bluuebunny/crossref_metadata_2025_split huggingface dataset:
Outer Membrane Vesicles Mediated Horizontal Transfer of an Aerobic Denitrification Gene betweenEscherichia coli
Authors: Luo Yang , Miao Jiahui , Qiao Weichuan 
Published: November 2019

AbstractBacterial genetic material can be horizontally transferred between microorganisms via outer membrane vesicles (OMVs) released by bacteria. Up to now, the application of vesicle-mediated horizontal transfer of “degrading genes” in environmental remediation has not been reported. In this study, thenirSgene from an aerobic denitrification bacterium,Pseudomonas stutzeri, was enclosed in a pET28a plasmid, transformed intoEscherichia coli(E. coli) DH5α and expressed inE. coliBL21. TheE. coliDH5α released OMVs containing the recombination plasmid pET28a–nirS. Moreover, the amount of released OMVs-protein and DNA in OMVs increase as heavy metal concentrations and temperature increased. When compared with the free pET28a–nirSplasmid’s inability to transform,nirSin OMVs could be transferred intoE. coliBL21 with the transformation frequency of 2.76×106CFU/g when the dosage of OMVs was 200 µg under natural conditions, andnirScould express successfully in recipient bacteria. Furthermore, the recipient bacteria that received OMVs could produce 18.16 U ml-1activity of nitrite reductase. Vesicle-mediated HGT of aerobic denitrification genes provides a novel bioaugmentation technology of nitrogen removal.ImportancePrevious studies have reported that bacterial genetic material can be horizontally transferred between microorganisms via outer membrane vesicles(OMVs) released by bacteria. However, the application of vesicle-mediated horizontal transfer of “degrading genes” in environmental remediation has not been reported. In this study, we found that OMVs could mediate horizontal transfer of pET28a–nirSplasmid between E. coli under natural condition. The transformation frequency reached to 2.76×106, which was higher than that of the free plasmid. Vesicle-mediated HGT of aerobic denitrification genes provides a novel bioaugmentation technology of nitrogen removal.
Hippocampus has lower oxygenation and weaker control of brain blood flow than cortex, due to microvascular differences
Authors: Shaw K. , Bell L. , Boyd K. , Grijseels D.M. , Clarke D. , Bonnar O. , Crombag H.S. , Hall C.N. 
Published: November 2019

AbstractThe hippocampus is essential for spatial and episodic memory but is damaged early in Alzheimer’s disease and is very sensitive to hypoxia. Understanding how it regulates its oxygen supply is therefore key for designing interventions to preserve its function. However, studies of neurovascular function in the hippocampusin vivohave been limited by its relative inaccessibility. Here we compared hippocampal and visual cortical neurovascular function in awake mice, using two photon imaging of individual neurons and vessels and measures of regional blood flow and haemoglobin oxygenation. We show that blood flow, blood oxygenation and neurovascular coupling were decreased in the hippocampus compared to neocortex, because of differences in both the vascular network and pericyte and endothelial cell function. Modelling oxygen diffusion indicates that these features of the hippocampal vasculature could explain its sensitivity to damage during neurological conditions, including Alzheimer’s disease, where the brain’s energy supply is decreased.
Mendelian randomisation for mediation analysis: current methods and challenges for implementation
Authors: Carter Alice R , Sanderson Eleanor , Hammerton Gemma , Richmond Rebecca C , Smith George Davey , Heron Jon , Taylor Amy E , Davies Neil M , Howe Laura D 
Published: November 2019

AbstractMediation analysis seeks to explain the pathway(s) through which an exposure affects an outcome. Mediation analysis experiences a number of methodological difficulties, including bias due to confounding and measurement error. Mendelian randomisation (MR) can be used to improve causal inference for mediation analysis. We describe two approaches that can be used for estimating mediation analysis with MR: multivariable Mendelian randomisation (MVMR) and two-step Mendelian randomisation. We outline the approaches and provide code to demonstrate how they can be used in mediation analysis. We review issues that can affect analyses, including confounding, measurement error, weak instrument bias, and analysis of multiple mediators. Description of the methods is supplemented by simulated and real data examples. Although Mendelian randomisation relies on large sample sizes and strong assumptions, such as having strong instruments and no horizontally pleiotropic pathways, our examples demonstrate that it is unlikely to be affected by confounders of the exposure or mediator and the outcome, reverse causality and non-differential measurement error of the exposure or mediator. Both MVMR and two-step MR can be implemented in both individual-level MR and summary data MR, and can improve causal inference in mediation analysis.
PCA-based source-space contrast maps reveal psychologically meaningful individual differences in continuous MEG activity
Authors: Heinilä Erkka , Hyvärinen Aapo , Ristaniemi Tapani , Parkkonen Lauri , Parviainen Tiina 
Published: November 2019

AbstractWithin the field of neuroimaging, there has been an increasing trend towards studying brain activity in naturalistic conditions, and it is possible to robustly estimate networks of on-going oscillatory activity in the brain. However, not many studies have focused on differences between individuals in on-going brain activity that would be associable to psychological or behavioral characteristics. Existing standard methods can perform well at single-participant level, but generalizing the methodology across many participants is challenging due to individual differences of brains. As an example of a clinically relevant, naturalistic condition we consider here mindfulness. Trait mindfulness, as well as a mindfulness-based intervention cultivating focused attention, is often associated with benefits for psychological health. Therefore, the manner in which the brain engages in focused attention vs. mind wandering is likely to associate with individual differences in psycho–behavioral tendencies.We recorded MEG from 29 participants both in a state of focused attention and in a state of simulated mind wandering. We used Principal Component Analysis to decompose spatial average activation maps of focused attention contrasted with two different mind wandering states. The first principal component, which reflected differential engagement of bilateral parietal areas during focused attention vs. mind wandering, was associated with behavioral characteristics of inhibition, anxiousness and depression, as measured by standard questionnaires. We demonstrated that such decomposition of time-averaged contrast maps can overcome some of the challenges in methods based on concatenated data, especially from the perspective of behaviorally and clinically relevant characteristics in the ongoing brain oscillatory activity.HighlightsWe present a specific method to analyse/establish associations between brain oscillations and behavioral characteristics.We found that activity levels in parietal areas during mind wandering compared to focused attention were associated with the behavioral trait of inhibition and anxiety.
gplas: a comprehensive tool for plasmid analysis using short-read graphs
Authors: Arredondo-Alonso Sergio , Bootsma Martin , Hein Yaïr , Rogers Malbert R.C. , Corander Jukka , Willems Rob JL , Schürch Anita C. 
Published: November 2019

ABSTRACTSummaryPlasmids can horizontally transmit genetic traits, enabling rapid bacterial adaptation to new environments and hosts. Short-read whole-genome sequencing data is often applied to large-scale bacterial comparative genomics projects but the reconstruction of plasmids from these data is facing severe limitations, such as the inability to distinguish plasmids from each other in a bacterial genome. We developed gplas, a new approach to reliably separate plasmid contigs into discrete components using sequence composition, coverage, assembly graph information and clustering based on a pruned network of plasmid unitigs. Gplas facilitates the analysis of large numbers of bacterial isolates and allows a detailed analysis of plasmid epidemiology based solely on short read sequence data.Availability and implementationGplas is written in R, Bash and uses a Snakemake pipeline as a workflow management system. Gplas is available under the GNU General Public License v3.0 at https://gitlab.com/sirarredondo/gplas.gitContacta.c.schurch@umcutrecht.nl
Integrated effect of plant growth regulators with boron sources on some biological parameters of sugar beet
Authors: Qotob Marwa A. , Nasef Mostafa A. , Elhakim Heba K. A. , Shaker Olfat G. , Habashy Nader R. , Abdelhamid Ismail A. 
Published: November 2019

ABSTRACTAny improvement in agricultural systems that results higher production aimed to reduce negative environmental impacts and enhance sustainability plant growth regulators (PGRs) such as gibberellin have similar physiological and biological effects to those of plant hormones, and therefore used widely in agriculture to minimize unwanted shoot growth without lowering plant productivity.An experimental field was conducted at Giza Experimental Station Egypt, on sugar beet plants (Beta vulgarisL.var.Sara poly) with some plant growth regulators (gibberellin and proline) foliar application at three rates of zero (control), 100 and 200 mg l−1and boron sources (Boric acid and B-NPs) with 75% of macro-nutrients from full dose.The main target of this study to evaluate another plant growth regulator source like proline which is safer than gibberellin for maximizing sugar beet biological parameters to reduce the gap between sugar consumption and production in presence of boron sources.Data showed that the foliar applications of gibberellin (GA3) at rate 100 mg l−1and proline at 200 mg l−1were found to be the more effective without significant differences for plant growth, productivity and quality may be due to increased N use efficiency, especially at sub-optimal macro nutrient fertilizers. Regard to boron sources, B-NPs had positive effect on all biological parameters under study due to sugar transport, cell membrane synthesis, nitrogen fixation, respiration, carbohydrate metabolisms, root growth, functional characteristics and development.
Reflections on interdisciplinary critical intellectual capital accounting research
Authors: Dumay John , Guthrie James 
Published: November 2019

Purpose
In 2001, the Accounting, Auditing & Accountability Journal (AAAJ) published a special issue entitled “Managing, measuring and reporting intellectual capital for the new millennium”. After 20 years, we revisit the eight articles in this special issue to trace early developments in interdisciplinary intellectual capital (IC) accounting research, link these developments to the current state of play, and set out an agenda for future research. The paper aims to discuss this issue.

Design/methodology/approach
This paper, written reflectively, includes an impact assessment of the articles using citation analysis and a thematic framing of the prominent issues they discussed. We critically reflect on the status of these eight foundational papers after 20 years, before presenting propositions for a multidisciplinary IC research future.

Findings
We find that IC research needs to extend beyond organisational boundaries to help improve human rights, human dignity and the human condition as part of the wider interdisciplinary accounting project. We argue that fifth stage IC research can assist because it explores beyond organisational boundaries and helps address the wicked problems of the world.

Research limitations/implications
This paper only investigates the themes found in the AAAJ special issue. However, the implications for researchers are intended to be transformational because, to go forward and help resolve the material issues facing society and the planet, researchers need to move from being observers to participants.

Originality/value
We argue that IC researchers must embrace both interdisciplinary and multidisciplinary IC research. This requires IC researchers to reflect on what they are trying to achieve and which issues facing the planet are material.
Does a creative identity encourage innovative behaviour? Evidence from knowledge-intensive IT service firms
Authors: Uddin Md. Aftab , Priyankara H.P. Rasika , Mahmood Monowar 
Published: November 2019

PurposeThe purpose of this paper is to investigate the influence of an employee’s personal creative identity on their innovation behaviour in knowledge-intensive information technology (IT) service provider firms. It further investigates the mediating role of an employee’s creative process engagement (CPE) and the moderating effects of the organizational creative climate on creative identity-innovative behaviour (IB) relationships.Design/methodology/approachThis study follows a quantitative method. Using a multi-item survey instrument, a total of 316 questionnaires were collected from the employees of IT service provider firms in Chittagong, Bangladesh. The collected data were analysed using structural equation modelling, factor analysis and path analysis to test the hypotheses and to assess the moderating and mediating effects of the variables.FindingsThe results revealed the significant influence of an employee’s creative personal identity (CPI) on their IB. The mediation analysis revealed that CPE mediates the association between a CPI and IB. The study also found a significant moderating effect of a creative organizational climate between a CPI and CPE.Research limitations/implicationsBased on the premise of the interactionist approach of creativity and role identity theory, this study contributes to the creativity and innovation literature by providing empirical support for the relationship between a personal creative identity, organizational creative culture, CPE and IB in IT service organizations.Originality/valueThis study adopts a distinct model comprising four different variables to investigate an employee’s IB from a multi-level perspective, i.e., a creative identity and CPE at the individual level and a creative climate and IB at the organizational level. This integrated model using predictors from multiple levels supports the theoretical assumption that IB results from the interaction of individual and organizational level factors.
Globalization and innovation with Chinese characteristics: the case of the automotive industry
Authors: Petti Claudio , Spigarelli Francesca , Lv Ping , Biggeri Mario 
Published: November 2019

Purpose
The purpose of this paper is to analyze the internationalization of Chinese new global players through innovation-oriented Mergers and Acquisitions (M&As).

Design/methodology/approach
The paper combines the analysis of East-Asian and Chinese multinationals’ international expansion within international business (IB) and innovation domains, with the “latecomer” perspective. It is a conceptual contribution, based on the role of local institutions and firm’s absorptive capacity. A theoretical framework is developed, and further elucidated with two illustrative cases of Chinese M&As abroad in the automotive sector. Implications for theoretical development and practical application are then drawn.

Findings
Chinese firms’ M&As abroad have become one of the preferential modes of developing innovation capabilities. The success of these endeavors is argued to be the result of a combination of a strong push from government industrial policies, along with significant internal knowledge assimilation and transformation capabilities.

Originality/value
The paper extends IB literature integrating the latecomer firms’ perspective within a novel conceptual framework, which adds to the traditional resource-based arguments about incumbent MNEs asset and knowledge-seeking internationalization modes, as well as institutional and multi-dimensional absorptive capacity perspectives.
Study of chiroptical effects on the novel chiral photonic structure
Authors: Zara Chemseddine , Mezache Zinelabiddine , Benabdelaziz Fatiha 
Published: November 2019

PurposeThe purpose of this paper is to demonstrate a novel chiral photonic crystal with thin thickness and small unit cells via numerical calculations. The multi-band circular dichroism is found in a wide frequency range from 400 to 600 THz by studying the transmission properties.Design/methodology/approachTo investigate this chiral photonic structure, refection coefficients are analytically computed using finite element method. Numerical results are given, and physical properties are discussed, including the optical rotation, the circular dichroism and the absorption.FindingsThe results of this modeling and simulation under COMSOL multiphysics environment have led the authors to study the scattered parameters such as the coefficient of transmission (S21) and the coefficient of reflection (S11) for a 2D CPC nanostructure. The authors have also developed script under the Matlab environment which studies absorption and circular dichroism and ensure the existence of optical activity. According to the obtained results, the coefficient of transmission is proportional to the parameter of chirality.Originality/valueThe authors have designed a novel chiral photonic structure that exhibits larger circular dichroism. The CD spectrum has typically both positive and negative bands. The design principles defined in this work, which combine the concepts of the photonic crystal with the chiral structure (optical activity, circular dichroism and absorption), represent a model for simulation of the properties of a more complex chiral photonic structure. These results led to realization of novel circularly polarized devices in nanotechnologies.
The relative importance of local and regional processes to metapopulation dynamics
Authors: Dallas Tad A. , Saastamoinen Marjo , Schulz Torsti , Ovaskainen Otso 
Published: November 2019

AbstractMetapopulation dynamics – patch occupancy, colonization and extinction – are the result of complex processes at both local (e.g. environmental conditions) and regional (e.g. spatial arrangement of habitat patches) scales. A large body of work has focused on habitat patch area and connectivity (area‐isolation paradigm). However, these approaches often do not incorporate local environmental conditions or fully address how the spatial arrangement of habitat patches (and resulting connectivity) can influence metapopulation dynamics.Here, we utilize long‐term data on a classic metapopulation system – the Glanville fritillary butterfly occupying a set of dry meadows and pastures in the Åland islands – to investigate the relative roles of local environmental conditions, geographic space and connectivity in capturing patch occupancy, colonization and extinction. We defined connectivity using traditional measures as well as graph‐theoretic measures of centrality. Using boosted regression tree models, we find roughly comparable model performance among models trained on environmental conditions, geographic space or patch centrality.In models containing all of the covariates, we find strong and consistent evidence for the roles of resource abundance, longitude and centrality (i.e. connectivity) in predicting habitat patch occupancy and colonization, while patch centrality (connectivity) was relatively unimportant for predicting extinction. Relative variable importance did not change when geographic coordinates were not considered and models underwent spatially stratified cross‐validation.Together, this suggests that the combination of regional‐scale connectivity measures and local‐scale environmental conditions is important for predicting metapopulation dynamics and that a stronger integration of ideas from network theory may provide insight into metapopulation processes.
Plasma D‐Dimer Level and the Failure of Forearm Autologous Arteriovenous Fistula in Patients With End‐Stage Renal Disease
Authors: Du Jing , Kong Xianglei , Liang Liming , Chen Qinlan , Yin Lili , Xu Dongmei 
Published: November 2019

AbstractFailed autologous arteriovenous fistula (AVF) is a major issue in the creation of functional hemodialysis vascular access. To date, the relationship between D‐dimer and AVF failure is still uncertain. Hence, we conducted a retrospective cohort study to explore the patency rate of forearm AVFs and to clarify whether plasma D‐dimer level can predict the failure of AVFs. In this study, 290 ESRD patients (the mean age 54.1 ± 14.6 years, 63.8% of them were males) receiving forearm AVFs surgery were consecutively enrolled with a median follow‐up time of 34 months. Primary patency rates and risk factors associated with AVFs failure were explored by the Kaplan–Meier method or Cox proportional hazards model. Patients were divided into two groups based on the median level of D‐dimer (group 1 <1.1 mg/L and group 2 ≥1.1 mg/L). The Kaplan–Meier survival analysis demonstrated that the patency of AVF in group 1 was similar in group 2, which were 92.4% versus 88.9%, 84.8% versus 84.0%, 80.0% versus 79.2%, 76.7% versus 78.5%, and 76.7% versus 78.5% at 12, 24, 36, 48, and 60 months (Log‐rank test, P = 0.8), respectively. In the crude analysis, D‐dimer (per 1 mg/L increase) was independently associated with AVFs failure, with OR of 1.08 (95% CI, 1.02–1.15). However, after adjusting for potential confounders, the D‐dimer (per 1 mg/L increase) was not associated with the AVFs failure (OR = 1.06, 95% CI = 0.99–1.13). This study did not find that the plasma D‐dimer level can predict the failure of forearm AVFs.
Long‐read metabarcoding of the eukaryotic rDNA operon to phylogenetically and taxonomically resolve environmental diversity
Authors: Jamy Mahwash , Foster Rachel , Barbera Pierre , Czech Lucas , Kozlov Alexey , Stamatakis Alexandros , Bending Gary , Hilton Sally , Bass David , Burki Fabien 
Published: November 2019

AbstractHigh‐throughput DNA metabarcoding of amplicon sizes below 500 bp has revolutionized the analysis of environmental microbial diversity. However, these short regions contain limited phylogenetic signal, which makes it impractical to use environmental DNA in full phylogenetic inferences. This lesser phylogenetic resolution of short amplicons may be overcome by new long‐read sequencing technologies. To test this idea, we amplified soil DNA and used PacBio Circular Consensus Sequencing (CCS) to obtain an ~4500‐bp region spanning most of the eukaryotic small subunit (18S) and large subunit (28S) ribosomal DNA genes. We first treated the CCS reads with a novel curation workflow, generating 650 high‐quality operational taxonomic units (OTUs) containing the physically linked 18S and 28S regions. To assign taxonomy to these OTUs, we developed a phylogeny‐aware approach based on the 18S region that showed greater accuracy and sensitivity than similarity‐based methods. The taxonomically annotated OTUs were then combined with available 18S and 28S reference sequences to infer a well‐resolved phylogeny spanning all major groups of eukaryotes, allowing us to accurately derive the evolutionary origin of environmental diversity. A total of 1,019 sequences were included, of which a majority (58%) corresponded to the new long environmental OTUs. The long reads also allowed us to directly investigate the relationships among environmental sequences themselves, which represents a key advantage over the placement of short reads on a reference phylogeny. Together, our results show that long amplicons can be treated in a full phylogenetic framework to provide greater taxonomic resolution and a robust evolutionary perspective to environmental DNA.