bluuebunny/crossref_metadata_2025_split huggingface dataset:
Coastal and river flood risk analyses for guiding economically optimal flood adaptation policies: a country-scale study for Mexico
Authors: Haer Toon , Botzen W. J. Wouter , van Roomen Vincent , Connor Harry , Zavala-Hidalgo Jorge , Eilander Dirk M. , Ward Philip J. 
Published: April 2018

Many countries around the world face increasing impacts from flooding due to socio-economic development in flood-prone areas, which may be enhanced in intensity and frequency as a result of climate change. With increasing flood risk, it is becoming more important to be able to assess the costs and benefits of adaptation strategies. To guide the design of such strategies, policy makers need tools to prioritize where adaptation is needed and how much adaptation funds are required. In this country-scale study, we show how flood risk analyses can be used in cost–benefit analyses to prioritize investments in flood adaptation strategies in Mexico under future climate scenarios. Moreover, given the often limited availability of detailed local data for such analyses, we show how state-of-the-art global data and flood risk assessment models can be applied for a detailed assessment of optimal flood-protection strategies. Our results show that especially states along the Gulf of Mexico have considerable economic benefits from investments in adaptation that limit risks from both river and coastal floods, and that increased flood-protection standards are economically beneficial for many Mexican states. We discuss the sensitivity of our results to modelling uncertainties, the transferability of our modelling approach and policy implications.
This article is part of the theme issue ‘Advances in risk assessment for climate change adaptation policy’.
Advances in risk assessment for climate change adaptation policy
Authors: Adger W. Neil , Brown Iain , Surminski Swenja 
Published: April 2018

Climate change risk assessment involves formal analysis of the consequences, likelihoods and responses to the impacts of climate change and the options for addressing these under societal constraints. Conventional approaches to risk assessment are challenged by the significant temporal and spatial dynamics of climate change; by the amplification of risks through societal preferences and values; and through the interaction of multiple risk factors. This paper introduces the theme issue by reviewing the current practice and frontiers of climate change risk assessment, with specific emphasis on the development of adaptation policy that aims to manage those risks. These frontiers include integrated assessments, dealing with climate risks across borders and scales, addressing systemic risks, and innovative co-production methods to prioritize solutions to climate challenges with decision-makers. By reviewing recent developments in the use of large-scale risk assessment for adaptation policy-making, we suggest a forward-looking research agenda to meet ongoing strategic policy requirements in local, national and international contexts.
This article is part of the theme issue ‘Advances in risk assessment for climate change adaptation policy’.
AMP-activated protein kinase is essential for the maintenance of energy levels during synaptic activation
Authors: Marinangeli Claudia , Didier Sébastien , Ahmed Tariq , Caillerez Raphaelle , Domise Manon , Laloux Charlotte , Bégard Séverine , Carrier Sébastien , Colin Morvane , Marchetti Philippe , Ghesquière Bart , Balschun Detlef , Buée Luc , Kluza Jérôme , Vingtdeux Valérie 
Published: April 2018

AbstractWhile accounting for 2% of the total body mass, the brain is the organ that consumes the most energy. Although it is widely acknowledged that neuronal energy metabolism is tightly regulated, the mechanism how neurons meet their energy demand to sustain synaptic transmission remains poorly studied. Here we provide substantial evidence that the AMP-activated protein kinase (AMPK) plays a leading role in this process. Our results show that following synaptic activation, AMPK activation is required to sustain neuronal energy levels particularly through mitochondrial respiration. Further, our studies revealed that this metabolic plasticity regulated by AMPK is required for the expression of immediate early genes, synaptic plasticity and memory formation. These findings are important in the context of neurodegenerative disorders, as AMPK deregulation as it is observed in Alzheimer’s disease, impairs the metabolic response to synaptic activation. Altogether, our data provides the proof of concept that AMPK is an essential player in the regulation of neuroenergetic metabolism plasticity induced in response to synaptic activation.
Precision Identification of Diverse Bloodstream Pathogens from the Gut Microbiome
Authors: Tamburini Fiona B. , Andermann Tessa M. , Tkatchenko Ekaterina , Senchyna Fiona , Banaei Niaz , Bhatt Ami S. 
Published: April 2018

AbstractBloodstream infection is the most common infectious complication in hematopoietic cell transplantation recipients. To evaluate the genomic concordance of bloodstream pathogens and bacterial strains within the intestinal microbiome using whole genome sequencing, we developed StrainSifter, a bioinformatic pipeline to compare nucleotide variation between bacterial isolate strains and stool metagenomes. We applied StrainSifter to bloodstream isolates and stool metagenome samples from hematopoietic stem cell transplant recipients with bloodstream infections. StrainSifter is designed to identify single nucleotide variants between isolate and metagenomic short reads using stringent alignment, coverage, and variant frequency criteria for strain comparison. We identified enteric BSI isolates that were highly concordant with those in the gut microbiota, as well as highly concordant strains of typically non-enteric bacteria. These findings demonstrate the utility of StrainSifter in strain matching and provide a more precise investigation of the intestine as a reservoir of diverse pathogens capable of causing bloodstream infections.
Identification of small regulatory RNAs involved in persister formation
Authors: Zhang Shanshan , Liu Shuang , Wu Nan , Zhang Wenhong , Zhang Ying 
Published: April 2018

AbstractSmall regulatory RNA (srRNA) is widely distributed in three kingdoms of life and fulfills functions in many aspects of cellular life, but their role in bacterial persistence remains unknown. In this study, we comprehensively interrogated the expression levels of the known srRNAs on three critical time points, stage 1 (S1) where no persisters are formed, stage 2 (S2) where persisters are beginning to appear, and stage 3 (S3) where persister numbers increase significantly. Three upregulated srRNAs (OmrB, an outer member associated srRNA; RdlB, a swarming motility and curli expression regulator; McaS, a flagellar motility and biofilm formation regulator) overlapping in S2/S1 and S3/S1, together with the other four upregulated srRNAs (MicF, a ribosome binding inhibitor; MicL, an outer membrane associated srRNA; RybB, a cell envelope stress regulator; RydB, regulator of a global regulator RpoS) in S2/S1 are of special interest. By constructing deletion mutants and overexpression strains in uropathogenic E. coli strain UTI89, we tested their persister-formation capabilities in log phase and stationary phase cultures exposed to antibiotics (gentamicin, cefotaxime and levofloxacin) and stresses (heat, hyperosmosis, H2O2, and acid). The results of the deletion mutant studies showed that all the seven identified sRNAs have varying effects on persister formation with different antibiotics or stresses. Moreover, we found all the deletion mutants of these srRNAs have reduced biofilm formation. Additionally, except the McaS and the RydB overexpression strains, all of the srRNAs overexpression strains demonstrated increased persister-formation in antibiotic and stress persister assays, confirming the role of these srRNAs in persistence. Together, we identified seven srRNAs (OmrB, RdlB, McaS, MicF, MicL, RybB, and RydB) that are involved in type II persister formation for the first time. These findings provide convincing evidence for a new level of rapid persistence regulation via srRNA and furnish novel therapeutic targets for intervention.
An RNAi screen in human cell lines reveals conserved DNA damage repair pathways that mitigate formaldehyde sensitivity
Authors: Juarez Eleonora , Chambwe Nyasha , Tang Weiliang , Mitchell Asia D. , Owen Nichole , Kumari Anuradha , Monnat Raymond J. , McCullough Amanda K. 
Published: April 2018

ABSTRACTFormaldehyde is a ubiquitous DNA damaging agent, with human exposures occuring from both exogenous and endogenous sources. Formaldehyde can also form DNA-protein crosslinks and is representative of other such DNA damaging agents including ionizing radiation, metals, aldehydes, chemotherapeutics, and cigarette smoke. In order to identify genetic determinants of cell proliferation in response to continuous formaldehyde exposure, we quantified cell proliferation after siRNA-depletion of a comprehensive array of over 300 genes representing all of the major DNA damage response pathways. Three unrelated human cell lines (SW480, U-2 OS and GM00639) were used to identify common or cell line-specific mechanisms. Four cellular pathways were determined to mitigate formaldehyde toxicity in all three cell lines: homologous recombination, double-strand break repair, ionizing radiation response, and DNA replication. Differences between cell lines were further investigated by using exome sequencing and Cancer Cell Line Encyclopedia genomic data. Our results reveal major genetic determinants of formaldehyde toxicity in human cells and provide evidence for the conservation of these formaldehyde responses between human and budding yeast.
The choice of the environmental covariate affects the power to detect variation in reaction norm slopes
Authors: Gienapp Phillip 
Published: April 2018

AbstractMany traits are phenotypically plastic, i.e. the same genotype expresses different phenotypes depending on the environment. Individuals and genotypes can vary in this response to the environment and this individual (IxE) and genetic variation in reaction norm slopes (GxE) can have important ecological or evolutionary consequences. Studies on variation in plasticity often fail to show IxE or GxE; this can indicate a genuine absence or simply a lack of power. There is, however, another factor that could potentially affect the power to detect IxE or GxE: the choice of the environmental variable included in the analysis. Identifying the genuine environmental driver of phenotypic plasticity will mostly be impossible and hence only a proxy is included in the analysis. However, if this proxy is too weakly correlated with the real driver of plasticity, this will bias IxE and GxE downwards, could lead to spurious negative results and invalid conclusions. As the mean phenotype in a given environment captures all environmental effects on the phenotype, using it as ‘environment’ in the analysis should increase the power to detect IxE or GxE. Using simulations I here showed that using weakly correlated proxies indeed biased estimates downwards but that when using the environment-specific means this was not the case. Using environment-specific means as a covariate has been commonly used in animal and plant breeding but rarely used outside these fields despite its potential usefulness as ‘yardstick’ to test whether IxE or GxE is present or absent in the phenotype of interest.
Inactivation of the monofunctional peptidoglycan glycosyltransferase SgtB allowsStaphylococcus aureusto survive in the absence of lipoteichoic acid
Authors: Karinou Eleni , Schuster Christopher F. , Pazos Manuel , Vollmer Waldemar , Gründling Angelika 
Published: April 2018

AbstractThe cell wall ofStaphylococcus aureusis composed of peptidoglycan and the anionic polymers lipoteichoic acid (LTA) and wall teichoic acid. LTA is required for growth and normal cell morphology inS. aureus.Strains lacking LTA are usually only viable when grown under osmotically stabilizing conditions or after the acquisition of compensatory mutations. LTA negative suppressor strains with inactivating mutations ingdpP, resulting in an increase in intracellular c-di-AMP levels, have been described previously. Here, we sought to identify factors other than c-di-AMP that allowS. aureusto survive without LTA. LTA-negative strains able to grow in un-supplemented medium were obtained and found to contain mutations insgtB, mazE, clpXorvraT. The growth improvement through mutations inmazEandsgtBwas confirmed by complementation analysis. We also show that anS. aureus sgtBtransposon mutant, inactivated for the monofunctional peptidoglycan glycosyltransferase SgtB, displays a 4-fold increase in the MIC towards a number of cell wall-targeting antibiotics, suggesting that alteration in the peptidoglycan structure could help bacteria compensate for the lack of LTA. Muropeptide analysis of peptidoglycan isolated from a WT andsgtBmutant strains did not reveal any sizable alternations in the peptidoglycan structure. In contrast, the peptidoglycan isolated from an LTA-negativeltaSmutant strain showed a significant reduction in the fraction of highly crosslinked peptidoglycan, which was partially rescued in thesgtB/ltaSdouble mutant suppressor strain. Taken together, these data point towards an important function of LTA in cell wall integrity through its requirement for proper peptidoglycan assembly.ImportanceThe bacterial cell wall acts as primary defence against environmental insults such as changes in osmolarity. It is also a vulnerable structure as defects in its synthesis can lead to growth arrest or cell death. The important human pathogenStaphylococcus aureushas a typical Gram-positive cell wall, which consists of peptidoglycan and the anionic polymers lipoteichoic acid (LTA) and wall teichoic acid. Several clinically relevant antibiotics inhibit the synthesis of peptidoglycan; hence it and teichoic acids are considered attractive targets for the development of new antimicrobials. We show that LTA is required for efficient peptidoglycan crosslinking inS. aureusand inactivation of a peptidoglycan glycosyltransferase can partially rescue this defect, altogether revealing an intimate link between peptidoglycan and LTA synthesis.
Divergent Roles for cAMP–PKA Signaling in the Regulation of Filamentous Growth inSaccharomyces cerevisiaeandSaccharomyces bayanus
Authors: Kayikci Ömur , Magwene Paul M. 
Published: April 2018

ABSTRACTThe cyclic AMP – Protein Kinase A (cAMP–PKA) pathway is an evolutionarily conserved eukaryotic signaling network that is essential for growth and development. In the fungi, cAMP–PKA signaling plays a critical role in regulating cellular physiology and morphological switches in response to nutrient availability. We undertook a comparative investigation of the role that cAMP-PKA signaling plays in the regulation of filamentous growth in two closely related budding yeast species,Saccharomyces cerevisiaeandSaccharomyces bayanus. Using chemical and genetic perturbations of this pathway and its downstream targets we discovered divergent roles for cAMP-PKA signaling in the regulation of filamentous growth. While cAMP-PKA signaling is required for the filamentous growth response in both species, increasing or decreasing the activity of this pathway leads to drastically different phenotypic outcomes. In S.cerevisiae, cAMP-PKA inhibition ameliorates the filamentous growth response while hyper-activation of the pathway leads to increased filamentous growth; the same perturbations in S.bayanusresult in the obverse. Divergence in the regulation of filamentous growth between S.cerevisiaeand S.bayanusextends to downstream targets of PKA, including several kinases, transcription factors, and effector proteins. Our findings highlight the potential for significant evolutionary divergence in gene network function, even when the constituent parts of such networks are well conserved.
Small RNAs gained during epididymal transit of sperm are essential for embryonic development in mice
Authors: Conine Colin C. , Sun Fengyun , Song Lina , Rivera-Pérez Jaime A. , Rando Oliver J. 
Published: April 2018

ABSTRACTThe small RNA payload of mammalian sperm undergoes dramatic remodeling during development, as several waves of microRNAs and tRNA fragments are shipped to sperm during post-testicular maturation in the epididymis. Here, we take advantage of this developmental process to probe the function of the sperm RNA payload in preimplantation development. We generated zygotes via intracytoplasmic sperm injection (ICSI) using sperm obtained from the proximal (caput) vs. distal (cauda) epididymis, then characterized development of the resulting embryos. Embryos generated using caput sperm significantly overexpress multiple regulatory factors throughout preimplantation development, and subsequently implant inefficiently and fail soon after implantation. Remarkably, microinjection of purified cauda-specific small RNAs into caput-derived embryos not only completely rescued preimplantation molecular defects, but also suppressed the postimplantation embryonic lethality phenotype. These findings reveal an essential role for small RNA remodeling during post-testicular maturation of mammalian sperm, and identify a specific preimplantation gene expression program responsive to sperm-delivered microRNAs.
Columnar vortex generator for flow control over a ski-jump ramp
Authors: Bardera Rafael , León-Calero Marina , de Nova-Trigueros Joaquín 
Published: April 2018

Purpose
Aircraft carriers are essential for modern naval operations. Takeoff maneuver is critical because of the short runway distance. The ski-jump ramp is a system which increases the angle of attack of the aircraft, so an extra lift is obtained. Regarding the flow configuration over the ski-jump ramp at ahead wind conditions, the complex aerodynamic environment generated by the ramp configuration influences aircraft operations. This flow field is mainly characterized by a low velocity recirculation bubble that reduces aircraft performances. The purpose of this paper is to find a solution to reduce these adverse effects, by means of flow control devices, which opens a wide field of research.

Design/methodology/approach
This paper presents wind tunnel tests performed to study the flow configuration in the vicinity of the ski-jump ramp and the flow control devices effects. A 1:100 scaled ship model was built to develop experimental tests by using flow control devices fabricated by means of additive manufacturing. Particle image velocimetry technique was used to measure the velocity flow field and the turbulence intensity maps.

Findings
Interesting results were obtained when the angle between the intersection of the ski-jump ramp and the columnar vortex generator (CVG) is modified. The results showed a high reduction of the recirculation bubble generated over the flight deck.

Originality/value
CVG has presented encouraging results as a passive flow control device. A study of the variation of CVG geometrical parameters has been developed.
Effects of free-stream turbulence on the global pressure fluctuation of compressible transitional flows in a low-pressure turbine cascade
Authors: Matsuura Kazuo , Matsui Kotaro , Tani Naoki 
Published: April 2018

Purpose
This paper aims to investigate global pressure fluctuations in compressible transitional flows in a low-pressure turbine cascade because of variations in the free-stream turbulence and its interaction with the boundary layers.

Design/methodology/approach
Transition process resolving numerical simulations are performed with different types of inflow turbulence. The unsteady three-dimensional fully compressible Navier–Stokes equations are solved using a sixth-order compact difference and a tenth-order filtering method. First, simulations of both K-regime and bypass transitions are conducted for a flat plate boundary layer to validate the use of the filter in computing different transition routes. Second, computations of the cascade flows are conducted. Cases of no free-stream turbulence, isotropic free-stream turbulence of 5 per cent and wakes from an upstream cylinder are compared. For wakes, variations in wake trajectory depending on the cylinder blade relative position are also taken into account.

Findings
The different transition routes are successfully reproduced by the present method even with strong filtering. When feedback phenomena occur near the trailing edge, high-frequency oscillations dominate in the flow field. Low-frequency oscillations become dominant when the blade boundary layer becomes turbulent. Thus, the effects of the free-stream turbulence and its interaction with the boundary layer appear as changes in the global pressure fluctuation.

Originality/value
The free-stream turbulence qualitatively affects global pressure fluctuations, which become a medium to convey boundary-layer information away from the cascade.
Aerodynamic prediction of a projectile fitted with fins
Authors: Decrocq Cédric , Martinez Bastien , Albisser Marie , Dobre Simona , Gnemmi Patrick , Bailly Yannick , Roy Jean-Claude 
Published: April 2018

Purpose
The present paper deals with weapon aerodynamics and aims to describe preliminary studies that were conducted for developing the next generation of long-range guided ammunition. Over history, ballistic research scientists were constantly investigating new artillery systems capable of overcoming limitations of range, accuracy and manoeuvrability. While futuristic technologies are increasingly under development, numerous issues concerning current powdered systems still need to be addressed. In this context, the present work deals with the design and the optimization of a new concept of long-range projectile with regard to multidisciplinary fields, including flight scenario, steering strategy, mechanical actuators or size of payload.

Design/methodology/approach
Investigations are conducted for configurations that combine existing full calibre 155 mm guided artillery shell with a set of lifting surfaces. As the capability of the ammunition highly depends on lifting surfaces in terms of number, shape or position, a parametric study has to be conducted for determining the best aerodynamic architecture. To speed-up this process, initial estimations are conducted thanks to low computational cost methods suitable for preliminary design requirements, in terms of time, accuracy and flexibility. The WASP code (Wing-Aerodynamic-eStimation-for-Projectiles) has been developed for rapidly predicting aerodynamic coefficients (static and dynamic) of a set of lifting surfaces fitted on a projectile fuselage, as a function of geometry and flight conditions, up to transonic velocities.

Findings
In the present study, WASP predictions at Mach 0.7 of both normal force and pitching moment coefficients are assessed for two configurations.

Originality/value
Analysis is conducted by gathering results from WASP, computational-fluid-dynamics (CFD) simulations, wind-tunnel experiments and free-flight tests. Obtained results demonstrate the ability of WASP code to be used for preliminary design steps.