The impact of chromosome sorting and painting on the comparative analysis of primate genomes

Chromosome sorting by flow cytometry is the main source of chromosome-specific DNA for the production of painting probes. These probes have been used for cross-species in situ hybridization in the construction of comparative maps, in the study of karyotype evolution and phylogenetics, in delineating territories in interphase nuclei, and in the analysis of chromosome breakpoints. We review here the contributions that this technology has made to the analysis of primate genomes. Copyright (C) 2005 S. Karger AG, Basel.

Kernelized sorting

Object matching is a fundamental operation in data analysis. It typically requires the definition of a similarity measure between the classes of objects to be matched. Instead, we develop an approach which is able to perform matching by requiring a similarity measure only within each of the classes. This is achieved by maximizing the dependency between matched pairs of observations by means of the Hilbert Schmidt Independence Criterion. This problem can be cast as one of maximizing a quadratic assignment problem with special structure and we present a simple algorithm for finding a locally optimal solution.

Context-dependent decay of motor memories during skill acquisition.

Current models of motor learning posit that skill acquisition involves both the formation and decay of multiple motor memories that can be engaged in different contexts. Memory formation is assumed to be context dependent, so that errors most strongly update motor memories associated with the current context. In contrast, memory decay is assumed to be context independent, so that movement in any context leads to uniform decay across all contexts. We demonstrate that for both object manipulation and force-field adaptation, contrary to previous models, memory decay is highly context dependent. We show that the decay of memory associated with a given context is greatest for movements made in that context, with more distant contexts showing markedly reduced decay. Thus, both memory formation and decay are strongest for the current context. We propose that this apparently paradoxical organization provides a mechanism for optimizing performance. While memory decay tends to reduce force output, memory formation can correct for any errors that arise, allowing the motor system to regulate force output so as to both minimize errors and avoid unnecessary energy expenditure. The motor commands for any given context thus result from a balance between memory formation and decay, while memories for other contexts are preserved.

Sorting nanoparticles by centrifugal fields in clean media

The on-demand availability of nanomaterials with selected size and well-defined chemical/physical properties is of fundamental importance for their widespread application. We report two clean, rapid, and non-destructive approaches for nanoparticle (NP) size selection in centrifugal fields. The first exploits rate zonal separation in a high viscosity gradient. The second exploits selective sedimentation of NPs with different sizes. These methods are here applied to metallic nanoparticles (MNPs) with different compositions and surface chemistry, dispersed either in water or organic solvents. The approach is general and can also be exploited for the separation of NPs of any material. We selectively sort both Au and AgNPs with sizes in the 10-30 nm range, achieving chemical-free MNPs with low polydispersivity. We do not use solutes, thus avoiding contamination, and only require low centrifugal fields, easily achievable in benchtop systems. © 2013 American Chemical Society.

Independent Transport and Sorting of Functionally Distinct Protein Families in Tetrahymena thermophila Dense Core Secretory Granules

Dense core granules (DCGs) in Tetrahymena thermophila contain two protein classes. Proteins in the first class, called granule lattice (Grl), coassemble to form a crystalline lattice within the granule lumen. Lattice expansion acts as a propulsive mechanism during DCG release, and Grl proteins are essential for efficient exocytosis. The second protein class, defined by a C-terminal beta/gamma-crystallin domain, is poorly understood. Here, we have analyzed the function and sorting of Grt1p (granule tip), which was previously identified as an abundant protein in this family. Cells lacking all copies of GRT1, together with the closely related GRT2, accumulate wild-type levels of docked DCGs. Unlike cells disrupted in any of the major GRL genes, Delta GRT1 Delta GRT2 cells show no defect in secretion, indicating that neither exocytic fusion nor core expansion depends on GRT1. These results suggest that Grl protein sorting to DCGs is independent of Grt proteins. Consistent with this, the granule core lattice in Delta GRT1 Delta GRT2 cells appears identical to that in wild-type cells by electron microscopy, and the only biochemical component visibly absent is Grt1p itself. Moreover, gel filtration showed that Grl and Grt proteins in cell homogenates exist in nonoverlapping complexes, and affinity-isolated Grt1p complexes do not contain Grl proteins. These data demonstrate that two major classes of proteins in Tetrahymena DCGs are likely to be independently transported during DCG biosynthesis and play distinct roles in granule function. The role of Grt1p may primarily be postexocytic; consistent with this idea, DCG contents from Delta GRT1 Delta GRT2 cells appear less adhesive than those from the wild type.

Manufacturing excellent engineers: Skill development in a Masters programme

An MPhil programme, delivered by the Engineering Department at the University of Cambridge, claims to be excellent at preparing graduates for manufacturing industry careers. The course uses a combination of different educational experiences, including industry-based assignments, industrial visits and practical exercises. This research explores how problem solving skills are developed during the first module, Induction, which is designed to enable students to undertake their first industrial assignment. From the literature, four conditions necessary for skill development were identified: Provision of a skill description, making explicit key components A number of different experiences with a range of contextual variables A teaching process which includes regular feedback and student reflection Students motivated to learn. These were used to construct a skill development framework (SDF). Using a case study research design, multiple types of evidence were collected to test for the above conditions using both classroom observation and questionnaire methods. The results confirmed the presence of the SDF conditions at different levels, with reflection aspects considered the weakest. Conflicting results were obtained regarding the students' self-awareness of skill levels. A plausible explanation is a change in the students' frame of reference. This initial study set out to develop a better understanding of the process of skill development. Whilst the SDF appears reasonable, there is a need for further work in three broad areas of defining skills, assessing skills and developing reflection skills.

Roles of sorting and chemical weathering in the geochemistry and magnetic susceptibility of Xiashu loess；East China

IEECAS SKLLQG

Effects of the initial size, stocking density and sorting on the growth of juvenile Pacific abalone, Haliotis discus hannai Ino

During winter months, a novel overwintering mode of transferring juvenile abalones to open seawaters in southern China rather than keeping them in closed land-based nursery systems in northern China is a popular practice. The initial size, stocking density and sorting are among the first considerations when establishing an abalone culture system. This study aimed to investigate the effects of these factors on the growth of juvenile Pacific abalone, Haliotis discus hannai Ino, during overwintering. Juvenile abalones were reared in multi-tier basket form for overwintering in open seawaters in southern China for 106 days. The daily growth rates (DGRs) in the shell length of all experimental groups ranged from 67.08 to 135.75 mu m day(-1), while the specific growth rates (SGRs) were 0.2447-0.3259% day(-1). Variance analysis indicated that both DGRs and SGRs in shell length were significantly affected by the initial body size and stocking density. Furthermore, the effects of stocking density on DGRs and SGRs varied with the initial size. However, sorting abalones according to their initial sizes may not be necessary in practice as sorting did not alter growth significantly at all densities in this study. Factors potentially affecting abalone growth such as genetic control and intraspecific competition were discussed.

A Computational Model of Skill Acquisition

This thesis confronts the nature of the process of learning an intellectual skill, the ability to solve problems efficiently in a particular domain of discourse. The investigation is synthetic; a computational performance model, HACKER, is displayed. Hacker is a computer problem-solving system whose performance improves with practice. HACKER maintains performance knowledge as a library of procedures indexed by descriptions of the problem types for which the procedures are appropriate. When applied to a problem, HACKER tries to use a procedure from this "Answer Library". If no procedure is found to be applicable, HACKER writes one using more general knowledge of the problem domain and of programming techniques. This new program may be generalized and added to the Answer Library.

A cognitive approach to identifying measurable milestones for programming skill acquisition

Mead, J., Gray, S., Hamer, J., James, R., Sorva, J., Clair, C. S., and Thomas, L. 2006. A cognitive approach to identifying measurable milestones for programming skill acquisition. SIGCSE Bull. 38, 4 (Dec. 2006), 182-194.

Sorting under partial information (without the ellipsoid algorithm)

We revisit the well-known problem of sorting under partial information: sort a finite set given the outcomes of comparisons between some pairs of elements. The input is a partially ordered set P, and solving the problem amounts to discovering an unknown linear extension of P, using pairwise comparisons. The information-theoretic lower bound on the number of comparisons needed in the worst case is log e(P), the binary logarithm of the number of linear extensions of P. In a breakthrough paper, Jeff Kahn and Jeong Han Kim (STOC 1992) showed that there exists a polynomial-time algorithm for the problem achieving this bound up to a constant factor. Their algorithm invokes the ellipsoid algorithm at each iteration for determining the next comparison, making it impractical. We develop efficient algorithms for sorting under partial information. Like Kahn and Kim, our approach relies on graph entropy. However, our algorithms differ in essential ways from theirs. Rather than resorting to convex programming for computing the entropy, we approximate the entropy, or make sure it is computed only once in a restricted class of graphs, permitting the use of a simpler algorithm. Specifically, we present: an O(n2) algorithm performing O(log n·log e(P)) comparisons; an O(n2.5) algorithm performing at most (1+ε) log e(P) + Oε(n) comparisons; an O(n2.5) algorithm performing O(log e(P)) comparisons. All our algorithms are simple to implement. © 2010 ACM.