Notes on bordered Floer homology

This is a survey of bordered Heegaard Floer homology, an extension of the Heegaard Floer invariant HF-hat to 3-manifolds with boundary. Emphasis is placed on how bordered Heegaard Floer homology can be used for computations.Comment: 73 pages, 29 figures. Based on lectures at the Contact and Symplectic Topology Summer School in Budapest, July 2012. v2: Fixed many small typo

Q&A: Epistasis

Molecular and Cellular Biolog

Parallelizing Gaussian Process Calculations in R

We consider parallel computation for Gaussian process calculations to overcome computational and memory constraints on the size of datasets that can be analyzed. Using a hybrid parallelization approach that uses both threading (shared memory) and message-passing (distributed memory), we implement the core linear algebra operations used in spatial statistics and Gaussian process regression in an R package called bigGP that relies on C and MPI. The approach divides the covariance matrix into blocks such that the computational load is balanced across processes while communication between processes is limited. The package provides an API enabling R programmers to implement Gaussian process-based methods by using the distributed linear algebra operations without any C or MPI coding. We illustrate the approach and software by analyzing an astrophysics dataset with n = 67, 275 observations

Grid Diagrams for Lens Spaces and Combinatorial Knot Floer Homology

Similar to knots in S^3, any knot in a lens space has a grid diagram from which one can combinatorially compute all of its knot Floer homology invariants. We give an explicit description of the generators, differentials, and rational Maslov and Alexander gradings in terms of combinatorial data on the grid diagram. Motivated by existing results for the Floer homology of knots in S^3 and the similarity of the combinatorics presented here, we conjecture that a certain family of knots is characterized by their Floer homology. Coupled with work of the third author, an affirmative answer to this would prove the Berge conjecture, which catalogs the knots in S^3 admitting lens space surgeries.Comment: 27 pages, 8 figures; Expositional improvements, corrected normalization of A grading in proof of Lemma 4.1

Genome-wide analysis of the maternal-to-zygotic transition in Drosophila primordial germ cells

Background: During the maternal-to-zygotic transition (MZT) vast changes in the embryonic transcriptome are produced by a combination of two processes: elimination of maternally provided mRNAs and synthesis of new transcripts from the zygotic genome. Previous genome-wide analyses of the MZT have been restricted to whole embryos. Here we report the first such analysis for primordial germ cells (PGCs), the progenitors of the germ-line stem cells. Results: We purified PGCs from Drosophila embryos, defined their proteome and transcriptome, and assessed the content, scale and dynamics of their MZT. Transcripts encoding proteins that implement particular types of biological functions group into nine distinct expression profiles, reflecting coordinate control at the transcriptional and posttranscriptional levels. mRNAs encoding germ-plasm components and cell-cell signaling molecules are rapidly degraded while new transcription produces mRNAs encoding the core transcriptional and protein synthetic machineries. The RNA-binding protein Smaug is essential for the PGC MZT, clearing transcripts encoding proteins that regulate stem cell behavior, transcriptional and posttranscriptional processes. Computational analyses suggest that Smaug and AU-rich element binding proteins function independently to control transcript elimination. Conclusions: The scale of the MZT is similar in the soma and PGCs. However, the timing and content of their MZTs differ, reflecting the distinct developmental imperatives of these cell types. The PGC MZT is delayed relative to that in the soma, likely because relief of PGC-specific transcriptional silencing is required for zygotic genome activation as well as for efficient maternal transcript clearance.http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000305391700004&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=8e1609b174ce4e31116a60747a720701Biotechnology & Applied MicrobiologyGenetics & HereditySCI(E)20ARTICLE2null1

Derivation of an optimal directivity pattern for sweet spot widening in stereo sound reproduction

In this paper the correction of the degradation of the stereophonic illusion during sound reproduction due to off-center listening is investigated. The main idea is that the directivity pattern of a loudspeaker array should have a well-defined shape such that a good stereo reproduction is achieved in a large listening area. Therefore, a mathematical description to derive an optimal directivity pattern lopt that achieves sweet spot widening in a large listening area for stereophonic sound applications is described. This optimal directivity pattern is based on parametrized time/intensity trading data coming from psycho-acoustic experiments within a wide listening area. After the study, the required digital FIR filters are determined by means of a least-squares optimization method for a given stereo base setup (two pair of drivers for the loudspeaker arrays and 2.5-m distance between loudspeakers), which radiate sound in a broad range of listening positions in accordance with the derived lopt. Informal listening tests have shown that the lopt worked as predicted by the theoretical simulations. They also demonstrated the correct central sound localization for speech and music for a number of listening positions. This application is referred to as "Position-Independent (PI) stereo.

A new approach to numerical characterisation of wear particle surfaces in three-dimensions for wear study

In the wear and tear process of synovial joints, wear particles generated and released from articular cartilage within the joints have surface topography and mechanical property which can be used to reveal wear conditions. Three-dimensional (3D) particle images acquired using laser scanning confocal microscopy (LSCM) contain appropriate surface information for quantitatively characterizing the surface morphology and changes to seek a further understanding of the wear process and wear features. This paper presents a new attempt on the 3D numerical characterisation of wear particle surfaces using the field and feature parameter sets which are defined in ISO/FDIS 25178-2. Based on the innovative pattern recognition capability, the feature parameters are, for the first time, employed for quantitative analysis of wear debris surface textures. Through performing parameter classification, ANOVA analysis and correlation analysis, typical changing trends of the surface transformation of the wear particles along with the severity of wear conditions and osteoarthritis (OA) have been observed. Moreover, the feature parameters have shown a significant sensitivity with the wear particle surfaces texture evolution under OA development. A correlation analysis of the numerical analysis results of cartilage surface texture variations and that of their wear particles has been conducted in this study. Key surface descriptors have been determined. Further research is needed to verify the above outcomes using clinic samples

Identification of the human factors contributing to maintenance failures in a petroleum operation

Objective: This research aimed to identify the most frequently occurring human factors contributing to maintenance-related failures within a petroleum industry organization. Commonality between failures will assist in understanding reliability in maintenance processes, thereby preventing accidents in high-hazard domains. Background: Methods exist for understanding the human factors contributing to accidents. Their application in a maintenance context mainly has been advanced in aviation and nuclear power. Maintenance in the petroleum industry provides a different context for investigating the role that human factors play in influencing outcomes. It is therefore worth investigating the contributing human factors to improve our understanding of both human factors in reliability and the factors specific to this domain. Method: Detailed analyses were conducted of maintenance- related failures (N = 38) in a petroleum company using structured interviews with maintenance technicians. The interview structure was based on the Human Factor Investigation Tool (HFIT), which in turn was based on Rasmussen’s model of human malfunction .Results: A mean of 9.5 factors per incident was identified across the cases investigated. The three most frequent human factors contributing to the maintenance failures were found to be assumption (79% of cases), design and maintenance (71%), and communication (66%).Conclusion: HFIT proved to be a useful instrument for identifying the pattern of human factors that recurred most frequently in maintenance-related failures. Application: The high frequency of failures attributed to assumptions and communication demonstrated the importance of problem-solving abilities and organizational communication in a domain where maintenance personnel have a high degree of autonomy and a wide geographical distribution

Cutoff Suppresses RNA Polymerase II Termination to Ensure Expression of piRNA Precursors

Small non-coding RNAs called piRNAs serve as guides for an adaptable immune system that represses transposable elements in germ cells of Metazoa. In Drosophila the RDC complex, composed of Rhino, Deadlock and Cutoff (Cuff) bind chromatin of dual-strand piRNA clusters, special genomic regions, which encode piRNA precursors. The RDC complex is required for transcription of piRNA precursors, though the mechanism by which it licenses transcription remained unknown. Here, we show that Cuff prevents premature termination of RNA polymerase II. Cuff prevents cleavage of nascent RNA at poly(A) sites by interfering with recruitment of the cleavage and polyadenylation specificity factor (CPSF) complex. Cuff also protects processed transcripts from degradation by the exonuclease Rat1. Our work reveals a conceptually different mechanism of transcriptional enhancement. In contrast to other factors that regulate termination by binding to specific signals on nascent RNA, the RDC complex inhibits termination in a chromatin-dependent and sequence-independent manner