Multidimensional scaling in the city-block metric: A combinatorial approach

We present an approach, independent of the common gradient-based necessary conditions for obtaining a (locally) optimal solution, to multidimensional scaling using the city-block distance function, and implementable in either a metric or nonmetric context. The difficulties encountered in relying on a gradient-based strategy are first reviewed: the general weakness in indicating a good solution that is implied by the satisfaction of the necessary condition of a zero gradient, and the possibility of actual nonconvergence of the associated optimization strategy. To avoid the dependence on gradients for guiding the optimization technique, an alternative iterative procedure is proposed that incorporates (a) combinatorial optimization to construct good object orders along the chosen number of dimensions and (b) nonnegative least-squares to re-estimate the coordinates for the objects based on the object orders. The re-estimated coordinates are used to improve upon the given object orders, which may in turn lead to better coordinates, and so on until convergence of the entire process occurs to a (locally) optimal solution. The approach is illustrated through several data sets on the perception of similarity of rectangles and compared to the results obtained with a gradient-based method.     

Ribosomal crystallization and hibernation in a viviparous lizard]

Part of the ribosomes crystallize in the ovarian follicles during hibernation. The association between ribosomes crystals and endoplasmic reticulum membranes depends on the cell types of the follicle. The cytoplasm of oocytes with a nucleolus shows ribosome crystals. In larger oocytes, without nucleolus, there is no ribosome crystallization. The ribosomes which crystallize would be newly synthesized.     

Emerging knowledge of regulatory roles of <Emphasis Type="SmallCaps">d-</Emphasis>amino acids in bacteria

The d-enantiomers of amino acids have been thought to have relatively minor functions in biological processes. While l-amino acids clearly predominate in nature, d-amino acids are sometimes found in proteins that are not synthesized by ribosomes, and d-Ala and d-Glu are routinely found in the peptidoglycan cell wall of bacteria. Here, we review recent findings showing that d-amino acids have previously unappreciated regulatory roles in the bacterial kingdom. Many diverse bacterial phyla synthesize and release d-amino acids, including d-Met and d-Leu, which were not previously known to be made. These noncanonical d-amino acids regulate cell wall remodeling in stationary phase and cause biofilm dispersal in aging bacterial communities. Elucidating the mechanisms by which d-amino acids govern cell wall remodeling and biofilm disassembly will undoubtedly reveal new paradigms for understanding how extracytoplasmic processes are regulated as well as lead to development of novel therapeutics.     

Collagens in the developing and diseased nervous system

Collagens are extracellular proteins characterized by a structure in triple helices. There are 28 collagen types which differ in size, structure and function. Their architectural and functional roles in connective tissues have been widely assessed. In the nervous system, collagens are rare in the vicinity of the neuronal soma, occupying mostly a “marginal” position, such as the meninges, the basement membranes and the sensory end organs. In neural development, however, where various ECM molecules are known to be determinant, recent studies indicate that collagens are no exception, participating in axonal guidance, synaptogenesis and Schwann cell differentiation. Insights on collagens function in the brain have also been derived from neural pathophysiological conditions. This review summarizes the significant advances which underscore the function and importance of collagens in the nervous system. Received 09 September 2008; received after revision 24 October 2008; accepted 28 October 2008     

Additive two-mode clustering: The error-variance approach revisited

The additive clustering approach is applied to the problem of two-mode clustering and compared with the recent error-variance approach of Eckes and Orlik (1993). Although the schemes of the computational algorithms look very similar in both of the approaches, the additive clustering has been shown to have several advantages. Specifically, two technical limitations of the error-variance approach (see Eckes and Orlik 1993, p. 71) have been overcome in the framework of the additive clustering. The research was supported by the Office of Naval Research under grant number N0014-93-1-0222 to Rutgers University. The authors are indebted both to Fionn Murtagh, who served as Acting Editor, and to anonymous Referees for thoughtful and constructive reviews.     

Survey of Wyoming crayfishes

Collections of crayfish by Wyoming Game and Fish Department biologists and University of Wyoming staff in 1985-1987 included five species: Pacifastacus gambelii , the only species found in the Snake River and Bear River drainages of western Wyoming; Orconectes neglectus neglectus , collected from one reservoir in the South Platte River drainage in southeastern Wyoming (its first reported occurrence in the state); O. immunis and O. virilis ,widespread east of the Continental Divide and in the Green River drainage of southwestern Wyoming; and Cambarus Diogenes Diogenes , collected from a tributary of the North Platte River in eastern Wyoming.     

The ciliary gene RPGRIP1L is mutated in cerebello-oculo-renal syndrome (Joubert syndrome type B) and Meckel syndrome

Cerebello-oculo-renal syndrome (CORS), also called Joubert syndrome type B, and Meckel (MKS) syndrome belong to the group of developmental autosomal recessive disorders that are associated with primary cilium dysfunction. Using SNP mapping, we identified missense and truncating mutations in RPGRIP1L (KIAA1005) in both CORS and MKS, and we show that inactivation of the mouse ortholog Rpgrip1l (Ftm) recapitulates the cerebral, renal and hepatic defects of CORS and MKS. In addition, we show that RPGRIP1L colocalizes at the basal body and centrosomes with the protein products of both NPHP6 and NPHP4, known genes associated with MKS, CORS and nephronophthisis (a related renal disorder and ciliopathy). In addition, the RPGRIP1L missense mutations found in CORS individuals diminishes the interaction between RPGRIP1L and nephrocystin-4. Our findings show that mutations in RPGRIP1L can cause the multiorgan phenotypic abnormalities found in CORS or MKS, which therefore represent a continuum of the same underlying disorder.     

ECB Projections as a Tool for Understanding Policy Decisions

The European Central Bank publishes inflation projections quarterly and we aim to establish empirically whether they influence private inflation forecasts and whether they may be considered as an enhanced means of implementing policy decisions by facilitating private agents’ information processing. We provide original evidence that ECB inflation projections do influence private inflation expectations positively, and that ECB projections convey signals about future ECB rate movements. This paper suggests that ECB projections enable private agents to correctly interpret and predict policy decisions. Copyright © 2015 John Wiley & Sons, Ltd.     

Inactivating mutations of the chromatin remodeling gene ARID2 in hepatocellular carcinoma

Through exomic sequencing of ten hepatitis C virus (HCV)-associated hepatocellular carcinomas (HCC) and subsequent evaluation of additional affected individuals, we discovered novel inactivating mutations of ARID2 in four major subtypes of HCC (HCV-associated HCC, hepatitis B virus (HBV)-associated HCC, alcohol-associated HCC and HCC with no known etiology). Notably, 18.2% of individuals with HCV-associated HCC in the United States and Europe harbored ARID2 inactivation mutations, suggesting that ARID2 is a tumor suppressor gene that is relatively commonly mutated in this tumor subtype.