Notropis hubbsi, a new cyprinid fish from the Mississippi River basin, with comments on Notropis welaka

http://deepblue.lib.umich.edu/bitstream/2027.42/57119/1/OP683.pd

The Shape of Dark Matter Haloes: Results from Weak Lensing

Dark matter haloes are expected to have a triaxial shape, appearing elliptical in projection. Understanding the orientation of these dark matter haloes, and how they are aligned, has implications for theories of structure formation in the universe. Additionally, a better understanding of halo alignment will allow us to account for intrinsic alignments and improve future weak lensing studies. We measure dark matter halo ellipticity using weak galaxy-galaxy lensing. We study the anisotropic shear around luminous red galaxies (LRGs) from the Baryon Oscillation Spectroscopic Survey (BOSS), using galaxies from the Canada-France Imaging Survey (CFIS) as background source galaxies. By aligning with the major axis of the galaxy light before measuring the shear, we can stack many lens galaxies to obtain a detection of halo ellipticity. We model the dark matter mass distribution as a multipole expansion, with an isotropic monopole component and a quadrupole that accounts for the angular dependence and ellipticity. We calculate 6 quadrupole estimators, which are designed to measure anisotropic lensing signal while minimising any isotropic contributions. Taking the results from these estimators into account, we obtain a mean halo ellipticity of e = 0.226 ± 0.102. We also study the lensing signal when aligning with filaments, using pairs of LRGs as a proxy. This also yields a detection of dark matter anisotropy. A meaningful measure of ellipticity along the filaments will require further development of the model to account for anisotropy on larger scales

Probabilistic Clustering of Sequences: Inferring new bacterial regulons by comparative genomics

Genome wide comparisons between enteric bacteria yield large sets of conserved putative regulatory sites on a gene by gene basis that need to be clustered into regulons. Using the assumption that regulatory sites can be represented as samples from weight matrices we derive a unique probability distribution for assignments of sites into clusters. Our algorithm, 'PROCSE' (probabilistic clustering of sequences), uses Monte-Carlo sampling of this distribution to partition and align thousands of short DNA sequences into clusters. The algorithm internally determines the number of clusters from the data, and assigns significance to the resulting clusters. We place theoretical limits on the ability of any algorithm to correctly cluster sequences drawn from weight matrices (WMs) when these WMs are unknown. Our analysis suggests that the set of all putative sites for a single genome (e.g. E. coli) is largely inadequate for clustering. When sites from different genomes are combined and all the homologous sites from the various species are used as a block, clustering becomes feasible. We predict 50-100 new regulons as well as many new members of existing regulons, potentially doubling the number of known regulatory sites in E. coli.Comment: 27 pages including 9 figures and 3 table

The shape of dark matter haloes: results from weak lensing in the Ultraviolet Near-Infrared Optical Northern Survey (UNIONS)

Cold dark matter haloes are expected to be triaxial, and so appear elliptical in projection. We use weak gravitational lensing from the Canada-France Imaging Survey (CFIS) component of the Ultraviolet-Near Infrared Optical Northern Survey (UNIONS) to measure the ellipticity of the dark matter haloes around Luminous Red Galaxies (LRGs) from the Sloan Digital Sky Survey Data Release 7 (DR7) and from the CMASS and LOWZ samples of the Baryon Oscillation Spectroscopic Survey (BOSS), assuming their major axes are aligned with the stellar light. We find that DR7 LRGs with masses $M \sim 2.5\times10^{13} \textrm{M}_{\odot}/h$ have halo ellipticities $e=0.35\pm0.09$. Expressed as a fraction of the galaxy ellipticity, we find $f_h = 1.4\pm0.4$. For BOSS LRGs, the detection is of marginal significance: $e = 0.17\pm0.10$ and $f_h=0.1\pm0.4$. These results are in agreement with other measurements of halo ellipticity from weak lensing and, taken together with previous results, suggest an increase of halo ellipticity of $0.10\pm0.05$ per decade in halo mass. This trend agrees with the predictions from hydrodynamical simulations, which find that at higher halo masses, not only do dark matter haloes become more elliptical, but that the misalignment between major axis of the stellar light in the central galaxy and that of the dark matter decreases

I feel you: the design and evaluation of a domotic affect-sensitive spoken conversational agent

We describe the work on infusion of emotion into a limited-task autonomous spoken conversational agent situated in the domestic environment, using a need-inspired task-independent emotion model (NEMO). In order to demonstrate the generation of affect through the use of the model, we describe the work of integrating it with a natural-language mixed-initiative HiFi-control spoken conversational agent (SCA). NEMO and the host system communicate externally, removing the need for the Dialog Manager to be modified, as is done in most existing dialog systems, in order to be adaptive. The first part of the paper concerns the integration between NEMO and the host agent. The second part summarizes the work on automatic affect prediction, namely, frustration and contentment, from dialog features, a non-conventional source, in the attempt of moving towards a more user-centric approach. The final part reports the evaluation results obtained from a user study, in which both versions of the agent (non-adaptive and emotionally-adaptive) were compared. The results provide substantial evidences with respect to the benefits of adding emotion in a spoken conversational agent, especially in mitigating users' frustrations and, ultimately, improving their satisfaction

Finding subtypes of transcription factor motif pairs with distinct regulatory roles

DNA sequences bound by a transcription factor (TF) are presumed to contain sequence elements that reflect its DNA binding preferences and its downstream-regulatory effects. Experimentally identified TF binding sites (TFBSs) are usually similar enough to be summarized by a ‘consensus’ motif, representative of the TF DNA binding specificity. Studies have shown that groups of nucleotide TFBS variants (subtypes) can contribute to distinct modes of downstream regulation by the TF via differential recruitment of cofactors. A TFA may bind to TFBS subtypes a1 or a2 depending on whether it associates with cofactors TFB or TFC, respectively. While some approaches can discover motif pairs (dyads), none address the problem of identifying ‘variants’ of dyads. TFs are key components of multiple regulatory pathways targeting different sets of genes perhaps with different binding preferences. Identifying the discriminating TF–DNA associations that lead to the differential downstream regulation is thus essential. We present DiSCo (Discovery of Subtypes and Cofactors), a novel approach for identifying variants of dyad motifs (and their respective target sequence sets) that are instrumental for differential downstream regulation. Using both simulated and experimental datasets, we demonstrate how current motif discovery can be successfully leveraged to address this question

Temporal and thematic trends in water, sanitation and hygiene (WaSH) research in Pacific Island Countries: a systematic review

Pacific Island Countries (PICs) lag behind global trends in water, sanitation and hygiene (WaSH) development. We conducted a systematic search of all English language papers (published before February 2015) about WaSH in PICs to evaluate the state of the peer-reviewed literature and explore thematic findings. A total of 121 papers met the criteria for full-text review following an initial search result of more than 6,000 papers. Two reviewers independently assessed the quality and relevance of each article and consolidated their findings according to four emergent themes: public health, environment, emergency response and interventions, and management and governance. Findings indicate a knowledge gap in evidence-guided WaSH management strategies that advocate for human health while concurrently protecting and preserving drinking water resources. Extreme weather events threaten the quantity and quality of limited freshwater resources, and cultural factors that are unique to PICs present challenges to hygiene and sanitation. This review highlights the strengths and weaknesses of the peer-reviewed literature on WaSH in PICs, addresses spatial and temporal publication trends, and suggests areas in need of further research to help PICs meet development goals

Extracting regulator activity profiles by integration of de novo motifs and expression data: characterizing key regulators of nutrient depletion responses in Streptomyces coelicolor

Determining transcriptional regulator activities is a major focus of systems biology, providing key insight into regulatory mechanisms and co-regulators. For organisms such as Escherichia coli, transcriptional regulator binding site data can be integrated with expression data to infer transcriptional regulator activities. However, for most organisms there is only sparse data on their transcriptional regulators, while their associated binding motifs are largely unknown. Here, we address the challenge of inferring activities of unknown regulators by generating de novo (binding) motifs and integrating with expression data. We identify a number of key regulators active in the metabolic switch, including PhoP with its associated directed repeat PHO box, candidate motifs for two SARPs, a CRP family regulator, an iron response regulator and that for LexA. Experimental validation for some of our predictions was obtained using gel-shift assays. Our analysis is applicable to any organism for which there is a reasonable amount of complementary expression data and for which motifs (either over represented or evolutionary conserved) can be identified in the genome

A combinatorial optimization approach for diverse motif finding applications

BACKGROUND: Discovering approximately repeated patterns, or motifs, in biological sequences is an important and widely-studied problem in computational molecular biology. Most frequently, motif finding applications arise when identifying shared regulatory signals within DNA sequences or shared functional and structural elements within protein sequences. Due to the diversity of contexts in which motif finding is applied, several variations of the problem are commonly studied. RESULTS: We introduce a versatile combinatorial optimization framework for motif finding that couples graph pruning techniques with a novel integer linear programming formulation. Our approach is flexible and robust enough to model several variants of the motif finding problem, including those incorporating substitution matrices and phylogenetic distances. Additionally, we give an approach for determining statistical significance of uncovered motifs. In testing on numerous DNA and protein datasets, we demonstrate that our approach typically identifies statistically significant motifs corresponding to either known motifs or other motifs of high conservation. Moreover, in most cases, our approach finds provably optimal solutions to the underlying optimization problem. CONCLUSION: Our results demonstrate that a combined graph theoretic and mathematical programming approach can be the basis for effective and powerful techniques for diverse motif finding applications