bluuebunny/crossref_metadata_2025_split huggingface dataset:
Man against machine: Do fungal fruitbodies and eDNA give similar biodiversity assessments across broad environmental gradients?
Authors: Frøslev Tobias Guldberg , Kjøller Rasmus , Bruun Hans Henrik , Ejrnæs Rasmus , Hansen Anders Johannes , Læssøe Thomas , Heilmann-Clausen Jacob 
Published: December 2018

AbstractThe majority of Earths biodiversity is unknown. This is particularly true for the vast part of soil biodiversity, which rarely can be observed directly. Metabarcoding of DNA extracted from the environment (eDNA) has become state-of-the-art in assessing soil biodiversity. Also for fungal community profiling eDNA is seen as an attractive alternative to classical surveying based on fruitbodies. However, it is unknown whether eDNA-metabarcoding provides a representative sample of fungal diversity and census of threatened species. Therefore conservation planning and assessment are still based on fruitbody inventories. Based on a dataset of unprecedented width and depth, representing both soil eDNA-metabarcoding and expert inventorying of fungal fruitbodies, we document for the first time the validity of eDNA as practical inventory method and measure of conservation value for fungi. Fruitbody data identified fewer species in total and per site, and had larger variance in site richness. Focusing on macrofungi – the class Agaricomycetes, and in turn the order Agaricales – metrics of total richness and compositional similarity converged between the methods. eDNA was suboptimal for recording the non-soil dwelling fungi. β-diversity was similar between methods, but more variation in community composition could be explained by environmental predictors in eDNA data. The fruitbody survey was slightly better in finding red-listed species. We find a better correspondence between biodiversity indices derived from fungal fruitbodies and DNA-based approaches than indicated in earlier studies. We argue that (historical) fungal community data based on fruitbody forays – with careful selection of taxonomic groups – may be interpreted together with modern DNA-based approaches.
SVIM: Structural Variant Identification using Mapped Long Reads
Authors: Heller David , Vingron Martin 
Published: December 2018

AbstractMotivationStructural variants are defined as genomic variants larger than 50bp. They have been shown to affect more bases in any given genome than SNPs or small indels. Additionally, they have great impact on human phenotype and diversity and have been linked to numerous diseases. Due to their size and association with repeats, they are difficult to detect by shotgun sequencing, especially when based on short reads. Long read, single molecule sequencing technologies like those offered by Pacific Biosciences or Oxford Nanopore Technologies produce reads with a length of several thousand base pairs. Despite the higher error rate and sequencing cost, long read sequencing offers many advantages for the detection of structural variants. Yet, available software tools still do not fully exploit the possibilities.ResultsWe present SVIM, a tool for the sensitive detection and precise characterization of structural variants from long read data. SVIM consists of three components for the collection, clustering and combination of structural variant signatures from read alignments. It discriminates five different variant classes including similar types, such as tandem and interspersed duplications and novel element insertions. SVIM is unique in its capability of extracting both the genomic origin and destination of duplications. It compares favorably with existing tools in evaluations on simulated data and real datasets from PacBio and Nanopore sequencing machines.Availability and implementationThe source code and executables of SVIM are available on Github: github.com/eldariont/svim. SVIM has been implemented in Python 3 and published on bioconda and the Python Package Index.Contactheller_d@molgen.mpg.de
Developmental Dieldrin Exposure Alters DNA Methylation at Genes Related to Dopaminergic Neuron Development and Parkinson’s Disease in Mouse Midbrain
Authors: Kochmanski Joseph , VanOeveren Sarah E. , Bernstein Alison I. 
Published: December 2018

AbstractHuman and animal studies have shown that exposure to the organochlorine pesticide dieldrin is associated with increased risk of Parkinson’s disease (PD). Despite previous work showing a link between developmental dieldrin exposure and increased neuronal susceptibility to MPTP toxicity in male C57BL/6 mice, the mechanism mediating this effect has not been identified. Here, we tested the hypothesis that developmental exposure to dieldrin increases neuronal susceptibility via genome-wide changes in DNA methylation. Starting at 8 weeks of age and prior to mating, female C57BL/6 mice were exposed to 0.3 mg/kg dieldrin by feeding (every 3 days) throughout breeding, gestation, and lactation. At 12 weeks of age, pups were sacrificed and midbrains were dissected. DNA was isolated and dieldrin-related changes in DNA methylation were assessed via reduced representation bisulfite sequencing (RRBS). We identified significant, sex-specific differentially methylated CpGs (DMCs) and regions (DMRs) by developmental dieldrin exposure (FDR<0.05), including DMCs at the Nr4a2 and Lmx1b genes, which are involved in dopaminergic neuron development and maintenance. Developmental dieldrin exposure had distinct effects on the male and female epigenome. Furthermore, a separate set of changes in DNA methylation was identified after adult exposure to dieldrin, suggesting that adult and developmental dieldrin toxicity may not act through a shared epigenetic mechanism. Together, our data suggest that developmental dieldrin exposure establishes sex-specific poised epigenetic states early in life. These poised epigenomes may mediate sensitivity to additional environmental stimuli and contribute to the development of late-life neurodegenerative disease, including PD.
Manganese influx and expression of ZIP8 is essential in primary myoblasts and contributes to activation of SOD2
Authors: Gordon Shellaina J. V. , Fenker Daniel E. , Vest Katherine E. , Padilla-Benavides Teresita 
Published: December 2018

ABSTRACTTrace elements such as copper (Cu), zinc (Zn), iron (Fe), and manganese (Mn) are enzyme cofactors and second messengers in cell signaling. Trace elements are emerging as key regulators of differentiation and development of mammalian tissues including blood, brain, and skeletal muscle. We previously reported an influx of Cu and dynamic expression of various metal transporters during differentiation of skeletal muscle cells. Here, we demonstrate that during differentiation of skeletal myoblasts an increase of additional trace elements such as Mn, Fe and Zn occurs. Interestingly the Mn increase is concomitant with increased Mn-dependent SOD2 levels. To better understand the Mn import pathway in skeletal muscle cells, we probed the functional relevance of the closely related proteins ZIP8 and ZIP14, which are implicated in Zn, Mn, and Fe transport. Partial depletion of ZIP8 severely impaired growth of myoblasts and led to cell death under differentiation conditions, indicating that ZIP8-mediated metal transport is essential in skeletal muscle cells. Moreover, knockdown ofZip8impaired activity of the Mn-dependent SOD2. Growth defects were partially rescued by Mn supplementation to the medium, suggesting additional functions for ZIP8 in the skeletal muscle lineage. Knockdown ofZip14, on the other hand, had only a mild effect on myotube size, consistent with a role for ZIP14 in muscle hypertrophy. This is the first report on the functional relevance of two members of the ZIP family of metal transporters in the skeletal muscle lineage, and further supports the paradigm that trace metal transporters are critical modulators of mammalian tissue development.
Chicory demonstrates substantial water uptake from below 2 m depth, but still did not escape topsoil drought
Authors: Rasmussen Camilla Ruø , Thorup-Kristensen Kristian , Dresbøll Dorte Bodin 
Published: December 2018

AbstractAimsDeep-rooted agricultural crops can potentially utilize deep water pools and thus reduce periods where growth is water limited. Chicory (Cichorium intybusL.) is known to be deep-rooted, but the contribution of deep roots to water uptake under well-watered and drought conditions by the deep root system has not been studied. The aim of this study was to investigate whether chicory could reach 3 m depth within a growing season and demonstrate significant water uptake from the deeper part of the root zone.MethodsWe tested if chicory exposed to either topsoil drought or resource competition from the shallow-rooted species ryegrass(Lolium perenne L.)and black medic (Medicago lupulina L.)would increase deep water uptake in compensation for reduced topsoil water uptake. We grew chicory in 4 m deep soil filled rhizotrons and found that the roots reached 3 m depth within a growing season.ResultsWater uptake from below 1.7 m depth in 2016 and 2.3 m depth in 2017 contributed significantly to chicory water use. However, neither drought nor intercropping increased the deep water uptake.ConclusionChicory benefits from being deep-rooted during drought events, yet deep water uptake cannot compensate for the reduced topsoil water uptake during drought.
Super-resolution modularity analysis shows polyhedral caveolin-1 oligomers combine to form scaffolds and caveolae
Authors: Khater Ismail M. , Liu Qian , Chou Keng C. , Hamarneh Ghassan , Nabi Ivan Robert 
Published: December 2018

ABSTRACTCaveolin-1 (Cav1), the coat protein for caveolae, also forms non-caveolar Cav1 scaffolds. Single molecule Cav1 super-resolution microscopy analysis previously identified caveolae and three distinct scaffold domains: smaller S1A and S2B scaffolds and larger hemispherical S2 scaffolds. Application here of network modularity analysis of SMLM data for endogenous Cav1 labeling in HeLa cells shows that small scaffolds combine to form larger scaffolds and caveolae. We find modules within Cav1 blobs by maximizing the intra-connectivity between Cav1 molecules within a module and minimizing the inter-connectivity between Cav1 molecules across modules, which is achieved via spectral decomposition of the localizations adjacency matrix. Features of modules are then matched with intact blobs to find the similarity between the module-blob pairs of group centers. Our results show that smaller S1A and S1B scaffolds are made up of small polygons, that S1B scaffolds correspond to S1A scaffold dimers and that caveolae and hemi-spherical S2 scaffolds are complex, modular structures formed from S1B and S1A scaffolds, respectively. Polyhedral interactions of Cav1 oligomers therefore leads progressively to the formation of larger and more complex scaffold domains and the biogenesis of caveolae.
The topology of DNA entrapment by cohesin rings
Authors: Chapard Christophe , Jones Robert , van Oepen Till , Scheinost Johanna C , Nasmyth Kim 
Published: December 2018

SummaryCohesin entraps sister DNAs within tripartite rings created by pairwise interactions between Smc1,Smc3, and Scc1. Because the ATPase heads of Smc1 and Smc3 can interact with each other, cohesin rings in fact have the potential to form a variety of sub-compartments. Using in vivo cysteine crosslinking,we show that when Smc1 and Smc3 ATPases are engaged in the presence of ATP (E heads)cohesin rings generate a “SMC (S) compartment” between hinge and E heads and a “kleisin (K)compartment” between E heads and their associated kleisin subunit. Upon ATP hydrolysis, cohesin’s heads associate with each other in a very different mode, in which their signature motifs and their coiled coils are closely juxtaposed (J heads), creating alternative S and K compartments. We show that all four sub-compartments exist in vivo, that acetylation of Smc3 during S phase is accompanied by an increase in the ratio of J to E heads, and that sister DNAs are entrapped in J-K but not E-K compartments or in either type of S compartment.
Liquid-crystal organization of liver tissue
Authors: Morales-Navarrete Hernán , Nonaka Hidenori , Scholich André , Segovia-Miranda Fabián , de Back Walter , Meyer Kirstin , Bogorad Roman L. , Koteliansky Victor , Brusch Lutz , Kalaidzidis Yannis , Jülicher Frank , Friedrich Benjamin M. , Zerial Marino 
Published: December 2018

AbstractFunctional tissue architecture originates by self-assembly of distinct cell types, following tissue-specific rules of cell-cell interactions. In the liver, a structural model of the lobule was pioneered by Elias in 1949. This model, however, is in contrast with the apparent random 3D arrangement of hepatocytes. Since then, no significant progress has been made to derive the organizing principles of liver tissue. To solve this outstanding problem, we computationally reconstructed 3D tissue geometry from microscopy images and analyzed it applying soft-condensed-matter-physics concepts. Surprisingly, analysis of the spatial organization of cell polarity revealed that hepatocytes are not randomly oriented but follow a long-range liquid-crystal order. This does not depend exclusively on hepatocytes receiving instructive signals by endothelial cells as generally assumed, since silencing Integrin-ß1 disrupted both liquid-crystal order and organization of the sinusoidal network. Our results suggest that bi-directional communication between hepatocytes and sinusoids underlies the self-organization of liver tissue.
A gene expression programming model for economy growth using knowledge-based economy indicators
Authors: Ahmadi Mohsen , Taghizadeh Rahim 
Published: December 2018

Purpose
The purpose of this paper is to focus on modeling economy growth with indicators of knowledge-based economy (KBE) introduced by World Bank for a case study in Iran during 1993-2013.

Design/methodology/approach
First, for grouping and reducing the number of variables, Tukey method and the principal component analysis are used. Also for modeling, 67 per cent of data is used for training in the two approaches of ARDL bounds testing and gene expression programming (GEP) and 33 per cent of them for testing the models. Then, the result models are compared with fitness function and Akaike information criteria (AIC).

Findings
The GEP model with fitness 945.7461 for training data and 954.8403 for testing data from 1000 is better than ARDL bounds testing model with fitness 335.5479 from 1000. In addition, according to model comparison tools (AIC), the GEP model has an extremely larger weight in comparison with ARDL bounds model. Therefore, the GEP model is introduced for future use in academia.

Practical implications
Knowledge and information is one of the most basic sources of wealth in economists’ sight. Thus, using KBE indicators appears essential in economic growth regarding daily progress in knowledge processes and its different theories. It is also extremely important to determine an appropriate model for KBE indicators which play a highly important role in the allocation of the economic resources of the country in an optimal manner.

Originality/value
This paper introduced a novel expression for economy growth using KBE indicators. All the data and the indicators are extracted from Word Bank service between 1993 and 2013.
Community policing and intelligence-led policing
Authors: Carter Jeremy G. , Fox Bryanna 
Published: December 2018

Purpose
Despite increased scholarly inquiry regarding intelligence-led policing (ILP) and popularity among law enforcement agencies around the globe, ambiguity remains regarding the conceptual foundation and appropriate measurement of ILP. Although most scholars agree that ILP is indeed a unique policing philosophy, there is less consensus regarding the relationship between ILP and the ever-present model of community-oriented policing (COP). Consequently, there is a clear need to study the empirical distinctions and overlaps in these policing philosophies as implemented by US law enforcement agencies. The paper aims to discuss these issues.

Design/methodology/approach
Data were gleaned from the 2007 LEMAS and 2009 NIJ Intelligence surveys. A total of 227 unique police agencies in the USA are included. A series of bivariate, exploratory factor analyses and structural models are used to determine discriminatory or convergent validity across COP and ILP constructs.

Findings
The goal was to answer the question: are these two policing philosophies are being implemented as separate and distinct strategies? Results of our exploratory and structural models indicate that COP and ILP loaded on unique latent constructs. This affirms the results of the bivariate correlations, and indicates that COP and ILP have discriminant measurement validity. In other words, COP and ILP are conceptually distinct, even when implemented in police departments across the USA. Implications of these findings and suggestions for future research are discussed.

Originality/value
This is the first study to empirically test the discriminant or convergent validity of COP and ILP.
The role of stressors in altering eco‐evolutionary dynamics
Authors: Theodosiou Loukas , Hiltunen Teppo , Becks Lutz 
Published: December 2018

AbstractWe review and synthesize evidence from the fields of ecology, evolutionary biology and population genetics to investigate how the presence of abiotic stress can affect the feedback between ecological and evolutionary dynamics.To obtain a better insight of how, and under what conditions, an abiotic stressor can influence eco‐evolutionary dynamics, we use a conceptual predator–prey model where the prey can rapidly evolve antipredator defences and stress resistance.We show how abiotic stress influences eco‐evolutionary dynamics by changing the pace and in some case the potential for evolutionary change and thus the evolution‐to‐ecology link. Whether and how the abiotic stress influences this link depends on the effect on population sizes, mutation rates, the presence of gene flow and the genetic architecture underlying the traits involved.Overall, we report ecological and population genetic mechanisms that have so far not been considered in studies on eco‐evolutionary dynamics and suggest future research directions and experiments to develop an understanding of the role of eco‐evolutionary dynamics in more complex ecological and evolutionary scenarios.Aplain language summaryis available for this article.
Carry‐over effects of early thermal conditions on somatic and germline oxidative damages are mediated by compensatory growth in sticklebacks
Authors: Kim Sin‐Yeon , Noguera José C. , Velando Alberto 
Published: December 2018

Abstract

Most studies of climate change impacts focus on the effects of summer temperatures, which can immediately impact fitness of breeders, but winter temperatures are expected to have a greater impact on development and growth of animals with long‐lasting consequences. Exposure to warmer temperatures can increase cellular oxidative damage in ectotherms. Yet, it is unknown whether thermal stress during early life has prolonged effects on oxidative status during adulthood.

In an experiment using F1 fish originated from a wild three‐spined stickleback population at the southern edge of its European distribution, we examined whether experimental thermal conditions experienced in winter had carry‐over effects on oxidative status and telomere length, a marker of accumulated stress, in the soma and germline during adulthood. For this, oxidative DNA damage, enzymatic antioxidant activities and telomere length were measured three months after the termination of the temperature manipulation. In addition, we tested whether such delayed effects, if any, were due to individuals’ compensatory growth after experiencing unfavourable growth conditions in winter.

Warm acclimation during winter induced increased levels of oxidative DNA damage in muscle and sperm and increased enzymatic antioxidant defences in muscle during the breeding season. Telomere length of adult fish was not influenced by thermal conditions experienced during early life.

Winter temperature manipulation influenced fish to alter the temporal pattern of growth trajectories across the juvenile and adult stages. Fish reared in warm winter conditions grew at a slower rate than the controls during the period of temperature manipulation then accelerated body mass gain to catch up during the breeding season. Faster somatic growth during the breeding season incurred a higher cost in terms of oxidative damage in the warm‐treated individuals.

For the first time, we experimentally show the long‐lasting detrimental effects of thermal stress on and the positive link between catch‐up growth and oxidative DNA damage in the soma and germline. Winter temperature increases due to climate change can reduce fertility and survival of fish by inducing catch‐up growth. The detrimental effects of winter climate change may accumulate across generations through the pre‐mutagenic DNA damage in the germline.
Linking the vectorial capacity of multiple vectors to observed patterns of West Nile virus transmission
Authors: McMillan Joseph R. , Blakney Rebekah A. , Mead Daniel G. , Koval William T. , Coker Sarah M. , Waller Lance A. , Kitron Uriel , Vazquez‐Prokopec Gonzalo M. 
Published: December 2018

Abstract

Theoretical models suggest that increased vector species participation in pathogen transmission significantly increases the prevalence of vector and host infections. However, there has been a lack of empirical evidence to support this.

We linked transmission potential of multiple vector species to observed patterns of enzootic pathogen transmission by conducting longitudinal field surveillance of West Nile virus (WNv) infections in Culex spp. mosquitoes and avian host communities in the southeast U.S. We then used a temperature‐dependent vectorial capacity model as a predictor of WNv infections in mosquitoes and birds using general linear mixed effects models.

Two WNv‐competent Culex spp. mosquitoes were present in our study sites, Culex restuans Theobald during the spring and Culex quinquefasciatus Say during the summer. Empirical evidence of WNv transmission was limited exclusively to time periods when night time temperatures were suitable for accelerated within‐vector viral replication, susceptible avian hosts (i.e. hatch year birds) were abundant and Cx. quinquefasciatus was the primary Culex spp. vector in the mosquito community.

Contrary to theoretical predictions, increased presence of competent vector species through time did not significantly increase the prevalence of infections in the WNv enzootic system.

Synthesis and applications. We extend a common theoretical model to both estimate the transmission potential of a mosquito community for West Nile virus (WNv) and quantify the relative contribution of two Culex mosquito species (Culex quinquefasciatus and Culex restuans) to observed patterns of WNv in the southeast U.S. Our findings suggest that to reduce the risk of human exposure to WNv in urban environments, vector control should focus on the primary WNv vector, Cx. quinquefasciatus. Additionally, vector control may be more effective if it coincides with the onset of the avian breeding season, when most WNv amplification occurs. Moreover, our results highlight relevant knowledge gaps pertaining to WNv transmission by secondary mosquito species that coexist either in time or space with Cx. quinquefasciatus. A better understanding of secondary WNv vector species is greatly needed in order to appropriately gauge their role in pathogen transmission dynamics.