bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sporadic Genetic Connectivity among Small Insular Populations of the Rare Geoendemic Plant Caulanthus amplexicaulis var. barbarae (Santa Barbara Jewelflower)
Authors: Burrell A Millie , Goddard Jeffrey H R , Greer Paul J , Williams Ryan J , Pepper Alan E 
Published: May 2019

AbstractGlobally, a small number of plants have adapted to terrestrial outcroppings of serpentine geology, which are characterized by soils with low levels of essential mineral nutrients (N, P, K, Ca, Mo) and toxic levels of heavy metals (Ni, Cr, Co). Paradoxically, many of these plants are restricted to this harsh environment. Caulanthus ampexlicaulis var. barbarae (Brassicaceae) is a rare annual plant that is strictly endemic to a small set of isolated serpentine outcrops in the coastal mountains of central California. The goals of the work presented here were to 1) determine the patterns of genetic connectivity among all known populations of C. ampexlicaulis var. barbarae, and 2) estimate contemporary effective population sizes (Ne), to inform ongoing genomic analyses of the evolutionary history of this taxon, and to provide a foundation upon which to model its future evolutionary potential and long-term viability in a changing environment. Eleven populations of this taxon were sampled, and population-genetic parameters were estimated using 11 nuclear microsatellite markers. Contemporary effective population sizes were estimated using multiple methods and found to be strikingly small (typically Ne &lt; 10). Further, our data showed that a substantial component of genetic connectivity of this taxon is not at equilibrium, and instead showed sporadic gene flow. Several lines of evidence indicate that gene flow between isolated populations is maintained through long-distance seed dispersal (e.g., &gt;1 km), possibly via zoochory.
FLASH: a next-generation CRISPR diagnostic for multiplexed detection of antimicrobial resistance sequences
Authors: Quan Jenai , Langelier Charles , Kuchta Alison , Batson Joshua , Teyssier Noam , Lyden Amy , Caldera Saharai , McGeever Aaron , Dimitrov Boris , King Ryan , Wilheim Jordan , Murphy Maxwell , Ares Lara Pesce , Travisano Katherine A , Sit Rene , Amato Roberto , Mumbengegwi Davis R , Smith Jennifer L , Bennett Adam , Gosling Roly , Mourani Peter M , Calfee Carolyn S , Neff Norma F , Chow Eric D , Kim Peter S , Greenhouse Bryan , DeRisi Joseph L , Crawford Emily D 
Published: May 2019

AbstractThe growing prevalence of deadly microbes with resistance to previously life-saving drug therapies is a dire threat to human health. Detection of low abundance pathogen sequences remains a challenge for metagenomic Next Generation Sequencing (NGS). We introduce FLASH (Finding Low Abundance Sequences by Hybridization), a next-generation CRISPR/Cas9 diagnostic method that takes advantage of the efficiency, specificity and flexibility of Cas9 to enrich for a programmed set of sequences. FLASH-NGS achieves up to 5 orders of magnitude of enrichment and sub-attomolar gene detection with minimal background. We provide an open-source software tool (FLASHit) for guide RNA design. Here we applied it to detection of antimicrobial resistance genes in respiratory fluid and dried blood spots, but FLASH-NGS is applicable to all areas that rely on multiplex PCR.
A Heterocyst-Specific Antisense RNA Contributes to Metabolic Reprogramming in Nostoc sp. PCC 7120
Authors: Olmedo-Verd Elvira , Brenes-�lvarez Manuel , Vioque Agust�n , Muro-Pastor Alicia M 
Published: May 2019

Abstract
Upon nitrogen deficiency, some filamentous cyanobacteria differentiate specialized cells, called heterocysts, devoted to N2 fixation. Heterocysts appear regularly spaced along the filaments and exhibit structural and metabolic adaptations, such as loss of photosynthetic CO2 fixation or increased respiration, to provide a proper microaerobic environment for its specialized function. Heterocyst development is under transcriptional control of the global nitrogen regulator NtcA and the specific regulator HetR. Transcription of a large number of genes is induced or repressed upon nitrogen deficiency specifically in cells undergoing differentiation. In recent years, the HetR regulon has been described to include heterocyst-specific trans-acting small RNAs and antisense RNAs (asRNAs), suggesting that there is an additional layer of post-transcriptional regulation involved in heterocyst development. Here, we characterize in the cyanobacterium Nostoc (Anabaena) sp. PCC 7120 an asRNA, that we call as_glpX, transcribed within the glpX gene encoding the Calvin cycle bifunctional enzyme sedoheptulose-1,7-bisphosphatase/fructose-1,6-bisphosphatase (SBPase). Transcription of as_glpX is restricted to heterocysts and is induced very early during the process of differentiation. Expression of as_glpX RNA promotes the cleavage of the glpX mRNA by RNase III, resulting in a reduced amount of SBPase. Therefore, the early expression of this asRNA could contribute to the quick shut-down of CO2 fixation in those cells in the filament that are undergoing differentiation into heterocysts. In summary, as_glpX is the first naturally occurring asRNA shown to rapidly and dynamically regulate metabolic transformation in Nostoc heterocysts. The use of antisense transcripts to manipulate gene expression specifically in heterocysts could became a useful tool for metabolic engineering in cyanobacteria.
Brassinosteroid Regulates Root Development with Highly Redundant Genes in Hexaploid Wheat
Authors: Hou Lijiang , Zhang Aihua , Wang Ruochen , Zhao Peng , Zhang Dongzhi , Jiang Yujie , Diddugodage Chamila Jeewani , Wang Xiaoming , Ni Zhongfu , Xu Shengbao 
Published: May 2019

Abstract
Brassinosteroid (BR) plays an important role in plant development and biotic and abiotic stress tolerance, but its specific function remains largely unknown in wheat (Triticum aestivum L.), preventing its utilization in this important crop. In this study, the function of BR and its underlying cytological role in wheat root development were comprehensively investigated. Our findings demonstrated that BR has a conserved function in regulating root length in wheat, and novel roles in regulating lateral root emergence and root diameter were uncovered. Analyses of BR homologous gene composition and evolutionary divergence demonstrated that the genetic framework of the wheat BR pathway was close to that of rice, but contained highly redundant homologous copies of genes from the subgenome A, B and D. These homologous copies showed active expression and shared a conserved BR response. The expression of wheat DWF4 and glycogen synthase kinase (GSK) genes in Arabidopsis confirmed that multiple homologous copies maintained their conserved function in regulating root development, highlighting their redundant status and indicating that a special challenge exists in wheat gene modification to deal with this high redundancy. However, our results suggested that the hypermorphic effect of T. aestivum GSK (TaGSK) genes with point mutations may be an effective approach to overcome this redundancy in the manipulation of BR signaling in wheat. Our study provides fundamental data uncovering the function of BR in wheat root development, the underlying genetic basis and a possible strategy to manipulate BR signaling in hexaploid wheat.
Identification of Arabidopsis CCR4-NOT Complexes with Pumilio RNA-Binding Proteins, APUM5 and APUM2
Authors: Arae Toshihiro , Morita Kotone , Imahori Riko , Suzuki Yuya , Yasuda Shigetaka , Sato Takeo , Yamaguchi Junji , Chiba Yukako 
Published: May 2019

Abstract
CCR4/CAF1 are widely conserved deadenylases in eukaryotes. They form a large complex that includes NOT1 as a scaffold protein and various NOT proteins that are core components of multiple levels of gene expression control. The CCR4-NOT complex also contains several RNA-binding proteins as accessory proteins, which are required for target recognition by CCR4/CAF1 deadenylases. AtCCR4a/b, orthologs of human CCR4 in Arabidopsis, have various physiological effects. AtCCR4 isoforms are likely to have specific target mRNAs related to each physiological effect; however, AtCCR4 does not have RNA-binding capability. Therefore, identifying factors that interact with AtCCR4a/b is indispensable to understand its function as a regulator of gene expression, as well as the target mRNA recognition mechanism. Here, we identified putative components of the AtCCR4-NOT complex using co-immunoprecipitation in combination with mass spectrometry using FLAG-tagged AtCCR4b and subsequent verification with a yeast two-hybrid assay. Interestingly, four of 11 AtCAF1 isoforms interacted with both AtCCR4b and AtNOT1, whereas two isoforms interacted only with AtNOT1 in yeast two-hybrid assays. These results imply that Arabidopsis has multiple CCR4-NOT complexes with various combinations of deadenylases. We also revealed that the RNA-binding protein Arabidopsis Pumilio 5 and 2 interacted with AtCCR4a/b in the cytoplasm with a few foci.
Essential and Detrimental — an Update on Intracellular Iron Trafficking and Homeostasis
Authors: Vigani Gianpiero , Solti ï¿½dï¿½m , Thomine Sï¿½bastien , Philippar Katrin 
Published: May 2019

Abstract
Chloroplasts, mitochondria and vacuoles represent characteristic organelles of the plant cell, with a predominant function in cellular metabolism. Chloroplasts are the site of photosynthesis and therefore basic and essential for photoautotrophic growth of plants. Mitochondria produce energy during respiration and vacuoles act as internal waste and storage compartments. Moreover, chloroplasts and mitochondria are sites for the biosynthesis of various compounds of primary and secondary metabolism. For photosynthesis and energy generation, the internal membranes of chloroplasts and mitochondria are equipped with electron transport chains. To perform proper electron transfer and several biosynthetic functions, both organelles contain transition metals and here iron is by far the most abundant. Although iron is thus essential for plant growth and development, it becomes toxic when present in excess and/or in its free, ionic form. The harmful effect of the latter is caused by the generation of oxidative stress. As a consequence, iron transport and homeostasis have to be tightly controlled during plant growth and development. In addition to the corresponding transport and homeostasis proteins, the vacuole plays an important role as an intracellular iron storage and release compartment at certain developmental stages. In this review, we will summarize current knowledge on iron transport and homeostasis in chloroplasts, mitochondria and vacuoles. In addition, we aim to integrate the physiological impact of intracellular iron homeostasis on cellular and developmental processes.
Against Contextualism about Prudential Discourse
Authors: Fletcher Guy 
Published: May 2019

Abstract
In recent times, there has been a surge of interest in, and enthusiasm for, contextualist views about prudential discourse—thought and talk about what has prudential value or contributes to someone's well-being. In this paper, I examine and reject two cases for radical forms of prudential contextualism, proposed by Anna Alexandrova and Steve Campbell. Alexandrova holds that the semantic content of terms like ‘well-being’ and ‘doing well’ varies across contexts. Campbell proposes that there are plural prudential concepts at play in prudential discourse (and in philosophical reflection upon such discourse) and that we find evidence of this in the conflicting commitments of prudential discourse. The negative aim of the paper is to show that Alexandrova and Campbell have not given us a good case for ambitious forms of contextualism about prudential discourse. The positive aim of the paper is to provide alternative, aspectualist, explanations of the features of prudential discourse that their discussions highlight.
Rolling back the prison estate: the pervasive impact of macroeconomic austerity on prisoner health in England
Authors: Ismail Nasrul 
Published: May 2019

AbstractPrisons offer policymakers an opportunity to address the pre-existing high prevalence of physical and mental health issues among prisoners. This notion has been widely integrated into international and national prison health policies, including the Healthy Prisons Agenda, which calls for governments to address the health needs of prisoners and safeguard their health entitlement during imprisonment, and the Sustainable Development Goals 2030 concerning reducing inequality among disadvantaged populations.However, the implementation of the austerity policy in the United Kingdom since the re-emergence of the global financial crisis in 2008 has impeded this aspiration. This interdisciplinary paper critically evaluates the impact of austerity on prison health. The aforementioned policy has obstructed prisoners’ access to healthcare, exacerbated the degradation of their living conditions, impeded their purposeful activities and subjected them to an increasing level of violence.This paper calls for alternatives to imprisonment, initiating a more informed economic recovery policy, and relying on transnational and national organizations to scrutinize prisoners’ entitlement to health. These systemic solutions could act as a springboard for political and policy discussions at national and international forums with regard to improving prisoners’ health and simultaneously meeting the aspirations of the Healthy Prisons Agenda and the Sustainable Development Goals.
Cross-Listings and the Dynamics between Credit and Equity Returns
Authors: Augustin Patrick , Jiao Feng , Sarkissian Sergei , Schill Michael J 
Published: May 2019

Abstract
We study how listing in multiple markets affects the dynamics between firms’ credit default swap (CDS) and stock returns. We find that cross-listing increases (1) the sensitivity of CDS to stock returns, (2) the integration of CDS with world equity and bond markets, and (3) the statistical synchronicity of CDS and stock prices. Our results are stronger for firms with greater media attention, analyst and CDS coverage, and Google search intensity and for listings in familiar markets. We suggest that a firm’s presence in global equity markets comes with an improvement in the credit-equity integration through a reduction of informational frictions.
Received April 20, 2017; editorial decision February 12, 2019 by Editor Andrew Karolyi. Authors have furnished an Internet Appendix, which is available on the Oxford University Press Web site next to the link to the final published paper online.
STRESS MANAGEMENT FOR DISASTER RECOVERY SUPPORT STAFF ASSISTING NUCLEAR DISASTER EVACUEES
Authors: Kawazoe I , Kidachi R , Norikane K , Tanaka M , Tanaba S 
Published: May 2019

Abstract
The residents of Town A have been taking shelter in various parts of Japan ever since the accident of Fukushima Daiichi Nuclear Power Plant. The staff members carry out their tasks in seven locations across the country under a great stress with the limited manpower. This study reports the present situation of the stress management for the disaster recovery support staff helping the evacuees living outside the prefecture. The subjects were the 19 members. The T-scores were calculated from Coping Inventory for Stressful Situations (CISS) by assessing their CISS before the mental health seminars commenced. There was a significant positive correlation between ‘task-oriented coping’ and ‘avoidance-oriented coping’ as well as ‘task-oriented coping’ and ‘amusement’. Between the genders, the male subjects expressed a significantly higher ‘amusement’ value.
APPLICABILITY OF AUTONOMOUS UNMANNED HELICOPTER SURVEY OF AIR DOSE RATE IN SUBURBAN AREA
Authors: Yoshimura K , Fujiwara K , Nakama S 
Published: May 2019

Abstract
An autonomous unmanned helicopter (AUH) survey is a useful tool for monitoring the distribution of ambient dose equivalent rates. However, the AUH survey method was developed for plane permeable fields such as agricultural land, and its applicability to urban areas is unclear. In this study, the applicability was investigated by comparing the results of AUH and ground-based surveys conducted in suburban areas, including residential and agricultural lands. The results of both surveys broadly agreed with each other within a factor of 2 in the range independent of land use, and the factor was the same as that reported for plane permeable fields. These results suggest that AUH surveys are applicable in urban areas. The measurement uncertainty of the AUH survey was largely affected by the patchy and local distribution of ambient dose equivalent rates on the ground and differences in the fields of view, rather than land use.
Electrical resistivity tomography: patterns in Betula pendula, Fagus sylvatica, Picea abies and Pinus sylvestris
Authors: Bär Andreas , Hamacher Monika , Ganthaler Andrea , Losso Adriano , Mayr Stefan 
Published: May 2019

Abstract
Electrical resistivity (ER) tomography is a promising technique to minimally invasively study stems of living trees. It allows insights into xylem properties based on the cross-sectional distribution of ER that is governed by the wood’s electrical conductance. In this study, ER measurements were carried out on four forest tree species, Betula pendula, Fagus sylvatica, Picea abies and Pinus sylvestris, to demonstrate interspecific, intraspecific and within-tree variation of ER tomograms. Further, ER patterns were linked to xylem moisture content (MC), electrolyte content and density obtained from wood core analyses. The ER patterns of both coniferous species, P. abies and P. sylvestris, were found to be more homogenous and concentric compared with the complex tomograms of angiosperms. However, the ER range of coniferous trees showed considerable intraspecific variation. Measurements near ground level showed pronounced effects on ER tomograms, highlighting the importance of the chosen measurement height. A strong relation between ER and wood density was found in F. sylvatica while ER patterns of conifers were mainly influenced by MC. Results demonstrate a high species specificity of ER tomograms and of respective influencing xylem traits. They underline the importance of reference measurements for a correct interpretation of ER studies.
Accounting for red blood cell accessibility reveals distinct invasion strategies inPlasmodium falciparumstrains
Authors: Cai Francisco , DeSimone Tiffany M. , Hansen Elsa , Jennings Cameron V. , Bei Amy K. , Ahouidi Ambroise D. , Mboup Souleymane , Duraisingh Manoj T. , Buckee Caroline O. 
Published: May 2019

AbstractThe growth of the malaria parasitePlasmodium falciparumin human blood causes all clinical manifestations of malaria, a process that begins with the invasion of red blood cells. Parasites enter red blood cells using distinct pairs of parasite ligands and host receptors that define particular invasion pathways. Parasite strains have the capacity to switch between invasion pathways. This flexibility is thought to facilitate immune evasion against particular parasite ligands, but may also reflect the fact that red blood cell surfaces are dynamic and composed of heterogeneous invasion targets. Different host genetic backgrounds affecting red blood cell structure have long been recognized to impact parasite growthin vivo, but even within a host, red blood cells undergo dramatic changes in morphology and receptor density as they age. The consequences of these heterogeneities for parasite growthin vivoremain unclear. Here, we measured the ability of laboratory strains ofP. falciparumrelying on distinct invasion pathways to enter red blood cells of different ages. We estimated invasion efficiency while accounting for the fact that even if the red blood cells display the appropriate receptors, not all are physically accessible to invading parasites. This approach revealed a tradeoff made by parasites between the fraction of susceptible cells and their invasion rate into them. We were able to distinguish between “specialist” strains exhibiting high invasion rate in fewer cells versus “generalist” strains invading less efficiently into a larger fraction of cells. We developed a mathematical model to predict that infection with a generalist strain would lead to higher peak parasitemiasin vivowhen compared with a specialist strain with similar overall proliferation rate. Thus, the heterogeneous ecology of red blood cells may play a key role in determining the rate of parasite proliferation between different strains ofP. falciparum.
Using Earth Mover’s Distance for Viral Outbreak Investigations
Authors: Melnyk Andrew , Knyazev Sergey , Vannberg Fredrik , Bunimovich Leonid , Skums Pavel , Zelikovsky Alex 
Published: May 2019

AbstractRNA viruses mutate at extremely high rates forming an intra-host viral population of closely related variants (or quasi-species) [4]. High variability of Human Immunodeficiency Virus (HIV) and Hepatitis C virus (HCV) making them particularly dangerous by allowing them to evade the host’s immune system. HIV and HCV outbreaks pose a significant problem for public health for solving which it is critical to infer transmission clusters, i.e., to decide whether two viral samples belong to the same outbreak. Initial approach [10] was based on estimating relatedness between two samples as the distance between consensuses of the corresponding viral populations. The distance between closest pair of representatives from two populations, MinDist, has been shown to be significantly more accurate [2]. Unfortunately, MinDist computation requires a cumbersome RNA-seq data assembly and identification of all viral sequences from a given project. We present a novel approach that allows to bypass read assembly and estimate the distance between viral samples based on k-mer (i.e. a substring of length k) distribution in RNA-seq reads. The experimental validation using sequencing data from HCV outbreaks shows that the proposed algorithms can successfully identify genetic relatedness between viral populations, infer transmission clusters and outbreak sources, as well decide whether the primary spreader is present in the sequenced outbreak sample.
Genome rearrangements and megaplasmid loss in the filamentous bacteriumKitasatospora viridifaciensare associated with protoplast formation and regeneration
Authors: Ramijan Karina , Zhang Zheren , van Wezel Gilles P. , Claessen D. 
Published: May 2019

AbstractFilamentous Actinobacteria are multicellular bacteria with linear replicons.Kitasatospora viridifaciensDSM 40239 contains a linear 7.8 Mb chromosome and an autonomously replicating plasmid KVP1 of 1.7 Mb. Here we show that lysozyme-induced protoplast formation of the multinucleated mycelium ofK. viridifaciensdrives morphological diversity. Characterization and sequencing of an individual revertant colony that had lost the ability to differentiate revealed that the strain had not only lost most of KVP1 but also carried lesions in the right arm of the chromosome. Strikingly, the lesion sites were preceded by insertion sequence elements, suggesting that the rearrangements may have been caused by replicative transposition and homologous recombination between both replicons. These data indicate that protoplast formation is a stressful process that can lead to profound genetic changes.RepositoriesGenomic sequence data for strain B3.1 has been deposited in the NCBI SRA database under accession code SAMN11514356.