bluuebunny/crossref_metadata_2025 huggingface dataset:
Assessing climate risks across different business sectors and industries: an investigation of methodological challenges at national scale for the UK
Authors: Surminski Swenja , Di Mauro Manuela , Baglee J. Alastair R. , Connell Richenda K. , Hankinson Joel , Haworth Anna R. , Ingirige Bingunath , Proverbs David
Published: April 2018

Climate change poses severe risks for businesses, which companies as well as governments need to understand in order to take appropriate steps to manage those. This, however, represents a significant challenge as climate change risk assessment is itself a complex, dynamic and geographically diverse process. A wide range of factors including the nature of production processes and value chains, the location of business sites as well as relationships and interdependencies with customers and suppliers play a role in determining if and how companies are impacted by climate risks. This research explores the methodological challenges for a national-scale assessment of climate risks through the lens of the UK Climate Change Risk Assessment (UKCCRA) process and compares the approaches adopted in the first and second UKCCRA (2011, 2016), while also reflecting on international experiences elsewhere. A review of these issues is presented, drawing on a wide body of contemporary evidence from a range of sources including the research disciplines, grey literature and government policy. The study reveals the methodological challenges and highlights six broad themes, namely scale, evidence base, adaptation responses, scope, interdependencies and public policy. The paper concludes by identifying suitable lessons for future national climate risk assessments, which should guide the next phase of research in preparation for UKCCRA3 and those of national-level risk assessments elsewhere.

This article is part of the theme issue ‘Advances in risk assessment for climate change adaptation policy’.
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

While 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

Bloodstream 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

Small 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

Formaldehyde 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

Many 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

The 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.

Importance

The 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

The 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

The 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.
A comparative transcriptional landscape of maize and sorghum obtained by single-molecule sequencing
Authors: Wang Bo , Regulski Michael , Tseng Elizabeth , Olson Andrew , Goodwin Sara , McCombie W. Richard , Ware Doreen
Published: April 2018

Maize and sorghum are both important crops with similar overall plant architectures, but they have key differences, especially in regard to their inflorescences. To better understand these two organisms at the molecular level, we compared expression profiles of both protein-coding and noncoding transcripts in 11 matched tissues using single-molecule, long-read, deep RNA sequencing. This comparative analysis revealed large numbers of novel isoforms in both species. Evolutionarily young genes were likely to be generated in reproductive tissues and usually had fewer isoforms than old genes. We also observed similarities and differences in alternative splicing patterns and activities, both among tissues and between species. The maize subgenomes exhibited no bias in isoform generation; however, genes in the B genome were more highly expressed in pollen tissue, whereas genes in the A genome were more highly expressed in endosperm. We also identified a number of splicing events conserved between maize and sorghum. In addition, we generated comprehensive and high-resolution maps of poly(A) sites, revealing similarities and differences in mRNA cleavage between the two species. Overall, our results reveal considerable splicing and expression diversity between sorghum and maize, well beyond what was reported in previous studies, likely reflecting the differences in architecture between these two species.
Decoupling anion-ordering and spin-Peierls transitions in a strongly one-dimensional organic conductor with a chessboard structure, (o-Me2TTF)2NO3
Authors: Jeannin Olivier , Reinheimer Eric W. , Foury-Leylekian Pascale , Pouget Jean-Paul , Auban-Senzier Pascale , Trzop Elzbieta , Collet Eric , Fourmigué Marc
Published: April 2018

A mixed-valence conducting cation radical salt of the unsymmetrically substituted o-Me2TTF donor molecule (TTF is tetrathiafulvalene) was obtained upon electrocrystallization in the presence of the non-centrosymmetric NO3
− anion. It crystallizes at room temperature in the monoclinic P21/c space group, with the anion disordered on an inversion centre. The donor molecules are stacked along the a axis. A 90° rotation of the longest molecular axis of o-Me2TTF generates a chessboard-like structure, preventing lateral S...S contacts between stacks and providing a strongly one-dimensional electronic system, as confirmed by overlap interaction energies and band structure calculations. A strong dimerization within the stacks explains the semiconducting behaviour of the salt, with σroom temp = 3–5 S cm−1 and E
activated = 0.12–0.14 eV. An X-ray diffuse scattering survey of reciprocal space, combined with full structure resolutions at low temperatures (250, 85 and 20 K), evidenced the succession of two structural transitions: a ferroelastic one with an anion-ordering (AO) process and the establishment of a (0, ½, ½) superstructure below 124 (±3) K, also visible via resistivity thermal dependence, followed by a stack tetramerization with the establishment of a (½, ½, ½) superstructure below 90 (±5) K. The latter ground state is driven by a spin-Peierls (SP) instability, as demonstrated by the temperature dependence of the magnetic susceptibility. Surprisingly, these two kinds of instability appear to be fully decoupled here, at variance with other tetramethyltetrathiafulvalene (TMTTF) or tetramethyltetraselenafulvalene (TMTSF) salts with such non-centrosymmetric counter-ions.
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.
Effective feedback for millennials in new organizations
Authors: Ray Prantika , Singh Manjari
Published: April 2018

Purpose

This paper aims to understand aspects of feedback given to the millennial generation, particularly in new organizations.

Design/methodology/approach

This paper is based on a review of existing literature from journals and magazines. The perspectives discussed in this paper have been substantiated with discussions with practicing line and HR managers. This paper has been further developed after conducting informal discussions with employees and their supervisors (both millennials and non-millennials). However, the synthesized perspectives expressed here are those of the authors.

Findings

The millennial generation has characteristics that relate to receiving feedback. Key aspects discussed in this paper are the purpose of feedback, formal versus informal methods, short versus long-term orientation, frequency, hierarchical relationships, and technology.

Practical implications

With the increasing entry of millennials into the workforce, organizations need to focus on the mechanisms and environments for effective feedback.

Originality/value

This paper is timely given the rising number of millennials entering the workforce. This work looks into the mechanisms for effective performance feedback, as well as creating a facilitating environment with the focus on employee development.
Automatic body measurement based on slicing loops
Authors: Zhong Yueqi , Li Duan , Wu Ge , Hu PengPeng
Published: April 2018

Purpose

The automatic body measurement is the key of tailoring, mass customization and fit/ease evaluation. The major challenges include finding the landmarks and extracting the sizes accurately. The purpose of this paper is to propose a new method of body measurement based on the loop structure.

Design/methodology/approach

The scanned human model is sliced equally to layers consist of various shapes of loops. The semantic feature analysis has been regarded as a problem of finding the points of interest (POI) and the loop of interest (LOI) according to the types of loop connections. Methods for determining the basic landmarks have been detailed.

Findings

The experimental results validate that the proposed methods can be used to locate the landmarks and to extract sizes on markless human scans robustly and efficiently.

Originality/value

With the method, the body measurement can be quickly performed with average errors around 0.5 cm. The results of segmentation, landmarking and body measurements also validate the robustness and efficiency of the proposed methods.
Biosynthesis of abscisic acid in fungi: identification of a sesquiterpene cyclase as the key enzyme in Botrytis cinerea
Authors: Izquierdo‐Bueno Inmaculada , González‐Rodríguez Victoria E. , Simon Adeline , Dalmais Bérengère , Pradier Jean‐Marc , Le Pêcheur Pascal , Mercier Alex , Walker Anne‐Sophie , Garrido Carlos , Collado Isidro González , Viaud Muriel
Published: April 2018

While abscisic acid (ABA) is known as a hormone produced by plants through the carotenoid pathway, a small number of phytopathogenic fungi are also able to produce this sesquiterpene but they use a distinct pathway that starts with the cyclization of farnesyl diphosphate (FPP) into 2Z,4E‐α‐ionylideneethane which is then subjected to several oxidation steps. To identify the sesquiterpene cyclase (STC) responsible for the biosynthesis of ABA in fungi, we conducted a genomic approach in Botrytis cinerea. The genome of the ABA‐overproducing strain ATCC58025 was fully sequenced and five STC‐coding genes were identified. Among them, Bcstc5 exhibits an expression profile concomitant with ABA production. Gene inactivation, complementation and chemical analysis demonstrated that BcStc5/BcAba5 is the key enzyme responsible for the key step of ABA biosynthesis in fungi. Unlike what is observed for most of the fungal secondary metabolism genes, the key enzyme‐coding gene Bcstc5/Bcaba5 is not clustered with the other biosynthetic genes, i.e., Bcaba1 to Bcaba4 that are responsible for the oxidative transformation of 2Z,4E‐α‐ionylideneethane. Finally, our study revealed that the presence of the Bcaba genes among Botrytis species is rare and that the majority of them do not possess the ability to produce ABA.
Shifting metabolic priorities among key protistan taxa within and below the euphotic zone
Authors: Hu Sarah K. , Liu Zhenfeng , Alexander Harriet , Campbell Victoria , Connell Paige E. , Dyhrman Sonya T. , Heidelberg Karla B. , Caron David A.
Published: April 2018

A metatranscriptome study targeting the protistan community was conducted off the coast of Southern California, at the San Pedro Ocean Time‐series station at the surface, 150 m (oxycline), and 890 m to link putative metabolic patterns to distinct protistan lineages. Comparison of relative transcript abundances revealed depth‐related shifts in the nutritional modes of key taxonomic groups. Eukaryotic gene expression in the sunlit surface environment was dominated by phototrophs, such as diatoms and chlorophytes, and high abundances of transcripts associated with synthesis pathways (e.g., photosynthesis, carbon fixation, fatty acid synthesis). Sub‐euphotic depths (150 and 890 m) exhibited strong contributions from dinoflagellates and ciliates, and were characterized by transcripts relating to digestion or intracellular nutrient recycling (e.g., breakdown of fatty acids and V‐type ATPases). These transcriptional patterns underlie the distinct nutritional modes of ecologically important protistan lineages that drive marine food webs, and provide a framework to investigate trophic dynamics across diverse protistan communities.
The distribution of active iron‐cycling bacteria in marine and freshwater sediments is decoupled from geochemical gradients
Authors: Otte Julia M. , Harter Johannes , Laufer Katja , Blackwell Nia , Straub Daniel , Kappler Andreas , Kleindienst Sara
Published: April 2018

Microaerophilic, phototrophic and nitrate‐reducing Fe(II)‐oxidizers co‐exist in coastal marine and littoral freshwater sediments. However, the in situ abundance, distribution and diversity of metabolically active Fe(II)‐oxidizers remained largely unexplored. Here, we characterized the microbial community composition at the oxic‐anoxic interface of littoral freshwater (Lake Constance, Germany) and coastal marine sediments (Kalø Vig and Norsminde Fjord, Denmark) using DNA‐/RNA‐based next‐generation 16S rRNA (gene) amplicon sequencing. All three physiological groups of neutrophilic Fe(II)‐oxidizing bacteria were found to be active in marine and freshwater sediments, revealing up to 0.2% anoxygenic photoferrotrophs (e.g., Rhodopseudomonas, Rhodobacter, Chlorobium), 0.1% microaerophilic Fe(II)‐oxidizers (e.g., Mariprofundus, Hyphomonas, Gallionella) and 0.3% nitrate‐reducing Fe(II)‐oxidizers (e.g., Thiobacillus, Pseudomonas, Denitromonas, Hoeflea). Active Fe(III)‐reducing bacteria (e.g., Shewanella, Geobacter) were most abundant (up to 2.8%) in marine sediments and co‐occurred with cable bacteria (up to 4.5%). Geochemical profiles of Fe(III), Fe(II), O2, light, nitrate and total organic carbon revealed a redox stratification of the sediments and explained 75%–85% of the vertical distribution of microbial taxa, while active Fe‐cycling bacteria were found to be decoupled from geochemical gradients. We suggest that metabolic flexibility, microniches in the sediments, or interrelationships with cable bacteria might explain the distribution patterns of active Fe‐cycling bacteria.
The path of electron transfer to nitrogenase in a phototrophic alpha‐proteobacterium
Authors: Fixen Kathryn R. , Pal Chowdhury Nilanjan , Martinez‐Perez Marta , Poudel Saroj , Boyd Eric S. , Harwood Caroline S.
Published: April 2018

The phototrophic alpha‐proteobacterium, Rhodopseudomonas palustris, is a model for studies of regulatory and physiological parameters that control the activity of nitrogenase. This enzyme produces the energy‐rich compound H2, in addition to converting N2 gas to NH3. Nitrogenase is an ATP‐requiring enzyme that uses large amounts of reducing power, but the electron transfer pathway to nitrogenase in R. palustris was incompletely known. Here, we show that the ferredoxin, Fer1, is the primary but not sole electron carrier protein encoded by R. palustris that serves as an electron donor to nitrogenase. A flavodoxin, FldA, is also an important electron donor, especially under iron limitation. We present a model where the electron bifurcating complex, FixABCX, can reduce both ferredoxin and flavodoxin to transfer electrons to nitrogenase, and we present bioinformatic evidence that FixABCX and Fer1 form a conserved electron transfer pathway to nitrogenase in nitrogen‐fixing proteobacteria. These results may be useful in the design of strategies to reroute electrons generated during metabolism of organic compounds to nitrogenase to achieve maximal activity.
Influence of the Hfq and Crc global regulators on the control of iron homeostasis in Pseudomonas putida
Authors: Sánchez‐Hevia Dione L. , Yuste Luis , Moreno Renata , Rojo Fernando
Published: April 2018

Metabolically versatile bacteria use catabolite repression control to select their preferred carbon sources, thus optimizing carbon metabolism. In pseudomonads, this occurs through the combined action of the proteins Hfq and Crc, which form stable tripartite complexes at target mRNAs, inhibiting their translation. The activity of Hfq/Crc is antagonised by small RNAs of the CrcZ family, the amounts of which vary according to carbon availability. The present work examines the role of Pseudomonas putida Hfq protein under conditions of low‐level catabolite repression, in which Crc protein would have a minor role since it is sequestered by CrcZ/CrcY. The results suggest that, under these conditions, Hfq remains operative and plays an important role in iron homeostasis. In this scenario, Crc appears to participate indirectly by helping CrcZ/CrcY to control the amount of free Hfq in the cell. Iron homeostasis in pseudomonads relies on regulatory elements such as the Fur protein, the PrrF1‐F2 sRNAs, and several extracytoplasmic sigma factors. Our results show that the absence of Hfq is paralleled by a reduction in PrrF1‐F2 small RNAs. Hfq thus provides a regulatory link between iron and carbon metabolism, coordinating the iron supply to meet the needs of the enzymes operational under particular nutritional regimes.
Harmless, friendly and lethal: antibiotic misuse in relation to the unpredictable bacterium Group A streptococcus
Authors: Gröndal Hedvig
Published: April 2018

Evidence‐based treatment guidelines for managing infections in health care are promoted as tools to prevent unnecessary use of antibiotics. Antibiotic misuse has been examined as regards the doctor‐patient relation and the social context of medical practice. Less attention has been paid to how the very conceptualisation of human‐microbial relations may influence understandings of antibiotic misuse. The article examines a medical controversy concerning guidelines for managing throat infection and antibiotic treatment in Sweden. It demonstrates how this controversy unfolds around two different ways of relating to a specific bacterium – Group A Streptococcus. The analysis shows how two ‘microbiopolitics’, involving different understandings of human‐microbial relations, are created in the controversy and how different antibiotic prescribing practices are justified. By focusing on Group A Streptococcus, which is commonly observed, but also unpredictable and potentially dangerous, the article provides new insights into the relations between bacteria, humans and policy in an age of antimicrobial resistance. It argues, in particular, that the definition of antibiotic misuse is unstable and consequently that policy measures aimed at reducing misuse must be related to how specific infections and bacteria are conceptualised in the actual context the policy addresses.
Human herpesvirus 8 infection DNA positivity is associated with low insulin secretion: A case‐control study in a sub‐Saharan African population with diabetes
Authors: Lontchi‐Yimagou Eric , Legoff Jérôme , Nguewa Jean‐Louis , Boudou Philippe , Balti Eric V. , Noubiap Jean J. , Kamwa Vicky , Atogho‐Tiedeu Barbara , Azabji‐Kenfack Marcel , Djahmeni Eric N. , Etoa Martine , Lemdjo Gaelle , Balla Vanessa , Dehayem Mesmin Y. , Foufelle Fabienne , Mbanya Jean‐Claude , Gautier Jean‐Francois , Sobngwi Eugene
Published: April 2018

Background

Viruses have been considered potential triggers for the development of diabetes. This study assessed insulin secretion and insulin sensitivity in human herpesvirus 8 (HHV8)‐infected and uninfected sub‐Saharan African people with diabetes.

Methods

In all, 173 people with non‐autoimmune diabetes were enrolled consecutively: 124 with type 2 diabetes mellitus (T2DM) and 49 with ketosis‐prone diabetes (KPD) admitted in hyperglycemic crisis. Those with KPD were further subdivided into those with new‐onset ketotic‐phase KPD (n = 34) or non‐ketotic phase KPD (n = 15). All participants were screened for HHV8‐specific antibodies and genomic DNA. Blood samples were collected for analysis of fasting glucose, HbA1c, lipid profile, and C‐peptide, with insulin resistance and secretion estimated by homeostasis model assessment.

Results

Among the 173 diabetic participants, 88 (50.9%) were positive for HHV8 antibodies (Ac‐HHV8+), including 15 (8.7%) positive for HHV8 DNA (DNA‐HHV8+). The seroprevalence of HHV8 was similar between T2DM (55.6%) and KPD (61.2%) subjects. Of those with and without ketotic‐phase KPD, 35.3% and 46.7% were Ac‐HHV8+, respectively. Body mass index was significantly in lower DNA‐HHV8+ than DNA‐HHV8– subjects. Low‐density lipoprotein and total cholesterol were significantly higher, but C‐peptide and homeostatic model assessment of β‐cell function (HOMA‐β) were significantly lower in DNA‐HHV8+ than DNA‐HHV8– participants. After excluding DNA‐HHV8+ participants, triglyceride concentrations were significantly higher in Ac‐HHV8+ (n = 73) than Ac‐HHV8– (n = 85) subjects. In contrast, HOMA‐β was significantly higher among Ac‐HHV8+ than Ac‐HHV8– participants.

Conclusions

In the present study, HHV8 DNA positivity was associated with low insulin secretion in this sub‐Saharan African diabetes population.
Evolving concepts in classification of systemic vasculitis: where are we and what is the way forward?
Authors: Watts Richard A.
Published: April 2018

The classification of the systemic vasculitides has been controversial for several decades. The Chapel Hill consensus Conference definitions originally developed in 1994, but revised and extended in 2012 are now widely accepted. The American College of Rheumatology (ACR) criteria were first published in 1990, are now generally accepted to be out of date and new criteria are needed. More recently the classical division of the ANCA vasculitides using clinical phenotype has come under scrutiny with evidence from epidemiological, genetic and outcome studies that perhaps these conditions should be classified on the basis of ANCA specificity into PR3‐ANCA positive and MPO‐ANCA positive groups. The traditional distinction between giant cell arteritis and Takayasu arteritis has been questioned and some recent studies of GCA have included patients with only extra‐cranial disease. The Diagnostic and Classification Criteria of Vasculitis study (DCVAS) will provide new validated classification criteria for the systemic vasculitides.
Oxygen supplementation for critically ill patients—A protocol for a systematic review
Authors: Barbateskovic M. , Schjørring O. L. , Jakobsen J. C. , Meyhoff C. S. , Rasmussen B. S. , Perner A. , Wetterslev J.
Published: April 2018

Background

In critically ill patients, hypoxaemia is a common clinical manifestation of inadequate gas exchange in the lungs. Supplemental oxygen is therefore given to all critically ill patients. This can result in hyperoxaemia, and some observational studies have identified harms with hyperoxia. The objective of this systematic review is to critically assess the evidence of randomised clinical trials on the effects of higher versus lower inspiratory oxygen fractions or targets of arterial oxygenation in critically ill adult patients.

Methods

We will search for randomised clinical trials in major international databases. Two authors will independently screen and select references for inclusion using Covidence, extract data and assess the methodological quality of the included randomised clinical trials using the Cochrane risk of bias tool. Any disagreement will be resolved by consensus. We will analyse the extracted data using Review Manager and Trial Sequential Analysis. To assess the quality of the evidence, we will create a ‘Summary of Findings’ table containing our primary and secondary outcomes using the GRADE assessment.

Discussion

Supplemental oxygen administration is widely recommended in international guidelines despite lack of robust evidence of its effectiveness. To our knowledge, no systematic review of randomised clinical trials has investigated the effects of oxygen supplementation in critically ill patients. This systematic review will provide reliable evidence to better inform future trialists and decision‐makers on clinical practice on supplemental oxygen administration in critically ill patients.
Standardised assessment of competence in Focused Assessment with Sonography for Trauma
Authors: Russell L. , Østergaard M. L. , Nielsen M. B. , Konge L. , Nielsen K. R.
Published: April 2018

Purpose

The aim of this study was to develop and gather validity evidence for a standardised test of competence in Focused Assessment with Sonography for Trauma (FAST) and to define the appropriate cut‐off point in simulation‐based learning of the FAST protocol.

Methods

A 20‐item simulation‐based test for assessing competence in FAST was created. The test was administered to thirteen novices and twelve radiologists experienced in abdominal ultrasound diagnostics. The Contrasting Groups’ method was used to establish a credible passing score.

Results

The internal consistency was high (Cronbach's α = 0.90) and the test had good discriminatory ability (P < .001). The mean score was 16.9 (95% CI: 15.5‐18.3) in the experienced group and 8.0 (95% CI: 5.8‐10.2) in the novice group, corresponding to 85% and 40% of the total score, respectively. A pass/fail standard of 14 points was established using the Contrasting Groups’ method.

Conclusions

The FAST simulation‐based test provided valid assessment of competence in FAST. The FAST test could be used to guide training and ensure basic competence of physicians using FAST.