bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diverse, abundant and novel viruses infecting “unculturable” but abundant marine bacteria
Authors: Zhang Zefeng , Chen Feng , Chu Xiao , Zhang Hao , Luo Haiwei , Qin Fang , Zhai Zhiqiang , Yang Mingyu , Sun Jing , Zhao Yanlin 
Published: July 2019

AbstractMany major marine bacterial lineages such as SAR11, Prochlorococcus, SAR116, and several Roseobacter lineages have members that are abundant, relatively slow-growing, and genome-streamlined. The isolation of phages that infect SAR11 and SAR116 have demonstrated the dominance of these phages in the marine virosphere. However, no phages have been isolated from bacteria in the Roseobacter RCA lineage, another abundant group of bacteria in the ocean. In this study, seven RCA phages that infect three different RCA strains were isolated and characterized. All seven RCA phages belong to the Podoviridae family and have genome sizes ranging from 39.6 to 58.1 kb. Interestingly, three RCA phages (CRP-1, CRP-2 and CRP-3) show a similar genomic content and architecture with SAR116 phage HMO-2011, which represents one of the most abundant known viral groups in the ocean. The high degree of homology between CRP-1, CRP-2, CRP-3 and HMO-2011 resulted in contribution of the RCA phages to the dominance of HMO-2011-type phage in the ocean. CRP-4 and CRP-5 are similar to the Siovirus roseophages in terms of gene content and organization. The remaining two RCA phages, CRP-6 and CRP-7, show limited genomic similarity with known phages and appear to form two new phage genera. Metagenomic fragment recruitment analyses reveal that these RCA phage groups are much more abundant in the ocean compared to most existing marine roseophage groups. The characterization of these RCA phages has greatly expanded our understanding of the genomic diversity and evolution of marine roseophages. Metagenomic fragment recruitment analyses suggest the critical need for isolating phages from the abundant but “unculturable” bacteria in the marine ecosystem.
Genetic basis of growth, phenology and susceptibility to biotic stressors in maritime pine
Authors: Hurel Agathe , de Miguel Marina , Dutech Cyril , Desprez-Loustau Marie-Laure , Plomion Christophe , Rodríguez-Quilón Isabel , Cyrille Agathe , Guzman Thomas , Alía Ricardo , González-Martínez Santiago C. , Budde Katharina B. 
Published: July 2019

AbstractForest ecosystems are increasingly challenged by extreme events, e.g. drought, storms, pest and pathogenic fungi outbreaks, causing severe ecological and economical losses. Understanding the genetic basis of adaptive traits in tree species is of key importance to preserve forest ecosystems, as genetic variation in a trait (i.e. heritability) determines its potential for human-mediated or evolutionary change. Maritime pine (Pinus pinaster Aiton), a conifer widely distributed in southwestern Europe and northwestern Africa, grows under contrasted environmental conditions promoting local adaptation. Genetic variation at adaptive phenotypes, including height, growth phenology and susceptibility to two fungal pathogens (Diplodia sapinea and Armillaria ostoyae) and an insect pest (Thaumetopoea pityocampa), were assessed in a range-wide clonal common garden of maritime pine. Broad-sense heritability was significant for height (0.219), growth phenology (0.165-0.310) and pathogen susceptibility (necrosis length caused by D. sapinea, 0.152; and by A. ostoyae, 0.021) measured after inoculation under controlled conditions, but not for pine processionary moth incidence in the common garden. The correlations of trait variation among populations revealed contrasting trends for pathogen susceptibility to D. sapinea and A. ostoyae with respect to height. Taller trees showed longer necrosis length caused by D. sapinea while shorter trees were more affected by A. ostoyae. Moreover, maritime pine populations from areas with high summer temperatures and frequent droughts were less susceptible to D. sapinea but more susceptible to A. ostoyae. Finally, an association study using 4,227 genome-wide SNPs revealed several loci significantly associated to each trait (range of 3-26), including a possibly disease-induced translation initiation factor, eIF-5. This study provides important insights to develop genetic conservation and breeding strategies integrating species responses to biotic stressors.
Characterising the mechanisms underlying genetic resistance to amoebic gill disease in Atlantic salmon using RNA sequencing
Authors: Robledo Diego , Hamilton Alastair , Gutiérrez Alejandro P. , Bron James E. , Houston Ross D. 
Published: July 2019

ABSTRACTBackgroundGill health is one of the main concerns for Atlantic salmon aquaculture, and Amoebic Gill Disease (AGD), attributable to infection by the amoebaNeoparamoeba perurans, is a frequent cause of morbidity. In the absence of preventive measures, increasing genetic resistance of salmon to AGD via selective breeding can reduce the incidence of the disease and mitigate gill damage. Understanding the mechanisms leading to AGD resistance and the underlying causative genomic features can aid in this effort, while also providing critical information for the development of other control strategies. AGD resistance is considered to be moderately heritable, and several putative QTL have been identified. The aim of the current study was to improve understanding of the mechanisms underlying AGD resistance, and to identify putative causative genomic factors underlying the QTL. To achieve this, RNA was extracted from the gill and head kidney of AGD resistant and susceptible animals following a challenge withN.perurans, and sequenced.ResultsComparison between resistant and susceptible animals pointed to differences mainly in the local immune response in the gill, involving red blood cell genes and genes related to immune function and cell adhesion. Differentially expressed immune genes highlighted differences in the Th2 and Th17 responses, which are consistent with the increased heritability observed after successive challenges with the amoeba. Five QTL-region candidate genes showed differential expression, including a gene connected to interferon responses (GVINP1), a gene involved in systemic inflammation (MAP4K4), and a positive regulator of apoptosis (TRIM39). Analyses of allele-specific expression highlighted a gene in the QTL region on chromosome 17, cellular repressor of E1A-stimulated genes 1 (CREG1), showing allelic differential expression suggestive of a cis-acting regulatory variant.ConclusionsIn summary, this study provides new insights into the mechanisms of resistance to AGD in Atlantic salmon, and highlights candidate genes for further functional studies that can further elucidate the genomic mechanisms leading to resistance and contribute to enhancing salmon health via improved genomic selection.
Functional harmonics reveal multi-dimensional basis functions underlying cortical organization
Authors: Glomb Katharina , Kringelbach Morten L. , Deco Gustavo , Hagmann Patric , Pearson Joel , Atasoy Selen 
Published: July 2019

ABSTRACTThe human brain consists of functionally specialized areas, which flexibly interact and integrate forming a multitude of complex functional networks. However, the nature and governing principles of these specialized areas remain controversial: a distinct modular architecture versus a smooth continuum across the whole cortex. Here, we demonstrate a candidate governing principle ubiquitous in nature, that resolves this controversy for the brain at rest, during perception, cognition and action: functional harmonic modes. We calculated the harmonic modes of the brain’s functional connectivity, called “functional harmonics”, from functional magnetic resonance imaging (fMRI) data in resting state of 812 participants. Each functional harmonic provides an elementary pattern of brain activity with a different spatial frequency. The set of all functional harmonics - ordered according to their spatial frequencies - can reconstruct any pattern of brain activity. The activity patterns elicited by 7 different tasks from the Human Connectome Project can be reconstructed from a very small subset of functional harmonics, suggesting a novel relationship between task and resting state brain activity. Further, the isolines of the continuous functional harmonic patterns delineate the borders of specialized cortical areas as well as somatotopic and retinotopic organization. Our results demonstrate a candidate scalable governing principle for functional brain organization, resolving the controversy between modular versus gradiental views, and demonstrate that a universal principle in nature also underlies human brain cortical organization.
Cryptogams signify key transition of bacteria and fungi in Arctic sand dune succession
Authors: Juottonen Heli , Männistö Minna , Tiirola Marja , Kytöviita Minna-Maarit 
Published: July 2019

SummaryPrimary succession models focus on aboveground vascular plants. However, the prevalence of mosses and lichens, i.e. cryptogams, suggests they play a role in soil successions. Here, we explore whether effects of cryptogams on belowground microbes can facilitate progressive shifts in sand dune succession.We linked aboveground vegetation, belowground bacterial and fungal community, and soil chemistry in six successional stages in Arctic inland sand dunes: bare sand, grass, moss, lichen, ericoid heath and mountain birch forest.Compared to the bare sand and grass stages, microbial biomass and the proportion of fungi increased in the moss stage, and later stage microbial groups appeared despite the absence of their host plants. The microbial communities of the lichen stage resembled the communities in the vascular plant stages. Bacterial community correlated better with soil chemistry than with vegetation, whereas the correlation of fungi with vegetation increased with vascular vegetation.Distinct bacterial and fungal patterns of biomass, richness, and plant-microbe interaction showed that the aboveground vegetation change structured the bacterial and fungal community differently. The nonalignment of aboveground vs. belowground changes suggests that cryptogams can drive succession towards vascular plant dominance through microbially mediated facilitation in eroded Arctic soil.
Har-P, ashortP-element variant, weaponizesP-transposase to severely impairDrosophiladevelopment
Authors: Srivastav Satyam P. , Rahman Reazur , Ma Qicheng , Lau Nelson C. 
Published: July 2019

ABSTRACTWithout transposon-silencing Piwi-interacting RNAs (piRNAs), transposition causes an ovarian atrophy syndrome inDrosophilacalled gonadal dysgenesis (GD).Harwich(Har) strains withP-elements cause severe GD in F1 daughters whenHarfathers mate with mothers lackingP-element-piRNAs (i.e.ISO1strain). To address the mystery of whyHarinduces severe GD, we bred hybridDrosophilawithHargenomic fragments into theISO1background to createHISR-D or HISR-Nlines that still causeDysgenesis or areNon-dysgenic, respectively. In these lines, we discovered a highly truncatedP-element variant we named “Har-P” as the most frequentde novoinsertion. AlthoughHISR-Dlines still contain full-lengthP-elements,HISR-Nlines lost functionalP-transposase but retainedHar-P’s that when crossed back toP-transposase restores GD induction. Finally, we uncoveredP-element-piRNA-directed repression onHar-P’stransmitted paternally to suppress somatic transposition. TheDrosophilashortHar-P’sand full-lengthP-elements relationship parallels the MITEs/DNA-transposase in plants and SINEs/LINEs in mammals.
Artifact Formation in Single Molecule Localization Microscopy
Authors: Reichel Jochen M. , Vomhof Thomas , Michaelis Jens 
Published: July 2019

AbstractWe investigate the influence of different accuracy-detection rate trade-offs on image reconstruction in single molecule localization microscopy. Our main focus is the investigation of image artifacts experienced when using low localization accuracy, especially in the presence of sample drift and inhomogeneous background. In this context we present a newly developed SMLM software termed FIRESTORM which is optimized for high accuracy reconstruction. For our analysis we used in silico SMLM data and compared the reconstructed images to the ground truth data. We observe two discriminable reconstruction populations of which only one shows the desired localization behavior.
Six Sigma with C-K theory for innovations in operational excellence: a case study
Authors: Sony Michael , Naik Subhash 
Published: July 2019

Purpose
Six Sigma is a well-established powerful business strategy for achieving operational excellence (OPEX). However, previous studies have suggested that the Six Sigma may negatively impact organizational creativity and innovation. The C-K theory is one of the most widely used technique for design reasoning which promotes the creativity and innovation. The purpose of this paper is to integrate the Six Sigma methodology and C-K theory for enhancing innovative capacity of Six Sigma for achieving OPEX.

Design/methodology/approach
The paper proposes an integration methodology of C-K theory and Six Sigma using the extant literature. Also, a case study is conducted based on the proposed integration model.

Findings
The paper suggests a step-by-step integration methodology for integrating Six Sigma with C-K theory for both (DMAIC and DMADV). The methodology when applied to a live case in mining logistics the results are very encouraging. The solution was cost effective and also technically superior compared to previous solutions.

Practical implications
The paper proposes a step-by-step methodology for the integration of Six Sigma with C-K tools. The methodology is practically applied in a live case. Organizations can use findings from this paper to implement an integration model of Six Sigma with C-K theory.

Originality/value
This is the first paper that proposes an integration methodology of Six Sigma with C-K theory to enhance the innovation capability to achieve the OPEX.
Divergent host plant utilization by adults and offspring is related to intra‐plant variation in chemical defences
Authors: Mason Charles J. , Long David C. , Lindroth Richard L. , Hoover Kelli 
Published: July 2019

Abstract

Adult and juvenile herbivores of the same species can use divergent feeding strategies, and thus may inhabit and consume different parts of the plant. Because the expression of chemical defences often differs between host plant tissues, this variation may result in disparate performance outcomes for adult and juvenile conspecifics that feed on distinct dietary substrates.

The goal of this study was to evaluate how host range may differ between adults and juveniles in a generalist herbivore. We addressed the impacts of among‐ and within‐plant defence variation using the wood‐feeding Asian longhorned beetle (Anoplophora glabripennis) and three host plants having a range of putative resistance.

Impacts of host plants on adult and offspring performance were assessed using a series of controlled bioassays. We evaluated adult‐feeding and egg‐laying behaviours in choice and no‐choice experiments using the different hosts, and subsequent offspring establishment. We then evaluated host plant chemical composition related to nutrition and defence.

Different plants had strong impacts on adult performance, but these patterns did not extend to effects on offspring. Females were capable of developing eggs when provided Acer rubrum, but not Populus deltoides or Populus tomentosa. Females that produced eggs by feeding on A. rubrum, however, deposited eggs into all three plant species. Larvae hatched and consumed tissues in all three hosts. The differences between adult and juvenile utilization of Populus spp. were reflected in markedly higher salicinoid phenolic concentrations in bark (>2% dw), while wood had trace quantities.

Our results demonstrate that plant resistance mechanisms can differentially act upon adult and juvenile life stages of a polyphagous herbivore when there is differential expression of chemical defences among plant tissue types. Anoplophora glabripennis has been a globally successful invader due in part to its broad host range, and our results suggest a mechanism that permits the beetle to exploit marginally resistant plants. This study has implications for how host range differs between insect feeding stages, which is particularly important for invasive, polyphagous species encountering novel food sources.
Global distribution of Trebouxiophyceae diversity explored by high‐throughput sequencing and phylogenetic approaches
Authors: Metz Sebastian , Singer David , Domaizon Isabelle , Unrein Fernando , Lara Enrique 
Published: July 2019

SummaryTrebouxiophyceae are a ubiquitous class of Chlorophyta encountered in aquatic and terrestrial environments. Most taxa are photosynthetic, and many acts as photobionts in symbiotic relationships, while others are free‐living. Trebouxiophyceae have also been widely investigated for their use for biotechnological applications. In this work, we aimed at obtaining a comprehensive image of their diversity by compiling the information of 435 freshwater, soil and marine environmental DNA samples surveyed with Illumina sequencing technology in order to search for the most relevant environments for bioprospecting. Freshwater and soil were most diverse and shared more than half of all operational taxonomic units (OTUs), however, their communities were significantly distinct. Oceans hosted the highest genetic novelty, and did not share any OTUs with the other environments; also, marine samples host more diversity in warm waters. Symbiotic genera usually found in lichens such as Trebouxia, Myrmecia and Symbiochloris were also abundantly detected in the ocean, suggesting either free‐living lifestyles or unknown symbiotic relationships with marine planktonic organisms. Altogether, our study opens the way to new prospection for trebouxiophycean strains, especially in understudied environments like the ocean.
Incidence and patterns of malignancies in a multi‐ethnic cohort of rheumatoid arthritis patients
Authors: Lim Xin Rong , Xiang Wenwei , Tan Justina Wei Lynn , Koh Li Wearn , Lian Tsui Yee , Leong Khai Pang , Koh Ee‐Tzun ,   TTSH Rheumatoid Arthritis Study Group
Published: July 2019

AbstractAimThis study was undertaken to determine the incidence and patterns of malignancies in rheumatoid arthritis (RA) patients in our cohort.MethodsBetween 2001 and 2013, we analyzed 1117 patients in the prospective Tan Tock Seng Hospital (TTSH) RA Registry. Patients who developed malignancies after the onset of RA were identified from this registry. Age‐ and sex‐adjusted standardized incidence ratios (SIRs) were calculated to compare observed to expected numbers of malignancies based on data from the Singapore Cancer Registry.ResultsOut of 19 839 person‐years of follow‐up, 132 incident malignancies were diagnosed during the observation period. There were 114 (86.4%) solid‐organ tumors and 18 (13.6%) hematological malignancies. The SIR (95% confidence interval) for all malignancies combined was 1.28 (0.88‐1.87) for males and 1.21 (1.00‐1.46) for females. Compared to the general population, we found a 4‐ to 5‐fold increase in lymphoma among our RA patients compared to the general population (SIR 5.05 [1.90‐13.46] for males and 3.75 [1.95‐7.20] for females). The SIR of lung malignancy in male RA patients is 2.36 (1.23‐4.53) and SIR of cervical malignancy in female RA patients is 3.72 (2.20‐6.23).ConclusionThere is a trend toward an overall increased malignancy risk in our RA patients compared to the general population. Specifically, there is an increased risk of lymphomas in all RA patients, lung malignancy in male patients, and cervical malignancy in female patients, compared to the general population.
Born this way: Hippocampal neurogenesis across the lifespan
Authors: Kozareva Danka A. , Cryan John F. , Nolan Yvonne M. 
Published: July 2019

AbstractThe capability of the mammalian brain to generate new neurons through the lifespan has gained much attention for the promise of new therapeutic possibilities especially for the aging brain. One of the brain regions that maintains a neurogenesis‐permissive environment is the dentate gyrus of the hippocampus. Here, new neurons are generated from a pool of multipotent neural progenitor cells to become fully functional neurons that are integrated into the brain circuitry. A growing body of evidence points to the fact that neurogenesis in the adult hippocampus is necessary for certain memory processes, and in mood regulation, while alterations in hippocampal neurogenesis have been associated with a myriad of neurological and psychiatric disorders. More recently, evidence has come to light that new neurons may differ in their vulnerability to environmental and disease‐related influences depending on the time during the life course at which they are exposed. Thus, it has been the topic of intense research in recent years. In this review, we will discuss the complex process and associated functional relevance of hippocampal neurogenesis during the embryonic/postnatal period and in adulthood. We consider the implications of hippocampal neurogenesis during the developmentally critical periods of adolescence and older age. We will further consider the literature surrounding hippocampal neurogenesis and its functional role during these critical periods with a view to providing insight into the potential of harnessing neurogenesis for health and therapeutic benefit.
The Rise and Fall of “Civil Society” in Bolivia
Authors: Shakow Miriam 
Published: July 2019

ABSTRACTAnthropologists have criticized “civil society” as a Eurocentric, bourgeois, and individualist concept that brands the Global South and Eastern Europe as inherently inferior. In this article, I introduce an understudied meaning of civil society as collective action inspired by indigenous cultural institutions, which has been operative in Bolivia during the 1990s and early 2000s, and, I suggest, more widely in the Global South. This variant of civil society, however, served as a framework for development professionals to blame failures of development upon local people. But I also argue that civil society's meaning is historically contingent. The concept diminished in Bolivia following Evo Morales's government's return to central state patronage after a decade of austerity and liberal state decentralization. Massive new funding for development in central Bolivia allayed development workers’ concerns that locals weren't doing their part to achieve development. If the reemergence of the civil society concept in Bolivia marked the rise of citizen participation as a substitute for state‐funded development, the decline of “civil society” marked the return to state‐led development. [civil society, neoliberalism, decentralization, development, indigeneity, Bolivia]