Delimiting genetic units in Neotropical toads under incomplete lineage sorting and hybridization

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Flow sorting and exome sequencing reveal the oncogenome of primary Hodgkin and Reed-Sternberg cells

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

The methylation patterns of the IGF2 and IGF2R genes in bovine spermatozoa are not affected by flow-cytometric sex sorting

The objectives of this study were to investigate the effect of sexing by flow cytometry on the methylation patterns of the IGF2 and IGF2R genes. Frozen-thawed, unsorted, and sex-sorted sperm samples from four Nellore bulls were used. Each ejaculate was separated into three fractions: non-sexed (NS), sexed for X-sperm (SX), and sexed for Y-sperm (SY). Sperm were isolated from the extender, cryoprotectant, and other cell types by centrifugation on a 40:70% Percoll gradient, and sperm pellets were used for genomic DNA isolation. DNA was used for analyses of the methylation patterns by bisulfite sequencing. Methylation status of the IGF2 and IGF2R genes were evaluated by sequencing 195 and 147 individual clones, respectively. No global differences in DNA methylation were found between NS, SX, and SY groups for the IGF2 (P=0.09) or IGF2R genes (P=0.38). Very specific methylation patterns were observed in the 25th and 26th CpG sites in the IGF2R gene. representing higher methylation in NS than in the SX and SY groups compared with the other CpG sites. Further, individual variation in methylation patterns was found among bulls. In conclusion, the sex-sorting procedure by flow cytometry did not affect the overall DNA methylation patterns of the IGF2 and IGF2R genes, although individual variation in their methylation patterns among bulls was observed. Mol. Reprod. Dev. 79:7784, 2012. (C) 2011 Wiley Periodicals, Inc.

Non-Dominated Sorting Genetic Algorithm Based on Reinforcement Learning to Optimization of Broad-Band Reflector Antennas Satellite

This paper aims to provide an improved NSGA-II (Non-Dominated Sorting Genetic Algorithm-version II) which incorporates a parameter-free self-tuning approach by reinforcement learning technique, called Non-Dominated Sorting Genetic Algorithm Based on Reinforcement Learning (NSGA-RL). The proposed method is particularly compared with the classical NSGA-II when applied to a satellite coverage problem. Furthermore, not only the optimization results are compared with results obtained by other multiobjective optimization methods, but also guarantee the advantage of no time-spending and complex parameter tuning.

Permutation classes, sorting algorithms, and lattice paths

A permutation is said to avoid a pattern if it does not contain any subsequence which is order-isomorphic to it. Donald Knuth, in the first volume of his celebrated book "The art of Computer Programming", observed that the permutations that can be computed (or, equivalently, sorted) by some particular data structures can be characterized in terms of pattern avoidance. In more recent years, the topic was reopened several times, while often in terms of sortable permutations rather than computable ones. The idea to sort permutations by using one of Knuth’s devices suggests to look for a deterministic procedure that decides, in linear time, if there exists a sequence of operations which is able to convert a given permutation into the identical one. In this thesis we show that, for the stack and the restricted deques, there exists an unique way to implement such a procedure. Moreover, we use these sorting procedures to create new sorting algorithms, and we prove some unexpected commutation properties between these procedures and the base step of bubblesort. We also show that the permutations that can be sorted by a combination of the base steps of bubblesort and its dual can be expressed, once again, in terms of pattern avoidance. In the final chapter we give an alternative proof of some enumerative results, in particular for the classes of permutations that can be sorted by the two restricted deques. It is well-known that the permutations that can be sorted through a restricted deque are counted by the Schrӧder numbers. In the thesis, we show how the deterministic sorting procedures yield a bijection between sortable permutations and Schrӧder paths.

Neuronal precursor cell-expressed developmentally down-regulated 4-1 (NEDD4-1) controls the sorting of newly synthesized Ca(V)1.2 calcium channels

Neuronal precursor cell-expressed developmentally down-regulated 4 (Nedd4) proteins are ubiquitin ligases, which attach ubiquitin moieties to their target proteins, a post-translational modification that is most commonly associated with protein degradation. Nedd4 ubiquitin ligases have been shown to down-regulate both potassium and sodium channels. In this study, we investigated whether Nedd4 ubiquitin ligases also regulate Ca(v) calcium channels. We expressed three Nedd4 family members, Nedd4-1, Nedd4-2, and WWP2, together with Ca(v)1.2 channels in tsA-201 cells. We found that Nedd4-1 dramatically decreased Ca(v) whole-cell currents, whereas Nedd4-2 and WWP2 failed to regulate the current. Surface biotinylation assays revealed that Nedd4-1 decreased the number of channels inserted at the plasma membrane. Western blots also showed a concomitant decrease in the total expression of the channels. Surprisingly, however, neither the Ca(v) pore-forming α1 subunit nor the associated Ca(v)β and Ca(v)α(2)δ subunits were ubiquitylated by Nedd4-1. The proteasome inhibitor MG132 prevented the degradation of Ca(v) channels, whereas monodansylcadaverine and chloroquine partially antagonized the Nedd4-1-induced regulation of Ca(v) currents. Remarkably, the effect of Nedd4-1 was fully prevented by brefeldin A. These data suggest that Nedd4-1 promotes the sorting of newly synthesized Ca(v) channels for degradation by both the proteasome and the lysosome. Most importantly, Nedd4-1-induced regulation required the co-expression of Ca(v)β subunits, known to antagonize the retention of the channels in the endoplasmic reticulum. Altogether, our results suggest that Nedd4-1 interferes with the chaperon role of Ca(v)β at the endoplasmic reticulum/Golgi level to prevent the delivery of Ca(v) channels at the plasma membrane.

Further Evidence for Hemisity Sorting During Career Specialization

Hemisity refers to binary thinking and behavioral style differences between right and left brain-oriented individuals. The inevitability of hemisity became clear when it was discovered by magnetic resonance imaging (MRI) that an anatomical element of the executive system was unilaterally embedded in either the right or the left side of the ventral gyrus of the anterior cingulate cortex in an idiosyncratic manner that was congruent with an individual's inherent hemisity subtype. Based upon the MRI-calibrated hemisity of many individuals, a set of earlier biophysical and questionnaire hemisity assays was calibrated for accuracy and found appropriate for use in the investigation of the hemisity of individuals and groups. It had been reported that a partial sorting of individuals into hemisity right and left brain-oriented subgroups occurred during the process of higher education and professional development. Here, these results were extended by comparison of the hemisity of a putative unsorted population of 1,049 high school upper classmen, with that of 228 university freshmen. These hemisity outcomes were further compared with that of 15 university librarians, here found to be predominantly left brain-oriented, and 91 academically trained musicians, including 47 professional pianists, here found to be mostly right brainers. The results further supported the existence of substantial hemisity selection occurring during the process of higher education and in professional development.

Sorting through the garbage can: under what conditions do governments adopt policy programs?

The paper aims at explaining the adoption of policy programs. We use the garbage can model of organizational choice as our theoretical framework and complement it with the institutional setting of administrative decision-making in order to understand the complex causation of policy program adoption. Institutions distribute decision power by rules and routines and coin actor identities and their interpretations of situations. We therefore expect institutions to play a role when a policy window opens. We explore the configurative explanations for program adoption in a systematic comparison of the adoption of new alcohol policy programs in the Swiss cantons employing Qualitative Comparative Analysis. The most important conditions are the organizational elements of the administrative structure decisive for the coupling of the streams. The results imply that classic bureaucratic structures are better suited to put policies into practice than limited government.

Utilizing the full Capacity of Sorting Systems with new Infeed Technology

Utilisation of sorting systems’ maximum performance demands continuous conveying of goods by infeed lines to sorters. This is the case especially for sorters with one single infeed line, because the sorters’ performance is limited by the performance of the infeed line. Within this paper different infeed line constructions at the Rotary Sorter with diverse performances will be presented. The focus lies on a specific conveying system to synchronise the goods with the sorter by a performance of 6000 pieces per hour with one dynamic infeed line. By this means there is no extensive adjustment control of serial conveyors in the infeed line any longer.

Effects of Sorting Steer Calves on Feedlot Performance and Carcass Value

Three groups of steer calves totaling 480 head were sorted into smaller and larger frame sizes, and those groups were sorted into groups with more and less backfat. There was no difference in age among the four sorted groups. The larger steers and steers with less fat had faster rates of gain and tended to have superior feed efficiencies. Steers with more initial fat were fed fewer days. The larger framed steers and steers with less fat had heavier carcasses, less carcass backfat, more yield grade 1 carcasses and a lower percentage of Choice carcasses, but they also had greater value per carcass when evaluated using a grid paying premiums for quality and yield grades. The greatest profit to the feedyard was realized from the smaller framed steers and those with less initial backfat. For similar profit it was calculated that the larger steers should have been discounted as feeders $3.50 per hundred compared with the smaller steers and the steers with more fat discounted $5.00 per hundred compared with those having less initial fat. The results of this study suggest that sorting based on initial fat thickness may have more potential for enhancing the value of finished cattle than sorting based on frame score.

Identifying Individual and Group Effects in the Presence of Sorting: A Neighborhood Effects Application

Researchers have long recognized that the non-random sorting of individuals into groups generates correlation between individual and group attributes that is likely to bias naive estimates of both individual and group effects. This paper proposes a non-parametric strategy for identifying these effects in a model that allows for both individual and group unobservables, applying this strategy to the estimation of neighborhood effects on labor market outcomes. The first part of this strategy is guided by a robust feature of the equilibrium in the canonical vertical sorting model of Epple and Platt (1998), that there is a monotonic relationship between neighborhood housing prices and neighborhood quality. This implies that under certain conditions a non- parametric function of neighborhood housing prices serves as a suitable control function for the neighborhood unobservable in the labor market outcome regression. The second part of the proposed strategy uses aggregation to develop suitable instruments for both exogenous and endogenous group attributes. Instrumenting for each individual's observed neighborhood attributes with the average neighborhood attributes of a set of observationally identical individuals eliminates the portion of the variation in neighborhood attributes due to sorting on unobserved individual attributes. The neighborhood effects application is based on confidential microdata from the 1990 Decennial Census for the Boston MSA. The results imply that the direct effects of geographic proximity to jobs, neighborhood poverty rates, and average neighborhood education are substantially larger than the conditional correlations identified using OLS, although the net effect of neighborhood quality on labor market outcomes remains small. These findings are robust across a wide variety of specifications and robustness checks.