bluuebunny/crossref_metadata_2025_split huggingface dataset:
A highly conserved metalloprotease effector enhances virulence in the maize anthracnose fungus Colletotrichum graminicola
Authors: Sanz‐Martín José M. , Pacheco‐Arjona José Ramón , Bello‐Rico Víctor , Vargas Walter A. , Monod Michel , Díaz‐Mínguez José M. , Thon Michael R. , Sukno Serenella A. 
Published: November 2015

SummaryColletotrichum graminicola causes maize anthracnose, an agronomically important disease with a worldwide distribution. We have identified a fungalysin metalloprotease (Cgfl) with a role in virulence. Transcriptional profiling experiments and live cell imaging show that Cgfl is specifically expressed during the biotrophic stage of infection. To determine whether Cgfl has a role in virulence, we obtained null mutants lacking Cgfl and performed pathogenicity and live microscopy assays. The appressorium morphology of the null mutants is normal, but they exhibit delayed development during the infection process on maize leaves and roots, showing that Cgfl has a role in virulence. In vitro chitinase activity assays of leaves infected with wild‐type and null mutant strains show that, in the absence of Cgfl, maize leaves exhibit increased chitinase activity. Phylogenetic analyses show that Cgfl is highly conserved in fungi. Similarity searches, phylogenetic analysis and transcriptional profiling show that C. graminicola encodes two LysM domain‐containing homologues of Ecp6, suggesting that this fungus employs both Cgfl‐mediated and LysM protein‐mediated strategies to control chitin signalling.
Transcriptome sequencing reveals population differentiation in gene expression linked to functional traits and environmental gradients in the South African shrub Protea repens
Authors: Akman Melis , Carlson Jane E. , Holsinger Kent E. , Latimer Andrew M. 
Published: November 2015

Summary

Understanding the environmental and genetic mechanisms underlying locally adaptive trait variation across the ranges of species is a major focus of evolutionary biology. Combining transcriptome sequencing with common garden experiments on populations spanning geographical and environmental gradients holds promise for identifying such mechanisms.

The South African shrub Protea repens displays diverse phenotypes in the wild along drought and temperature gradients. We grew plants from seeds collected at 19 populations spanning this species’ range, and sequenced the transcriptomes of these plants to reveal gene pathways associated with adaptive trait variation. We related expression in co‐expressed gene networks to trait phenotypes measured in the common garden and to source population climate.

We found that expression in gene networks correlated with source‐population environment and with plant traits. In particular, the activity of gene networks enriched for growth related pathways correlated strongly with source site minimum winter temperature and with leaf size, stem diameter and height in the garden. Other gene networks with enrichments for photosynthesis related genes showed associations with precipitation.

Our results strongly suggest that this species displays population‐level differences in gene expression that have been shaped by source population site climate, and that are reflected in trait variation along environmental gradients.
Genetic architecture of wood properties based on association analysis and co‐expression networks in white spruce
Authors: Lamara Mebarek , Raherison Elie , Lenz Patrick , Beaulieu Jean , Bousquet Jean , MacKay John 
Published: November 2015

Summary

Association studies are widely utilized to analyze complex traits but their ability to disclose genetic architectures is often limited by statistical constraints, and functional insights are usually minimal in nonmodel organisms like forest trees.

We developed an approach to integrate association mapping results with co‐expression networks. We tested single nucleotide polymorphisms (SNPs) in 2652 candidate genes for statistical associations with wood density, stiffness, microfibril angle and ring width in a population of 1694 white spruce trees (Picea glauca).

Associations mapping identified 229–292 genes per wood trait using a statistical significance level of P < 0.05 to maximize discovery. Over‐representation of genes associated for nearly all traits was found in a xylem preferential co‐expression group developed in independent experiments. A xylem co‐expression network was reconstructed with 180 wood associated genes and several known MYB and NAC regulators were identified as network hubs. The network revealed a link between the gene PgNAC8, wood stiffness and microfibril angle, as well as considerable within‐season variation for both genetic control of wood traits and gene expression. Trait associations were distributed throughout the network suggesting complex interactions and pleiotropic effects.

Our findings indicate that integration of association mapping and co‐expression networks enhances our understanding of complex wood traits.
Accounting for the nested nature of genetic variation across levels of organization improves our understanding of biodiversity and community ecology
Authors: Read Quentin D. , Hoban Sean M. , Eppinga Maarten B. , Schweitzer Jennifer A. , Bailey Joseph K. 
Published: November 2015

Recent work has demonstrated that the presence or abundance of specific genotypes, populations, species and phylogenetic clades may influence community and ecosystem properties such as resilience or productivity. Many ecological studies, however, use simple linear models to test for such relationships, including species identity as the predictor variable and some measured trait or function as the response variable without accounting for the nestedness of genetic variation across levels of organization. This omission may lead to incorrect inference about which source of variation influences community and ecosystem properties. Here, we explicitly compare this common approach to alternative ways of modeling variation in trait data, using simulated trait data and empirical results of common‐garden trials using multiple levels of genetic variation within Eucalyptus, Populus and Picea. We show that: 1) when nested variation is ignored, an incorrect conclusion of species effect is drawn in up to 20% of cases; 2) overestimation of the species effect increases – up to 60% in some scenarios – as the nested term explains more of the variation; and 3) the sample sizes needed to overcome these potential problems associated with aggregating nested hierarchical variation may be impractically large. In common‐garden trials, incorporating nested models increased explanatory power twofold for mammal browsing rate in Eucalyptus, threefold for leaf area in Populus, and tenfold for branch number in Picea. Thoroughly measuring intraspecific variation and characterizing hierarchical genetic variation beyond the species level has implications for developing more robust theory in community ecology, managing invaded natural systems, and improving inference in biodiversity–ecosystem functioning research.SynthesisUntil recently, ecologists acknowledged the ubiquity of within‐species trait variation, but paid scant attention to how much it affects communities and ecosystems. Here, the authors used simulated trait data and common‐garden studies to demonstrate that we ignore intraspecific trait variation at our peril. In both simulated and experimental systems, in many cases ignoring intraspecific variation led to incorrect statistical inferences and inflated the effect size of species identity.This study shows that ecologists must characterize hierarchically nested genetic and phenotypic variation to fully understand the links between individual traits, community structure and ecosystem functioning.
Orienting versus inhibition in the Concealed Information Test: Different cognitive processes drive different physiological measures
Authors: klein Selle Nathalie , Verschuere Bruno , Kindt Merel , Meijer Ewout , Ben‐Shakhar Gershon 
Published: November 2015

AbstractThe Concealed Information Test (CIT) provides a valid tool for psychophysiological detection of concealed knowledge. However, its precise theoretical underpinnings remain a matter of debate. The differential physiological responses elicited by concealed, relevant items, relative to control items, were traditionally explained as reflecting an orienting response (OR). According to an alternative account, these responses reflect attempts to inhibit arousal. The present study examined whether and to what extent CIT detection efficiency is affected by instructions aimed at manipulating arousal inhibition (AI). One hundred and forty‐eight undergraduate students completed a CIT, while electrodermal, cardiac, and respiratory measures were recorded. Half of the participants were requested to imagine that they are suspected of committing a crime and were motivated to avoid detection (presumably eliciting both OR and AI), while the other half were requested to imagine that they are witnesses of a crime and were motivated to be detected (presumably eliciting OR only). All participants were further requested to remain silent throughout the test. In both conditions, concealed items led to a similar increase in skin conductance as compared to the control items. However, the typically observed heart rate deceleration and respiratory suppression were found in suspects, but not in witnesses. These data imply that different mechanisms drive the responding of different psychophysiological measures used in the CIT, with skin conductance reflecting OR, and heart rate and respiration primarily reflecting AI.
Transition to Sustainable Fertilisation in Agriculture, A Practices Approach
Authors: Huttunen Suvi , Oosterveer Peter 
Published: November 2015

AbstractIt is argued that sustainability transition in agriculture requires a shift from a regime oriented towards increasing agricultural productivity to a regime in which the environmental and social effects of production are regarded as central. Practice theories represent an emerging perspective on analysing sustainability transitions and provide a way to focus on farming activities and their changes. Focusing on practice elements – materials, meanings and competences – we explore the prospects of applying practice theory when analysing differentiation and change in agricultural fertilisation practices. Empirically, the article is based on semi‐open qualitative interviews among Finnish farmers. We identified five different fertilisation practices. The differences and changes in practices could be explained by the diverse and hierarchically organised purposes in farming which contributed to different elements and their linkages in the performance of the practices. Consciously cultivating changes in meaning are especially important in facilitating the change in practices.
Differential effects of sex in a West African cohort of HIV‐1, HIV‐2 and HIV‐1/2 dually infected patients: men are worse off
Authors: Jespersen Sanne , Hønge Bo Langhoff , Esbjörnsson Joakim , Medina Candida , da Silva Té David , Correira Faustino Gomes , Laursen Alex Lund , Østergaard Lars , Andersen Andreas , Aaby Peter , Erikstrup Christian , Wejse Christian ,   the Bissau HIV Cohort study group
Published: November 2015

AbstractObjectivesSeveral studies have reported conflicting effects of sex on HIV‐1 infection. We describe differences in baseline characteristics and assess the impact of sex on HIV progression among patients at a clinic with many HIV‐2 and HIV‐1/2 dually infected patients.MethodsThis study utilised a retrospective cohort of treatment‐naïve adults at the largest HIV clinic in Guinea‐Bissau from 6 June 2005 to 1 December 2013. Baseline characteristics were assessed and the patients followed until death, transfer, loss to follow‐up, or 1 June 2014. We estimated the time from the first clinic visit until initiation of ART, death or loss to follow‐up using Cox proportional hazard models.ResultsA total of 5694 patients were included in the study, 3702 women (65%) and 1992 men (35%). Women were more likely than men to be infected with HIV‐2 (19% vs. 15%, P < 0.01) or dually infected with HIV‐1/2 (11% vs. 9%, P = 0.02). For all HIV types, women were younger (median 35 vs. 40 years), less likely to have schooling (55% vs. 77%) or to be married (46% vs. 67%), and had higher baseline CD4 cell counts (median 214 vs. 178 cells/μl). Men had a higher age‐adjusted mortality rate (hazard rate ratio (HRR) 1.29, 95% confidence interval (CI) 1.09–1.52) and were more often lost to follow‐up (HRR 1.27, 95% CI 1.17–1.39).ConclusionSignificant differences exist between HIV‐infected men and women regardless of HIV type. Men seek treatment at a later stage and, despite better socio‐economic status, have higher mortality and loss to follow‐up than women.
Trading with Conditions: The Effect of Sanitary and Phytosanitary Measures on the Agricultural Exports from Low‐income Countries
Authors: Murina Marina , Nicita Alessandro 
Published: November 2015

AbstractMarket access for agricultural products is increasingly determined by capability to comply with a wide array of regulatory measures. From a trade perspective, one of the most important aspects of such regulatory measures is their potential distortionary effect, as their cost of compliance is often asymmetrical across countries. This paper investigates the effect of the European Union's sanitary and phytosanitary (SPS) measures on the exports from low income countries. This study finds that SPS measures result in relatively higher burden for low income countries but that membership in deep trade agreements seems to reduce the difficulties related to compliance with SPS measures. These results are consistent with the hypothesis that while many middle and high income countries have the internal capacity to comply with SPS measures, most low income countries do not.
Report on the 40th International Symposium on Symbolic and Algebraic Computation
Authors: England Matthew 
Published: November 2015

The 40th International Symposium on Symbolic and Algebraic Computation (ISSAC 2015) was held at The University of Bath, Bath, UK from 6 - 9 July 2015. It featured:
• 43 Contributed Paper talks selected by the ISSAC 2015 Program Committee;
• 3 Invited Speakers;
• 3 Tutorial Sessions;
• 12 Poster Presentations;
• 6 Software Demonstrations.
Aphrodite of the dawn: indo-european heritage in greek divine epithets and theonyms
Authors: Kölligan Daniel 
Published: November 2015

§1. Afrodite, originalmente um epíteto do PIE *<em>h₂éu̯sōs</em>, incorporou inúmeros aspectos da deusa da aurora. À maneira da Uṣas védica, é a “filha do céu”, relacionada à calmaria do mar (γαλήνη) e à salvadora dos marinheiros, função exercida pelos pretendentes de Uṣas na mitologia védica. Seu nome pode derivar de *<em>abʰro-dih<em>₂</em>-to-</em> “brilhando a partir da névoa, ou espuma”. § 2.1 Os epítetos de Afrodite derivados de nome de cor, ou que o incluem (χρυσής, χρυσοστέφανος, etc.), talvez se refiram ao caráter original da deusa como personificação da aurora. § 2.2 Sua relação com carruagens, como se vê, p. ex., em χρυσάνιος, talvez derive da associação da deusa com a carruagem do sol, o que poderia também ser o caso de χρυσόθρονος. § 2.3 O uso de λευκός em conexão com Afrodite pode ser comparado com o véd. <em>rocamāna-</em>, que se diz de Uṣas. § 2.4 Seu epíteto Ἀργυννίς corresponde ao véd. <em>arjunī-</em>. § 2.5 Afrodite ῥοδέη e ῥοδόχρους corresponde a Eos ῥοδοδάκτυλος. § 3. A figura védica das “vacas da aurora” pode ser comparada com a das vacas de Hélio em Trinácia. Os epítetos épicos ἕλιξ e ἑλικοβλέφαρος talvez se refiram ao movimento celeste. § 4. A Afrodite Ὀρθροῦ da inscrição pode ser a aurora ou a estrela da manhã, como filha da alvorada, e pode equiparar-se ao Ὀρθρία do frg. 1 de Álcman e a um enigma de Teógnis (vv. 861-4). O Ἐρίβοια atestado junto a Afrodite Ὀρθροῦ pode ser entendido como “rica em vacas da aurora”.
<em>Odisseia</em> XIX: Penélope anfitriã
Authors: Sais Lilian Amadei 
Published: November 2015

<span>O presente artigo aborda um canto chave tanto para a interpretação da </span><em>Odisseia</em><span> homérica como para o entendimento da personagem Penélope: nele, Penélope faz as vezes de anfitriã ao "mendigo-Odisseu" e, após a entrevista entre ambos, decide propor o desafio do arco e contrair novas bodas com seu vencedor. Trataremos das questões centrais da passagem: elas são relativas, principalmente, (1) ao poder que Penélope tem dentro da sociedade ficcional itacense e dentro de seu </span><em>oikos</em><span>, (2) à teoria do </span><em>early recognition</em><span> e (3) à motivação real de Penélope ao tomar a decisão de casar novamente.</span>
O orador perfeito (Cícero, O melhor gênero de oradores 1–4; 5.15–6; 6.16–7)
Authors: Alonso Júnior Clóvis Luiz 
Published: November 2015

Tradução de <span>CÍCERO. </span><span>O melhor gênero de oradores. </span><span>I-IV; V, 15-16; VI, 16-17 </span>
La actualidad de la Ilíada: de la poesía oral a internet
Authors: Güemes Emilio Crespo 
Published: November 2015

<p>Este artigo apresenta numerosas e variadas informações sobre a <em>Ilíada</em>, remetendo o leitor à vasta bibliografia moderna (tanto impressa quanto eletrônica) da filologia, arqueologia e historiografia modernas. Entre as informações estão a autoria e a datação da <em>Ilíada</em>; a unidade da ação narrada; os resquícios da composição oral, tais como repetição de epítetos, de partes de verso, de estruturas narrativas; a variedade dialetal; o testemunho homérico do ofício do aedo; dados homéricos, geográficos e culturais da cidade de Troia e dos invasores micênicos; a vida de Homero e a origem e transmissão do texto da <em>Ilíada</em>.</p>
Mitos en la literatura griega arcaica y clásica; Mitos en la literatura griega helenística e imperial
Authors: Torrano JAA 
Published: November 2015

<div class="column"><p><span>LÓPEZ FÉREZ, Juan Antonio (ed.). </span><em>Mitos en la Literatura Griega Arcaica y Clásica</em>. Estudios de Filologia Griega. Vol. 7. Madrid, Ediciones Clásicas, 2002. 608 páginas. I.S.B.N 84-78824-84-7.</p><p><span>LÓPEZ FÉREZ, Juan Antonio (ed.). </span><em>Mitos en la Literatura Griega Helenística e Imperial</em>. Estudios de Filologia Griega. Vol. 8. Ediciones Clásicas, 2003. 582 páginas. I.S.B.N. 84-78825-41-X.</p><p> </p></div>
Os heróis se armam para a guerra (Ilíada, 3.328-338; 9.15-48; 16.130-147; 19.367-395)
Authors: Zanon Camila Aline 
Published: November 2015

A tradução das quatro cenas de armamento descritas na Ilíada foi realizada com o intuito de proporcionar ao leitor um quadro mais preciso no que se refere às armas que o herói, particularmente, carrega para a batalha. Distintamente das cenas em que a massa de guerreiros se utiliza das armas ou nas suas breves descrições que se encontram alhures na Ilíada, as cenas de armamento fornecem elementos que compõem quase todo o arsenal do qual o herói dispõe. Como se poderá perceber pela leitura da tradução proposta aqui, as fórmulas presentes nas quatro cenas foram mantidas para possibilitar a fruição do caráter formular de tais cenas, sem limitar essa característica da poesia homérica a uma mera (re)produção mecânica de fórmulas repetitivas desconsiderando a complexidade de suas variações. Apesar da seqüência de colocação das armas ser apresentada numa ordem quase ritualística nas quatro cenas (primeiro as cnêmides, depois a couraça, a espada, o escudo, o elmo e, finalmente, a lança) não se pode deixar de perceber as variações expressas pelas descrições particularizantes.
Asymmetric Processing of Numerical and Nonnumerical Magnitudes in the Brain: An fMRI Study
Authors: Leibovich Tali , Vogel Stephan E. , Henik Avishai , Ansari Daniel 
Published: November 2015

Abstract
It is well established that, when comparing nonsymbolic magnitudes (e.g., dot arrays), adults can use both numerical (i.e., the number of items) and nonnumerical (density, total surface areas, etc.) magnitudes. It is less clear which of these magnitudes is more salient or processed more automatically. In this fMRI study, we used a nonsymbolic comparison task to ask if different brain areas are responsible for the automatic processing of numerical and nonnumerical magnitudes, when participants were instructed to attend to either the numerical or the nonnumerical magnitudes of the same stimuli. An interaction of task (numerical vs. nonnumerical) and congruity (congruent vs. incongruent) was found in the right TPJ. Specifically, this brain region was more strongly activated during numerical processing when the nonnumerical magnitudes were negatively correlated with numerosity (incongruent trials). In contrast, such an interference effect was not evident during nonnumerical processing when the task-irrelevant numerical magnitude was incongruent. In view of the role of the right TPJ in the control of stimulus-driven attention, we argue that these data demonstrate that the processing of nonnumerical magnitudes is more automatic than that of numerical magnitudes and that, therefore, the influence of numerical and nonnumerical variables on each other is asymmetrical.
The Role of the Frontal and Parietal Cortex in Proactive and Reactive Inhibitory Control: A Transcranial Direct Current Stimulation Study
Authors: Cai Ying , Li Siyao , Liu Jing , Li Dawei , Feng Zifang , Wang Qiang , Chen Chuansheng , Xue Gui 
Published: November 2015

Abstract
Mounting evidence suggests that response inhibition involves both proactive and reactive inhibitory control, yet its underlying neural mechanisms remain elusive. In particular, the roles of the right inferior frontal gyrus (IFG) and inferior parietal lobe (IPL) in proactive and reactive inhibitory control are still under debate. This study aimed at examining the causal role of the right IFG and IPL in proactive and reactive inhibitory control, using transcranial direct current stimulation (tDCS) and the stop signal task. Twenty-two participants completed three sessions of the stop signal task, under anodal tDCS in the right IFG, the right IPL, or the primary visual cortex (VC; 1.5 mA for 15 min), respectively. The VC stimulation served as the active control condition. The tDCS effect for each condition was calculated as the difference between pre- and post-tDCS performance. Proactive control was indexed by the RT increase for go trials (or preparatory cost), and reactive control by the stop signal RT. Compared to the VC stimulation, anodal stimulation of the right IFG, but not that of the IPL, facilitated both proactive and reactive control. However, the facilitation of reactive control was not mediated by the facilitation of proactive control. Furthermore, tDCS did not affect the intraindividual variability in go RT. These results suggest a causal role of the right IFG, but not the right IPL, in both reactive and proactive inhibitory control.
Biased Competition during Long-term Memory Formation
Authors: Hutchinson J. Benjamin , Pak Sarah S. , Turk-Browne Nicholas B. 
Published: November 2015

Abstract
A key task for the brain is to determine which pieces of information are worth storing in memory. To build a more complete representation of the environment, memory systems may prioritize new information that has not already been stored. Here, we propose a mechanism that supports this preferential encoding of new information, whereby prior experience attenuates neural activity for old information that is competing for processing. We evaluated this hypothesis with fMRI by presenting a series of novel stimuli concurrently with repeated stimuli at different spatial locations in Experiment 1 and from different visual categories (i.e., faces and scenes) in Experiment 2. Subsequent memory for the novel stimuli could be predicted from the reduction in activity in ventral temporal cortex for the accompanying repeated stimuli. This relationship was eliminated in control conditions where the competition during encoding came from another novel stimulus. These findings reveal how prior experience adaptively guides learning toward new aspects of the environment.