bluuebunny/crossref_metadata_2025_split huggingface dataset:
Trollism, Reality Hunger, and Vulnerability. Trolls in film and literature in the 2000’s
Authors: Dancus Adriana Margareta 
Published: October 2016

Abstract
Trolls have become increasingly salient in contemporary Nordic film and literature. This article sets up to understand the dissemination of cinematic and literary trolls of the 2000’s by providing a comparative analysis of three contemporary texts: the Norwegian mockumentary Trollhunter (André Øvredal, 2010) and two fantasy novels, Troll: A Love Story by Finnish writer Johanna Sinisalo (2000) and Stallo by Swedish author Stefan Spjut (2012). In addition to comparing contemporary trolls to more established troll conceptualizations from Nordic folklore and children’s literature, I will also analyze trolls in a larger cultural and socio-political context by tying them to aesthetic movements such as the reality hunger in contemporary Scandinavian art and the vulnerability of the contemporary socio-political moment.
Application of Static Var Compensator (SVC) With PI Controller for Grid Integration of Wind Farm Using Harmony Search
Authors: Keshta H. E. , Ali A. A. , Saied E. M. , Bendary F. M. 
Published: October 2016

Abstract
Large-scale integration of wind turbine generators (WTGs) may have significant impacts on power system operation with respect to system frequency and bus voltages. This paper studies the effect of Static Var Compensator (SVC) connected to wind energy conversion system (WECS) on voltage profile and the power generated from the induction generator (IG) in wind farm. Also paper presents, a dynamic reactive power compensation using Static Var Compensator (SVC) at the a point of interconnection of wind farm while static compensation (Fixed Capacitor Bank) is unable to prevent voltage collapse. Moreover, this paper shows that using advanced optimization techniques based on artificial intelligence (AI) such as Harmony Search Algorithm (HS) and Self-Adaptive Global Harmony Search Algorithm (SGHS) instead of a Conventional Control Method to tune the parameters of PI controller for SVC and pitch angle. Also paper illustrates that the performance of the system with controllers based on AI is improved under different operating conditions. MATLAB/Simulink based simulation is utilized to demonstrate the application of SVC in wind farm integration. It is also carried out to investigate the enhancement in performance of the WECS achieved with a PI Controller tuned by Harmony Search Algorithm as compared to a Conventional Control Method.
The Duality of Page and Stage: Constructing Lyrical Voices in Contemporary British Poetry Written for Performance
Authors: Tönnies Merle , Brüning Joana , Sand Andrea 
Published: October 2016

AbstractThe paper uses an interdisciplinary approach to analyse characteristic works by three contemporary British authors who come from different backgrounds but have all, in various ways, brought a performative perspective to bear on their poetry: Patience Agbabi, Jackie Kay, and Ben Mellor. The focus is on the concrete techniques which the poets use to construct different lyrical voices in the written texts as well as in performance. With their emphasis on difference(s), they seem to align themselves closely with broader literary and cultural developments like postmodernism or Stuart Hall’s ‘politics of representation,’ while nevertheless repeatedly suggesting the possibility of a unifying centre behind the text. All in all, the detailed analyses of the poems show the authors to take up different positions in the continuum between orality and writing, unity and diversity, as well as political intervention and playfulness.
Activation of a Habenulo–Raphe Circuit Is Critical for the Behavioral and Neurochemical Consequences of Uncontrollable Stress in the Male Rat
Authors: Dolzani Samuel D. , Baratta Michael V. , Amat Jose , Agster Kara L. , Saddoris Michael P. , Watkins Linda R. , Maier Steven F. 
Published: October 2016

AbstractExposure to uncontrollable stress [inescapable tailshock (IS)] produces behavioral changes that do not occur if the stressor is controllable [escapable tailshock (ES)] an outcome that is mediated by greater IS-induced dorsal raphe nucleus (DRN) serotonin [5-hydroxytryptamine (5-HT)] activation. It has been proposed that this differential activation occurs because the presence of control leads to top–down inhibition of the DRN from medial prefrontal cortex (mPFC), not because uncontrollability produces greater excitatory input. Although mPFC inhibitory regulation over DRN 5-HT activation has received considerable attention, the relevant excitatory inputs that drive DRN 5-HT during stress have not. The lateral habenula (LHb) provides a major excitatory input to the DRN, but very little is known about the role of the LHb in regulating DRN-dependent behaviors. Here, optogenetic silencing of the LHb during IS blocked the typical anxiety-like behaviors produced by IS in male rats. Moreover, LHb silencing blocked the increase in extracellular basolateral amygdala 5-HT during IS and, surprisingly, during behavioral testing the following day. We also provide evidence that LHb–DRN pathway activation is not sensitive to the dimension of behavioral control. Overall, these experiments highlight a critical role for LHb in driving DRN activation and 5-HT release into downstream circuits that mediate anxiety-like behavioral outcomes of IS and further support the idea that behavioral control does not modulate excitatory inputs to the DRN.
Autosomal and X-Linked Additive Genetic Variation for Lifespan and Aging: Comparisons Within and Between the Sexes in Drosophila melanogaster
Authors: Griffin Robert M , Schielzeth Holger , Friberg Urban 
Published: October 2016

Abstract
Theory makes several predictions concerning differences in genetic variation between the X chromosome and the autosomes due to male X hemizygosity. The X chromosome should: (i) typically show relatively less standing genetic variation than the autosomes, (ii) exhibit more variation in males compared to females because of dosage compensation, and (iii) potentially be enriched with sex-specific genetic variation. Here, we address each of these predictions for lifespan and aging in Drosophila melanogaster. To achieve unbiased estimates of X and autosomal additive genetic variance, we use 80 chromosome substitution lines; 40 for the X chromosome and 40 combining the two major autosomes, which we assay for sex-specific and cross-sex genetic (co)variation. We find significant X and autosomal additive genetic variance for both traits in both sexes (with reservation for X-linked variation of aging in females), but no conclusive evidence for depletion of X-linked variation (measured through females). Males display more X-linked variation for lifespan than females, but it is unclear if this is due to dosage compensation since also autosomal variation is larger in males. Finally, our results suggest that the X chromosome is enriched for sex-specific genetic variation in lifespan but results were less conclusive for aging overall. Collectively, these results suggest that the X chromosome has reduced capacity to respond to sexually concordant selection on lifespan from standing genetic variation, while its ability to respond to sexually antagonistic selection may be augmented.
First Draft Assembly and Annotation of the Genome of a California Endemic OakQuercus lobataNée (Fagaceae)
Authors: Sork Victoria L , Fitz-Gibbon Sorel T , Puiu Daniela , Crepeau Marc , Gugger Paul F , Sherman Rachel , Stevens Kristian , Langley Charles H , Pellegrini Matteo , Salzberg Steven L 
Published: October 2016

AbstractOak represents a valuable natural resource across Northern Hemisphere ecosystems, attracting a large research community studying its genetics, ecology, conservation, and management. Here we introduce a draft genome assembly of valley oak (Quercus lobata) using Illumina sequencing of adult leaf tissue of a tree found in an accessible, well-studied, natural southern California population. Our assembly includes a nuclear genome and a complete chloroplast genome, along with annotation of encoded genes. The assembly contains 94,394 scaffolds, totaling 1.17 Gb with 18,512 scaffolds of length 2 kb or longer, with a total length of 1.15 Gb, and a N50 scaffold size of 278,077 kb. The k-mer histograms indicate an diploid genome size of ∼720–730 Mb, which is smaller than the total length due to high heterozygosity, estimated at 1.25%. A comparison with a recently published European oak (Q. robur) nuclear sequence indicates 93% similarity. The Q. lobata chloroplast genome has 99% identity with another North American oak, Q. rubra. Preliminary annotation yielded an estimate of 61,773 predicted protein-coding genes, of which 71% had similarity to known protein domains. We searched 956 Benchmarking Universal Single-Copy Orthologs, and found 863 complete orthologs, of which 450 were present in &gt; 1 copy. We also examined an earlier version (v0.5) where duplicate haplotypes were removed to discover variants. These additional sources indicate that the predicted gene count in Version 1.0 is overestimated by 37–52%. Nonetheless, this first draft valley oak genome assembly represents a high-quality, well-annotated genome that provides a tool for forest restoration and management practices.
Genomic Prediction of Single Crosses in the Early Stages of a Maize Hybrid Breeding Pipeline
Authors: Kadam Dnyaneshwar C , Potts Sarah M , Bohn Martin O , Lipka Alexander E , Lorenz Aaron J 
Published: October 2016

Abstract
Prediction of single-cross performance has been a major goal of plant breeders since the beginning of hybrid breeding. Recently, genomic prediction has shown to be a promising approach, but only limited studies have examined the accuracy of predicting single-cross performance. Moreover, no studies have examined the potential of predicting single crosses among random inbreds derived from a series of biparental families, which resembles the structure of germplasm comprising the initial stages of a hybrid maize breeding pipeline. The main objectives of this study were to evaluate the potential of genomic prediction for identifying superior single crosses early in the hybrid breeding pipeline and optimize its application. To accomplish these objectives, we designed and analyzed a novel population of single crosses representing the Iowa Stiff Stalk synthetic/non-Stiff Stalk heterotic pattern commonly used in the development of North American commercial maize hybrids. The performance of single crosses was predicted using parental combining ability and covariance among single crosses. Prediction accuracies were estimated using cross-validation and ranged from 0.28 to 0.77 for grain yield, 0.53 to 0.91 for plant height, and 0.49 to 0.94 for staygreen, depending on the number of tested parents of the single cross and genomic prediction method used. The genomic estimated general and specific combining abilities showed an advantage over genomic covariances among single crosses when one or both parents of the single cross were untested. Overall, our results suggest that genomic prediction of single crosses in the early stages of a hybrid breeding pipeline holds great potential to redesign hybrid breeding and increase its efficiency.
Depletion of Shine-Dalgarno Sequences Within Bacterial Coding Regions Is Expression Dependent
Authors: Yang Chuyue , Hockenberry Adam J , Jewett Michael C , Amaral Luís A N 
Published: October 2016

Abstract
Efficient and accurate protein synthesis is crucial for organismal survival in competitive environments. Translation efficiency (the number of proteins translated from a single mRNA in a given time period) is the combined result of differential translation initiation, elongation, and termination rates. Previous research identified the Shine-Dalgarno (SD) sequence as a modulator of translation initiation in bacterial genes, while codon usage biases are frequently implicated as a primary determinant of elongation rate variation. Recent studies have suggested that SD sequences within coding sequences may negatively affect translation elongation speed, but this claim remains controversial. Here, we present a metric to quantify the prevalence of SD sequences in coding regions. We analyze hundreds of bacterial genomes and find that the coding sequences of highly expressed genes systematically contain fewer SD sequences than expected, yielding a robust correlation between the normalized occurrence of SD sites and protein abundances across a range of bacterial taxa. We further show that depletion of SD sequences within ribosomal protein genes is correlated with organismal growth rates, supporting the hypothesis of strong selection against the presence of these sequences in coding regions and suggesting their association with translation efficiency in bacteria.
Predictive Model and Software for Inbreeding-Purging Analysis of Pedigreed Populations
Authors: García-Dorado Aurora , Wang Jinliang , López-Cortegano Eugenio 
Published: October 2016

Abstract
The inbreeding depression of fitness traits can be a major threat to the survival of populations experiencing inbreeding. However, its accurate prediction requires taking into account the genetic purging induced by inbreeding, which can be achieved using a “purged inbreeding coefficient”. We have developed a method to compute purged inbreeding at the individual level in pedigreed populations with overlapping generations. Furthermore, we derive the inbreeding depression slope for individual logarithmic fitness, which is larger than that for the logarithm of the population fitness average. In addition, we provide a new software, PURGd, based on these theoretical results that allows analyzing pedigree data to detect purging, and to estimate the purging coefficient, which is the parameter necessary to predict the joint consequences of inbreeding and purging. The software also calculates the purged inbreeding coefficient for each individual, as well as standard and ancestral inbreeding. Analysis of simulation data show that this software produces reasonably accurate estimates for the inbreeding depression rate and for the purging coefficient that are useful for predictive purposes.
The Genetic Basis of Upland/Lowland Ecotype Divergence in Switchgrass (Panicum virgatum)
Authors: Milano Elizabeth R , Lowry David B , Juenger Thomas E 
Published: October 2016

Abstract
The evolution of locally adapted ecotypes is a common phenomenon that generates diversity within plant species. However, we know surprisingly little about the genetic mechanisms underlying the locally adapted traits involved in ecotype formation. The genetic architecture underlying locally adapted traits dictates how an organism will respond to environmental selection pressures, and has major implications for evolutionary ecology, conservation, and crop breeding. To understand the genetic architecture underlying the divergence of switchgrass (Panicum virgatum) ecotypes, we constructed a genetic mapping population through a four-way outbred cross between two northern upland and two southern lowland accessions. Trait segregation in this mapping population was largely consistent with multiple independent loci controlling the suite of traits that characterizes ecotype divergence. We assembled a joint linkage map using ddRADseq, and mapped quantitative trait loci (QTL) for traits that are divergent between ecotypes, including flowering time, plant size, physiological processes, and disease resistance. Overall, we found that most QTL had small to intermediate effects. While we identified colocalizing QTL for multiple traits, we did not find any large-effect QTL that clearly controlled multiple traits through pleiotropy or tight physical linkage. These results indicate that ecologically important traits in switchgrass have a complex genetic basis, and that similar loci may underlie divergence across the geographic range of the ecotypes.
Regulation of Secondary Metabolism by the Velvet Complex Is Temperature-Responsive in Aspergillus
Authors: Lind Abigail L , Smith Timothy D , Saterlee Timothy , Calvo Ana M , Rokas Antonis 
Published: October 2016

Abstract
Sensing and responding to environmental cues is critical to the lifestyle of filamentous fungi. How environmental variation influences fungi to produce a wide diversity of ecologically important secondary metabolites (SMs) is not well understood. To address this question, we first examined changes in global gene expression of the opportunistic human pathogen, Aspergillus fumigatus, after exposure to different temperature conditions. We found that 11 of the 37 SM gene clusters in A. fumigatus were expressed at higher levels at 30° than at 37°. We next investigated the role of the light-responsive Velvet complex in environment-dependent gene expression by examining temperature-dependent transcription profiles in the absence of two key members of the Velvet protein complex, VeA and LaeA. We found that the 11 temperature-regulated SM gene clusters required VeA at 37° and LaeA at both 30 and 37° for wild-type levels of expression. Interestingly, four SM gene clusters were regulated by VeA at 37° but not at 30°, and two additional ones were regulated by VeA at both temperatures but were substantially less so at 30°, indicating that the role of VeA and, more generally of the Velvet complex, in the regulation of certain SM gene clusters is temperature-dependent. Our findings support the hypothesis that fungal secondary metabolism is regulated by an intertwined network of transcriptional regulators responsive to multiple environmental factors.
Prevention of DNA Rereplication Through a Meiotic Recombination Checkpoint Response
Authors: Najor Nicole A , Weatherford Layne , Brush George S 
Published: October 2016

AbstractIn the budding yeast Saccharomyces cerevisiae, unnatural stabilization of the cyclin-dependent kinase inhibitor Sic1 during meiosis can trigger extra rounds of DNA replication. When programmed DNA double-strand breaks (DSBs) are generated but not repaired due to absence of DMC1, a pathway involving the checkpoint gene RAD17 prevents this DNA rereplication. Further genetic analysis has now revealed that prevention of DNA rereplication also requires MEC1, which encodes a protein kinase that serves as a central checkpoint regulator in several pathways including the meiotic recombination checkpoint response. Downstream of MEC1, MEK1 is required through its function to inhibit repair between sister chromatids. By contrast, meiotic recombination checkpoint effectors that regulate gene expression and cyclin-dependent kinase activity are not necessary. Phosphorylation of histone H2A, which is catalyzed by Mec1 and the related Tel1 protein kinase in response to DSBs, and can help coordinate activation of the Rad53 checkpoint protein kinase in the mitotic cell cycle, is required for the full checkpoint response. Phosphorylation sites that are targeted by Rad53 in a mitotic S phase checkpoint response are also involved, based on the behavior of cells containing mutations in the DBF4 and SLD3 DNA replication genes. However, RAD53 does not appear to be required, nor does RAD9, which encodes a mediator of Rad53, consistent with their lack of function in the recombination checkpoint pathway that prevents meiotic progression. While this response is similar to a checkpoint mechanism that inhibits initiation of DNA replication in the mitotic cell cycle, the evidence points to a new variation on DNA replication control.
A Natural Mutation Involving both Pathogenicity and Perithecium Formation in theFusarium graminearumSpecies Complex
Authors: Suga Haruhisha , Kageyama Koji , Shimizu Masafumi , Hyakumachi Misturo 
Published: October 2016

AbstractMembers of the Fusarium graminearum species complex (Fg complex or FGSC) are the primary pathogens causing Fusarium head blight in wheat and barley worldwide. A natural pathogenicity mutant (strain 0225022) was found in a sample of the Fg complex collected in Japan. The mutant strain did not induce symptoms in wheat spikes beyond the point of inoculation, and did not form perithecia. No segregation of phenotypic deficiencies occurred in the progenies of a cross between the mutant and a fully pathogenic wild-type strain, which suggested that a single genetic locus controlled both traits. The locus was mapped to chromosome 2 by using sequence-tagged markers; and a deletion of ∼3 kb was detected in the mapped region of the mutant strain. The wild-type strain contains the FGSG_02810 gene, encoding a putative glycosylphosphatidylinositol anchor protein, in this region. The contribution of FGSG_02810 to pathogenicity and perithecium formation was confirmed by complementation in the mutant strain using gene transfer, and by gene disruption in the wild-type strain.
Suitability of Different Mapping Algorithms for Genome-Wide Polymorphism Scans with Pool-Seq Data
Authors: Kofler Robert , Langmüller Anna Maria , Nouhaud Pierre , Otte Kathrin Anna , Schlötterer Christian 
Published: October 2016

Abstract
The cost-effectiveness of sequencing pools of individuals (Pool-Seq) provides the basis for the popularity and widespread use of this method for many research questions, ranging from unraveling the genetic basis of complex traits, to the clonal evolution of cancer cells. Because the accuracy of Pool-Seq could be affected by many potential sources of error, several studies have determined, for example, the influence of sequencing technology, the library preparation protocol, and mapping parameters. Nevertheless, the impact of the mapping tools has not yet been evaluated. Using simulated and real Pool-Seq data, we demonstrate a substantial impact of the mapping tools, leading to characteristic false positives in genome-wide scans. The problem of false positives was particularly pronounced when data with different read lengths and insert sizes were compared. Out of 14 evaluated algorithms novoalign, bwa mem and clc4 are most suitable for mapping Pool-Seq data. Nevertheless, no single algorithm is sufficient for avoiding all false positives. We show that the intersection of the results of two mapping algorithms provides a simple, yet effective, strategy to eliminate false positives. We propose that the implementation of a consistent Pool-Seq bioinformatics pipeline, building on the recommendations of this study, can substantially increase the reliability of Pool-Seq results, in particular when libraries generated with different protocols are being compared.