bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogenomics reveals dynamic evolution of fungal nitric oxide reductases and their relationship to secondary metabolism
Authors: Higgins Steven A. , Schadt Christopher W. , Matheny Patrick B. , Löffler Frank E. 
Published: April 2018

AbstractFungi expressing P450nor, an unconventional nitric oxide (NO) reducing cytochrome P450, are thought to be significant contributors to soil nitrous oxide (N2O) emissions. However, fungal contributions to N2O emissions remain uncertain due to inconsistencies in measurements of N2O formation by fungi. Much of the N2O emitted from antibiotic-amended soil microcosms is attributed to fungal activity, yet fungal isolates examined in pure culture are poor N2O producers. To assist in reconciling these conflicting observations and produce a benchmark genomic analysis of fungal denitrifiers, genes underlying fungal denitrification were examined in >700 fungal genomes. Of 167p450nor–containing genomes identified, 0, 30, and 48 also harbored the denitrification genesnarG,napAornirK, respectively. Compared tonapAandnirK,p450norwas twice as abundant and exhibited two to five-fold more gene duplications, losses, and transfers, indicating a disconnect betweenp450norpresence and denitrification potential. Furthermore, co-occurrence ofp450norwith genes encoding NO-detoxifying flavohemoglobins (Spearman r = 0.87,p= 1.6e−10) confounds hypotheses regarding P450nor’s primary role in NO detoxification. Instead, ancestral state reconstruction united P450nor with actinobacterial cytochrome P450s (CYP105) involved in secondary metabolism (SM) and 19 (11 %)p450nor-containing genomic regions were predicted to be SM clusters. Another 40 (24 %) genomes harbored genes nearbyp450norpredicted to encode hallmark SM functions, providing additional contextual evidence linkingp450norto SM. These findings underscore the potential physiological implications of widespreadp450norgene transfer, support the novel affiliation ofp450norwith fungal SM, and challenge the hypothesis ofp450nor’s primary role in denitrification.
Loss of function mutations inepaRconfer resistance to phage NPV1 infection inEnterococcus faecalisOG1RF
Authors: Ho Khang , Huo Wenwen , Pas Savannah , Dao Ryan , Palmer Kelli L. 
Published: April 2018

AbstractEnterococcus faecalisis a Gram-positive opportunistic pathogen that inhabits the human gastrointestinal tract. Because of the high frequency of antibiotic resistance amongEnterococcusclinical isolates, interest in using phage to treat enterococcal infections and to decolonize high-risk patients for antibiotic-resistantEnterococcusis rising. Bacteria can evolve phage resistance, but there is little published information on these mechanisms inE. faecalis. In this report, we identified genetic determinants ofE. faecalisresistance to ϕNPV1. We found that loss-of-function mutations inepaRconfer ϕNPV1 resistance by blocking phage adsorption. We attribute the inability of the phage to adsorb to the modification or loss of an extracellular polymer in strains with inactivatedepaR. Phage-resistantepaRmutants exhibited increased daptomycin and osmotic stress susceptibilities. Our results demonstrate thatin vitrospontaneous resistance to ϕNPV1 comes at a cost inE. faecalisOG1RF.
Insufficient fumarase contributes to generating reactive oxygen species in Dahl salt sensitive rats
Authors: Hou Entai , Zheng Xuewei , Yang Zhe , Li Xian , Liu Zerong , Chen Meng , Li Xiaoxue , Liang Mingyu , Tian Zhongmin 
Published: April 2018

AbstractDahl SS rats exhibit greater levels of renal medullary oxidative stress and lower levels of fumarase activities. Fumarase insufficiencies can increase reactive oxygen species (ROS), the mechanism of which, however, is not clear. A proteomic analysis indicated fumarase knockdown in HK-2 cells resulted in changes in the expression or activity of NADPH oxidase, mitochondrial respiratory chain complex I and III, ATP synthase subunits, and α-oxoglutarate dehydrogenase, all of which are sites of ROS formation. Meantime, the activities of key antioxidant enzymes such as G6PD, 6PGD, GR, GPx and GST increased significantly too. The apparent activation of antioxidant defense appeared insufficient as glutathione precursors, glutathione and GSH/GSSG ratio were decreased. SS rats exhibited changes in redox metabolism similar to HK-2 cells with fumarase knockdown. Supplementation with fumarate and malate, the substrate and product of fumarase, increased and decreased, respectively, blood pressure and the levels of H2O2and MDA in kidney tissues of SS rats. These results indicate fumarase insufficiencies cause a wide range of changes at several sites of ROS production and antioxidant mechanisms.
Sparse reduced-rank regression for exploratory visualization of paired multivariate datasets
Authors: Kobak Dmitry , Bernaerts Yves , Weis Marissa A. , Scala Federico , Tolias Andreas , Berens Philipp 
Published: April 2018

AbstractIn genomics, transcriptomics, and related biological fields (collectively known as omics), it is common to work with n ≪ p datasets with the dimensionality much larger than the sample size. In recent years, combinations of experimental techniques began to yield multiple sets of features for the same set of biological replicates. One example is Patch-seq, a method combining single-cell RNA sequencing with electrophysiological recordings from the same cells. Here we present a framework based on sparse reduced-rank regression for obtaining an interpretable visualization of the relationship between the transcriptomic and the electrophysiological data. We use an elastic net regularization penalty that yields sparse solutions and allows for an efficient computational implementation. Using several publicly available Patch-seq datasets, we show that sparse reduced-rank regression outperforms both sparse full-rank regression and non-sparse reduced-rank regression in terms of predictive performance, and can outperform existing methods for sparse partial least squares and sparse canonical correlation analysis in terms of out-of-sample correlations. We introduce a bibiplot visualization in order to display the dominant factors determining the relationship between transcriptomic and electrophysiological properties of neurons. We believe that sparse reduced-rank regression can provide a valuable tool for the exploration and visualization of paired multivariate datasets, including Patch-seq.
Computational-Observer Analysis of Illumination Discrimination
Authors: Ding Xiaomao , Radonjić Ana , Cottaris Nicolas P. , Jiang Haomiao , Wandell Brian A. , Brainard David H. 
Published: April 2018

AbstractThe spectral properties of the ambient illumination provide useful information about time of day and weather. We study the perceptual representation of illumination by analyzing measurements of how well people discriminate between illuminations across scene configurations. More specifically, we compare human performance to a computational-observer analysis that evaluates the information available in the isomerizations of the cones in a model human photoreceptor mosaic. Some patterns of human performance are predicted by the computational observer, other aspects are not. The analysis clarifies which aspects of performance require additional explanation in terms of the action of visual mechanisms beyond the isomerization of light by the cones.
Experimental and numerical study of ventilation cavitation around a NACA0015 hydrofoil with special emphasis on bubble evolution and air-vapor interactions
Authors: Yu An , Luo Xianwu , Yang Dandan , Zhou Jiajian 
Published: April 2018

Purpose
This paper aims to gain a clear understanding of the ventilated cavity evolution around an NACA0015 hydrofoil by using both experimental and numerical investigation.

Design/methodology/approach
The bubble evolution around an NACA0015 hydrofoil with or without air injection was observed in a water tunnel, and the simulation was conducted using a modified turbulence model and homogeneous cavitation model.

Findings
The present simulation method can successfully predict the bubble evolutions around the NACA0015 hydrofoil with or without air injection. Air injection can alleviate the nature cavitation oscillation, and the suppression effect on nature cavitation depends on the air-entrant coefficient. It is confirmed that the air and vapor cavity have the same shedding frequency. It is seen that the air sheet closely attaches to the hydrofoil surface and is surrounded by the vapor sheet. Thus, the injected air promotes vapor growth and results in an increase in the cavity shedding frequency. Further, with a large air-entrant coefficient, the pressure fluctuation is suppressed completely.

Originality/value
The new simulation method is adopted to explore the mechanism of ventilated cavitation. The bubble evolutions with and without air injection have been comprehensively studied by experimental and numerical investigation. The effects of air injection on natural cavity oscillations and pressure fluctuations have been revealed in the present study.
FGA-MMF method for the simulation of two-phase flows
Authors: Behrangi Farhang , Banihashemi Mohammad Ali , Montazeri Namin Masoud , Bohluly Asghar 
Published: April 2018

Purpose
This paper aims to present a novel numerical technique for solving the incompressible multiphase mixture model.

Design/methodology/approach
The multiphase mixture model contains a set of momentum and continuity equations for the mixture phase, a second phase continuity equation and the algebraic equation for the relative velocity. For solving continuity equation for the second phase and advection term of momentum, an improved approach fine grid advection-multiphase mixture flow (FGA-MMF) is developed. In the FGA-MMF method, the continuity equation for the second phase is solved with higher-order schemes in a two times finer grid. To solve the advection term of the momentum equation, the advection fluxes of the volume fraction in the continuity equation for the second phase are used.

Findings
This approach has been used in various tests to simulate unsteady flow problems. Comparison between numerical results and experimental data demonstrates a satisfactory performance. Numerical examples show that this approach increases the accuracy and stability of the solution and decreases non-monotonic results.

Research limitations/implications
The solver for the multi-phase mixture model can only be adopted to solve the incompressible fluid flow.

Originality/value
The paper developed an innovative solution (FGA-MMF) to find multi-phase flow field value in the multi-phase mixture model. Advantages of the FGA-MMF technique are the ability to accurately determine the phases interpenetrating, decreasing the numerical diffusion of the interface and preventing instability and non-monotonicity in solution of large density variation problems.
Adaptive finite element analysis for damage detection of non-uniform Euler–Bernoulli beams with multiple cracks based on natural frequencies
Authors: Wang Yongliang , Ju Yang , Zhuang Zhuo , Li Chenfeng 
Published: April 2018

Purpose
This study aims to develop an adaptive finite element method for structural eigenproblems of cracked Euler–Bernoulli beams via the superconvergent patch recovery displacement technique. This research comprises the numerical algorithm and experimental results for free vibration problems (forward eigenproblems) and damage detection problems (inverse eigenproblems).

Design/methodology/approach
The weakened properties analogy is used to describe cracks in this model. The adaptive strategy proposed in this paper provides accurate, efficient and reliable eigensolutions of frequency and mode (i.e. eigenpairs as eigenvalue and eigenfunction) for Euler–Bernoulli beams with multiple cracks. Based on the frequency measurement method for damage detection, using the difference between the actual and computed frequencies of cracked beams, the inverse eigenproblems are solved iteratively for identifying the residuals of locations and sizes of the cracks by the Newton–Raphson iteration technique. In the crack detection, the estimated residuals are added to obtain reliable results, which is an iteration process that will be expedited by more accurate frequency solutions based on the proposed method for free vibration problems.

Findings
Numerical results are presented for free vibration problems and damage detection problems of representative non-uniform and geometrically stepped Euler–Bernoulli beams with multiple cracks to demonstrate the effectiveness, efficiency, accuracy and reliability of the proposed method.

Originality/value
The proposed combination of methodologies described in the paper leads to a very powerful approach for free vibration and damage detection of beams with cracks, introducing the mesh refinement, that can be extended to deal with the damage detection of frame structures.
Automated layout design of multi-span reinforced concrete beams using charged system search algorithm
Authors: Uz Mehmet Eren , Sharafi Pezhman , Askarian Mahya , Fu Weiqing , Zhang Chunmei 
Published: April 2018

Purpose
The preliminary layout design of structures impacts upon the entire design process and, consequently, the total cost. The purpose of this paper is to select the most economical layouts that satisfy structural and architectural requirements, while considering the reciprocal effects of cost factors and layout variables at the preliminary stages of design.

Design/methodology/approach
This paper presents an automated method for cost optimization of geometric layout design of multi-span reinforced concrete (RC) beams subjected to dynamic loading by using the charged system search (CSS) algorithm. First, a novel cost optimization approach for geometric layout problems is introduced, in which both cost parameters and dynamic responses are considered in the preliminary layout design of beams. The proposed structural optimization problem with constraints on the static and dynamic equilibrium, architectural dimensions and structural action effects is solved using the CSS algorithm.

Findings
The proposed CSS algorithm for solving the cost optimization problem can be easily used for optimizing the span lengths and is also capable of working with various cost functions. The presented examples show that the proposed algorithm using the new cost optimization function provides satisfactory results and can result in over 7 per cent cost saving.

Originality/value
This is an original paper proposing a novel methodology for preliminary layout design of concrete beams.
Nonlinear temperature and thermal stress analysis of annular fins with time dependent boundary condition
Authors: Lee Sen-Yung , Chou Li-Kuo , Chen Chao Kuang 
Published: April 2018

PurposeThe purpose of this paper is to propose the Laplace Adomian Decomposition Method (LADM) for studying the nonlinear temperature and thermal stress analysis of annular fins with time-dependent boundary condition.Design/methodology/approachThe nonlinear behavior of temperature and thermal stress distribution in an annular fin with rectangular profile subjected to time-dependent periodic temperature variations at the root is studied by the LADM. The radiation effect is considered. The convective heat transfer coefficient is considered as a temperature function.FindingsThe proposed solution method is helpful in overcoming the computational bottleneck commonly encountered in industry and in academia. The results show that the circumferential stress at the root of the fin will be important in the fatigue analysis.Originality/valueThis study presents an effective solution method to analyze the nonlinear behavior of temperature and thermal stress distribution in an annular fin with rectangular profile subjected to time-dependent periodic temperature variations at the root by using LADM.
A note on the stiffness and flexibility natural approach to the triangular spring cell
Authors: Doltsinis I. St 
Published: April 2018

Purpose
An intended numerical analysis of solids and structures by spring cell substitutes in place of finite elements has occasioned considerable research on the subject. This paper aims to expose two alternative concepts evolving out of Argyris’ natural approach to the simplex triangular element. One is based on an approximation of the element flexibility and the other approximates the stiffness with coincidence at the ideal conditions of complete substitution.

Design/methodology/approach
Characteristic of the natural formalism is the homogeneous definition of strain and stress along the sides of the triangular element. The associated elastic compliance offers itself for the transition to the spring cell. The diagonal entities are interpreted immediately as springs along the element sides, and the off-diagonal terms account for the completeness of the substitution. In addition to the flexibility concept, the spring cell is deduced alternatively from the element’s natural stiffness. The difference in the flexibility result lies in the calculatory cross-sectional areas of the elastic bar members.

Findings
From the natural point of view, the spring cell evolves out of the continuum element to the desired degree of substitution. The simplest configuration of pin-joined bars discards all geometrical and physical cross effects. The approach is attractive because of its transparent simplicity.

Research limitations/implications
The difference between the stiffness and the flexibility approach to spring cells is demonstrated for triangular elements that suit the problems lying in plane stress or plane strain. More general states of stress and strain involve spring cell counterparts of the tetrahedral finite element.

Practical implications
Apart from plane geometries, triangular spring cells are assembled to lattice models of space structures, such as membrane shells and similar.

Originality/value
The natural formalism of simplex finite elements is used for deducing spring cells in two variants and exploring their properties. This is a novel approach to spring cells and an original employment of the natural concept.
Development of a crisis in a project: a process perspective
Authors: Simard Magali , Laberge Danielle 
Published: April 2018

PurposeThe purpose of this paper is to analyze the development and outbreak of a crisis in a high-priority project within a large organization.Design/methodology/approachSingle-case study using extreme case sampling, a type of purposeful sampling, because this case provides rich information on a rare research opportunity: a project crisis that emerged during the fieldwork. Research data are semi-structured interviews, observations, project and organization documentation, logbook, notes and memos.FindingsThe paper shows the relevance of notions from organizational crisis management to an internal crisis in a temporary setting. This allowed a deeper understanding of crisis development. The paper reveals the wealth of meaningful, transparent data that can be collected when a crisis emerges. It highlights the high potential of project crises to reveal parent organizations’ dysfunctions. Indeed, findings suggest that the parent organization’s usual project management practices greatly contributed to the crisis affecting this project, which was unusually large and complex.Research limitations/implicationsThe main potential limitation relates to transferability. However, a single-case study is appropriate when it represents a rare phenomenon that is not easily accessible for researchers – a crisis outbreak.Practical implicationsResults can provide insights enabling practitioners to improve their understanding of the ambiguous, stressful situations created by a crisis.Originality/valueThe results show the relevance of notions from organizational crisis management to the development of a project crisis and demonstrate the potentially harmful impact of a parent organization’s “usual” practices, especially on “unusually” large and complex projects.
Environmental performance measurement for green supply chains
Authors: Tuni Andrea , Rentizelas Athanasios , Duffy Alex 
Published: April 2018

PurposeThe majority of the environmental impacts in a typical supply chain can arise beyond the focal firm boundaries. However, no standardised method to quantify these impacts at the supply chain level currently exists. The purpose of this paper is to identify the quantitative methods developed to measure the environmental performance of supply chains and evaluate their key features.Design/methodology/approachA systematic literature review is conducted at the intersection of performance measurement and green supply chain management (GSCM) fields, covering 78 publications in peer-reviewed academic journals. The literature is reviewed according to several perspectives, including the environmental aspects considered, the main purpose of measurement, model types and the extent of supply chain covered by performance measurements.FindingsAdopted environmental metrics show a low degree of standardisation and focus on natural resources, energy and emissions to air. The visibility and traceability of environmental aspects are still limited; the assessment of environmental impacts does not span in most cases beyond the direct business partners of the focal firms. A trade-off was observed between the range of environmental aspects and the extent of the supply chain considered with no method suitable for a holistic evaluation of the environmental supply chain performance identified. Three major streams of research developing in the field are identified, based on different scope.Originality/valueThis paper is the first attempt to examine in detail what tiers of the supply chain are actually involved in green performance assessment, ultimately contributing to clarify the scope of the supply chain dimension in GSCM performance measurement research. The work also recognises which methods are applicable to extended supply chains and explores how different methodologies perform in terms of supply chain extent covered.