Three New Species of Saccocirrus (Polychaeta: Saccocirridae) from Hawai'i

Three new species of saccocirrids from interstitial sand habitats off O'ahu, Hawai'i, are described. Two are from subtidal depths, 9-33 m, and the third is from the intertidal to 3.5 m deep on a fringing reef and at Hanauma Bay, the Marine Life Conservation District and public park. The two deeper-water species, Saccocirrus oahuensis, n. sp. and S. waianaensis, n. sp., have 76-119 and 157-210 segments, respectively; they also have bilateral gonads but lack a pharyngeal pad. The third, S. alanhongi, n. sp., has 35-47 segments, unilateral gonads, and a muscular pharyngeal pad. These species are distinguished from 18 known Saccocirrus spp. by their unique chaetation, number of segments, presence or absence of ventral cilia, and pygidial adhesive structures. Saccocirms oahuensis consumes foraminiferans, and S. alanhongi contained diatoms, unicellular algae, and ostracods. These species add to the interstitial fauna of O'ahu and cooccur with polychaetes Nerilla antennata (Nerillidae) and protodrilids (Protodrilidae), and Kinorhyncha. Saccocirrus alanhongi withstands almost daily disturbance by 600-1200 bathers per day entering the sandy swimming holes in the reef at Hanauma Bay

Fast computation of Bernoulli, Tangent and Secant numbers

We consider the computation of Bernoulli, Tangent (zag), and Secant (zig or Euler) numbers. In particular, we give asymptotically fast algorithms for computing the first n such numbers in O(n^2.(log n)^(2+o(1))) bit-operations. We also give very short in-place algorithms for computing the first n Tangent or Secant numbers in O(n^2) integer operations. These algorithms are extremely simple, and fast for moderate values of n. They are faster and use less space than the algorithms of Atkinson (for Tangent and Secant numbers) and Akiyama and Tanigawa (for Bernoulli numbers).Comment: 16 pages. To appear in Computational and Analytical Mathematics (associated with the May 2011 workshop in honour of Jonathan Borwein's 60th birthday). For further information, see http://maths.anu.edu.au/~brent/pub/pub242.htm

Motif Discovery through Predictive Modeling of Gene Regulation

We present MEDUSA, an integrative method for learning motif models of transcription factor binding sites by incorporating promoter sequence and gene expression data. We use a modern large-margin machine learning approach, based on boosting, to enable feature selection from the high-dimensional search space of candidate binding sequences while avoiding overfitting. At each iteration of the algorithm, MEDUSA builds a motif model whose presence in the promoter region of a gene, coupled with activity of a regulator in an experiment, is predictive of differential expression. In this way, we learn motifs that are functional and predictive of regulatory response rather than motifs that are simply overrepresented in promoter sequences. Moreover, MEDUSA produces a model of the transcriptional control logic that can predict the expression of any gene in the organism, given the sequence of the promoter region of the target gene and the expression state of a set of known or putative transcription factors and signaling molecules. Each motif model is either a $k$-length sequence, a dimer, or a PSSM that is built by agglomerative probabilistic clustering of sequences with similar boosting loss. By applying MEDUSA to a set of environmental stress response expression data in yeast, we learn motifs whose ability to predict differential expression of target genes outperforms motifs from the TRANSFAC dataset and from a previously published candidate set of PSSMs. We also show that MEDUSA retrieves many experimentally confirmed binding sites associated with environmental stress response from the literature.Comment: RECOMB 200

Genome And Secretome Analysis Of The Hemibiotrophic Fungal Pathogen, Moniliophthora Roreri, Which Causes Frosty Pod Rot Disease Of Cacao: Mechanisms Of The Biotrophic And Necrotrophic Phases

Background: The basidiomycete Moniliophthora roreri is the causal agent of Frosty pod rot (FPR) disease of cacao (Theobroma cacao), the source of chocolate, and FPR is one of the most destructive diseases of this important perennial crop in the Americas. This hemibiotroph infects only cacao pods and has an extended biotrophic phase lasting up to sixty days, culminating in plant necrosis and sporulation of the fungus without the formation of a basidiocarp.Results: We sequenced and assembled 52.3 Mb into 3,298 contigs that represent the M. roreri genome. Of the 17,920 predicted open reading frames (OFRs), 13,760 were validated by RNA-Seq. Using read count data from RNA sequencing of cacao pods at 30 and 60 days post infection, differential gene expression was estimated for the biotrophic and necrotrophic phases of this plant-pathogen interaction. The sequencing data were used to develop a genome based secretome for the infected pods. Of the 1,535 genes encoding putative secreted proteins, 1,355 were expressed in the biotrophic and necrotrophic phases. Analysis of the data revealed secretome gene expression that correlated with infection and intercellular growth in the biotrophic phase and invasive growth and plant cellular death in the necrotrophic phase.Conclusions: Genome sequencing and RNA-Seq was used to determine and validate the Moniliophthora roreri genome and secretome. High sequence identity between Moniliophthora roreri genes and Moniliophthora perniciosa genes supports the taxonomic relationship with Moniliophthora perniciosa and the relatedness of this fungus to other basidiomycetes. Analysis of RNA-Seq data from infected plant tissues revealed differentially expressed genes in the biotrophic and necrotrophic phases. The secreted protein genes that were upregulated in the biotrophic phase are primarily associated with breakdown of the intercellular matrix and modification of the fungal mycelia, possibly to mask the fungus from plant defenses. Based on the transcriptome data, the upregulated secreted proteins in the necrotrophic phase are hypothesized to be actively attacking the plant cell walls and plant cellular components resulting in necrosis. 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International Trade and Investment Sanctions

The purpose of this paper is to clarify the theory of international economic sanctions and to provide estimates of the short-run economic impact on South Africa of externally imposed reductions of the imports and capital flows into that country. A macroeconomic picture of South Africa's "dependence" is drawn, and the economy's vulnerability in the short run is seen to be in its capacity to import, not in exports or capital flows. Trade and capital sanctions most clearly damage South Afnca's growth potential; the short-run impact is harder to quantify. A static linear programming model of the South African economy is constructed in an attempt at this quantification. This model estimates that small sanctions would have small impact—i.e., if imports were reduced by less than one-fourth, GDP would be cut by only about one half as large a percentage as imports. Larger import reductions cause greater damage. If imports were to be cut in half, not only would GDP be seriously reduced but massive unemployment and relocation of white labor would occur.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/68182/2/10.1177_002200277902300401.pd

Charged lepton electric dipole moments with the localized leptons and the new Higgs doublet in the two Higgs doublet model

We study the lepton electric dipole moments in the split fermion scenario, in the two Higgs doublet model, where the new Higgs scalars are localized around the origin in the extra dimension, with the help of the localizer field. We observe that the numerical value of the electron (muon, tau) electric dipole moment is at the order of the magnitude of 10^{-31} (10^{-24}, 10^{-22}) (e-cm) and this quantity is sensitive the new Higgs localization in the extra dimension.Comment: 20 pages, 7 figure

Understanding preventive behaviors among mid-Western African-American men: a pilot qualitative study of prostate screening

http://dx.doi.org/10.1016/j.jomh.2011.03.00

Changing patterns of eastern Mediterranean shellfish exploitation in the Late Glacial and Early Holocene: Oxygen isotope evidence from gastropod in Epipaleolithic to Neolithic human occupation layers at the Haua Fteah cave, Libya

The seasonal pattern of shellfish foraging at the archaeological site of Haua Fteah in the Gebel Akhdar, Libya was investigated from the Epipaleolithic to the Neolithic via oxygen isotope (d18O) analyses of the topshell Phorcus (Osilinus) turbinatus. To validate this species as faithful year-round palaeoenvironmental recorder, the intra-annual variability of d18O in modern shells and sea water was analysed and compared with measured sea surface temperature (SST). The shells were found to be good candidates for seasonal shellfish forging studies as they preserve nearly the complete annual SST cycle in their shell d18O with minimal slowing or stoppage of growth. During the terminal Pleistocene Early Epipaleolithic (locally known as the Oranian, with modeled dates of 17.2-12.5 ka at 2sigma probability, Douka et al., 2014), analysis of archaeological specimens indicates that shellfish were foraged year-round. This complements other evidence from the archaeological record that shows that the cave was more intensively occupied in this period than before or afterwards. This finding is significant as the period of the Oranian was the coldest and driest phase of the last glacial cycle in the Gebel Akhdar, adding weight to the theory that the Gebel Akhdar may have served as a refugium for humans in North Africa during times of global climatic extremes. Mollusc exploitation in the Latest Pleistocene and Early Holocene, during the Late Epipaleolithic (locally known as the Capsian, c. 12.7 to 9 ka) and the Neolithic (c. 8.5 to 5.4 ka), occurred predominantly during winter. Other evidence from these archaeological phases shows that hunting activities occurred during the warmer months. Therefore, the timing of Holocene shellfish exploitation in the Gebel Akhdar may have been influenced by the seasonal availability of other resources at these times and possibly shellfish were used as a dietary supplement when other foods were less abundant

Caste development and reproduction: a genome-wide analysis of hallmarks of insect eusociality

The honey bee queen and worker castes are a model system for developmental plasticity. We used established expressed sequence tag information for a Gene Ontology based annotation of genes that are differentially expressed during caste development. Metabolic regulation emerged as a major theme, with a caste-specific difference in the expression of oxidoreductases vs. hydrolases. Motif searches in upstream regions revealed group-specific motifs, providing an entry point to cis-regulatory network studies on caste genes. For genes putatively involved in reproduction, meiosis-associated factors came out as highly conserved, whereas some determinants of embryonic axes either do not have clear orthologs (bag of marbles, gurken, torso), or appear to be lacking (trunk) in the bee genome. Our results are the outcome of a first genome-based initiative to provide an annotated framework for trends in gene regulation during female caste differentiation (representing developmental plasticity) and reproduction