Configurations and relative efficiencies of shrimp trawls employed in southeastern United States waters

Common shrimp trawl designs employed in the southeastern United States shrimp fishery are the flat, balloon, semiballoon, jib, and super X-3. Recent innovations in trawl design and rigging, including the twin trawl rigging and tongue trawl design, have improved the efficiency of shrimp trawling gear. A description of the construction techniques for the different designs indicate differences which affect gear performance. Measurements of horizontal spread and vertical opening for 76 trawl configurations indicate the relative efficiencies of the different designs. Maximum horizontal spreading efficiency was achieved by the "twin" and "tongue" trawl designs followed by the super X-3, jib, balloon, and semiballoon designs. Designs having the greatest vertical openings were the tongue and flat trawl designs followed by the semiballoon. Maximum total gape dimension was demonstrated by the "Mongoose" tongue trawl. Comparison of trawl spreading efficiency and door area to headrope length ratio indicates that a range of 70-80 in square (per door) of door area is required for each foot of trawl headrope length for maximum efficiency with conventional trawl designs and 66-75 in square per foot of headrope for tongue trawl designs. (PDF file contains 18 pages.

Lower Bounds on the Redundancy of Huffman Codes with Known and Unknown Probabilities

In this paper we provide a method to obtain tight lower bounds on the minimum redundancy achievable by a Huffman code when the probability distribution underlying an alphabet is only partially known. In particular, we address the case where the occurrence probabilities are unknown for some of the symbols in an alphabet. Bounds can be obtained for alphabets of a given size, for alphabets of up to a given size, and for alphabets of arbitrary size. The method operates on a Computer Algebra System, yielding closed-form numbers for all results. Finally, we show the potential of the proposed method to shed some light on the structure of the minimum redundancy achievable by the Huffman code

Investigating Cancer Molecular Genetics using Genome-wide RNA Interference Screens: A Dissertation

The development of RNAi based technologies has given researchers the tools to interrogate processes as diverse as cancer biology, metabolism and organ development. Here I employ genome-wide shRNA screens to discover the genes involved in two different processes in carcinogenesis, oncogene-induced senescence [OIS] and epigenetic silencing of tumor suppressor genes [TSGs]. OIS is a poorly studied yet significant tumor suppressing mechanism in normal cells where they enter cell cycle arrest [senescence] or programmed cell death [apoptosis] in the presence of an activated oncogene. Here I employ a genomewide shRNA screen and identify a secreted protein, IGFBP7, that induces senescence and apoptosis in melanocytes upon introduction of the oncogene BRAFV600E. Expression of BRAFV600E in primary cells leads to synthesis and secretion of IGFBP7, which acts through autocrine/paracrine pathways to inhibit BRAF-MEK-ERK signaling and induce senescence and apoptosis. Apoptosis results from IGFBP7-mediated upregulation of BNIP3L, a proapoptotic BCL2 family protein. Recombinant IGFBP7 has potent pro-apoptotic and anti-tumor activity in mouse xenograft models using BRAFV600E-postive melanoma cell lines. Finally, IGFBP7 is epigenetically silenced in human melanoma samples suggesting IGFBP7 expression is a key barrier to melanoma formation. Next I investigated the factors involved in epigenetic silencing in cancer. The TSG p14ARFis inactivated in a wide range of cancers by promoter hypermethylation through unknown mechanisms. To discover p14ARF epigenetic silencing factors, I performed a genome-wide shRNA screen and identified ZNF304, a zinc finger transcription factor that contains a Krüppel-associated box [KRAB] repressor domain. I show that ZNF304 binds to the p14ARF promoter and recruits a KRAB co-repressor complex containing KAP1, SETDB1 and DNMT1 for silencing. We find oncogenic RAS signaling to promote the silencing of p14ARF by USP28-mediated stabilization of ZNF304. In addition I find ZNF304 to be overexpressed in human colorectal cancers and responsible for hypermethylation of over 50 TSGs known as Group 2 CIMP marker genes. My findings establish ZNF304 as a novel oncogene that directs epigenetic silencing and facilitates tumorigenicity in colorectal cancer

On electrons and hydrogen-bond connectivity in liquid water

The network connectivity in liquid water is revised in terms of electronic signatures of hydrogen bonds (HBs) instead of geometric criteria, in view of recent X-ray absorption studies. The analysis is based on ab initio molecular-dynamics simulations at ambient conditions. Even if instantaneous thread-like structures are observed in the electronic network, they continuously reshape in oscillations reminiscent of the r and t modes in ice (tau~170 fs). However, two water molecules initially joint by a HB remain effectively bound over many periods regardless of its electronic signature.Comment: 4 pages, 4 figure

Penicillium astrolabium and penicillium neocrassum, two new species isolated from grapes and their phylogenetic placement in the P. olsonii and P. brevicompactum clade

We describe two new terverticillate Penicillium species isolated from grapes on the basis of phenotypic and phylogenetic differences from known species. The strains were isolated in the course of a study to establish the mycobiota of grapes in Portugal. Penicillium astrolabium is phenotypically similar to P. olsonii but differs from it by two cultural characters, growth rates and the colony reverse color. P. neocrassum is similar to P. brevicompactum but is readily distinguished by sclerotia production. Phylogenetically P. astrolabium and P. neocrassum are placed respectively in the P. olsonii and P. brevicompactum clade. Multilocus analysis confirmed the genetic distinctiveness of both species. The parsimony trees obtained for ITS-lsu rDNA region and two protein coding genes, calmodulin and b-tubulin, show congruence for all the species in the Olsonii series: P. brevicompactum, P. bialowiezense, P. olsonii, P. astrolabium and P. neocrassum, indicating that these taxa are genetically well isolated.Fundação para a Ciência e a Tecnologia (FCT

Far-infrared edge modes in quantum dots

We have investigated edge modes of different multipolarity sustained by quantum dots submitted to external magnetic fields. We present a microscopic description based on a variational solution of the equation of motion for any axially symmetric confining potential and multipole mode. Numerical results for dots with different number of electrons whose ground-state is described within a local Current Density Functional Theory are discussed. Two sum rules, which are exact within this theory, are derived. In the limit of a large neutral dot at B=0, we have shown that the classical hydrodynamic dispersion law for edge waves \omega(q) \sim \sqrt{q \ln (q_0/q)} holds when quantum and finite size effects are taken into account.Comment: We have changed some figures as well as a part of the tex

Far-infrared edge modes in quantum dots

We have investigated edge modes of different multipolarity sustained by quantum dots submitted to external magnetic fields. We present a microscopic description based on a variational solution of the equation of motion for any axially symmetric confining potential and multipole mode. Numerical results for dots with different number of electrons whose ground-state is described within a local Current Density Functional Theory are discussed. Two sum rules, which are exact within this theory, are derived. In the limit of a large neutral dot at B=0, we have shown that the classical hydrodynamic dispersion law for edge waves \omega(q) \sim \sqrt{q \ln (q_0/q)} holds when quantum and finite size effects are taken into account.Comment: We have changed some figures as well as a part of the tex

Spatial Configuration and Vehicular Movement: a nationwide correlational study

We provide the most comprehensive study to date on the correlation between network centrality measures and vehicular movement flows, using a model of the UK’s entire road network (2,031,971 nodes) and a very large dataset of vehicular movement counts (20,752 instances, evenly distributed over the UK’s territory). We describe the statistical associations between observed vehicular flows and the values of betweenness centrality of the road-network nodes where such flows were measured, the latter calculated using Euclidean and angular distance functions, across a number of increasing radii, from the local to the supra-regional scales. Relations to road capacity are also discussed in principal road networks where this is known. The geographical comprehensiveness of our model and the size of our movement sample allows us to state, with unprecedented statistical validity, the clear outperformance of angular distance over Euclidean distance, on what concerns the effect sizes of the studied correlations. We also demonstrate the existence of two clearly different regimes of association between movement and centrality, occurring on the background and foreground networks of cities, which may be interpreted as new evidence of the dual structure of urban form, proposed by space syntax

The influence of skull shape modularity on internal skull structures: a 3D-Pilot study using bears

In order to capture the phenotypic variation of the internal skull structures, such as the sinuses or the brain, it is necessary to perform CT scans in a large number of specimens, which is difficult and expensive. Therefore, while the external morphology of the mammalian cranium has been the subject of many morphometric studies, the internal structures of the cranium have been comparatively less studied. Here, we explore how the variation of external shape reflects the morphology of internal structures. We use the family Ursidae (Carnivora, Mammalia) as a case study because bears have a wide variability of cranial morphologies in part associated with different trophic ecologies. To do this, we digitized a set of landmarks in 3D with a Microscribe G2X from the external surface of the cranium in a wide sample of bears. Additionally, the crania of seven bear species were CT-scanned and prepared digitally to visualize the 3D models of the external cranium morphology and of internal structures. Subsequently, we divided the landmarks into two modules, splanchnocranium and neurocranium, and we perform a two-block partial least squares analysis (2B PLS) to explore the intraspecific (static) morphological changes associated with the covariation between them. These morphological changes were visualized using the morphing technique with the 3D models, looking at both the external shape and the internal structures. In addition, we inferred the volume of the sinuses and of the brain in each hypothetical model. Our results show that the first two PLS axes are associated externally with changes in the basicranial angle, face length and cranium height and width. Concerning the internal structures, there are parallel changes in dorso-ventral and medio-lateral expansion of sinuses and brain, accompanied by their corresponding changes in volume. In contrast, the third PLS axis is related to opposite changes in the volume of sinuses and brain. These preliminary results suggest that the opposite relationship between sinuses and brain volumes in the bear cranium is not as evident as expected, at least at intraspecific level.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Self-avoiding walks on a bilayer Bethe lattice

We propose and study a model of polymer chains in a bilayer. Each chain is confined in one of the layers and polymer bonds on first neighbor edges in different layers interact. We also define and comment results for a model with interactions between monomers on first neighbor sites of different layers. The thermodynamic properties of the model are studied in the grand-canonical formalism and both layers are considered to be Cayley trees. In the core region of the trees, which we may call a bilayer Bethe lattice, we find a very rich phase diagram in the parameter space defined by the two activities of monomers and the Boltzmann factor associated to the interlayer interaction between bonds or monomers. Beside critical and coexistence surfaces, there are tricritical, bicritical and critical endpoint lines, as well as higher order multicritical points.Comment: 21 pages, 10 figures. Journal of Statistical Mechanics: Theory and Experiment (in press