bluuebunny/crossref_metadata_2025_split huggingface dataset:
How normative interpretations of climate risk assessment affect local decision-making: an exploratory study at the city scale in Cork, Ireland
Authors: McDermott T. K. J. , Surminski S. 
Published: April 2018

Urban areas already suffer substantial losses in both economic and human terms from climate-related disasters. These losses are anticipated to grow substantially, in part as a result of the impacts of climate change. In this paper, we investigate the process of translating climate risk data into action for the city level. We apply a commonly used decision-framework as our backdrop and explore where in this process climate risk assessment and normative political judgements intersect. We use the case of flood risk management in Cork city in Ireland to investigate what is needed for translating risk assessment into action at the local city level. Evidence presented is based on focus group discussions at two stakeholder workshops, and a series of individual meetings and phone-discussions with stakeholders involved in local decision-making related to flood risk management and adaptation to climate change, in Ireland. Respondents were chosen on the basis of their expertise or involvement in the decision-making processes locally and nationally. Representatives of groups affected by flood risk and flood risk management and climate adaptation efforts were also included. The Cork example highlights that, despite ever more accurate data and an increasing range of theoretical approaches available to local decision-makers, it is the normative interpretation of this information that determines what action is taken. The use of risk assessments for decision-making is a process that requires normative decisions, such as setting ‘acceptable risk levels' and identifying ‘adequate’ protection levels, which will not succeed without broader buy-in and stakeholder participation. Identifying and embracing those normative views up-front could strengthen the urban adaptation process—this may, in fact, turn out to be the biggest advantage of climate risk assessment: it offers an opportunity to create a shared understanding of the problem and enables an informed evaluation and discussion of remedial action.This article is part of the theme issue ‘Advances in risk assessment for climate change adaptation policy’.
Turning risk assessment and adaptation policy priorities into meaningful interventions and governance processes
Authors: Brown Kathryn , DiMauro Manuela , Johns Daniel , Holmes Gemma , Thompson David , Russell Andrew , Style David 
Published: April 2018

The UK is one of the first countries in the world to have set up a statutory system of national climate risk assessments followed by a national adaptation programme. Having this legal framework has been essential for enabling adaptation at the government level in a challenging political environment. However, using this framework to create an improvement in resilience to climate change across the country requires more than publishing a set of documents; it requires careful thought about what interventions work, how they can be enabled and what level of risk acceptability individuals, organizations and the country should be aiming for.
This article is part of the theme issue ‘Advances in risk assessment for climate change adaptation policy'.
Evidence of an Unusual Poly(A) RNA Signature Detected by High-throughput Chemical Mapping
Authors: Wellington-Oguri Roger , Fisker Eli , Zada Mat , Wiley Michelle ,   Eterna Players
Published: April 2018

ABSTRACTHomopolymeric adenosine RNA plays numerous roles in both cells and non-cellular genetic material, and for lack of evidence to the contrary, it is generally accepted to form a random coil under physiological conditions. However, chemical mapping data generated by the Eterna Massive Open Laboratory indicates that a poly (A) sequence of length seven or more, at pH 8.0 and MgCl concentrations of 10 mM, develops unexpected protection to selective 2’-hydroxyl acylation read out by primer extension (SHAPE) and dimethyl sulfate (DMS) chemical probing. This protection first appears in poly(A) sequences of length 7 and grows to its maximum strength at length ~10. In a long poly(A) sequence, substitution of a single A by any other nucleotide disrupts the protection, but only for the 6 or so nucleotides on the 5’ side of the substitution. The authors are grateful for pre-publication comments; please use https://docs.google.com/document/d/14972Q36IDTYMglwMXTOrqd4P9orQ6-P3bPbCuITdv6A.
Genetic regulatory mechanisms of smooth muscle cells map to coronary artery disease risk loci
Authors: Liu Boxiang , Pjanic Milos , Wang Ting , Nguyen Trieu , Gloudemans Michael , Rao Abhiram , Castano Victor G. , Nurnberg Sylvia , Rader Daniel J. , Elwyn Susannah , Ingelsson Erik , Montgomery Stephen B. , Miller Clint L. , Quertermous Thomas 
Published: April 2018

AbstractCoronary artery disease (CAD) is the leading cause of death globally. Genome-wide association studies (GWAS) have identified more than 95 independent loci that influence CAD risk, most of which reside in non-coding regions of the genome. To interpret these loci, we generated transcriptome and whole-genome datasets using human coronary artery smooth muscle cells (HCASMC) from 52 unrelated donors, as well as epigenomic datasets using ATAC-seq on a subset of 8 donors. Through systematic comparison with publicly available datasets from GTEx and ENCODE projects, we identified transcriptomic, epigenetic, and genetic regulatory mechanisms specific to HCASMC. We assessed the relevance of HCASMC to CAD risk using transcriptomic and epigenomic level analyses. By jointly modeling eQTL and GWAS datasets, we identified five genes (SIPA1, TCF21, SMAD3, FES, and PDGFRA) that modulate CAD risk through HCASMC, all of which have relevant functional roles in vascular remodeling. Comparison with GTEx data suggests that SIPA1 and PDGFRA influence CAD risk predominantly through HCASMC, while other annotated genes may have multiple cell and tissue targets. Together, these results provide new tissue-specific and mechanistic insights into the regulation of a critical vascular cell type associated with CAD in human populations.
Diversity of Culturable Endophytic bacteria from Wild and Cultivated Rice showed potential Plant Growth Promoting activities
Authors: Borah Madhusmita , Das Saurav , Baruah Himangshu , Boro Robin C. , Barooah Madhumita 
Published: April 2018

AbstractIn this paper, we report the endophytic microbial diversity of cultivated and wild Oryza sativa plants including their functional traits related to multiple traits that promote plant growth and development. Around 255 bacteria were isolated out of which 70 isolates were selected for further studies based on their morphological differences. The isolates were characterized both at biochemical and at the molecular level by 16s rRNA gene sequencing. Based on 16S rRNA gene sequencing the isolates were categorized into three major phyla, viz, Firmicutes (57.1 %), Actinobacteria (20.0 %) and Proteobacteria (22.8 %). Firmicutes was the dominant group of bacteria of which the most abundant genus was Bacillus. The isolates were further screened in vitro for plant growth promoting activities which revealed a hitherto unreported endophytic bacterial isolate, Microbacteriaceae bacterium RS01 11 as the highest secretor of a phytohormone, IAA (28.39 ± 1.39 μg/ml) and GA (67.23 ± 1.83 μg/ml). Bacillus subtilis RHS 01 displayed highest phosphate solubilizing activity (81.70 ± 1.98 μg/ml) while, Microbacterium testaceum MK LS01, and Microbacterium trichothecenolyticum MI03 L05 exhibited highest potassium solubilizing activity (53.42±0.75μg/ml) and zinc solubilizing efficiency (157.50%) respectively. Bacillus barbaricus LP20 05 produced highest siderophore units (64.8 %). Potential plant growth promoting isolated were tested in vivo in pot culture under greenhouse conditions. A consortium consisting of Microbacteriaceae bacterium RS01 11, Bacillus testaceum MK LS01 and Bacillus subtilis RHS promoted plant growth and increased the yield 3.4 fold in rice when compared to control T0 when tested in pot culture and reduce application rates of chemical fertilizer to half the recommended dose. Our study confirms the potentiality of the rice endophytes isolated as good plant growth promoter and effective biofertilizer.
Super-enhancers are transcriptionally more active and cell-type-specific than stretch enhancers
Authors: Khan Aziz , Mathelier Anthony , Zhang Xuegong 
Published: April 2018

AbstractBackgroundSuper-enhancers and stretch enhancers represent classes of transcriptional enhancers that have been shown to control the expression of cell identity genes and carry disease- and trait-associated variants. Specifically, super-enhancers are clusters of enhancers defined based on the binding occupancy of master transcription factors (TFs), chromatin regulators, or chromatin marks, while stretch enhancers are large chromatin-defined regulatory regions of at least 3,000 base pairs. Several studies have characterized these regulatory regions in numerous cell types and tissues to decipher their functional importance. However, the differences and similarities between these regulatory regions have not been fully assessed.ResultsWe integrated genomic, epigenomic, and transcriptomic data from ten human cell types to perform a comparative analysis of super and stretch enhancers with respect to their chromatin profiles, cell-type-specificity, and ability to control gene expression. We found that stretch enhancers are more abundant, more distal to transcription start sites, cover twice as much the genome and are significantly less conserved than super-enhancers. In contrast, super-enhancers are significantly more enriched for active chromatin marks and cohesin complex and transcriptionally active than stretch enhancers. Importantly, a vast majority of superenhancers (85%) overlap with only a small subset of stretch enhancers (13%), which are enriched for cell-type-specific biological functions, and control cell identity genes.ConclusionsThese results suggest that super-enhancers are transcriptionally more active and cell-type-specific than stretch enhancers, and importantly, most of the stretch enhancers that are distinct from superenhancers do not show an association with cell identity genes, are less active, and more likely to be poised enhancers.
Biogenesis of a young, 22-nt microRNA in Phaseoleae species by precursor-programmed uridylation
Authors: Fei Qili , Yu Yu , Liu Li , Zhang Yu , Baldrich Patricia , Dai Qing , Chen Xuemei , Meyers Blake C. 
Published: April 2018

ABSTRACTPhased, secondary siRNAs (phasiRNAs) represent a class of small RNAs in plants generated via distinct biogenesis pathways, predominantly dependent on the activity of 22 nt miRNAs. Most 22 nt miRNAs are processed by DCL1 from miRNA precursors containing an asymmetric bulge, yielding a 22/21 nt miRNA/miRNA* duplex. Here we show that miR1510, a soybean miRNA capable of triggering phasiRNA production from numerousNB-LRRs, previously described as 21 nt in its mature form, primarily accumulates as a 22 nt isoform via monouridylation. We demonstrate that in Arabidopsis, this uridylation is performed by HESO1. Biochemical experiments showed that the 3’ terminus of miR1510 is only partially 2’-O-methylated, because of the terminal mispairing in the miR1510/miR1510* duplex that inhibits HEN1 activity in soybean. miR1510 emerged in the Phaseoleae ~41 to 42 MYA with a conserved precursor structure yielding a 22 nt monouridylated form, yet a variant in mung bean is processed directly in a 22 nt mature form. This analysis of miR1510 yields two observations: (1) plants can utilize post-processing modification to generate abundant 22 nt miRNA isoforms to more efficiently regulate target mRNA abundances; (2) comparative analysis demonstrates an example of selective optimization of precursor processing of a young plant miRNA.
To B or not to B: Arsenophonus as a source of B-vitamins in whiteflies
Authors: Santos-Garcia Diego , Juravel Ksenia , Freilich Shiri , Zchori-Fein Einat , Latorre Amparo , Moya Andrés , Morin Shai , Silva Francisco J. 
Published: April 2018

1AbstractInsect lineages feeding on nutritionally restricted diets such as phloem, xylem, or blood, were able to diversify by acquiring bacterial species that complemented the missing nutrients. These bacteria, considered obligate/primary endosymbionts, share a long evolutionary history with their hosts. In some cases, however, these endosymbionts are not able to fulfill all the nutritional requirements of their host, driving the acquisition of additional symbiotic species. Whiteflies, which feed on phloem, established an obligate relationship with Candidatus Portiera aleyrodidarum, who provides essential amino acids and carotenoids to the host. As many Whiteflies species harbor additional endosymbionts, they could provide their hosts with missing nutrients. To test this hypothesis, genomes of several endosymbionts from the whiteflies Aleurodicus dispersus, A. floccissimus and Trialeurodes vaporariorum were sequenced and analyzed. All three species were found to harbor an endosymbiont from the genus Arsenophonus, and the two former also host Wolbachia. A comparative analysis of the three Arsenophonus genomes revealed that although all of them are capable of synthesizing B-vitamins and cofactors, such as pyridoxal, riboflavin, or folate, their genomes and phylogenetic relationship vary greatly. Arsenophonus of A. floccissimus and T. vaporariorum belong to the same clade and display characteristics of facultative endosymbionts, such as large genomes (3 Mb) with thousands of genes, many pseudogenes, intermediate GC content, and mobile genetic elements (MGEs). In contrast, Arsenophonus of A. dispersus belongs to a different lineage and displays the characteristics of a primary endosymbiont, such as a reduced genome (670 kb) with 400 genes, 32% GC content, and no MGEs. However, the presence of 274 pseudogenes suggests that this symbiotic association is more recent than other reported hemipteran’s primary endosymbionts. Arsenophonus of A. dispersus gene repertoire is completely integrated in the symbiotic consortia, and the biosynthesis of most vitamins occurs in shared pathways with its host. In addition, Wolbachia have also retained the ability to produce riboflavin, FAD, and folate, and may have a nutritional contribution. Taken together, our results show that Arsenophonus have a pivotal place in whiteflies nutrition by their ability to produce B-vitamins, even if they diverge and/or go through a genome reduction process.
A functional different immune capacity in cattle is associated with higher mastitis incidence
Authors: Lutterberg Karina , Kleinwort Kristina J. H. , Hobmaier Bernhard F. , Hauck Stefanie M. , Nüske Stefan , Scholz Armin M. , Deeg Cornelia A. 
Published: April 2018

ABSTRACTBovine neonatal pancytopenia (BNP) was a deadly disease transferred by antibodies from 5-10% of cows given a novel BVD vaccine. Disease was lethal in 90% of calves receiving colostrum with BNP antibodies. The cause of BNP is not fully understood to date. We revealed a profound difference in immune capacities between BNP dams and non-responders. Significant differences were detectable in response toin vitrostimulation of peripheral blood derived lymphocytes to several mitogens and IL-2. BNP cows regulated their immune proteomes completely different from controls with other immune response master regulators. Since we detected this response pattern also in 22% of cows that were never vaccinated at all, this immune deviant (ID) phenotype is still present in cattle and probably inherited. Immune response pattern of these cows was stable over an observation period of 38 months. Importantly, ID have a significant increased prevalence of mastitis underscoring the clinical importance.
Automated Segmentation of Epithelial Tissue Using Cycle-Consistent Generative Adversarial Networks
Authors: Häring Matthias , Großhans Jörg , Wolf Fred , Eule Stephan 
Published: April 2018

AbstractA central problem in biomedical imaging is the automated segmentation of images for further quantitative analysis. Recently, fully convolutional neural networks, such as the U-Net, were applied successfully in a variety of segmentation tasks. A downside of this approach is the requirement for a large amount of well-prepared training samples, consisting of image - ground truth mask pairs. Since training data must be created by hand for each experiment, this task can be very costly and time-consuming. Here, we present a segmentation method based on cycle consistent generative adversarial networks, which can be trained even in absence of prepared image - mask pairs. We show that it successfully performs image segmentation tasks on samples with substantial defects and even generalizes well to different tissue types.
Gating Mechanisms during Actin Filament Elongation by Formins
Authors: Aydin Fikret , Courtemanche Naomi , Pollard Thomas D. , Voth Gregory A. 
Published: April 2018

ABSTRACTFormins play an important role in the polymerization of unbranched actin filaments, and particular formins slow elongation by 5-95%. We studied the interactions between actin and the FH2 domains of formins Cdc12, Bni1 and mDia1 to understand the factors underlying their different rates of polymerization. All-atom molecular dynamics simulations revealed two factors that influence actin filament elongation and correlate with the rates of elongation. First, FH2 domains can sterically block the addition of new actin subunits. Second, FH2 domains flatten the helical twist of the terminal actin subunits, making the end less favorable for subunit addition. Coarse-grained simulations over longer time scales support these conclusions. The simulations show that filaments spend time in states that either allow or block elongation. The rate of elongation is a time-average of the degree to which the formin compromises subunit addition rather than the formin-actin complex literally being in ‘open’ or ‘closed’ states.
Numerical and experimental analysis of rotating wheel in contact with the ground
Authors: Kulak Michal , Karczewski Maciej , Lesniewicz Pawel , Olasek Krzysztof , Hoogterp Bas , Spolaore Guillaume , Józwik Krzysztof 
Published: April 2018

Purpose
This paper aims to provide the results of investigations concerning an influence of the tyre with longitudinal grooves on the car body aerodynamics. It is considered as an important aspect affecting the vehicle aerodynamic drag.

Design/methodology/approach
To investigate a contribution of grooved tyres to the overall vehicle drag, three wind tunnel experimental campaigns were performed (two by Peugeot Société Anonyme Peugeot Citroen, one at the Lodz University of Technology). In parallel, computational fluid dynamics (CFD) simulations were conducted with the ANSYS CFX software to enable formulation of wider conclusions.

Findings
The research shows that optimised tread patterns can be derived on a single tyre via a CFD study in combination with a controlled experiment to deliver designs actively lowering the overall vehicle aerodynamic drag.

Practical implications
A reduction in the aerodynamic drag is one of ways to decrease vehicle fuel consumption. Alternatively, it can be translated into an increase in the maximum travel velocity and the maximum distance driven (key factor in electric vehicles), as well as in a reduction of CO2 emissions. Finally, it can improve the vehicle driving and steering stability.

Originality/value
The tyre tread pattern analysis on isolated wheels provides an opportunity to cut costs of R&D and could be a step towards isolating aerodynamic properties of tyres, irrespective of the car body on which they are applied.
Restructuring for relevance: a paradigm shift for academic libraries
Authors: Raju Reggie , Claassen Jill , Adam Amina , DAngelo Alexander , Keraan Sadiq , Mostert Niel , Vonk Saskia 
Published: April 2018

Purpose
The purpose of this paper is to report on the development of a flexible and robust academic library structure that meets the demands of an ever changing user community and remains relevant and fit for purpose in a technology-driven age. The new structure makes provision for the delivery of new and innovative services responding to the need for a paradigm shift in twenty-first century academic librarianship. The move away from subject librarianship, which has been the bastion of South African academic librarianship, is significant.

Design/methodology/approach
This paper used the exploratory method to gain new insights into library structures that have restructured for the twenty-first century. The exploratory study was used to gain new insights into functional librarianship. Despite the short comings of the exploratory method, the method was deemed most appropriate as UCT Libraries was not seeking definitive answers but a process that would provide opportunities to explore possibilities for subsequent processes.

Findings
The move from subject librarianship to functional librarianship has given the library the opportunity to restructure. The restructured library can now offer new and/or radically expanded services to meet the demands of a twenty-first century academic library.

Practical implications
The development of new and future roles and responsibilities commensurate with a robust and “future-driven” structure will consolidate the library’s role as a collaborator in the teaching and learning, and research agendas of a higher education institution.

Originality/value
This paper will be of interest and value to library managers and staff wanting to develop a library structure that responds positively to the redefinition of the professional roles and functions of the library and to strategically position the academic library for the future. It will also be of interest to library and information science academics who may want to re-examine their curricula for the incorporation of new trends.
Exploring attitudes related to sweetened soft drinks consumption among adults in Saudi Arabia
Authors: Benajiba Nada , Eldib Rokkaya Sami 
Published: April 2018

Purpose
Soft drinks consumption in Saudi Arabia is high, although these drinks are nutritionally poor and might lead to various health problems. This paper aims to assess sweetened soft drinks consumption patterns among adult Saudis and explore the association between different attitudes and these patterns.

Design/methodology/approach
In total, 1,194 eligible Saudi adults answered an online questionnaire including soft drinks consumption patterns (frequency of consumption and quantity) and attitudes influencing them. Statistical analysis was performed using SPSS. Pearson test was used to assess the association of attitudes with frequency of sweetened soft drinks consumption. A p-value of <0.05 was set as the significance cut-off.

Findings
Sixteen per cent of participants consumed sweetened soft drinks either daily or usually. Frequency and quantity of consumption were significantly and positively associated (R2 = 0.4, p < 0.0001). The highest correlations were obtained between frequency of consumption and positive attitudes towards perceiving sweetened soft drinks as enjoyable, value for money and indispensable at eating (R2 = 0.55; 0.43 and 0.6, respectively, p < 0.0001). Average score in different attitudes was significantly lower frequency of consumption “never” compared to “always” (p < 0.001) (Healthy: 1 vs 1.9, Enjoyable: 1.5 vs 4.4, value for money: 1.7 vs 3.9, indispensable at eating: 1.1 vs 4.0 and social gathering: 1.2 vs 3.8, respectively).

Research limitations/implications
Main limitation of this study relates to the sampling technique through a snowballing, which could influence on the representativeness of the study population.

Originality/value
Findings advance the understanding on the high consumption of sweetened soft drinks among Saudis, making an emphasis on the complexity of this dietary pattern and the importance of different attitudes influencing on it. Thus, changing this pattern implies a global strategy to reduce both frequency and quantity of consumption.