bluuebunny/crossref_metadata_2025 huggingface dataset:
Rab GAP cascade regulates dynamics of Ypt6 in the Golgi traffic
Authors: Suda Yasuyuki , Kurokawa Kazuo , Hirata Ryogo , Nakano Akihiko
Published: November 2013

Significance

The Golgi apparatus functions as the central station of membrane traffic in cells. A series of Rab GTPases, which control various steps in membrane traffic, act consecutively during the course of Golgi maturation. Here, we report that Ypt6, a Rab6 homologue in yeast, resides temporarily at the Golgi and dissociates into the cytosol upon arrival of Ypt32, another Rab GTPase functioning in the late Golgi. We have found that Gyp6, a putative GTPase-activating protein for Ypt6, specifically interacts with Ypt32 as an effector. Taken together with the previously proposed Rab cascade within the Golgi, we propose that multiple Rab cascades interact at the intersection of secretory and endosomal pathways and play significant roles in traffic within and around the Golgi apparatus.
High-speed holographic microscopy of malaria parasites reveals ambidextrous flagellar waveforms
Authors: Wilson Laurence G. , Carter Lucy M. , Reece Sarah E.
Published: November 2013

Significance

Cilia and flagella are ubiquitous in eukaryotes, enabling cells to move and pump fluid. Understanding how flagella beat is critical in understanding medical “ciliopathies” (e.g., hydrocephalus, male and female infertility). We introduce a unique flagellar model system: the male microgametes of the malaria parasite
Plasmodium berghei
. These microorganisms are isolated swimming flagella, unencumbered by large structures such as a cell body (as in
Chlamydomonas
algae). We measure their 3D beating patterns using high-speed holographic microscopy and find a surprising diversity of waveforms. Structural chirality (handedness) in the flagellum is not manifested in the beat patterns. This interrupts the link between the molecular structure of the flagellum and its dynamics, which was believed to break left-right symmetry in developing embryos.
Discourse markers as stance markers
Authors: Sakita Tomoko I.
Published: November 2013

Stance is inherent in conversational interaction and is interactional in nature. When speakers take a stance, they pay attention to both prior stances and stance relations, as well as to the anticipated consequences of their stancetaking. They manage stance relations as a way of dealing with the “sociocognitive relations” of intersubjectivity (Du Bois 2007). Using the dialogic framework proposed by Du Bois, this paper shows that the discourse marker well in American English works as a resource for the management of relationships among stances. With its referential and grammatical flexibility, it is uniquely characterized as a meta-stance marker because, rather than indexing a specific stance, it negotiates and regulates stance relations. Well is analyzed in two contextual categories: first, at stance divergence among utterances, and second, at stance shifts embedded in topic shift.
WaveCNV: allele-specific copy number alterations in primary tumors and xenograft models from next-generation sequencing
Authors: Holt Carson , Losic Bojan , Pai Deepa , Zhao Zhen , Trinh Quang , Syam Sujata , Arshadi Niloofar , Jang Gun Ho , Ali Johar , Beck Tim , McPherson John , Muthuswamy Lakshmi B.
Published: November 2013

Motivation: Copy number variations (CNVs) are a major source of genomic variability and are especially significant in cancer. Until recently microarray technologies have been used to characterize CNVs in genomes. However, advances in next-generation sequencing technology offer significant opportunities to deduce copy number directly from genome sequencing data. Unfortunately cancer genomes differ from normal genomes in several aspects that make them far less amenable to copy number detection. For example, cancer genomes are often aneuploid and an admixture of diploid/non-tumor cell fractions. Also patient-derived xenograft models can be laden with mouse contamination that strongly affects accurate assignment of copy number. Hence, there is a need to develop analytical tools that can take into account cancer-specific parameters for detecting CNVs directly from genome sequencing data.

Results: We have developed WaveCNV, a software package to identify copy number alterations by detecting breakpoints of CNVs using translation-invariant discrete wavelet transforms and assign digitized copy numbers to each event using next-generation sequencing data. We also assign alleles specifying the chromosomal ratio following duplication/loss. We verified copy number calls using both microarray (correlation coefficient 0.97) and quantitative polymerase chain reaction (correlation coefficient 0.94) and found them to be highly concordant. We demonstrate its utility in pancreatic primary and xenograft sequencing data.

Availability and implementation: Source code and executables are available at https://github.com/WaveCNV. The segmentation algorithm is implemented in MATLAB, and copy number assignment is implemented Perl.

Contact:  lakshmi.muthuswamy@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Stunting of Onion in the Columbia Basin of Oregon and Washington Caused byRhizoctoniaspp.
Authors: Patzek L. J. , du Toit L. J. , Paulitz T. C. , Jones S. S.
Published: November 2013

During 2009 and 2010, 45 isolates of Rhizoctonia spp. were recovered from onion bulb crops in the semiarid Columbia Basin of Oregon and Washington, in which patches of severely stunted onion plants developed following rotation with winter cereal cover crops. Characterization of isolates recovered from naturally infested soil and roots was performed by sequence analysis of the ribosomal DNA (rDNA) internal transcribed spacer region, with the majority of isolates (64%) identified as Rhizoctonia solani. In steam-pasteurized field soil, stunting of onion was caused by isolates of R. solani anastamosis groups (AGs) 2-1, 3, 4, and 8, as well as Waitea circinata var. circinata and binucleate Rhizoctonia AG E evaluated at 13 and 8 or 15 and 15°C day and night temperatures, respectively, typical of spring planting conditions in the Columbia Basin. Isolates of R. solani AG 5 as well as binucleate AG A and I were nonpathogenic. The most virulent isolates belonged to AG 8, although an AG 3 and an AG E isolate were also highly virulent. Isolates of AG 2-1 and 3 caused moderate levels of disease, while isolates of AG 4 and W. circinata var. circinata caused low levels of disease. Emergence was reduced by isolates of AG 2-1, 3, and E. When the various AGs were grown at temperatures of 5 to 30°C, the relative growth rate of the Rhizoctonia isolates was not positively correlated with virulence on onion within an AG.
2P2I
HUNTER
: a tool for filtering orthosteric protein–protein interaction modulators via a dedicated support vector machine
Authors: Hamon Véronique , Bourgeas Raphael , Ducrot Pierre , Theret Isabelle , Xuereb Laura , Basse Marie Jeanne , Brunel Jean Michel , Combes Sebastien , Morelli Xavier , Roche Philippe
Published: November 2013

Over the last 10 years, protein–protein interactions (PPIs) have shown increasing potential as new therapeutic targets. As a consequence, PPIs are today the most screened target class in high-throughput screening (HTS). The development of broad chemical libraries dedicated to these particular targets is essential; however, the chemical space associated with this ‘high-hanging fruit’ is still under debate. Here, we analyse the properties of 40 non-redundant small molecules present in the 2P2I database (
http://2p2idb.cnrs-mrs.fr/
) to define a general profile of orthosteric inhibitors and propose an original protocol to filter general screening libraries using a support vector machine (SVM) with 11 standard D
ragon
molecular descriptors. The filtering protocol has been validated using external datasets from PubChem BioAssay and results from in-house screening campaigns
.
This external blind validation demonstrated the ability of the SVM model to reduce the size of the filtered chemical library by eliminating up to 96% of the compounds as well as enhancing the proportion of active compounds by up to a factor of 8. We believe that the resulting chemical space identified in this paper will provide the scientific community with a concrete support to search for PPI inhibitors during HTS campaigns.
Differential equations with general highly oscillatory forcing terms
Authors: Condon M. , Iserles A. , Nørsett S. P.
Published: November 2013

The concern of this paper is in expanding and computing initial-value problems of the form

y

′=

f

(

y

)+

h

ω

(
t
), where the function

h

ω

oscillates rapidly for
ω
≫1. Asymptotic expansions for such equations are well understood in the case of modulated Fourier oscillators

and they can be used as an organizing principle for very accurate and affordable numerical solvers. However, there is no similar theory for more general oscillators, and there are sound reasons to believe that approximations of this kind are unsuitable in that setting. We follow in this paper an alternative route, demonstrating that, for a much more general family of oscillators, e.g. linear combinations of functions of the form e

i
ωg

k

(
t
)

, it is possible to expand

y

(
t
) in a different manner. Each
r
th term in the expansion is

for some
ς
>0 and it can be represented as an
r
-dimensional highly oscillatory integral. Because computation of multivariate highly oscillatory integrals is fairly well understood, this provides a powerful method for an effective discretization of a numerical solution for a large family of highly oscillatory ordinary differential equations.
Subglacial hydrology and the formation of ice streams
Authors: Kyrke-Smith T. M , Katz R. F , Fowler A. C
Published: November 2013

Antarctic ice streams are associated with pressurized subglacial meltwater but the role this water plays in the dynamics of the streams is not known. To address this, we present a model of subglacial water flow below ice sheets, and particularly below ice streams. The base-level flow is fed by subglacial melting and is presumed to take the form of a rough-bedded film, in which the ice is supported by larger clasts, but there is a millimetric water film which submerges the smaller particles. A model for the film is given by two coupled partial differential equations, representing mass conservation of water and ice closure. We assume that there is no sediment transport and solve for water film depth and effective pressure. This is coupled to a vertically integrated, higher order model for ice-sheet dynamics. If there is a sufficiently small amount of meltwater produced (e.g. if ice flux is low), the distributed film and ice sheet are stable, whereas for larger amounts of melt the ice–water system can become unstable, and ice streams form spontaneously as a consequence. We show that this can be explained in terms of a multi-valued sliding law, which arises from a simplified, one-dimensional analysis of the coupled model.
Experimental elimination of parasites in nature leads to the evolution of increased resistance in hosts
Authors: Dargent Felipe , Scott Marilyn E. , Hendry Andrew P. , Fussmann Gregor F.
Published: November 2013

A reduction in the strength of selection is expected to cause the evolution of reduced trait expression. Elimination of a parasite should thus cause the evolution of reduced resistance to that parasite. To test this prediction in nature, we studied the fourth- and eighth-generation descendants of guppies (
Poecilia reticulata
) introduced into four natural streams following experimental elimination of a common and deleterious parasite (
Gyrodactylus
spp.). After two generations of laboratory rearing to control for plasticity and maternal effects, we infected individual fish to assess their resistance to the parasite. Contrary to theoretical expectations, the introduced guppy populations had rapidly and repeatably evolved increased resistance to the now-absent parasite. This evolution was not owing to a resistance-tolerance trade-off, nor to differences in productivity among the sites. Instead, a leading candidate hypothesis is that the rapid life-history evolution typical in such introductions pleiotropically increases parasite resistance. Our study adds a new dimension to the growing evidence for contemporary evolution in the wild, and also points to the need for a re-consideration of simple expectations from host–parasite theory. In particular, our results highlight the need for increased consideration of multiple sources of selection and pleiotropy when studying evolution in natural contexts.
Molecular epidemiology and genetic diversity of Entamoeba species in a chelonian collection
Authors: García Gabriela , Ramos Fernando , Pérez Rodrigo Gutiérrez , Yañez Jorge , Estrada Mónica Salmerón , Mendoza Lilian Hernández , Martinez-Hernandez Fernando , Gaytán Paul
Published: November 2013

Veterinary medicine has focused recently on reptiles, due to the existence of captive collections in zoos and an increase in the acquisition of reptiles as pets. The protozoan parasite,Entamoebacan cause amoebiasis in various animal species and humans. Although amoebiasis disease is remarkably rare in most species of chelonians and crocodiles, these species may serve asEntamoebaspecies carriers that transmit parasites to susceptible reptile species, such as snakes and lizards, which can become sick and die. In this study, we identified theEntamoebaspecies in a population of healthy (disease-free) chelonians, and evaluated their diversity through the amplification and sequencing of a small subunit rDNA region. Using this procedure, threeEntamoebaspecies were identified:Entamoeba invadensin 4.76 % of chelonians,Entamoeba moshkovskiiin 3.96 % andEntamoeba terrapinaein 50 %. We did not detect mixedEntamoebainfections. Comparative analysis of the amplified region allowed us to determine the intra-species variations. TheE. invadensandE. moshkovskiistrains isolated in this study did not exhibit marked differences with respect to the sequences reported in GenBank. The analysis of theE. terrapinaeisolates revealed three different subgroups (A, B and C). Although subgroups A and C were very similar, subgroup B showed a relatively marked difference with respect to subgroups A and C (Fst = 0.984 andFst = 1.000, respectively; 10–14 % nucleotide variation, as determined byblast) and with respect to the sequences reported in GenBank. These results suggested thatE. terrapinaesubgroup B may be either in a process of speciation or belong to a different lineage. However, additional research is necessary to support this statement conclusively.
Antigenic variation of foot-and-mouth disease virus serotype A
Authors: Ludi A. B. , Horton D. L. , Li Y. , Mahapatra M. , King D. P. , Knowles N. J. , Russell C. A. , Paton D. J. , Wood J. L. N. , Smith D. J. , Hammond J. M.
Published: November 2013

The current measures to control foot-and-mouth disease (FMD) include vaccination, movement control and slaughter of infected or susceptible animals. One of the difficulties in controlling FMD by vaccination arises due to the substantial diversity found among the seven serotypes of FMD virus (FMDV) and the strains within these serotypes. Therefore, vaccination using a single vaccine strain may not fully cross-protect against all strains within that serotype, and therefore selection of appropriate vaccines requires serological comparison of the field virus and potential vaccine viruses using relationship coefficients (r
1 values). Limitations of this approach are that antigenic relationships among field viruses are not addressed, as comparisons are only with potential vaccine virus. Furthermore, inherent variation among vaccine sera may impair reproducibility of one-way relationship scores. Here, we used antigenic cartography to quantify and visualize the antigenic relationships among FMD serotype A viruses, aiming to improve the understanding of FMDV antigenic evolution and the scope and reliability of vaccine matching. Our results suggest that predicting antigenic difference using genetic sequence alone or by geographical location is not currently reliable. We found co-circulating lineages in one region that were genetically similar but antigenically distinct. Nevertheless, by comparing antigenic distances measured from the antigenic maps with the full capsid (P1) sequence, we identified a specific amino acid substitution associated with an antigenic mismatch among field viruses and a commonly used prototype vaccine strain, A22/IRQ/24/64.
Terpene Down-Regulation Triggers Defense Responses in Transgenic Orange Leading to Resistance against Fungal Pathogens
Authors: Rodríguez Ana , Shimada Takehiko , Cervera Magdalena , Alquézar Berta , Gadea José , Gómez-Cadenas Aurelio , De Ollas Carlos José , Rodrigo María Jesús , Zacarías Lorenzo , Peña Leandro
Published: November 2013

Terpenoid volatiles are isoprene compounds that are emitted by plants to communicate with the environment. In addition to their function in repelling herbivores and attracting carnivorous predators in green tissues, the presumed primary function of terpenoid volatiles released from mature fruits is the attraction of seed-dispersing animals. Mature oranges (Citrus sinensis) primarily accumulate terpenes in peel oil glands, with d-limonene accounting for approximately 97% of the total volatile terpenes. In a previous report, we showed that down-regulation of a d-limonene synthase gene alters monoterpene levels in orange antisense (AS) fruits, leading to resistance against Penicillium digitatum infection. A global gene expression analysis of AS versus empty vector (EV) transgenic fruits revealed that the down-regulation of d-limonene up-regulated genes involved in the innate immune response. Basal levels of jasmonic acid were substantially higher in the EV compared with AS oranges. Upon fungal challenge, salicylic acid levels were triggered in EV samples, while jasmonic acid metabolism and signaling were drastically increased in AS orange peels. In nature, d-limonene levels increase in orange fruit once the seeds are fully viable. The inverse correlation between the increase in d-limonene content and the decrease in the defense response suggests that d-limonene promotes infection by microorganisms that are likely involved in facilitating access to the pulp for seed-dispersing frugivores.
Lattice strain distribution resolved by X-ray Bragg-surface diffraction in an Si matrix distorted by embedded FeSi2nanoparticles
Authors: Lang Rossano , de Menezes Alan S. , dos Santos Adenilson O. , Reboh Shay , Meneses Eliermes A. , Amaral Livio , Cardoso Lisandro P.
Published: November 2013

Out-of-plane and primarily in-plane lattice strain distributions, along the two perpendicular crystallographic directions on the subsurface of a silicon layer with embedded FeSi2nanoparticles, were analyzed and resolved as a function of the synchrotron X-ray beam energy by using ω:φ mappings of the ({\overline 1}11) and (111) Bragg-surface diffraction peaks. The nanoparticles, synthesized by ion-beam-induced epitaxial crystallization of Fe+-implanted Si(001), were observed to have different orientations and morphologies (sphere- and plate-like nanoparticles) within the implanted/recrystallized region. The results show that the shape of the synthesized material singularly affects the surrounding Si lattice. The lattice strain distribution elucidated by the nonconventional X-ray Bragg-surface diffraction technique clearly exhibits an anisotropic effect, predominantly caused by plate-shaped nanoparticles. This type of refined detection reflects a key application of the method, which could be used to allow discrimination of strains in distorted semiconductor substrate layers.
The marine environment as a reservoir of enterococci carrying resistance and virulence genes strongly associated with clinical strains
Authors: Di Cesare Andrea , Pasquaroli Sonia , Vignaroli Carla , Paroncini Paolo , Luna Gian Marco , Manso Esther , Biavasco Francesca
Published: November 2013

To gain insights into the relationships and the genetic exchange among environmental and clinical enterococci, 59 strains (29 from marine aquaculture sites and 30 from clinical settings) resistant to tetracycline, erythromycin, ampicillin and/or gentamicin were analysed for the antibiotic resistance tet(M), tet(L), tet(O), erm(A), erm(B), mef blaZ, aac(6′)‐Ie aph(2″)‐Ia and virulence gelE, cylB, efaA and esp genes, and for the copper resistance gene tcrB. Antibiotic resistance and virulence genes were detected more frequently in clinical than in environmental enterococci; the opposite was true for copper resistance. Conjugation experiments demonstrated the transfer of antibiotic resistance genes from marine to clinical enterococci in interspecific mating and the uncommon joint transfer of tet(L) and erm(B). Enterobacterial repetitive intergenic consensus polymerase chain reaction typing evidenced a cluster (90% similarity) encompassing strains carrying multiple antibiotic resistance genes from both sets; the others marine isolates exhibited polyclonality and bore tcrB. Our results demonstrate that antibiotic‐resistant marine enterococci bear antibiotic resistance genes transferable to humans and suggest that copper resistance, not observed among clinical strains, may be useful for survival in the environment, whereas virulence genes likely confer no advantage to enterococcal populations adapted to a lifestyle outside the host.
Trading fours: Creativity, analogy, and exchange
Authors: BRENNEIS DON
Published: November 2013

In commenting on Eitan Wilf's “Sociable robots, jazz music, and divination,” I consider contemporary practices of spontaneous algorithmic composition designed to help produce new, unpredictable, and “interesting” jazz music. I focus, in particular, on five themes that emerge in Wilf's article: emotion, grooves and grooving, routinization, affordances and constraints, and analogy as both cultural practice and theory‐making strategy. I also draw on a comparison between the emergent compositional practices Wilf documents and ethnographic accounts of other improvisatory practices in jazz.
Limited ability of existing nomograms to predict outcomes in men undergoing active surveillance for prostate cancer
Authors: Wang Siao‐Yi , Cowan Janet E. , Cary K. Clint , Chan June M. , Carroll Peter R. , Cooperberg Matthew R.
Published: November 2013

Objective

To assess the ability of current nomograms to predict disease progression at repeat biopsy or at delayed radical prostatectomy (RP) in a prospectively accrued cohort of patients managed by active surveillance (AS).

Materials and Methods

A total of 273 patients meeting low‐risk criteria who were managed by AS and who underwent multiple biopsies and/or delayed RP were included in the study.

The Kattan (base, medium and full), Steyerberg, Nakanishi and Chun nomograms were used to calculate the likelihood of indolent disease (‘nomogram probability’) as well as to predict ‘biopsy progression’ by grade or volume, ‘surgical progression’ by grade or stage, or ‘any progression’ on repeat biopsy or surgery.

We evaluated the associations between each nomogram probability and each progression outcome using logistic regression with (area under the receiver‐operating characteristic curve (AUC) values and decision curve analysis.

Results

The nomogram probabilities of indolent disease were lower in patients with biopsy progression (P < 0.01) and any progression on repeat biopsy or surgical pathology (P < 0.05).

In regression analyses, nomograms showed a modest ability to predict biopsy progression, adjusted for total number of biopsies (AUC range 0.52–0.67) and any progression (AUC range 0.52–0.70).

Decision curve analyses showed that all the nomograms, except for the Kattan base model, have similar value in predicting biopsy progression and any progression.

Nomogram probabilities were not associated with surgical progression in a subgroup of 58 men who underwent delayed RP.

Conclusions

Existing nomograms have only modest accuracy in predicting the outcomes of patients undergoing AS.

Improvements to existing nomograms should be made before they are implemented in clinical practice and used to select patients for AS.
The cognition‐enhancing activity of E1R, a novel positive allosteric modulator of sigma‐1 receptors
Authors: Zvejniece L , Vavers E , Svalbe B , Vilskersts R , Domracheva I , Vorona M , Veinberg G , Misane I , Stonans I , Kalvinsh I , Dambrova M
Published: November 2013

Background and Purpose

Here, we describe the in vitro and in vivo effects of (4R,5S)‐2‐(5‐methyl‐2‐oxo‐4‐phenyl‐pyrrolidin‐1‐yl)‐acetamide (E1R), a novel positive allosteric modulator of sigma‐1 receptors.

Experimental Approach

E1R was tested for sigma receptor binding activity in a [3H](+)‐pentazocine assay, in bradykinin (BK)‐induced intracellular Ca2+ concentration ([Ca2+]i) assays and in an electrically stimulated rat vas deferens model. E1R's effects on cognitive function were tested using passive avoidance (PA) and Y‐maze tests in mice. A selective sigma‐1 receptor antagonist (NE‐100), was used to study the involvement of the sigma‐1 receptor in the effects of E1R. The open‐field test was used to detect the effects of E1R on locomotion.

Key Results

Pretreatment with E1R enhanced the selective sigma‐1 receptor agonist PRE‐084's stimulating effect during a model study employing electrically stimulated rat vasa deferentia and an assay measuring the BK‐induced [Ca2+]i increase. Pretreatment with E1R facilitated PA retention in a dose‐related manner. Furthermore, E1R alleviated the scopolamine‐induced cognitive impairment during the PA and Y‐maze tests in mice. The in vivo and in vitro effects of E1R were blocked by treatment with the selective sigma‐1 receptor antagonist NE‐100. E1R did not affect locomotor activity.

Conclusion and Implications

E1R is a novel 4,5‐disubstituted derivative of piracetam that enhances cognition and demonstrates efficacy against scopolamine‐induced cholinergic dysfunction in mice. These effects are attributed to its positive modulatory action on the sigma‐1 receptor and this activity may be relevant when developing new drugs for treating cognitive symptoms related to neurodegenerative diseases.
Novel bioresorbable strontium hydroxyapatite membrane for guided bone regeneration
Authors: Hao J. , Acharya A. , Chen K. , Chou J. , Kasugai S. , Lang N. P.
Published: November 2013

Objectives

Membrane materials have been widely used for guided bone regeneration (GBR). However, due to bio‐functional limitation of the current membranes, the ideal resorbable membrane that can stimulate bone regeneration has yet to be developed. This study seeks to investigate the effects of a strontium hydroxyapatite (SrHA)‐containing membrane for GBR.

Material and methods

Strontium hydroxyapatite powder was synthesized and mixed with gelatin solution to the final concentration of 10 mg/ml (Sr10) and 20 mg/ml (Sr20). Approximately 100‐μm‐thick membranes were fabricated, and the mechanical properties and strontium ion release pattern were analyzed. Rat bone marrow stromal cell (BMSC) responses were investigated in vitro. Bilaterial rat calvarial defects were used in vivo to compare the SrHA membranes against commercially available collagen membranes and evaluated radiologically and histologically.

Results

Strontium hydroxyapatite membranes exhibited higher elasticity and strength than the collagen membrane, and slow strontium ion release was also confirmed. No BMSC cytotoxicity was found on the SrHA membranes, and the alkaline phosphatase positively stained area was significantly greater than the collagen membrane at earlier time point. At 4 weeks, both micro‐CT and histological analyses revealed that the Sr20 group yielded significantly greater bone formation.

Conclusions

The SrHA‐containing membrane developed in this study was found to be a biocompatible material that can stimulate BMSC differentiation as well as bone regeneration and maturation in rat calvarial defects at early time point compared with collagen membrane. The best result was observed in Sr20 group, which can be potentially effective for GBR.
Effects of anonymous peer observation on adolescents' preference for immediate rewards
Authors: Weigard Alexander , Chein Jason , Albert Dustin , Smith Ashley , Steinberg Laurence
Published: November 2013

Research suggests that the presence of peers influences adolescent risk‐taking by increasing the perceived reward value of risky decisions. While prior work has involved observation of participants by their friends, the current study examined whether observation by an anonymous peer could elicit similarly increased reward sensitivity. Late adolescent participants completed a delay discounting task either alone or under the belief that performance was being observed from a neighboring room by an unknown viewer of the same gender and age. Even in this limited social context, participants demonstrated a significantly increased preference for smaller, immediate rewards when they believed that they were being watched. This outcome challenges several intuitive accounts of the peer effect on adolescent risk‐taking, and indicates that the peer influence on reward sensitivity during late adolescence is not dependent on familiarity with the observer. The findings have both theoretical and practical implications for our understanding of social influences on adolescents' risky behavior.
Inter‐Vendor Variability of Left Ventricular Volumes and Strains Determined by Three‐Dimensional Speckle Tracking Echocardiography
Authors: Yuda Satoshi , Sato Yasumi , Abe Kiyoshi , Kawamukai Mina , Kouzu Hidemichi , Muranaka Atsuko , Kokubu Nobuaki , Hashimoto Akiyoshi , Tsuchihashi Kazufumi , Watanabe Naoki , Miura Tetsuji
Published: November 2013

Background

Inter‐vendor discordance in three‐dimensional speckle‐tracking echocardiography (3DS) remains uncharacterized. We aimed to examine inter‐vendor discordance of left ventricular (LV) volumes, and functional parameters and their reproducibilities between two commercially available 3DS systems.

Methods

Echocardiographic examinations with 3DS were performed in 26 healthy subjects (age 34 ± 13 years, 85% men) using a Vivid E9 system (V1) with 4V probe (GE Health Care) and Artida (V2) with PST‐25SX probe (Toshiba Medical Systems) on the same day. LV variables and global LV longitudinal, circumferential, radial, and area strains were measured by vendor‐specific softwares, 4D strain EchoPAC BT11 (for V1) and 3D WMT (for V2), respectively. Reproducibility of data was assessed by an intra‐class correlation coefficient (ICC).

Results

The mean time required for 3DS analysis was 5.4 ± 1.5 min for V1, being 21% less than that for V2 (6.8 ± 1.9 min, P < 0.01). Reproducibilities of all LV strains were comparable between V1 (ICC 0.50–0.82) and V2 (ICC 0.51–0.76), except for intra‐observer and inter‐observer reproducibilities of radial strain being lower in V2 (ICC for V1 0.82 and 0.82 and ICC for V2 0.44 and 0.40, respectively). LV strains in all directions and area were significantly different between V1 and V2, though LV volumes and ejection fraction were comparable.

Conclusions

Global longitudinal, circumferential, and area LV strains are reproducible in both 3DS vendors. However, values of three‐dimensional LV strains by 3DS are highly vendor‐dependent.
Lp‐PLA2 is associated with structural valve degeneration of bioprostheses
Authors: Mahmut Ablajan , Mahjoub Haïfa , Boulanger Marie‐Chloé , Fournier Dominique , Després Jean‐Pierre , Pibarot Philippe , Mathieu Patrick
Published: November 2013

Objectives

In this study, we sought to determine the metabolic markers associated with structural valve degeneration (SVD).

Background

Structural valve degeneration (SVD) is the major cause of bioprosthetic valve failure leading to bioprostheses (BPs) stenosis or regurgitation. We hypothesized that lipoprotein‐associated phospholipase A2 (Lp‐PLA2) is involved in the SVD of BPs.

Methods

We included 197 patients who underwent aortic valve replacement with a bioprosthetic valve and had echocardiographic follow‐up to evaluate valve function. Moreover, explanted BPs (n = 39) were analysed by immunohistochemistry for the expression of Lp‐PLA2.

Results

After a mean follow‐up of 7·9 ±0·2 years, forty‐one patients (21%) were identified as developing SVD. Patients with SVD had significantly higher plasma level of Lp‐PLA2 mass (151·8 ± 9·2 ng/mL vs. 133·2 ± 3·4 ng/mL, P = 0·03) and activity (27·6 ± 0·9 nmol/min/mL vs. 25·0 ± 0·4 nmol/min/mL, P = 0·005). Multivariate analysis revealed that Lp‐PLA2 activity (OR: 1·09, 95% CI: 1·01–1·18; P = 0·03) was the strongest independent predictor of SVD. Immunohistochemistry studies of explanted BP showed that 77% of explanted BPs had the expression of Lp‐PLA2, which correlated with the density of macrophages (CD68), and ox‐LDL levels in bioprosthetic tissues.

Conclusions

Increased blood plasma activity of Lp‐PLA2 is associated with higher prevalence of SVD. These findings open new avenues for the identification of patients at risk for SVD and for the development of pharmacotherapy aiming at the prevention of SVD.
The RIAD peptidomimetic inhibits HIV‐1 replication in humanized NSG mice
Authors: Singh Maneesh , Singh Pratibha , Vaira Dolores , Torheim Eirik A. , Rahmouni Souad , Taskén Kjetil , Moutschen Michel
Published: November 2013

Background

Increased intracellular concentration of cyclic AMP (cAMP) in T cells is associated with various immunodeficiency conditions including human immunodeficiency virus (HIV) infection. Several reports indicate a critical role of activated protein kinase A (PKA) in the susceptibility of cells to HIV infection. We have used a cell permeable, stable peptidomimetic version (P3) of the RI‐anchoring disruptor (RIAD), which prevents PKA interaction with A‐kinase‐anchoring proteins (AKAPs). It is known that RIAD peptide abrogates effects of localized cAMP signalling through anchored type I PKA in lymphocytes and prevents murine AIDS (MAIDS) infection when expressed as a transgene in mice.

Methods and Results

In vitro HIV‐infected human peripheral blood mononuclear cells (PBMCs) show reduced levels of p24 and intracellular cAMP in T cells when treated with RIAD peptidomimetic (RIAD‐P3). Humanized NOD/SCID/IL2γnull (NSG) mice infected with HIV‐1 JRCSF and treated with RIAD‐P3 (3·5 mg) once every 2 weeks showed significantly reduced levels of viral load at +28, +42 and +56 days and increased CD4 numbers at +56 days after the start of treatment. RIAD‐P3‐treated humanized mice had lower levels of intracellular cAMP in T cells sorted from splenocytes.

Conclusions

Treatment with RIAD‐P3 limits HIV‐1 viral replication and stabilizes CD4 levels by mechanisms involving cAMP/PKA‐I pathway in human PBMCs and humanized NSG mice.
Periodic properties of the histaminergic system of the mouse brain
Authors: Rozov Stanislav V. , Zant Janneke C. , Karlstedt Kaj , Porkka‐Heiskanen Tarja , Panula Pertti
Published: November 2013

Brain histamine is involved in the regulation of the sleep–wake cycle and alertness. Despite the widespread use of the mouse as an experimental model, the periodic properties of major markers of the mouse histaminergic system have not been comprehensively characterized. We analysed the daily levels of histamine and its first metabolite, 1‐methylhistamine, in different brain structures of C57BL/6J and CBA/J mouse strains, and the mRNA level and activity of histidine decarboxylase and histamine‐N‐methyltransferase in C57BL/6J mice. In the C57BL/6J strain, histamine release, assessed by in vivo microdialysis, underwent prominent periodic changes. The main period was 24 h peaking during the activity period. Additional 8 h periods were also observed. The release was highly positively correlated with active wakefulness, as shown by electroencephalography. In both mouse strains, tissue histamine levels remained steady for 24 h in all structures except for the hypothalamus of CBA/J mice, where 24‐h periodicity was observed. Brain tissue 1‐methylhistamine levels in both strains reached their maxima in the periods of activity. The mRNA level of histidine decarboxylase in the tuberomamillary nucleus and the activities of histidine decarboxylase and histamine‐N‐methyltransferase in the striatum and cortex did not show a 24‐h rhythm, whereas in the hypothalamus the activities of both enzymes had a 12‐h periodicity. These results show that the activities of histamine‐metabolizing enzymes are not under simple direct circadian regulation. The complex and non‐uniform temporal patterns of the histaminergic system of the mouse brain suggest that histamine is strongly involved in the maintenance of active wakefulness.
Potential impacts of climate change on distribution range of Nabis pseudoferus and N. palifer (Hemiptera: Nabidae) in Iran
Authors: Solhjouy‐Fard Samaneh , Sarafrazi Alimorad
Published: November 2013

Nabis pseudoferus Remane and N. palifer Seidenstucker are predators that feed on a wide range of insect pests. To reveal their current potential habitats, the effects of climate change and their future distribution in various areas of Iran we used maximum entropy modeling (Maxent). To produce the models, samples were collected from 218 areas of Iran resulting in discovering 271 points where the nabids were found. The accuracy and performance of distribution models were also evaluated by the area under receiver operating characteristic curve and jack‐knife analysis. In the Maxent model, the climatic, elevation and land cover layers were the major bases for the current models. In modeling future distribution, the land cover layer was excluded. The distribution of N. pseudoferus was independent of the type of vegetation while the distribution of N. palifer varied according to differences in type of vegetation. Using jack‐knife analysis, the land cover and precipitation were the most effective predictors driving the two Nabis species range expansion. From 2013 to 2050 the impacts of climate change on N. pseudoferus distribution was predicted to have a negative impact but have a positive effect on N. palifer range expansion. Results could be used in preparation of predators' conservation, translocation and reintroduction programs and application in pest management strategies.
Contemporary climate change and terrestrial invertebrates: evolutionary versus plastic changes
Authors: Schilthuizen Menno , Kellermann Vanessa
Published: November 2013

To forecast the responses of species to future climate change, an understanding of the ability of species to adapt to long‐term shifts in temperature is crucial. We present a review on evolutionary adaptation and phenotypic plasticity of temperature‐related traits in terrestrial invertebrates. The evidence for adaptive evolution in melanization is good, but we caution that genetic determination needs to be tested in each individual species, and complex genetic correlations may exist. For phenological traits allochronic data sets provide powerful means to track climate‐induced changes; however, rarely are responses deconstructed into evolutionary and plastic responses. Laboratory studies suggest climate change responses in these traits will be driven by both. For stress resistance, the evidence for shifts in traits is poor. Studies leaning heavily onDrosophilahave demonstrated potential limits to evolutionary responses in desiccation and heat resistance. Quantifying the capacity for these species to respond plastically and extending this work to other taxa will be an important next step. We also note that, although not strictly speaking a species trait, the response of endosymbionts to heat stress requires further study. Finally, while clearly genetic, and possibly adaptive, the anonymous nature of latitudinal shifts in clines of genetic markers inDrosophilaprevents further interpretation.
Protein universe containing a PUA RNA‐binding domain
Authors: Cerrudo Carolina S. , Ghiringhelli Pablo D. , Gomez Daniel E.
Published: November 2013

Here, we review current knowledge about pseudouridine synthase and archaeosine transglycosylase (PUA)‐domain‐containing proteins to illustrate progress in this field. A methodological analysis of the literature about the topic was carried out, together with a ‘qualitative comparative analysis’ to give a more comprehensive review. Bioinformatics methods for whole‐protein or protein‐domain identification are commonly based on pairwise protein sequence comparisons; we added comparison of structures to detect the whole universe of proteins containing the PUA domain. We present an update of proteins having this domain, focusing on the specific proteins present in Homo sapiens (dyskerin, MCT1, Nip7, eIF2D and Nsun6), and explore the existence of these in other species. We also analyze the phylogenetic distribution of the PUA domain in different species and proteins. Finally, we performed a structural comparison of the PUA domain through data mining of structural databases, determining a conserved structural motif, despite the differences in the sequence, even among eukaryotes, archaea and bacteria. All data discussed in this review, both bibliographic and analytical, corroborate the functional importance of the PUA domain in RNA‐binding proteins.
Researching language needs using ‘insiders’: Mediated trilingualism and other issues of power asymmetries
Authors: Androulakis George
Published: November 2013

This paper exposes researching multilingually processes and findings from a research project investigating the provision of specialized Greek courses for immigrants from Albania, Pakistan and Romania. Linguistic mediators from the respective communities were appointed in order to facilitate qualitative research for the exploration of immigrants' needs. The research process proved to be more multilingual than what was initially planned. A mediated trilingualism emerged for the research within the communities, with the use of ‘international’ languages (Italian, English, French) between home languages and Greek. Faced with issues of power asymmetries, and of data translation and management, the project leader opted for an approach encouraging multilingualism and code‐switching in all its stages, from collection of data to presentation of outcomes.
Identification of taste receptors and proteomic characterization of the antenna and legs of Tribolium brevicornis, a stored food product pest
Authors: Alabi T. , Marion‐Poll F. , Danho M. , Mazzucchelli G. D. , De Pauw E. , Haubruge E. , Francis F.
Published: November 2013

Chemoreception plays an important role in mediating a diverse range of behaviours, including predation and food selection. In the present study, we combined anatomical observations, electrophysiology and proteomics to investigate sensilla that mediate chemoreception on the antenna and the legs of Tribolium. Scanning electron microscopy was used to differentiate the coxal and trochanteral segments of the pro‐, meso‐ and metathoracic legs by the presence of sensilla trichoidea and chaetica, while the antennae were covered with five types of sensilla (chaetica, basiconica, trichoidea, squamiformia and coeloconica). Antenna morphology and ultrastructure were similar in both sexes. Electrophysiological recordings allowed us to characterize a row of small sensilla basiconica on the terminal segment of the antenna as taste receptors, responding to sucrose and NaCl. Proteomics investigations of antennae and legs yielded several proteins with specific interest for those involved in chemoreception. Odorant‐binding proteins were antenna‐specific, while chemosensory proteins were detected in both tissues.
Staphylococcus aureusconvert neonatal conventionalCD4+Tcells intoFOXP3+ CD25+ CD127lowTcells via thePD‐1/PD‐L1 axis
Authors: Rabe Hardis , Nordström Inger , Andersson Kerstin , Lundell Anna‐Carin , Rudin Anna
Published: November 2013

The gut microbiota provides an important stimulus for the induction of regulatoryT(Treg) cells in mice, whether this applies to newborn children is unknown. InSwedish children,Staphylococcus aureushas become a common early colonizer of the gut. Here, we sought to study the effects of bacterial stimulation on neonatalCD4+Tcells for the induction ofCD25+ CD127lowTreg cellsin vitro. The proportion of circulatingCD25+ CD127lowTreg cells and their expression ofFOXP3,Helios andCTLA‐4 was examined in newborns and adults. To evaluate if commensal gut bacteria could induceTreg cells,CellTrace violet‐stained non‐Treg cells from cord or peripheral blood from adults were co‐cultured with autologousCD25+ CD127lowTreg cells and remaining mononuclear cells and stimulated withS. aureus. Newborns had a significantly lower proportion ofCD25+ CD127lowTreg cells than adults, but these cells wereHelios+andCTLA‐4+to a higher extent than in adults.FOXP3+ CD25+ CD127lowTcells were induced mainly in neonatalCellTrace‐stained non‐Treg cells after stimulation withS. aureus. In cell cultures from adults,S. aureusinducedCD25+ CD127lowTcells only if sorted naiveCD45RA+non‐Treg cells were used, but these cells expressed lessFOXP3 than those induced from newborns. Sorted neonatalCD25+ CD127lowTcells fromS. aureus‐stimulated cultures were still suppressive. Finally, blockingPD‐L1 during stimulation reduced the induction ofFOXP3+ CD25+ CD127lowTcells. These results suggest that newborns have a higher proportion of circulating thymically derivedHelios+Treg cells than adults and thatS. aureuspossess an ability to convert neonatal conventionalCD4+Tcells intoFOXP3+ CD25+CD127lowTreg cells via thePD‐1/PD‐L1 axis.
Cryptic yet colorful: anatomy and relationships of a new genus of Cerithiidae (Caenogastropoda, Cerithioidea) from coral reef drop‐offs
Authors: Strong Ellen E. , Bouchet Philippe
Published: November 2013

Cerithium koperbergi is a rare gastropod of the family Cerithiidae from the tropical Indo‐West Pacific. The species has a small, unusual shell and often inhabits deeper water, fore‐reef habitats that are atypical for the genus. Anatomical investigations reveal that it possesses a combination of features heretofore considered diagnostic of two main cerithiid subfamilies: Cerithiinae and Bittiinae. While the shell is bittiine, the animal lacks mesopodial pedal glands and possesses a seminal receptacle (vs. a spermatophore bursa) in the lateral lamina of the oviduct, which are considered to be cerithiine features. Re‐evaluation of the anatomy of Bittium reticulatum, the type species of Bittium, indicates the defining anatomical difference in oviduct anatomy between the two subfamilies does not stand up to closer scrutiny. Partial mitochondrial cytochrome c oxidase I (COI) sequences support the interpretation that C. koperbergi is a species complex around the western Pacific rim comprising three divergent mitochondrial lineages. Bayesian analysis of partial mitochondrial COI and 16S rRNA sequences confirm the placement of the C. koperbergi complex within a monophyletic Bittiinae, despite the apparent absence of a unifying anatomical feature. Species in the C. koperbergi complex are here united in Pictorium nov. gen. and two species are described as new. It is hypothesized that features of the midgut may be diagnostic of the Bittiinae, but more comparative data are needed.