kif9, has recently been implicated in maintaining a physical connection between the centrosome and nucleus in Dictyostelium discoideum. However, the mechanism by which Kif9 functions to link these two organelles remains obscure. Here we demonstrate that the Kif9 protein is localized to the nuclear envelope and is concentrated in the region underlying the centrosome point of attachment. Nuclear anchorage appears mediated through a specialized transmembrane domain located in the carboxyl terminus. Kif9 interacts with microtubules in in vitro binding assays and effects an endwise depolymerization of the polymer. These results suggest a model whereby Kif9 is anchored to the nucleus and generates a pulling force that reels the centrosome up against the nucleus. This is a novel activity for a kinesin motor, one important for progression of cells into mitosis and to ensure centrosome-nuclear parity in a multinuclear environment.