bluuebunny/crossref_metadata_2025_split huggingface dataset:
RegCyanoDB: a database of regulatory interactions in cyanobacteria
Authors: Nair Ajay , Chetty Madhu , Vinh Nguyen Xuan 
Published: March 2017

AbstractBackgroundCyanobacteria are photoautotrophic organisms with environmental, evolutionary, and industrial importance. Knowledge of its regulatory interactions are important to predict, optimise, and engineer their characteristics. However, at present, very few of their regulatory interactions are known. The regulatory interactions are known only for a few model organisms such asEscherichia colidue to technical and economical constraints, which are unlikely to change soon. Thus, mapping of regulatory interactions from well-studied organisms to less-studied organisms by using computational techniques is widely used. Reverse Best Hit (RBH), with appropriate algorithm parameters, is a simple and efficient method for detecting functional homologs.DescriptionWe predict the regulatory interactions in 30 strains of cyanobacteria using the known regulatory interactions from the best-studied organism,E. coli.RBH method with appropriate parameters is used to identify the functional homologs. An interaction is mapped to a cyanobacterial strain if functional homologs exist for a known transcription factor and its target gene. The confidence of the detected homologs and interactions are also provided. Since RBH is a conservative method, homolog-grouping is performed to recover lost putative interactions. A database of the predicted interactions from all the 30 strains of cyanobacteria is constructed.ConclusionRegcyanoDB contains 20,280 interactions with confidence levels for 30 cyanobacterial strains. The predicted regulatory interactions exhibit a scale free network topology as observed in model organisms. The interacting genes inE. coliand cyanobacteria are mostly found to have the same gene annotation. This database can be used for posing novel hypotheses and validation studies in wet-lab and computational domains.The database is available athttp://www.che.iitb.ac.in/grn/RegCyanoDB/
Amending published articles: time to rethink retractions and corrections?
Authors: Barbour Virginia , Bloom Theo , Lin Jennifer , Moylan Elizabeth 
Published: March 2017

AbstractAcademic publishing is evolving and our current system of correcting research post-publication is failing, both ideologically and practically. It does not encourage researchers to engage in consistent post-publication changes. Worse yet, post-publication ‘updates’ are misconstrued as punishments or admissions of guilt. We propose a different model that publishers of research can apply to the content they publish, ensuring that any post-publication amendments are seamless, transparent and propagated to all the countless places online where descriptions of research appear. At the center, the neutral term “amendment” describes all forms of post-publication change to an article. We lay out a straightforward and consistent process that applies to each of the three types of amendments: insubstantial, substantial, and complete. This proposed system supports the dynamic nature of the research process itself as researchers continue to refine or extend the work, removing the emotive climate particularly associated with retractions and corrections to published work. It allows researchers to cite and share the correct versions of articles with certainty, and for decision makers to have access to the most up to date information.
A porcine ex vivo model of pigmentary glaucoma
Authors: Dang Yalong , Waxman Susannah , Wang Chao , Loewen Ralista T. , Sun Ming , Loewen Nils A. 
Published: March 2017

AbstractPigment dispersion syndrome can lead to pigmentary glaucoma (PG), a poorly understood condition of younger, myopic eyes with fluctuating, high intraocular pressure (IOP). The absence of a model similar in size and behavior to human eyes has made it difficult to investigate its pathogenesis. Here, we present a porcine ex vivo model that recreates the features of PG including intraocular hypertension, pigment accumulation in the trabecular meshwork and relative failure of phagocytosis. Inin vitromonolayer cultures as well as inex vivoeye perfusion cultures, we found that the trabecular meshwork (TM) cells that regulate outflow, form actin stress fibers and have a decreased phagocytosis. Gene expression microarray and pathway analysis indicated key roles of RhoA in regulating the TM cytoskeleton, motility, and phagocytosis thereby providing new targets for PG therapy.
Mercury and water level fluctuations in lakes of northern Minnesota
Authors: Larson James H. , Maki Ryan P. , Christensen Victoria G. , Sandheinrich Mark B. , LeDuc Jaime F. , Kissane Claire , Knights Brent C. 
Published: March 2017

AbstractLarge lake ecosystems support a variety of ecosystem services in surrounding communities, including recreational and commercial fishing. However, many northern temperate fisheries are contaminated by mercury. Annual variation in mercury accumulation in fish has previously been linked to water level (WL) fluctuations, opening the possibility of regulating water levels in a manner that minimizes or reduces mercury contamination in fisheries. Here, we compiled a long-term dataset (1997–2015) of mercury content in young-of-year Yellow Perch (Perca flavescens) from six lakes on the border between the U.S. and Canada and examined whether mercury content appeared to be related to several metrics of WL fluctuation (e.g., spring WL rise, annual maximum WL, and year-to-year change in maximum WL). Using simple correlation analysis, several WL metrics appear to be strongly correlated to Yellow Perch mercury content, although the strength of these correlations varies by lake. We also used many WL metrics, water quality measurements, temperature and annual deposition data to build predictive models using partial least squared regression (PLSR) analysis for each lake. These PLSR models showed some variation among lakes, but also supported strong associations between WL fluctuations and annual variation in Yellow Perch mercury content. The study lakes underwent a modest change in WL management in 2000, when winter WL minimums were increased by about 1 m in five of the six study lakes. Using the PLSR models, we estimated how this change in WL management would have affected Yellow Perch mercury content. For four of the study lakes, the change in WL management that occurred in 2000 likely reduced Yellow Perch mercury content, relative to the previous WL management regime.
Discoveringin vivocytokine eQTL interactions from a lupus clinical trial
Authors: Davenport Emma E. , Amariuta Tiffany , Gutierrez-Arcelus Maria , Slowikowski Kamil , Westra Harm-Jan , Luo Yang , Shen Ciyue , Rao Deepak A. , Zhang Ying , Pearson Stephen , von Schack David , Beebe Jean S. , Bing Nan , John Sally , Vincent Michael S. , Zhang Baohong , Raychaudhuri Soumya 
Published: March 2017

AbstractBackgroundCytokines are critical to human disease and are attractive therapeutic targets given their widespread influence on gene regulation and transcription. Defining the downstream regulatory mechanisms influenced by cytokines is central to defining drug and disease mechanisms. One promising strategy is to use interactions between expression quantitative trait loci (eQTLs) and cytokine levels to define target genes and mechanisms.ResultsIn a clinical trial for anti-IL-6 in patients with systemic lupus erythematosus we measured interferon (IFN) status, anti-IL-6 drug exposure and genome-wide gene expression at three time points (379 samples from 157 individuals). First, we show that repeat transcriptomic measurements increases the number ofciseQTLs identified compared to using a single time point by 64%. Then, after identifying 4,818 cis-eQTLs, we observed a statistically significant enrichment ofin vivoeQTL interactions with IFN status (p<0.001 by permutation) and anti-IL-6 drug exposure (p<0.001). We observed 210 and 72 interactions for IFN and anti-IL-6 respectively (FDR<20%). Anti-IL-6 interactions have not yet been described while 99 of the IFN interactions are novel. Finally, we found transcription factor binding motifs interrupted by eQTL interaction SNPs, pointing to key regulatory mediators of these environmental stimuli and therefore potential therapeutic targets for autoimmune diseases. In particular, genes with IFN interactions are enriched for ISRE binding site motifs, while those with anti-IL-6 interactions are enriched for IRF4 motifs.ConclusionThis study highlights the potential to exploit clinical trial data to discoverin vivoeQTL interactions with therapeutically relevant environmental variables.
Influence of the electrical circuit configurations of a DVR coupling transformer with a magnetic bypass
Authors: Majchrzak Virginie , Parent Guillaume , Brudny Jean-François , Costan Valentin , Guuinic Philippe 
Published: March 2017

Purpose
For the proposed coupling transformer, a magnetic bypass based on the virtual air gap principle is realized by inserting auxiliary windings in a return leg added to a standard transformer. With such a setup, it is able to act as a voltage regulator as well as protect the power electronics of the dynamic voltage restorer from electrical grid fault currents. This paper focuses on the electrical design part of the coupling transformer. It aims to explain how the behavior of the auxiliary windings electrical circuit of the magnetic bypass impacts the performances of the device.

Design/methodology/approach
The influence of the electrical auxiliary windings circuit configurations on the operation of the coupling transformer is studied by finite element analyses with nonlinear and isotropic magnetic materials.

Findings
A configuration for the realization of the electrical circuit of the auxiliary windings is determined according to the finite element simulation results to achieve the design of the coupling transformer whose magnetic core was previously designed.

Originality/value
By studying the operation of a special coupling transformer with nonlinear saturation phenomenon by finite element analyses, a to-do list of the electrical circuit parameters is described to design this device well.
Minimization of a SynRel’s oscillating torque by calculation of the appropriate skew angle
Authors: Martinez Javier , Krischan Klaus , Muetze Annette 
Published: March 2017

Purpose
Synchronous Reluctance (SynRel) motors are known to suffer from excessive torque ripples. The classical way to avoid this drawback of the motor is skewing the slots. This paper aims to provide an analytic estimation of the best skew angle to minimize the ripples in such SynRel motors with tooth windings. The approach used in this paper consists of the minimization of the spectral components of the magnetic energy that cause these oscillation torques. The method was validated by means of a multi-slice finite element model (FEM).

Design/methodology/approach
An analytic model, based on permeance theory, is derived to analyse the electromagnetic phenomena taking place inside of the motor. This model allows the identification of the causes underlying the torque ripple production. Based on this understanding, the most suitable skew angle can be determined. The analytic method, together with the best skew angle, is validated by means of an FEM of a SynRel machine.

Findings
A method to determine the optimum skew angle for a SynRel machine is presented. It depends on the wave-number of the magnetic waves producing the torque ripple. It is twice the one typically chosen for induction machines.

Practical/implications
The proposed approach allows improving on the design methodology for the production of smoothly running SynRel machines.

Originality/value
The methodology utilized in this paper is based on the relationship between the mechanical torque and the magnetic energy stored in the motor (virtual work law). From this, the best skew angle to eliminate the magnetic energy causing torque ripple can be determined. It, therefore, proposes an effective alternative to the common use of inductance models to determine such angles.
Parallelized numerical modeling of the interaction of a solid object with immiscible incompressible two-phase fluid flow
Authors: Ghasemi Amirmahdi , Nikbakhti R. , Ghasemi Amirreza , Hedayati Faraz , Malvandi Amir 
Published: March 2017

Purpose
A numerical method is developed to capture the interaction of solid object with two-phase flow with high density ratios. The current computational tool would be the first step of accurate modeling of wave energy converters in which the immense energy of the ocean can be extracted at low cost.

Design/methodology/approach
The full two-dimensional Navier–Stokes equations are discretized on a regular structured grid, and the two-step projection method along with multi-processing (OpenMP) is used to efficiently solve the flow equations. The level set and the immersed boundary methods are used to capture the free surface of a fluid and a solid object, respectively. The full two-dimensional Navier–Stokes equations are solved on a regular structured grid to resolve the flow field. Level set and immersed boundary methods are used to capture the free surface of liquid and solid object, respectively. A proper contact angle between the solid object and the fluid is used to enhance the accuracy of the advection of the mass and momentum of the fluids in three-phase cells.

Findings
The computational tool is verified based on numerical and experimental data with two scenarios: a cylinder falling into a rectangular domain due to gravity and a dam breaking in the presence of a fixed obstacle. In the former validation simulation, the accuracy of the immersed boundary method is verified. However, the accuracy of the level set method while the computational tool can model the high-density ratio is confirmed in the dam-breaking simulation. The results obtained from the current method are in good agreement with experimental data and other numerical studies.

Practical/implications
The computational tool is capable of being parallelized to reduce the computational cost; therefore, an OpenMP is used to solve the flow equations. Its application is seen in the following: wind energy conversion, interaction of solid object such as wind turbine with water waves, etc.

Originality/value
A high efficient CFD approach method is introduced to capture the interaction of solid object with a two-phase flow where they have high-density ratio. The current method has the ability to efficiently be parallelized.
A comparative study of wall jet flow containing carbon nanotubes with convective heat transfer and MHD
Authors: Ali Zaidi Syed Zulfiqar , Mohyud-din Syed Tauseef , Bin-Mohsen Bandar 
Published: March 2017

Purpose
The purpose of this study is to conduct a comparative investigation for incompressible electrically conducting nanofluid fluid through wall jet. Single-walled carbon nanotubes (SWCNTs) and multiple-walled carbon nanotubes (MWCNTs) are considered as the nanoparticles. To record the effect of Lorentz forces, a magnetic field is applied normally with the assumption that the induced magnetic field is negligible.

Design/methodology/approach
Boundary layer approximation is used to convert governing equations into ordinary differential equations along with appropriate boundary conditions. To obtain the results, used homotopy analysis method (HAM) has been used as an analytical technique and to validate the obtained results a famous numerical Runge–Kutta–Fehlberg method is also exploited. It has been observed that the results obtained through both of the methods are in excellent agreement with exact solution.

Findings
The Hartmann number is used as controlling parameter for velocity and temperature profile. That can be recorded as its extended values help to normalize the velocity, whereas it controls the rapid increase in temperature. The temperature profile is boosted by increasing the value of the Biot number, a physical parameter. Similarly, it also increases for an increased percentage of volume fraction of particles (SWCNTs/MWCNTs). The Hartmann number plays an important role in decreasing local skin friction coefficient. The influence of the Biot number and volume fraction of nanoparticles caused similar increasing effects on the local Nusselt number. Nanoparticles of the form SWCNT provide better heat transfer as compared to MWCNTs. Influence of the Biot number and volume fraction of nanoparticles caused similar increasing effects on the local Nusselt number. Nanoparticles of the form SWCNT provide better heat transfer as compared to MWCNTs.

Originality/value
To gain insight into the problem, the effects of various emerging parameters and physical quantities such as Biot number, Nusselt number and skin friction coefficient, have been explored.
Simulation of partial differential equations models in Java
Authors: Cano María José , Chacon-Vera Eliseo , Esquembre Francisco 
Published: March 2017

Purpose
Computer simulations improve the knowledge of physical models and are widely used in teaching and research. Key aspects are to understand their solutions and to make interactive changes to the models, observing their effects in real-time. The drawback of creating interactive simulations of physical models is the high level of programming expertise required. The purpose of this study is to facilitate this task.

Design/methodology/approach
Java is the perfect language for this task; it yields high-quality graphics and is widely spread in the scientific community. Because many important physical models are described by means of partial differential equations (PDEs), the combination of Java with FreeFem++, a C++ PDE solver based on the finite element method, is considered.

Findings
In this study, a Java library is introduced to numerically solve PDE equations via a run-time connection with FreeFem++. The solution is encapsulated into Java objects that are ready to be used in different programming tasks. The library also includes new Java visualization elements for solutions and meshes in the context of the Open Source Physics project library. Together, the connection features and the visualization elements facilitate the creation of Java simulations by programming researchers. For those with less programming capabilities, this work has been included into Easy Java Simulations, a tool to further ease the creation of interactive simulations.

Originality/value
The present study approach allows simulating models given PDEs. The equations are solved either in local or in remote mode (e.g. by a network accessible to a high-performance computer) and visualized locally, providing a high degree of interactivity to the end user.
MHD squeezing flow between two parallel disks with suction or injection via Legendre wavelet-quasilinearization technique
Authors: Mohyud-din Syed Tauseef , Iqbal Muhammad Asad , Khan Umar , Yang Xiao-Jun 
Published: March 2017

Purpose
This paper aims to propose a method by merging Legendre wavelets method and quasilinearization technique to tackle with the nonlinearity and to get better and more accurate results.

Design/methodology/approach
To test the significance of the proposed scheme, the authors applied the method on the model representing magneto-hydrodynamic squeezing flow of a viscous fluid between two parallel infinite disks, where one disk is impermeable and the other is porous with either suction or injection of the fluid. For the sake of comparison, numerical solution by using RK-4 is also computed. From the graphs and tables, it is evident that the proposed method shows an excellent accordance with the numerical solution.

Findings
The solution converges to the numerical solution when the degree of Legendre polynomials m is increased. For m = 20 in all the three cases, for different values of S, M and A, the graphs of solutions obtained by Legendre wavelet quasilinearization technique show an excellent agreement with numerical solution. Also, it is evident from figures that suction and injection affects the velocity profile in opposite way. For suction, maximum velocity is seen to be at the center of the channel. Magnetic field can be used to regularize the flow and it stabilizes the flow behavior.

Originality/value
Magnetic field can be used to regularize the flow and it stabilizes the flow behavior.
International construction joint ventures between Singapore and developing countries
Authors: Hwang Bon-Gang , Zhao Xianbo , Chin Eileen Wei Yan 
Published: March 2017

Purpose
The purposes of this paper is twofold: first, to assess the risks associated with the international construction joint ventures (ICJVs) between Singapore and developing countries and second, to investigate the risk allocation preferences in these ICJVs.

Design/methodology/approach
A questionnaire survey was conducted and responses were received from 38 firms that had participated in ICJVs with developing countries. A risk criticality (RC) index was adopted to evaluate the criticality of each risk.

Findings
The survey results reported “political instability” as the most critical risk and market-level risks were less critical than country and project-level risks. Additionally, the results showed agreement on the risk ranking between building and infrastructure ICJVs, despite significant differences in the criticalities of five risks. Furthermore, five risks were preferably allocated to host and foreign partners, respectively, while 13 risks could be shared among partners.

Research limitations/implications
First, due to the sample size, one should be cautious when interpreting and generalizing the results. Second, the RC index proposed in this study was subjective as it was influenced by the individual experience and risk attitude of the respondents. Also, the RC values were calculated without considering the weights of the respondents. Lastly, the questionnaire survey, which has been widely used in identifying risk allocation preferences, may not identify the insights of practitioners into the risk allocation practices.

Practical implications
This study provides a clear understanding of the risks associated with forming ICJVs with developing countries and the preferred risk allocation. Although, this study is focused on the risks faced by the Singapore-developing country ICJVs, the identification of the potential risks allows companies from other countries to customize their risk profile and assess the risks before they form ICJVs with developing countries.

Originality/value
As few studies have explored the risk allocation preferences in ICJVs, this study expands the literature and provides practitioners with important information for preparing joint venture contracts or agreements. Thus, this study can contribute to the literature relating to ICJVs.