bluuebunny/crossref_metadata_2025 huggingface dataset:
Mathematical modelling of shallow flows: Closure models drawn from grain-scale mechanics of sediment transport and flow hydrodynamicsThis paper is one of a selection of papers in this Special Issue in honour of Professor M. Selim Yalin (1925–2007).
Authors: Ferreira Rui M. L. , Franca Mário J. , Leal João G. A. B. , Cardoso António H.
Published: November 2009

Mathematical modelling of river processes is, nowadays, a key element in river engineering and planning. River modelling tools should rest on conceptual models drawn from mechanics of sediment transport, river mechanics, and river hydrodynamics. The objectives of the present work are (i) to describe conceptual models of sediment transport, deduced from grain-scale mechanics of sediment transport and turbulent flow hydrodynamics, and (ii) to present solutions to specific river morphology problems. The conceptual models described are applicable to the morphologic evolution of rivers subjected to the transport of poorly sorted sediment mixtures at low shear stresses and to geomorphic flows featuring intense sediment transport at high shear stresses. In common, these applications share the fact that sediment transport and flow resistance depend, essentially, on grain-scale phenomena. The idealized flow structures are presented and discussed. Numerical solutions for equilibrium and nonequilibrium sediment transport are presented and compared with laboratory and field data.
On bedform growth and nonequilibrium sediment transportThis paper is one of a selection of papers in this Special Issue in honour of Professor M. Selim Yalin (1925-2007).
Authors: Zhou Donghuo , Mendoza Cesar
Published: November 2009

Starting from the model proposed by the authors to analyze the time-evolution of bedforms growing on the surface of an initially flat sand bed, the present study explores associated features of the bedform growth processes, including (i) mechanisms of growth, (ii) evolution of the bedform-induced drag, (iii) transition to antidunes, and (iv) non-equilibrium bedload sediment transport.
Size and effect on the mean flow of large-scale horizontal coherent structures in open-channel flows: an experimental studyThis paper is one of a selection of papers in this Special Issue in honour of Professor M. Selim Yalin (1925–2007).
Authors: Ferreira da Silva Ana Maria , Ahmari Habib
Published: November 2009

The size of the largest horizontal coherent structures (HCSs) of turbulence in open-channel flows is investigated experimentally on the basis of three series of flow velocity measurements. These are further used to explore the dynamics and morphological consequences of HCSs. The flow velocity measurements were carried out in a 21 m long and 1 m wide channel, with a bed formed by sand with average grain size of 2 mm. The bed surface was flat. The turbulent and subcritical flow under investigation was uniform, with a flow depth of 4 cm. The bed slope of 0.0015 was such that, for the present flow depth, the bed shear stress acting on the bed was substantially below the threshold for initiation of motion, thus ensuring that the bed remained flat throughout the measurements. To the knowledge of the writers, this work is a first attempt to systematically investigate HCSs in open-channel flows. It should be viewed as an extension to the case of horizontal structures of work previously carried out by a number of authors on large-scale organized turbulence motion in open-channel flows, so far focusing exclusively on vertical coherent structures (VCSs). The horizontal burst length was found to be between five and seven times the flow width. A slight internal meandering of the flow caused by the superimposition of burst sequences on the mean flow was detectable. Both of these findings lend support to the longstanding belief expressed by many prominent researchers that the formation of large-scale river forms is directly related to the large-scale turbulence. In particular, the present measurements for the first time provide some direct evidence in support of hypotheses previously raised by Yalin and da Silva regarding the formation of alternate bars and meanders through the action of HCSs on the mean flow and the mobile bed and banks.
Actin polymerization is controlled by residue size at position 204
Authors: Yates Susan P. , Loncar Ana , Dawson John F.
Published: November 2009

Previous work has shown that purified double mutant A204C/C374A yeast actin is polymerization-deficient in vitro under physiological concentrations. To understand the importance of the 204 residue in subdomain 4, a series of actin proteins with a single mutation at this position were created with Cys-374 retained. Only yeast expressing A204G-, A204S-, or A204C-actin were viable. The A204G and A204S strains were sensitive to cold temperature and hyperosmolarity, whereas the A204C strain showed more profound effects on growth under these conditions. Cells expressing A204C-actin exhibited anomalies previously observed for A204C/C374A actin, including abnormal actin structures. A204G- and A204S-actin proteins had 12- and 13-fold increased critical concentrations, respectively, relative to wild-type. Only at very high concentrations could A204C actin polymerize when ATP was bound; when hydrolyzed, the ADP-containing A204C filaments depolymerized, demonstrating a profound difference in critical concentration between ATP and ADP states with A204C actin. A correlation between size of the residue substituted at position 204 and energy minimization of actin filament models was observed. We propose that the region surrounding residue 204 is involved in interactions that change depending on the phosphorylation state of the bound nucleotide that might reflect different conformations of F-actin subunits.
Molecular disruption of oncogenic signal transducer and activator of transcription 3 (STAT3) protein
Authors: Fletcher Steven , Drewry Joel A. , Shahani Vijay M. , Page Brent D. G. , Gunning Patrick T.
Published: November 2009

Signal transducer and activator of transcription protein 3 (STAT3) is a latent cytosolic transcription factor that is widely recognized as being a master regulator of the cellular functions that lead to the cancer phenotype. Constitutively activated STAT3 protein activity is routinely observed in human cancers, promoting uncontrolled cell proliferation and suppressing apoptosis. Until relatively recently, inhibition of STAT3 transcriptional activity was achieved indirectly via suppression of upstream kinase activators and extracellular cytokine and (or) growth factor stimuli. However, activated STAT3 forms transcriptionally functional STAT3–STAT3 dimers, providing a valid juncture for targeted downstream molecular inhibition. STAT3's prominent role in cancer has seen a decade of innovative and novel approaches to targeting constitutively active STAT3 protein–protein complexes. This mini-review outlines the progress made towards identifying molecular agents capable of silencing aberrant STAT3 signalling through the disruption of STAT3 complexation events.
Cloning and sequencing of tubulin cDNAs fromArtemia franciscana: evidence for differential expression of α- and β-tubulin genes
Authors: Garant Katy A. , MacRae Thomas H.
Published: November 2009

Tubulin is a heterodimeric protein composed of α- and β-tubulin. In most organisms, they are encoded by multiple gene families whose members are subject to differential regulation. The objective of the work described herein was to better understand tubulin gene expression in the extremophile Artemia franciscana To this end tubulin cDNAs were cloned and sequenced. αAT2, an α-tubulin cDNA, differed by one nucleotide from αAT1, a previously cloned Artemia cDNA. This change, possibly generated by allelic variation, caused an M313V substitution in α-tubulin. The amino acid sequence of β-tubulin encoded by βAT1, one of only a very limited number of cloned crustacean β-tubulin cDNA sequences yet available, and the first from Artemia, was similar to other β-tubulins. However, βAT1 possessed four degenerate TATA boxes in the 5′ untranslated region, although authentic TATA and CCAAT boxes occurred in the 3′ non-coding sequence. Analyses by quantitative PCR demonstrated that the amount of tubulin mRNA declined relative to total mRNA in progressive life history stages of Artemia and also that the organism contained more αAT2- than βAT1-tubulin mRNA at all developmental phases examined.
Functional cooperation between Stat-1 and ets-1 to optimizeicam-1gene transcription
Authors: Yockell-Lelièvre Julien , Spriet Corentin , Cantin Paule , Malenfant Patrick , Heliot Laurent , de Launoit Yvan , Audette Marie
Published: November 2009

Intercellular adhesion molecule-1 (ICAM-1) plays an important role in the immune system, enabling the interactions between effector cells and target cells. It is also known to be involved in tumor growth and metastasis. Its expression is transcriptionally regulated by several proinflammatory cytokines including IFN-γ, which induces ICAM-1 transcription via the JAK–STAT signaling pathway in a Stat1-dependent fashion. The ICAM-1 promoter contains several cis-active regulatory elements including 2 Ets binding sites (EBSs) located at positions –158 and –138 relatively to the AUG, which were previously shown to play a role in the constitutive activity of the ICAM-1 promoter. In the present study, we have determined whether the EBSs are also involved in the regulation of ICAM-1 gene transcription by pro-inflammatory cytokines. Transient transfection assays were performed with reporter genes containing ICAM-1 promoter constructions cloned upstream from the firefly luciferase gene. Site-specific mutations of the EBS diminished the promoter activity stimulated by IFN-γ, although the IFN-γ responsive element (pIγRE), which binds Stat1, was intact. Stimulation of the transcriptional activity following IFN-γ treatment was significantly reduced when both EBSs were inactivated. Co-immunoprecipitation experiments provided evidence of a physical interaction involving Ets1 and Stat1. In COS-1 and HEK 293 cells cotransfected with CFP-Stat1 and YFP-Ets fusion protein, fluorescence resonance energy transfer experiments confirmed the close proximity of these 2 proteins in living cells following treatment with IFN-γ.
Platelet-derived endothelial cell growth factor mediates angiogenesis and antiapoptosis in rat aortic endothelial cells
Authors: Hemalatha Thiagarajan , Tiwari Mitali , Balachandran Chidambaram , Manohar Bhakthavatsalam Murali , Puvanakrishnan Rengarajulu
Published: November 2009

This study explores the angiogenic and antiapoptotic activities of platelet-derived endothelial cell growth factor (PDECGF) in rat aortic endothelial cells. The effects of PDECGF on rat aortic endothelial cell (RAEC) proliferation, migration, chemotaxis, and tubule formation were investigated in vitro at various concentrations viz., 1, 2, 4, 8, 16, and 32 ng·mL–1on endothelial cells. Endothelial cells were induced with hypoxic stress and the antiapoptotic effects of PDECGF were analysed by cell survival assay, fluorescence microscopy, cell viability assay, and flow cytometry. The results demonstrated the angiogenic potential of PDECGF on endothelial cells in a dose-dependent manner. PDECGF at 16 and 32 ng·mL–1increased cell proliferation (>80%), induced cell migration (>4 fold), stimulated chemotaxis (>2 fold), and increased tubule formation (>3 fold) compared with the control. Studies on hypoxic stress revealed the antiapoptotic nature of PDECGF on endothelial cells. PDECGF treatment enhanced cell survival by 14%, as well as cell viability by 13%, and decreased the percentage of apoptotic cells by 13% as demonstrated by fluorescence-activated cell sorter studies (FACS). In conclusion, this study demonstrated the angiogenic and antiapoptotic potentials of PDECGF on RAEC.
Characterization of the O-antigen in the lipopolysaccharide of Cronobacter (Enterobacter) malonaticus 3267
Authors: MacLean Leann L. , Vinogradov Evgeny , Pagotto Franco , Farber Jeffrey M. , Perry Malcolm B.
Published: November 2009

Cronobacter malonaticus, a Gram-negative bacterium previously known as Enterobacter sakazakii, is an opportunistic pathogen known to cause serious infection in infants and neonates. To provide aid for the serological and chemical identification of clinical, environmental, or food isolates of this emerging pathogen, the characterization of the lipopolysaccharide (LPS) O-polysaccharide (O-PS) antigens of Cronobacter spp. is being undertaken. The structural analysis of the O-PS, obtained by hydrazinolysis of the lipopolysaccharide produced by Cronobacter malonaticus HPB 3267, was investigated by composition, methylation, and two-dimensional high-resolution nuclear magnetic resonance methods, and was found to be a polymer of a branched pentasaccharide unit. This unit is composed of d-glucose (d-Glc), d-galactose (d-Gal), 2-amino-2-deoxy-d-glucose (d-GlcN), 2-amino-2-deoxy-d-galactose (d-GalN) and 3-deoxy-d-manno-oct-2-ulosonic acid (Kdo) residues (1: 1: 1: 1: 1), forms the repeating oligosaccharide in the O-PS antigen, and has the structure: [Formula: see text]
Inhibition of Hes1 activity in gall bladder epithelial cells promotes insulin expression and glucose responsiveness
Authors: Coad R. A. , Dutton J. R. , Tosh D. , Slack J. M.W.
Published: November 2009

The biliary system has a close developmental relationship with the pancreas, evidenced by the natural occurrence of small numbers of biliary-derived β-cells in the biliary system and by the replacement of biliary epithelium with pancreatic tissue in mice lacking the transcription factor Hes1. In normal pancreatic development, Hes1 is known to repress endocrine cell formation. Here we show that glucose-responsive insulin secretion can be induced in biliary epithelial cells when activity of the transcription factor Hes1 is antagonised. We describe a new culture system for adult murine gall bladder epithelial cells (GBECs), free from fibroblast contamination. We show that Hes1 is expressed both in adult murine gall bladder and in cultured GBECs. We have created a new dominant negative Hes1 (ΔHes1) by removal of the DNA-binding domain, and show that it antagonises Hes1 function in vivo. When ΔHes1 is introduced into the GBEC it causes expression of insulin RNA and protein. Furthermore, it confers upon the cells the ability to secrete insulin following exposure to increased external glucose. GBEC cultures are induced to express a wider range of mature β cell markers when co-transduced with ΔHes1 and the pancreatic transcription factor Pdx1. Introduction of ΔHes1 and Pdx1 can therefore initiate a partial respecification of phenotype from biliary epithelial cell towards the pancreatic β cell.
Selenoprotein T deficiency alters cell adhesion and elevates selenoprotein W expression in murine fibroblast cells
Authors: Sengupta Aniruddha , Carlson Bradley A. , Labunskyy Vyacheslav M. , Gladyshev Vadim N. , Hatfield Dolph L.
Published: November 2009

Mammalian selenoproteins have diverse functions, cellular locations, and evolutionary histories, but all use the amino acid selenocysteine (Sec), often present in the enzyme’s active site. Only about half of mammalian selenoproteins have been functionally characterized, with most being oxidoreductases. The cellular role of selenoprotein T (SelT), manifesting a CxxU motif in a thioredoxin-like fold and localized to Golgi and the endoplasmic reticulum, is not known. To examine its biological function, we knocked down SelT expression in mouse fibroblast cells and found that SelT deficiency alters cell adhesion and enhances the expression of several oxidoreductase genes, while decreasing the expression of genes involved in cell structure organization, suggesting the involvement of SelT in redox regulation and cell anchorage. Furthermore, we found that the loss of SelT elevates expression of another selenoprotein, selenoprotein W (SepW1). SelT and SepW1 belong to the same protein family, suggesting that SepW1 may functionally compensate for SelT.
Antioxidative activities of white rose flower extract and pharmaceutical advantages of its hexane fraction via free radical scavenging effects
Authors: Park Dongsun , Jeon Jeong Hee , Kwon Sang-Chul , Shin Sunhee , Jang Ja Young , Jeong Heon Sang , Lee Do Ik , Kim Yun-Bae , Joo Seong Soo
Published: November 2009

In this study, we determined the antioxidant activities of two different solvent fractions(butanol and hexane) obtained from white Rosa rugosa flowers by employing various assays such as 2,2-diphenyl-1-picrylhydrazyl hydrate (DPPH), 2,2′-azino-bis(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS) radical scavenging activity, and nitric oxide (NO) scavenging and inhibition activity in S-nitroso-N-acetylpenicillamine (SNAP) in the RAW264.7 model. In addition, more advanced antioxidant assays were conducted, including lipid peroxidation, hydroxyl radical-mediated oxidation, DNA fragmentation, apoptosis, and cell growth. The results revealed that the hexane fraction, which contained a significant amount of polyphenols and volatile components, had excellent antioxidant potency and could scavenge free radicals of DPPH and ABTS. Interestingly, the hexane fraction inhibited lipid peroxidation to almost the same degree as a chemical antioxidant. In the NO assay, the hexane fraction effectively scavenged free radicals at all dose ranges and is expected to inhibit NO production in mammalian cells. The hexane fraction effectively prevented oxidative damage, which was induced by Cu2+/H2O2, to target proteins at lower concentrations (>1 μg·mL–1). The DNA fragmentation and the cell-level assays suggest that the hexane fraction may play a crucial role in inhibiting peroxynitrite and H2O2 attack. Based on the findings described in this study, the hexane fraction holds promise for use as a novel pharmaceutical antioxidant.
Reproductive periodicity and host-specific settlement and growth of a deep-water symbiotic sea anemone
Authors: Mercier Annie , Hamel Jean-François
Published: November 2009

Sea anemones Allantactis parasitica Danielssen, 1890 (Actiniaria: Hormathiidae) living as epibionts on various gastropods were found at depths of ~725–1100 m off Labrador (eastern Canada). Live specimens collected with their hosts were studied in the laboratory to elucidate the role of the gastropod host in the reproductive and colonizing success of its actinian symbiont. Broadcast spawning occurred twice a year, in spring and late fall, in correlation with maximum phytoplankton or phytodetritus abundance, often during copulation of the gastropod hosts. The fully developed planula stage was reached after ~22 d. Settlement on the host’s shell generally occurred 40–44 d postfertilization, although some larvae delayed settlement for up to 22 weeks in the absence of a host. Independent and pairwise settlement trials showed that shells of live bathyal gastropods were highly favoured compared with shells of shallow-water gastropods, empty shells, pebbles, or sand. Juveniles developed 24 tentacles and reached ~10 mm in basal disk diameter and ~12 mm in stalk height after 21 months of growth. The estimated growth rates of A. parasitica suggest that symbiotic individuals would require 6–7 years to reach the mean maximum adult size (~35 mm, basal disk diameter), whereas asymbiotic individuals would need 11–12 years.
Using stable isotopes to track frugivory in migratory passerines
Authors: Gagnon Chantal , Hobson Keith A.
Published: November 2009

Several species of North American migratory songbirds undergo seasonal diet shifts from insects to fruits, but this phenomenon is poorly quantified. Measurement of naturally occurring stable isotopes of carbon (δ13C) and nitrogen (δ15N) are linked to sources of diets and trophic level, respectively. We used stable carbon (δ13C) and nitrogen (δ15N) isotope analyses of blood and claw tissues of 16 species of migratory songbirds to evaluate the timing and extent of frugivory over different periods. Species differed considerably in their tissue δ15N values, but we found poor isotopic segregation of species according to our a priori classifications as insectivores or omnivores. Season accounted for considerable variance in tissue δ15N values. However, only American Robin ( Turdus migratorius L., 1766), Northern Oriole ( Icterus galbula (L., 1758)), Gray Catbird ( Dumetella carolinensis (L., 1766)), Least Flycatcher ( Empidonax minimus (W.M. Baird and S.F. Baird, 1843)), and Warbling Vireo ( Vireo gilvus (Vieillot, 1808)) showed expected decrease in winter-grown tissue δ15N values compared with those grown in late summer. This indicates either that our a priori guild associations were incorrect and (or) that using stable isotopes to track frugivory at continental scales is problematic. We recommend that the isotope technique be used to track frugivory only in well-constrained systems where food-web δ15N follows reliable and understood trophic enrichment patterns.
Foods and nutritional components of diets of black bear in Rocky Mountain National Park, Colorado
Authors: Baldwin Roger A. , Bender Louis C.
Published: November 2009

We used scat analysis to determine diets and relative nutritional values of diets for black bears ( Ursus americanus Pallas, 1780) in Rocky Mountain National Park, Colorado, from 2003 to 2006, and compared foods consumed and nutritional components to identify important sources of fecal gross energy (GE), crude fat (CF), and fecal nitrogen (FN) in annual and seasonal diets. Patterns of use of food classes followed typical seasonal patterns for bears, although use of animal matter was among the highest reported (>49% annually). Use of animal matter increased after spring, although crude protein levels in bear diets were always >25%. GE was typically lowest for grasses and other herbaceous plants and highest for ants and ungulates; FN was strongly positively related to most animal sources, but negatively correlated with vegetative matter; and CF showed the strongest positive relationship with ungulates and berries, with the latter likely influenced by the presence of seeds. Compared with historic data (1984–1991), contemporary diets included substantially greater prevalence of anthropogenic foods, which likely contributed to increases in size, condition, and productivity of the contemporary bear population. Management strategies are needed to increase quantity and quality of natural foods while minimizing dependence on anthropogenic sources.
Seasonal detection rates of river otters (Lontra canadensis) using bridge-site and random-site surveys
Authors: Crimmins S. M. , Roberts N. M. , Hamilton D. A. , Mynsberge A. R.
Published: November 2009

Randomization of survey sites is generally desired because of its unbiased approach, but is often abandoned because of logistical constraints. This is true for river otters ( Lontra canadensis (Schreber, 1777)), with bridges commonly determining survey locations. We conducted seasonal sign surveys for river otters on two rivers in southern Missouri, USA, using randomized survey points and fixed bridge-crossing points in 2001–2003. Otter sign was more likely to be detected at randomized sites than at bridge sites in summer (P < 0.0001), with sign being detected on 68% of visits to random sites (n = 348) and on 40% of visits to bridge sites (n = 60). Scat abundance was higher (P = 0.0001) at random sites (8.82 ± 0.6, mean ± SE) than at bridge sites (3.96 ± 1.0) during the summer. Similar but nonsignificant trends were found during the winter. Detection probabilities were significantly higher at random sites than at bridge sites in both seasons. Our results indicate that surveys of bridge sites for river otters may yield inaccurate results for distribution and relative abundance, particularly if conducted during the summer.
Isometric scaling in home-range size of male and female bobcats (Lynx rufus)
Authors: Ferguson Adam W. , Currit Nathan A. , Weckerly Floyd W.
Published: November 2009

For solitary carnivores a polygynous mating system should lead to predictable patterns in space-use dynamics. Females should be most influenced by resource distribution and abundance, whereas polygynous males should be strongly influenced by female spatial dynamics. We gathered mean annual home-range-size estimates for male and female bobcats ( Lynx rufus (Schreber, 1777)) from previous studies to address variation in home-range size for this solitary, polygynous carnivore that ranges over much of North America. Mean annual home ranges for bobcats (171 males, 214 females) from 29 populations covering the entire north to south and east to west range demonstrated female home-range sizes varied more than an order of magnitude and that, on average, males maintained home ranges 1.65 times the size of females. Male home-range sizes scaled isometrically with female home-range sizes indicating that male bobcats increase their home-range size proportional to female home-range size. Using partial correlation analysis we also detected an inverse relationship between environmental productivity, estimated using the normalized difference vegetation index, and home-range size for females but not males. This study provides one of the few empirical assessments of how polygyny influences home-range dynamics for a wide-ranging carnivore.
Forming foci of transmission: the effects of resource utilization, species interaction, and parasitism on molluscan movement
Authors: Gray T. T. , Detwiler J. T. , Minchella D. J.
Published: November 2009

Animal aggregation to environmental cues provides opportunities for parasite transmission between individual hosts of the same or different species. Better characterization of host behavioral responses to environmental stimuli in the absence and presence of parasites will improve our understanding of how foci of transmission form. The behavioral response patterns of two co-occurring freshwater snail species ( Lymnaea elodes (Say, 1821) and Helisoma trivolvis (Say, 1817) (=  Planorbella trivolvis (Say, 1817))) were assessed in response to three environmental stimuli (crayfish (genus Orconectes  Cope, 1872) carrion, vegetation, or temperature gradient). Experiments were conducted with single species and species interactions. In addition, parasitized L. elodes were included in a single-species experiment and a species-interaction experiment. Snail species differed in the direction and magnitude of their responses to the environmental stimuli. Species interactions did not affect the responses to two of the stimuli for either species; however, interspecific interactions affected the response to high temperature in both species. Behavioral responses were altered in the presence of parasites for both the infected and uninfected hosts, suggesting parasitism is an important biotic factor in animal movement. This experimental study indicates co-occurring species respond to environmental factors in different ways. Furthermore, species interactions and parasitism within a guild can have strong effects on animal movement and potentially on parasite transmission.
Tapeworm (Hymenolepis diminuta) infection in flour beetles (Tribolium confusum): does it cause a trade-off between host fecundity and egg size?
Authors: Shostak Allen W.
Published: November 2009

Inter- and intra-specific comparisons commonly reveal an inverse relationship between fecundity and offspring size. Many animals also vary egg size in response to environmental conditions. Infection of flour beetles Tribolium confusum Jaquelin Du Val, 1868 with the rat tapeworm Hymenolepis diminuta (Rudolphi, 1819) causes a major reduction in host fecundity. This study tested if this fecundity reduction was associated with changes in host egg size. Age-matched beetles were either fasted and then exposed to parasites, fasted only, or neither, and egg production and egg length determined for 5 weeks postexposure. Control beetles that were neither fasted nor exposed to parasites had steady egg production, but produced smaller eggs as they aged. Beetles that were fasted only, produced fewer but larger eggs for 1–2 weeks after the fast ended. Then, fecundity and egg size returned to control levels. Infected beetles also produced fewer, larger eggs for 1–2 weeks, but at levels indistinguishable from beetles that had been fasted only. After 2 weeks, while fecundity of infected beetles remained low, egg size became similar to noninfected hosts. Beetles appeared to trade-off fecundity and egg size in response to reduced feeding, but not to the presumed nutritional stress of parasitic infection.
EFFICIENT VARIANTS OF THE BACKWARD-ORACLE-MATCHING ALGORITHM
Authors: FARO SIMONE , LECROQ THIERRY
Published: November 2009

In this article we present two efficient variants of the BOM string matching algorithm which are more efficient and flexible than the original algorithm. We also present bit-parallel versions of them obtaining an efficient variant of the BNDM algorithm. Then we compare the newly presented algorithms with some of the most recent and effective string matching algorithms. It turns out that the new proposed variants are very flexible and achieve very good results, especially in the case of large alphabets.
THE VIRTUAL SUFFIX TREE
Authors: LIN JIE , JIANG YUE , ADJEROH DON
Published: November 2009

We introduce the VST (virtual suffix tree), an efficient data structure for suffix trees and suffix arrays. Starting from the suffix array, we construct the suffix tree, from which we derive the virtual suffix tree. Later, we remove the intermediate step of suffix tree construction, and build the VST directly from the suffix array. The VST provides the same functionality as the suffix tree, including suffix links, but at a much smaller space requirement. It has the same linear time construction even for large alphabets, Σ, requires O(n) space to store (n is the string length), and allows searching for a pattern of length m to be performed in O(m log |Σ|) time, the same time needed for a suffix tree. Given the VST, we show an algorithm that computes all the suffix links in linear time, independent of Σ. The VST requires less space than other recently proposed data structures for suffix trees and suffix arrays, such as the enhanced suffix array [1], and the linearized suffix tree [17]. On average, the space requirement (including that for suffix arrays and suffix links) is 13.8n bytes for the regular VST, and 12.05n bytes in its compact form.
Irrelevant Singletons in Visual Search Do Not Capture Attention but Can Produce Nonspatial Filtering Costs
Authors: Wykowska Agnieszka , Schubö Anna
Published: November 2009

It is not clear how salient distractors affect visual processing. The debate concerning the issue of whether irrelevant salient items capture spatial attention [e.g., Theeuwes, J., Atchley, P., & Kramer, A. F. On the time course of top–down and bottom–up control of visual attention. In S. Monsell & J. Driver (Eds.), Attention and performance XVIII: Control of cognitive performance (pp. 105–124). Cambridge, MA: MIT Press, 2000] or produce only nonspatial interference in the form of, for example, filtering costs [Folk, Ch. L., & Remington, R. Top–down modulation of preattentive processing: Testing the recovery account of contingent capture. Visual Cognition, 14, 445–465, 2006] has not yet been settled. The present ERP study examined deployment of attention in visual search displays that contained an additional irrelevant singleton. Display-locked N2pc showed that attention was allocated to the target and not to the irrelevant singleton. However, the onset of the N2pc to the target was delayed when the irrelevant singleton was presented in the opposite hemifield relative to the same hemifield. Thus, although attention was successfully focused on the target, the irrelevant singleton produced some interference resulting in a delayed allocation of attention to the target. A subsequent probe discrimination task allowed for locking ERPs to probe onsets and investigating the dynamics of sensory gain control for probes appearing at relevant (target) or irrelevant (singleton distractor) positions. Probe-locked P1 showed sensory gain for probes positioned at the target location but no such effect for irrelevant singletons in the additional singleton condition. Taken together, the present data support the claim that irrelevant singletons do not capture attention. If they produce any interference, it is rather due to nonspatial filtering costs.
Neural Changes Associated with Nonspeech Auditory Category Learning Parallel Those of Speech Category Acquisition
Authors: Liu Ran , Holt Lori L.
Published: November 2009

Native language experience plays a critical role in shaping speech categorization, but the exact mechanisms by which it does so are not well understood. Investigating category learning of nonspeech sounds with which listeners have no prior experience allows their experience to be systematically controlled in a way that is impossible to achieve by studying natural speech acquisition, and it provides a means of probing the boundaries and constraints that general auditory perception and cognition bring to the task of speech category learning. In this study, we used a multimodal, video-game-based implicit learning paradigm to train participants to categorize acoustically complex, nonlinguistic sounds. Mismatch negativity (MMN) responses to the nonspeech stimuli were collected before and after training, and changes in MMN resulting from the nonspeech category learning closely resemble patterns of change typically observed during speech category learning. This suggests that the often-observed “specialized” neural responses to speech sounds may result, at least in part, from the expertise we develop with speech categories through experience rather than from properties unique to speech (e.g., linguistic or vocal tract gestural information). Furthermore, particular characteristics of the training paradigm may inform our understanding of mechanisms that support natural speech acquisition.
Hyporesponsive Reward Anticipation in the Basal Ganglia following Severe Institutional Deprivation Early in Life
Authors: Mehta Mitul A. , Gore-Langton Emma , Golembo Nicole , Colvert Emma , Williams Steven C. R. , Sonuga-Barke Edmund
Published: November 2009

Severe deprivation in the first few years of life is associated with multiple difficulties in cognition and behavior. However, the brain basis for these difficulties is poorly understood. Structural and functional neuroimaging studies have implicated limbic system structures as dysfunctional, and one functional imaging study in a heterogeneous group of maltreated individuals has confirmed the presence of abnormalities in the basal ganglia. Based on these studies and known dopaminergic abnormalities from studies in experimental animals using social isolation, we used a task of monetary reward anticipation to examine the functional integrity of brain regions previously shown to be implicated in reward processing. Our sample included a group of adolescents (n = 12) who had experienced global deprivation early in their lives in Romania prior to adoption into UK families. In contrast to a nonadopted comparison group (n = 11), the adoptees did not recruit the striatum during reward anticipation despite comparable performance accuracy and latency. These results show, for the first time, an association between early institutional deprivation and brain reward systems in humans and highlight potential neural vulnerabilities resulting from such exposures.
Sound Categorization and Conceptual Priming for Nonlinguistic and Linguistic Sounds
Authors: Aramaki Mitsuko , Marie Céline , Kronland-Martinet Richard , Ystad Sølvi , Besson Mireille
Published: November 2009

The aim of these experiments was to compare conceptual priming for linguistic and for a homogeneous class of nonlinguistic sounds, impact sounds, by using both behavioral (percentage errors and RTs) and electrophysiological measures (ERPs). Experiment 1 aimed at studying the neural basis of impact sound categorization by creating typical and ambiguous sounds from different material categories (wood, metal, and glass). Ambiguous sounds were associated with slower RTs and larger N280, smaller P350/P550 components, and larger negative slow wave than typical impact sounds. Thus, ambiguous sounds were more difficult to categorize than typical sounds. A category membership task was used in Experiment 2. Typical sounds were followed by sounds from the same or from a different category or by ambiguous sounds. Words were followed by words, pseudowords, or nonwords. Error rate was highest for ambiguous sounds and for pseudowords and both elicited larger N400-like components than same typical sounds and words. Moreover, both different typical sounds and nonwords elicited P300 components. These results are discussed in terms of similar conceptual priming effects for nonlinguistic and linguistic stimuli.
Establishing a sexual identity
Authors: Tissot Catherine
Published: November 2009

The physical and emotional changes that occur in adolescence are part of the process of sexual maturity. These changes occur irrespective of ability and are often aligned with psychological and social factors. When the nature of a disability has an inherent limitation in social awareness, as is the case for individuals with autism, the achievement of personal sexual identity can become much more complex. Challenges in supporting individuals in this respect can be caused by the sensitive aspects of inappropriate behaviour, the abstract nature of teaching the topic, and the general reluctance on the part of parents and staff to discuss sexuality in individuals with disabilities. This article explores how a residential school addressed this gap. It provides details of how this need was met for seven students and the process undertaken to involve staff, parents and other stakeholders to establish ongoing support.
Autistic disorder symptoms in Rett syndrome
Authors: Wulffaert Josette , Van Berckelaer-Onnes Ina A. , Scholte Evert M.
Published: November 2009

According to the major classification systems it is not possible to diagnose a comorbid autistic disorder in persons with Rett syndrome. However, this is a controversial issue, and given the level of functioning of persons with Rett syndrome, the autistic disorder is expected to be present in a comparable proportion as in people with the same level of functioning. To investigate, parents of 52 females with classical and atypical Rett syndrome (2.4—49.3 years) completed the Developmental Behavior Checklist (DBC), the Diagnostic Interview for Social and Communication Disorders (DISCO) and the Dutch Vineland Screener 0—6 (VS 0—6). All participants had a severe to profound intellectual disability (ID) according to the VS 0—6. Behavior indicated an autistic disorder in 42 (DBC) to 58 percent (DISCO) of the Rett cases. Autistic behavior had decreased in 19 percent such that they no longer met the criteria for autistic disorder. Some participants were suspected of having a comorbid autistic disorder, though not more often than can be expected at their level of functioning. Clinicians should be aware of the possibility of a comorbid autistic disorder as much as they should be in other people with this level of functioning.
Assessing progress during treatment for young children with autism receiving intensive behavioural interventions
Authors: Hayward Diane , Eikeseth Svein , Gale Catherine , Morgan Sally
Published: November 2009

This study examined progress after 1 year of treatment for children with autism who received a mean of 36 hours per week one-to-one University of California at Los Angeles Applied Behavior Analysis (UCLA ABA) treatment. Two types of service provision were compared: an intensive clinic based treatment model with all treatment personnel ( N = 23), and an intensive parent managed treatment model with intensive supervision only ( N = 21). A non-concurrent multiple baseline design across participants ( N = 13) examined whether progress was associated with ABA treatment or confounders. Between intake and follow-up, children in both groups improved significantly on IQ, visual-spatial IQ, language comprehension, expressive language, social skills, motor skills and adaptive behaviour. There were no significant differences between the two groups on any of the measures at follow-up. Mean IQ for participants in both groups increased by 16 points between intake and follow-up. These findings are consistent with previous studies demonstrating the benefits of ABA treatment.
Efficacy of pre-procedural rinsing in reducing aerosol contamination during dental procedures
Authors: Purohit Bharathi , Priya Harsh , Acharya Shashidhar , Bhat Meghashyam , Ballal Mamtha
Published: November 2009

Our objective was to determine the efficacy of pre-procedural rinsing with chlorhexidine in reducing bacterial aerosol contamination during use of ultrasonic scaler and high speed air turbine handpiece. Twenty patients, ten each for the two groups who were found to satisfy the inclusion criteria were selected for the study. Four predesignated locations of the dental clinic were chosen to be evaluated for each patient using blood agar plates. Aerosols were collected during treatment procedures for control and experimental quadrants. Results showed that a regimen of 30-seconds pre-procedural rinsing with 0.12% chlorhexidine gluconate before dental procedures consistently reduced colony-forming units than without rinsing due to the ability of antiseptic mouthwash to inhibit microbial growth. There was more aerosol contamination during scaling procedures than during the use of a high speed air turbine handpiece. The conclusion is that chlorhexidine is an effective primary measure in reducing aerosol cross-contamination when using dental devices in a dental set up.
Correlation between the incidence of nosocomial aspergillosis and room reconstruction of a haematological ward
Authors: Hütter G. , Ganepola S. , Thiel E. , Blau IW
Published: November 2009

Invasive pulmonary aspergillosis (IPA) represents ~ a major cause of morbidity and mortality in patients I with impaired function of the immune system such as in patients with acute myeloid leukaemia (AML). We investigated the in uence of the patients’ room occu- pancy and the sanitary facilities with regard to the inci- dence of IPA after reconstruction of a haematological ward. This is a retrospective cohort-control study in patients with newly diagnosed AML. Thirty ve patients were treated before and 28 patients in the time after the reconstruction works. The median time of neutropenia was 18.5 days vs. 19.5 days. Twelve patients before and 11 patients after the reconstruction developed IPA (p = 0.794). The incidence of IPA did not decrease after a reduction in the patients’ occupancy and improvement of the sanitary equipment. This study emphasises the presumed importance of optimal physical barriers, e.g. air ltration and/or antimycotic prophylaxis in high-risk patients.
Innovative infection prevention and control teaching for nursing students: a personal reflection
Authors: Burnett E.
Published: November 2009

A crucial part of our role as Infection Prevention and Control Practitioners is to develop, facilitate and evaluate the teaching and learning of students and healthcare workers. However, creating an environment for participation, interaction and socialisation whilst effectively stimulating reflective and critical thinking in order to promote good practice can be challenging. This paper is a critical reflection, based on Gibb’s model of reflection to demonstrate the development, facilitation, support and evaluation of learning using an innovative, interactive method.
An adjusted funnel plot methodology for benchmarking targeted local healthcare associated prevalence surveys
Authors: Cairns S. , Stewart S. , Allardice G. , Reilly J.
Published: November 2009

We report the development of a local healthcare associated infection prevalence survey methodology that uses multivariate adjustment and funnel plots to facilitate benchmarking of local survey results against Scottish National HAI Prevalence Survey data. The tool provides robust and consistent results that can be used to inform infection control strategy.
Characterisation of microRNA expression in post-natal mouse mammary gland development
Authors: Avril-Sassen Stefanie , Goldstein Leonard D , Stingl John , Blenkiron Cherie , Le Quesne John , Spiteri Inmaculada , Karagavriilidou Konstantina , Watson Christine J , Tavaré Simon , Miska Eric A , Caldas Carlos
Published: November 2009

Background

The differential expression pattern of microRNAs (miRNAs) during mammary gland development might provide insights into their role in regulating the homeostasis of the mammary epithelium. Our aim was to analyse these regulatory functions by deriving a comprehensive tissue-specific combined miRNA and mRNA expression profile of post-natal mouse mammary gland development.

We measured the expression of 318 individual murine miRNAs by bead-based flow-cytometric profiling of whole mouse mammary glands throughout a 16-point developmental time course, including juvenile, puberty, mature virgin, gestation, lactation, and involution stages. In parallel whole-genome mRNA expression data were obtained.

Results

One third (n = 102) of all murine miRNAs analysed were detected during mammary gland development. MicroRNAs were represented in seven temporally co-expressed clusters, which were enriched for both miRNAs belonging to the same family and breast cancer-associated miRNAs. Global miRNA and mRNA expression was significantly reduced during lactation and the early stages of involution after weaning. For most detected miRNA families we did not observe systematic changes in the expression of predicted targets. For miRNA families whose targets did show changes, we observed inverse patterns of miRNA and target expression. The data sets are made publicly available and the combined expression profiles represent an important community resource for mammary gland biology research.

Conclusion

MicroRNAs were expressed in likely co-regulated clusters during mammary gland development. Breast cancer-associated miRNAs were significantly enriched in these clusters. The mechanism and functional consequences of this miRNA co-regulation provide new avenues for research into mammary gland biology and generate candidates for functional validation.