bluuebunny/crossref_metadata_2025 huggingface dataset:
Measuring rewilding progress
Authors: Torres Aurora , Fernández Néstor , zu Ermgassen Sophus , Helmer Wouter , Revilla Eloy , Saavedra Deli , Perino Andrea , Mimet Anne , Rey-Benayas José M. , Selva Nuria , Schepers Frans , Svenning Jens-Christian , Pereira Henrique M.
Published: October 2018

Rewilding is emerging as a promising restoration strategy to enhance the conservation status of biodiversity and promote self-regulating ecosystems while re-engaging people with nature. Overcoming the challenges in monitoring and reporting rewilding projects would improve its practical implementation and maximize its conservation and restoration outcomes. Here, we present a novel approach for measuring and monitoring progress in rewilding that focuses on the ecological attributes of rewilding. We devised a bi-dimensional framework for assessing the recovery of processes and their natural dynamics through (i) decreasing human forcing on ecological processes and (ii) increasing ecological integrity of ecosystems. The rewilding assessment framework incorporates the reduction of material inputs and outputs associated with human management, as well as the restoration of natural stochasticity and disturbance regimes, landscape connectivity and trophic complexity. Furthermore, we provide a list of potential activities for increasing the ecological integrity after reviewing the evidence for the effectiveness of common restoration actions. For illustration purposes, we apply the framework to three flagship restoration projects in the Netherlands, Switzerland and Argentina. This approach has the potential to broaden the scope of rewilding projects, facilitate sound decision-making and connect the science and practice of rewilding.

This article is part of the theme issue ‘Trophic rewilding: consequences for ecosystems under global change’.
Island rewilding with giant tortoises in an era of climate change
Authors: Falcón Wilfredo , Hansen Dennis M.
Published: October 2018

Replacing recently extinct endemic giant tortoises with extant, functional analogues provide the perhaps best examples of island rewilding to date. Yet, an efficient future application of this conservation action is challenging in an era of climate change. We here present and discuss a conceptual framework that can serve as a roadmap for the study and application of tortoise rewilding in an uncertain future. We focus on three main ecological functions mediated by giant tortoises, namely herbivory, seed dispersal and nutrient cycling, and discuss how climate change is likely to impact these. We then propose and discuss mitigation strategies such as artificial constructed shade sites and water holes that can help drive and maintain the ecosystem functions provided by the tortoises on a landscape scale. The application of the framework and the mitigation strategies are illustrated with examples from both wild and rewilded populations of the Aldabra giant tortoise,Aldabrachelys gigantea, in the Western Indian Ocean.

This article is part of the theme issue ‘Trophic rewilding: consequences for ecosystems under global change’.
Soil biological responses to, and feedbacks on, trophic rewilding
Authors: Andriuzzi W. S. , Wall D. H.
Published: October 2018

Trophic rewilding—the (re)introduction of missing large herbivores and/or their predators—is increasingly proposed to restore biodiversity and biotic interactions, but its effects on soils have been largely neglected. The high diversity of soil organisms and the ecological functions they perform mean that the full impact of rewilding on ecosystems cannot be assessed considering only above-ground food webs. Here we outline current understanding on how animal species of rewilding interest affect soil structure, processes and communities, and how in turn soil biota may affect species above ground. We highlight considerable uncertainty in soil responses to and feedbacks on above-ground consumers, with potentially large implications for rewilding interactions with global change. For example, the impact of large herbivores on soil decomposers and plant–soil interactions could lead to reduced carbon sequestration, whereas herbivore interactions with keystone biota such as mycorrhizal fungi, dung beetles and bioturbators could promote native plants and ecosystem heterogeneity. Moreover, (re)inoculation of keystone soil biota could be considered as a strategy to meet some of the objectives of trophic rewilding. Overall, we call for the rewilding research community to engage more with soil ecology experts and consider above-ground–below-ground linkages as integral to assess potential benefits as well as pitfalls.

This article is part of the theme issue ‘Trophic rewilding: consequences for ecosystems under global change'.
mTORC1 Restricts Hepatitis C Virus Replication Through ULK1-mediated Suppression of miR-122 and Facilitates Post-replication Events
Authors: Johri Manish Kumar , Lashkari Hiren Vasantrai , Vedagiri Dhiviya , Gupta Divya , Harshan Krishnan Harinivas
Published: October 2018

Mechanistic target of rapamycin (mTOR) is an important kinase that assimilates several upstream signals including viral infection and facilitates appropriate response by the cell through two unique complexes mTORC1 and mTORC2. Here, we demonstrate that mTORC1 is activated early during HCV infection as antiviral response. Pharmacological inhibition of mTORC1 promoted HCV replication as suggested by elevated levels of HCV (+) and (-) RNA strands. This was accompanied by significant drop in extracellular HCV RNA levels indicating defective post-replication stages. The increase in viral RNA levels failed to augment intracellular infectious virion levels, suggesting that mTORC1 inhibition is detrimental to post-replication steps. Lower infectivity of the supernatant confirmed this observation. Depletion of Raptor and ULK1 accurately reproduced these results suggesting that mTORC1 imparted these effects on HCV through mTORC1-ULK1 arm. Interestingly, ULK1 depletion resulted in increased levels of miR-122, a critical host factor for HCV replication, thus revealing a new mechanism of regulation by ULK1. The binary effect of mTORC1 on HCV replication and egress suggests that mTORC1-ULK1 could be critical in replication: egress balance. Interestingly we discover that ULK1 depletion did not interfere with autophagy in Huh7.5 cells and hence the effects on HCV replication and post-replication events are not resultant of involvement of autophagy. Our studies demonstrate an overall ULK1 mediated anti-HCV function of mTORC1 and identifies an ULK1-independent autophagy that allows HCV replication in spite of mTORC1 activation.
Reconstructing the origins of the space-number association: spatial and number-magnitude codes must be used jointly to elicit spatially organised mental number lines
Authors: Pinto Mario , Pellegrino Michele , Marson Fabio , Lasaponara Stefano , Doricchi Fabrizio
Published: October 2018

In a series of recent studies we have pointed out that the use of contrasting left/right spatial codes, whether indirectly related to number magnitudes through response selection or directly associated to the same magnitudes to guide their spatial positioning on a mental number line, is crucial in eliciting space-number associations (Aiello, 2012; Fattorini et al., 2015; 2016; Pinto et al., 2018). Nonetheless, this conclusion is based on experiments in which spatial and number-magnitudes codes are used jointly during task performance. Here, in a series of unimanual Go/No-Go tasks with intermixed central numerical and pictorial targets, i.e. arrows pointing to the left or to the right, we explore whether spatial codes used in isolation inherently evoke the left-to-right representation of number magnitudes and, vice-versa, whether number-magnitude codes used in isolation inherently evoke the conceptual activation of left/right spatial codes. In a first series of experiments participants were asked to provide unimanual Go/N-Go responses based on instructions that activated only magnitude codes, e.g. “push only if the number is lower than 5 and whenever an arrow appears”, or only spatial codes, e.g. “push only when an arrow points to the left and whenever a number appears”. In a second series of experiments, the same numerical instructions were combined with the request of responding only to arrows in a specific colour, e.g. “push when the number is lower than 5 and whenever a blue arrow appears”. At variance with a recent experiment by Shaki and Fischer (2018), in our experiments no constant association was present between a specific arrow colour and a specific arrow direction. The results of these experiments highlight no space-number congruency effects: e.g. no faster RTs to arrows pointing to the left rather than to the right when participants attend to numbers lower than 5 and, vice-versa, no faster RTs to numbers lower than 5 rather than higher, when participants attend to arrows pointing to the left. Based on these findings it must be concluded that neither space codes used in isolation can elicit a spatial representation of number magnitudes nor number-magnitude codes used in isolation can trigger the activation of spatial codes. Thus, spatial and numerical codes must be used jointly to evoke spatially organised mental number lines.
Electron microscopic analysis of the exo-skeleton of hadal zone amphipodHirondellea gigas
Authors: Kobayashi Hideki , Shimoshige Hirokazu , Nakajima Yoshikata , Arai Wataru , Takami Hideto
Published: October 2018

The amphipodHirondellea gigasinhabits the deepest regions of the oceans in extra high-pressure. However, the mechanisms by which they adapt to their high-pressure environments remain unknown. In this study, we investigated elements of the exoskeleton ofH. gigascaptured from the deepest points of the Mariana Trench. TheH. gigasexoskeleton contained aluminum, as well as a major amount of calcium carbonate. Unlike other accumulated metals, aluminum was distributed on the surface of exoskeletons. To investigate howH. gigasobtains aluminum, we conducted a metabolome analysis and found that gluconic acid/gluconolactone was capable of extracting metals from the sediment under the habitat conditions ofH. gigas. The extracted aluminum ions are transformed into the gel state of aluminum hydroxide in alkaline seawater, and this gel covers the body to protect the amphipod. The aluminum gel would be one of good materials to adapt to such high-pressure environment.
Mechanistic basis for decreased antimicrobial susceptibility in a clinical isolate ofNeisseria gonorrhoeaepossessing a mosaic-likemtrefflux pump locus
Authors: Rouquette-Loughlin Corinne E. , Reimche Jennifer L. , Balthazar Jacqueline T. , Dhulipala Vijaya , Gernert Kim M. , Kersh Ellen N. , Pham Cau D. , Pettus Kevin , Abrams A. Jeanine , Trees David L. , Cyr Sancta St , Shafer William M.
Published: October 2018

Recent reports suggest that mosaic-like sequences within themtr(multipletransferableresistance) efflux pump locus ofNeisseria gonorrhoeaelikely originating from commensalNeisseria sp.by transformation can increase the ability of gonococci to resist structurally diverse antimicrobials. Thus, acquisition of numerous nucleotide changes within themtrRgene encoding the transcriptional repressor (MtrR) of themtrCDEefflux pump-encoding operon or overlapping promoter region for both along with those that cause amino acid changes in the MtrD transporter protein were recently reported to decrease gonococcal susceptibility to numerous antimicrobials, including azithromycin (Azi) (Wadsworthet al.2018. MBio. doi.org/10.1128/mBio.01419-18). We performed detailed genetic and molecular studies to define the mechanistic basis for why such strains can exhibit decreased susceptibility to MtrCDE antimicrobial substrates including Azi. We report that a strongcis-acting transcriptional impact of a single nucleotide change within the -35 hexamer of themtrCDEpromoter as well gain-of-function amino acid changes at theC-terminal region of MtrD can mechanistically account for the decreased antimicrobial susceptibility of gonococci with a mosaic-likemtrlocus.

IMPORTANCE

Historically, after introduction of an antibiotic for treatment of gonorrhea, strains ofN. gonorrhoeaeemerge that display clinical resistance due to spontaneous mutation or acquisition of resistance genes. Genetic exchange between members of theNeisseriagenus occurring by transformation can cause significant changes in gonococci that impact the structure of an antibiotic target or expression of genes involved in resistance. The results presented herein provide a framework for understanding how mosaic-like DNA sequences from commensalNeisseriathat recombine within the gonococcalmtrefflux pump locus function to decrease bacterial susceptibility to antimicrobials including antibiotics used in therapy of gonorrhea.
Assessing mitochondrial function in angiosperms with highly divergent mitochondrial genomes
Authors: Havird Justin C. , Noe Gregory R. , Link Luke , Torres Amber , Logan David C. , Sloan Daniel B. , Chicco Adam J.
Published: October 2018

Angiosperm mitochondrial (mt) genes are generally slow-evolving, but multiple lineages have undergone dramatic accelerations in rates of nucleotide substitution and extreme changes in mt genome structure. While molecular evolution in these lineages has been investigated, very little is known about their mt function. Here, we develop a new protocol to characterize respiration in isolated plant mitochondria and apply it to species ofSilenewith mt genomes that are rapidly evolving, highly fragmented, and exceptionally large (∼11 Mbp). This protocol, complemented with traditional measures of plant fitness, cytochrome c oxidase activity assays, and fluorescence microscopy, was used to characterize inter-and intraspecific variation in mt function. Contributions of the individual “classic” OXPHOS complexes, the alternative oxidase, and external NADH dehydrogenases to overall mt respiratory flux were found to be similar to previously studied angiosperms with more typical mt genomes. Some differences in mt function could be explained by inter-and intraspecific variation, possibly due to local adaptation or environmental effects. Although this study suggests that theseSilenespecies with peculiar mt genomes still show relatively normal mt function, future experiments utilizing the protocol developed here can explore such questions in a more detailed and comparative framework.
Rapid high throughput SYBR green assay for identifying the malaria vectors Anopheles arabiensis, Anopheles coluzzii and Anopheles gambiae s.s. Giles
Authors: Chabi Joseph , Van’t Hof Arjen , N’dri Louis K. , Datsomor Alex , Okyere Dora , Njoroge Harun , Pipini Dimitra , Hadi Melinda P. , de Souza Dziedzom K. , Suzuki Takashi , Dadzie Samuel K. , Jamet Helen P.
Published: October 2018

The Anopheles gambiae sensu lato species complex consists of a number of cryptic species with different habitats and behaviours. These morphologically indistinct species are identified by chromosome banding and molecular diagnostic techniques which are still under improvement even though the current SINE method for identification between An. coluzzii and An. gambiae works reliably. This study describes a refinement of the SINE method to increase sensitivity and high throughput method for the identification of both species and An. arabiensis using amplicon dissociation characteristics.

Field collected samples, laboratory reared colonies and crossed specimens of the two species were used for the design of the protocol. An. gambiae, An. coluzzii, and hybrids of the two species were provided by the insectary of Vestergaard-NMIMR Vector Labs at the Noguchi Memorial Institute for Medical Research (Ghana) and An. arabiensis from Kenya. Samples were first characterised using conventional SINE PCR method, and further assayed using SYBR green, an intercalating fluorescent dye.

The three species and hybrids were clearly differentiated using the melting temperature of the dissociation curves, with derivative peaks at 72 Celsius for An. arabiensis, 75°C for An. gambiae and 86°C for An. coluzzii. The hybrids (An. gambiae / An. coluzzii) showed both peaks. This work is the first to describe a SYBR green real time PCR method for the characterization of An. arabiensis, An. gambiae and An. coluzzii and was purposely designed for basic melt-curve analysis (rather than high-resolution melt-curve) to allow it to be used on a wide range of real-time PCR machines.
Mutualism outcome across plant populations, microbes, and environments in the duckweedLemna minor
Authors: O’Brien Anna M. , Laurich Jason , Lash Emma , Frederickson Megan E
Published: October 2018

The picture emerging from the rapidly growing literature on host-associated micro-biota is that host traits and fitness often depend on complex and interactive effects of host genotype, microbial interactions, and abiotic environment. However, testing these main and interactive effects typically requires large, multi-factorial experiments and thus remains challenging in many systems. Furthermore, most studies of plant microbiomes focus on terrestrial hosts and microbes. Aquatic habitats may confer unique properties to plant micriobiomes. We grew different populations of duck-weed (Lemna minor), a floating aquatic plant of increasing popularity in freshwater phytoremediation, in three microbial treatments (adding no, “home”, or “away” microbes) at two levels of zinc, a common water contaminant in urban areas. Thus, we simultaneously manipulated plant source population, microbial community, and the abiotic environment, and measured both plant and microbial performance as well as plant traits. Although we found little evidence of interactive effects, we found strong main effects of plant source, microbial treatment, and zinc on both duckweed and microbial growth, with significant variation among both duckweed and microbial communities. Despite strong growth alignment between duckweed and microbes, zinc consistently decreased plant growth, but increased microbial growth. Furthermore, as in recent studies of terrestrial plants, microbial interactions altered a duckweed phenotype (frond aggregation). Our results suggest that the duckweed source population, its associated microbiome, and the contaminant environment may all need to be considered in real-world phytoremediation efforts. Lastly, we propose that duckweed microbes offer a robust experimental system for study of host-microbiota interactions under a range of environmental stresses.
Shifting up a gear with iDNA: from mammal detection events to standardized surveys
Authors: Abrams Jesse F , Hoerig Lisa , Brozovic Robert , Axtner Jan , Crampton-Platt Alex , Mohamed Azlan , Wong Seth T , Sollmann Rahel , Yu Douglas W , Wilting Andreas
Published: October 2018

Invertebrate-derived DNA (iDNA), in combination with high throughput sequencing, has been proposed as a cost-efficient and powerful tool to survey vertebrate species. Previous studies, however, have only provided evidence that vertebrates can be detected using iDNA, but have not taken the next step of placing these detection events within a statistical framework that allows for robust biodiversity assessments. Here, we compare concurrent iDNA and camera-trap surveys. Leeches were repeatedly collected in close vicinity to 64 camera-trap stations in Sabah, Malaysian Borneo. We analyze iDNA-derived mammalian detection events in a modern occupancy model that accounts for imperfect detection and compare the results with those from occupancy models parameterized with camera-trap-derived detection events. We also combine leech-iDNA and camera-trap data in a single occupancy model. We found consistent estimates of occupancy probabilities produced by our camera-trap and leech datasets. This indicates that the metabarcoding of leech-iDNA method provides reasonable estimates of occupancy and can be a suitable method for studying and monitoring mammal species in tropical rainforests. However, we also show that a more extensive collection of leeches would be needed to assess mammal biodiversity with a similar robustness as with camera traps. As certain taxa were only detected in leeches, we see great potential in complementing camera-trap studies with the iDNA approach, as long as the collection of leeches follows a similar robust and standardized sampling scheme. Synthesis and applications: The approach we describe here is not restricted to the processing of leech samples, but can be used for the analysis of other iDNA and environmental DNA (eDNA) data. Our study is the first step to shift the application of e/iDNA studies from opportunistic ad-hoc collections to systematic surveys required for long-term wildlife populations and biodiversity monitoring programs.
Deciphering epigenomic code for cell differentiation using deep learning
Authors: Ni Pengyu , Su Zhengchang
Published: October 2018

Epigenomic markers, such as histone modifications, play important roles in cell fate determination and type maintenance during cell differentiation. Although genomic sequence plays a crucial role in establishing the unique epigenome in each cell type produced during cell differentiation, little is known about the sequence determinants that lead to the unique epigenomes of the cells. Here, using a dataset of six histone markers measured in four human CD4+ T cell types produced at different stages of T cell development, we showed that two types of highly accurate deep convolutional neural networks (CNNs) constructed for each cell type and for each histone marker are a powerful strategy to uncover the sequence determinants of the various histone modification patterns in difference cell types. We found that sequence motifs learned by the CNN models are highly similar to known binding motifs of transcription factors known to play important roles in CD4+ T cell differentiation. Our results suggest that both the unique histone modification patterns in each cell type and the different patterns of the same histone marker in different cell types are determined by a set of motifs with unique combinations. Interestingly, the level of shared few motifs learned in the different cell models reflect the lineage relationships of the cells, while the level of few shared motifs learned in different histone marker models reflect their functional relationships. Furthermore, using these models, we can predict the importance of the learned motifs and their interactions in determining specific histone marker patterns in the cell types.
Predicting the Future with Multi-scale Successor Representations
Authors: Momennejad Ida , Howard Marc W.
Published: October 2018

The successor representation (SR) is a candidate principle for generalization in reinforcement learning, computational accounts of memory, and the structure of neural representations in the hippocampus. Given a sequence of states, the SR learns a predictive representation for every given state that encodes how often, on average, each upcoming state is expected to be visited, even if it is multiple steps ahead. A discount or scale parameter determines how many steps into the future SR’s generalizations reach, enabling rapid value computation, subgoal discovery, and flexible decision-making in large trees. However, SR with a single scale could discard information for predicting both the sequential order of and the distance between states, which are common problems in navigation for animals and artificial agents. Here we propose a solution: an ensemble of SRs with multiple scales. We show that the derivative of multi-scale SR can reconstruct both the sequence of expected future states and estimate distance to goal. This derivative can be computed linearly: we show that a multi-scale SR ensemble is the Laplace transform of future states, and the inverse of this Laplace transform is a biologically plausible linear estimation of the derivative. Multi-scale SR and its derivative could lead to a common principle for how the medial temporal lobe supports both map-based and vector-based navigation.
Direct and transgenerational effects of an experimental heat wave on early life stages in a freshwater snail
Authors: Leicht Katja , Seppälä Otto
Published: October 2018

Global climate change imposes a serious threat to natural populations of many species. Estimates of the effects of climate change-mediated environmental stresses are, however, often based only on their direct effects on organisms, and neglect the potential transgenerational effects. We investigated whether high temperature (i.e. an experimental heat wave) that is known to reduce performance of adultLymnaea stagnalissnails affects their offspring through maternal effects. Specifically, we tested whether eggs and hatched juveniles are affected by maternal thermal environment, and how strong these effects are compared with direct effects of temperature on offspring. We examined the effect of maternal thermal environment (15°C versus 25°C) on per offspring investment (egg size), and the role of both maternal and offspring thermal environments (15°C versus 25°C) on hatching success and developmental time of eggs, offspring survival after hatching, and hatchling size at the age of five weeks. Exposure of mothers to high temperature increased hatching success of eggs, and also made the onset of hatching earlier. However, high maternal temperature reduced the survival and the final size of hatched juveniles. Direct effects of high temperature on offspring survival were negative (both eggs and hatchlings), but increased the developmental rate and growth of those eggs and hatchlings that survived. Interestingly, the magnitude of transgenerational effects of high temperature on hatching success of eggs and hatchling survival were similar to its direct effects. This indicates that heat waves can affect natural populations through transgenerational effects, and that the magnitude of such effects can be equally strong to the direct effects of temperature, although this depends on the trait considered. Our results highlight the importance of considering transgenerational effects of climate warming when estimating its effects in the wild.
The impact of bilingualism on executive functions and working memory in young adults
Authors: Antón Eneko , Carreiras Manuel , Duñabeitia Jon Andoni
Published: October 2018

A bilingual advantage in a form of a better performance of bilinguals in tasks tapping into executive function abilities has been reported repeatedly in the literature. However, recent research defends that this advantage does not stem from bilingualism, but from uncontrolled factors or imperfectly matched samples. In this study we explored the potential impact of bilingualism on executive functioning abilities by testing large groups of young adult bilinguals and monolinguals in the tasks that were most extensively used when the advantages were reported. Importantly, the recently identified factors that could be disrupting the between groups comparisons were controlled for, and both groups were matched. We found no differences between groups in their performance. Additional bootstrapping analyses indicated that, when the bilingual advantage appeared, it very often co-occurred with unmatched socio-demographic factors. The evidence presented here indicates that the bilingual advantage might indeed be caused by spurious uncontrolled factors rather than bilingualism per se. Secondly, bilingualism has been argued to potentially affect working memory also. Therefore, we tested the same participants in both a forward and a backward version of a visual and an auditory working memory task. We found no differences between groups in either of the forward versions of the tasks, but bilinguals systematically outperformed monolinguals in the backward conditions. The results are analyzed and interpreted taking into consideration different perspectives in the domain-specificity of the executive functions and working memory.
Full Title: Growth substrate may influence biofilm susceptibility to antibiotics
Authors: Williams Dustin L. , Smith Scott R. , Peterson Brittany R. , Allyn Gina , Epperson Richard Tyler , Looper Ryan E.
Published: October 2018

The CDC biofilm reactor is a robust culture system with high reproducibility in which biofilms can be grown for a wide variety of analyses. Multiple material types are available as growth substrates, yet data from biofilms grown on biologically relevant materials is scarce, particularly for antibiotic efficacy against differentially supported biofilms. In this study, CDC reactor holders were modified to allow growth of biofilms on collagen, a biologically relevant substrate. Susceptibility to multiple antibiotics was compared between biofilms of varying species grown on collagen versus standard polycarbonate coupons. Data indicated that in 13/18 instances, biofilms on polycarbonate were more susceptible to antibiotics than those on collagen, suggesting that when grown on a complex substrate, biofilms may be more tolerant to antibiotics. These outcomes may influence the translatability of antibiotic susceptibility profiles that have been collected for biofilms on hard plastic materials. Data may also help to advance information on antibiotic susceptibility testing of biofilms grown on biologically relevant materials for futurein vitroandin vivoapplications.
Are working memory training effects paradigm-specific?
Authors: Holmes Joni , Woolgar Francesca , Hampshire Adam , Gathercole Susan E.
Published: October 2018

A randomized controlled trial compared complex span and n-back training regimes to investigate the generality of training benefits across materials and paradigms. The memory items and training intensities were equated across programs, providing the first like-with-like comparison of transfer in these two widely-used training paradigms. The stimuli in transfer tests of verbal and visuo-spatial n-back and complex span differed from the trained tasks, but were matched across the untrained paradigms. Pre-to-post changes were observed for untrained n-back tasks following n-back training. Following complex span training there was equivocal evidence for improvements on a verbal complex span task, but no evidence for changes on an untrained visuo-spatial complex span activity. Relative to a no intervention group, the evidence supported no change on an untrained verbal complex span task following either n-back or complex span training. Equivocal evidence was found for improvements on visuo-spatial complex span and verbal and visuo-spatial n-back tasks following both training regimes. Evidence for selective transfer (comparing the two active training groups) was only found for an untrained visuo-spatial n-back task following n-back training. There was no evidence for cross-paradigm transfer. Thus transfer is constrained by working memory paradigm and the nature of individual processes executed within complex span tasks. However, within-paradigm transfer can occur when the change is limited to stimulus category, at least for n-back.
Aging Boosts Antiviral CD8+T Cell Memory Through Improved Engagement Of Diversified Recall Response Determinants
Authors: Davenport Bennett , Eberlein Jens , Nguyen Tom T. , Victorino Francisco , Jhun Kevin , Abuirqeba Haedar , van der Heide Verena , Heeger Peter , Homann Dirk
Published: October 2018

The determinants of protective CD8+memory T cell (CD8+TM) immunity remain incompletely defined and may in fact constitute an evolving agency as aging CD8+TMprogressively acquire enhanced rather than impaired recall capacities. Here, we show that old as compared to young antiviral CD8+TMmore effectively harness disparate molecular processes (cytokine signaling, trafficking, effector functions, and co-stimulation/inhibition) that in concert confer greater secondary reactivity. The relative reliance on these pathways is contingent on the nature of the secondary challenge (greater for chronic than acute viral infections) and over time, aging CD8+TMre-establish a dependence on the same accessory signals required for effective priming of naïve CD8+T cells in the first place. Thus, our findings are consistent with the recently proposed “rebound model” that stipulates a gradual alignment of naïve and CD8+TMproperties, and identify a diversified collection of potential targets that may be exploited for the therapeutic modulation of CD8+TMimmunity.
Meta-analysis of Drought-tolerant Genotypes inOryza sativa: A Network-based Approach
Authors: Sircar Sanchari , Parekh Nita
Published: October 2018

Background

Drought is a severe environmental stress. It is estimated that about 50% of the world rice production is affected mainly by drought. Apart from conventional breeding strategies to develop drought-tolerant crops, innovative computational approaches may provide insights into the underlying molecular mechanisms of stress response and identify drought-responsive markers. Here we propose a network-based computational approach involving a meta-analytic study of seven drought-tolerant rice genotypes under drought stress.

Results

Co-expression networks enable large-scale analysis of gene-pair associations and tightly coupled clusters that may represent coordinated biological processes. Considering differentially expressed genes in the co-expressed modules and supplementing external information such as, resistance/tolerance QTLs, transcription factors, network-based topological measures, we identify and prioritize drought-adaptive co-expressed gene modules and potential candidate genes. Using the candidate genes that are well-represented across the datasets as ‘seed’ genes, two drought-specific protein-protein interaction networks (PPINs) are constructed with up-and down-regulated genes. Cluster analysis of the up-regulated PPIN revealed ABA signaling pathway as a central process in drought response with a probable crosstalk with energy metabolic processes. Tightly coupled gene clusters representing up-regulation of core cellular respiratory processes and enhanced degradation of branched chain amino acids and cell wall metabolism are identified. Cluster analysis of down-regulated PPIN provides a snapshot of major processes associated with photosynthesis, growth, development and protein synthesis, most of which are shut down during drought. Differential regulation of phytohormones, e.g., jasmonic acid, cell wall metabolism, signaling and posttranslational modifications associated with biotic stress are elucidated. Functional characterization of topologically important, drought-responsive uncharacterized genes that may play a role in important processes such as ABA signaling, calcium signaling, photosynthesis and cell wall metabolism is discussed. Further transgenic studies on these genes may help in elucidating their biological role under stress conditions.

Conclusion

Currently, a large number of resources for rice functional genomics exist which are mostly underutilized by the scientific community. In this study, a computational approach integrating information from various resources such as gene co-expression networks, protein-protein interactions and pathway-level information is proposed to provide a systems-level view of complex drought-responsive processes across the drought-tolerant genotypes.
Cortisol Predicts Antidepressant Treatment Outcome, Memory Improvement, and Brain Response to Negative Emotions: The Importance of Aging
Authors: Jain Felipe A. , Connolly Colm G. , Reus Victor I. , Meyerhoff Dieter J. , Yang Tony T. , Mellon Synthia H. , Mackin Scott , Hough Christina M. , Morford Alexandra , Epel Elissa S. , Wolkowitz Owen M.
Published: October 2018

Background

Studies testing the relationship between cortisol levels, depression, and antidepressant treatment response have yielded divergent results suggesting the possibility of moderators of a cortisol effect. Several studies indicate that age may moderate the relationship between cortisol and psychopathology. In patients with Major Depressive Disorder (MDD), we studied the interactive effects of age and cortisol on predicting diagnostic status, improvement in mood and memory function with antidepressant treatment, and brain response to negative emotional stimuli.

Methods

66 unmedicated patients with MDD and 75 matched healthy controls had serum assayed at pre-treatment baseline for cortisol. Logistic regression was used to determine an association of age, cortisol and their interaction with MDD diagnosis. Thirty-four of the MDD participants (age range: 19-65 years; median: 36) underwent treatment with a selective serotonin reuptake inhibitor (SSRl) for 8 weeks. Clinician and self-ratings of depression symptoms, as well as tests of verbal and visual delayed recall were obtained at baseline and post treatment. Moderation analyses determined the effect of age on the relationship between baseline cortisol and treatment outcome. A separate sample of 8 MDD participants prospectively underwent fMRI neuroimaging and cortisol collection while viewing negative emotional faces.

Results

Age moderated the effects of cortisol on predicting MDD diagnosis (p<.05), treatment-associated reduction of depression symptoms (p<.001), improvement of delayed recall (p<.001), and baseline brain response to negative emotions (p<.05, whole brain corrected). Modeling the Age X Cortisol interaction suggested that for the participants below the median age of our sample, lower cortisol levels predicted a lower rate of MDD diagnosis, higher antidepressant effects and decreased brain reactivity in emotion regulation regions such as the anterior cingulate gyrus. On the contrary, in those above the median sample age, lower cortisol predicted a higher rate of MDD, less improvement in depression symptoms and memory performance, and more brain reactivity in the anterior cingulate.

Conclusions

Our results indicate that age moderates the relationship between peripheral cortisol levels and (1) MDD diagnosis, (2) brain reactivity to emotional stimuli, and (3) antidepressant-associated improvement in depression and memory symptoms. These results indicate that previous disparities in the literature linking peripheral cortisol levels with depression characteristics and treatment response may critically relate, at least in part, to the age of the patients studied.
Bayesian reassessment of the epigenetic architecture of complex traits
Authors: Banos Daniel Trejo , McCartney Daniel L. , Battram Tom , Hemani Gibran , Walker Rosie M. , Morris Stewart W. , Zhang Qian , Porteous David J. , McRae Allan F. , Wray Naomi R. , Visscher Peter M. , Haley Chris S. , Evans Kathryn L. , Deary Ian J. , McIntosh Andrew M. , Marioni Riccardo E. , Robinson Matthew R.
Published: October 2018

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Epigenetic DNA modification is partly under genetic control, and occurs in response to a wide range of environmental exposures. Linking epigenetic marks to clinical outcomes may provide greater insight into underlying molecular processes of disease, assist in the identification of therapeutic targets, and improve risk prediction. Here, we present a statistical approach, based on Bayesian inference, that estimates associations between disease risk and all measured epigenetic probes jointly, automatically controlling for both data structure (including cell-count effects, relatedness, and experimental batch effects) and correlations among probes. We benchmark our approach in simulation study, finding improved estimation of probe associations across a wide range of scenarios over existing approaches. Our method estimates the total proportion of disease risk captured by epigenetic probe variation, and when we applied it to measures of body mass index (BMI) and cigarette consumption behaviour in 5,101 individuals, we find that 66.7% (95% CI 60.0-72.8) of the variation in BMI and 67.7% (95% CI 58.4-76.9) of the variation in cigarette consumption can be captured by methylation array data from whole blood, independent of the variation explained by single nucleotide polymorphism markers. We find novel associations, with smoking behaviour associated with a methylation probe at the MNDA gene with >95% posterior inclusion probability, which is a myeloid cell nuclear differentiation antigen gene previously implicated as a biomarker for inflammation and non-Hodgkin lymphoma risk. We conduct unique genome-wide enrichment analyses, identifying blood cholesterol, lipid transport and sterol metabolism pathways for BMI, and response to xenobiotic stimulus and negative regulation of RNA polymerase II promoter transcription for smoking, all with >95% posterior inclusion probability of having methylation probes with associations >1.5 times larger than the average. Finally, we improve phenotypic prediction in two independent cohorts by 28.7% and 10.2% for BMI and smoking respectively over a LASSO model. These results imply that probe measures may capture large amounts of variance because they are likely a consequence of the phenotype rather than a cause. As a result, ‘omics’ data may enable accurate characterization of disease progression and identification of individuals who are on a path to disease. Our approach facilitates better understanding of the underlying epigenetic architecture of complex common disease and is applicable to any kind of genomics data.
I know that I don’t know: Structural and functional connectivity underlying meta-ignorance in pre-schoolers
Authors: Filevich Elisa , Forlim Caroline Garcia , Fehrman Carmen , Forster Carina , Paulus Markus , Shing Yee Lee , Kühn Simone
Published: October 2018

Research Highlights

[1] Children develop the ability to report that they do not know something at around five years of age.

[2] Children who could correctly report their own ignorance in a partial-knowledge task showed thicker cortices within medial orbitofrontal cortex.

[3] This region was functionally connected to parts of the default-mode network.

[4] The default-mode network might support the development of correct metacognitive monitoring.

Metacognition plays a pivotal role in human development. The ability to realize that we do not know something, or meta-ignorance, emerges after approximately five years of age. We aimed at identifying the brain systems that underlie the developmental emergence of this ability in a preschool sample.

Twenty-four children aged between five and six years answered questions under three conditions of a meta-ignorance task twice. In the criticalpartial knowledgecondition, an experimenter first showed two toys to a child, then announced that she would place one of them in a box behind a screen, out of sight from the child. The experimenter then asked the child whether or not she knew which toy was in the box.

Children who answered correctly both times to the metacognitive question in the partial knowledge condition (n=9) showed greater cortical thickness in a cluster within left medial orbitofrontal cortex than children who did not (n=15). Further, seed-based functional connectivity analyses of the brain during resting state revealed that this region is functionally connected to the medial orbitofrontal gyrus, posterior cingulate gyrus and precuneus, and mid- and inferior temporal gyri.

This finding suggests that the default mode network, critically through its prefrontal regions, supports introspective processing. It leads to the emergence of metacognitive monitoring allowing children to explicitly report their own ignorance.
Corporate governance integration with sustainability: a systematic literature review
Authors: E-Vahdati Sahar , Zulkifli Norhayah , Zakaria Zarina
Published: October 2018

Purpose

The purpose of this paper is to systematically review the literature on corporate governance and sustainability integration in identifying the main rigidity, infirmity and gaps in the current literature, and also to mention future research paths.

Design/methodology/approach

A systematic literature review of existing international papers is used through quantitative and qualitative approach by selecting 27 articles published in Scopus.

Findings

The review suggests although integration of governance into sustainability is interpreted differently in a geographical area, vision, mission and leadership are the most significant drivers of sustainability framework dealing corporate governance. Despite the limitation which is related to the choice of number and type of keywords and journals, outcomes and the interpretation, generalization and application of results, sustainability frameworks suggest a number of avenues for investors, policy makers and future market scenario which will increase the efficiency of companies.

Research limitations/implications

This research uses limited number of reviews by the common features of Scopus search as previous studies. This review study reflects corporate governance to sustainability models and provides opportunities to researchers for a more in-depth investigation into the theoretical advancement and joint work of sustainability and corporate governance which better inform strategies and implementations of governmental structures.

Originality/value

This paper undertakes a significant thorough systematic review for sustainability integration with corporate governance literature. It gives a written work review and reference index from1995 to 2017, useful for both academics and professionals.
Construction projects as mechanisms for knowledge integration
Authors: Lindgren John , Emmitt Stephen , Widén Kristian
Published: October 2018

Purpose

The purpose of this paper is to study knowledge integration (KI) when diffusing a systemic innovation. The objectives are to understand what mechanisms are used and when and what their effects are in terms of knowledge development.

Design/methodology/approach

The method comprised a longitudinal case study which followed a firm’s attempts to develop and diffuse a timber multi-storey building system (the systemic innovation) over a number of projects.

Findings

The findings emphasize actual projects as the most crucial activity for KI and when and why soft personalization mechanisms and codified knowledge should be mixed. Furthermore, it shows how different types of knowledge are built-up including construction process effects over a series of projects.

Research limitations/implications

The research contributes with knowledge about mechanisms for the diffusion of a specific systemic innovation type and provides input regarding mechanisms to use. The introduction of the concepts “domain-specific,” “procedural” and “general knowledge” into construction has increased understanding of innovation diffusion and knowledge flows and where and how they are integrated.

Practical implications

The research shows how knowledge develops and through which mechanisms, and where problems occur. Construction organizations can learn from this to avoid mistakes and potentially better understand how to manage knowledge to diffuse a systemic innovation.

Originality/value

The research provides insight into systemic innovation diffusion over a series of projects and focuses on both projects and the construction process.