bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of the habitat- and season-independent increase in fungal biomass induced by the invasive giant goldenrod and its impact on the fungivorous nematode community
Authors: Harkes Paula , van Heumen Lisa J.M. , van den Elsen Sven J.J. , Mooijman Paul J.W. , Quist Casper W. , Vervoort Mariëtte T. W. , Gort Gerrit , Holterman Martijn H.M. , van Steenbrugge Joris J.M. , Helder Johannes 
Published: September 2020

AbstractOutside its native range, the invasive plant species giant goldenrod (Solidago gigantea) has been shown to increase belowground fungal biomass. This non-obvious effect is poorly characterized; we don’t know whether it is plant developmental stage-dependent, which fractions of the fungal community are affected, and whether it is reflected in the next trophic level. To address the questions, fungal assemblages in soil samples collected from invaded and non-invaded plots in two soil types were compared. Whereas ergosterol as a marker for fungal biomass demonstrated a significant increase in fungal biomass, specific qPCR assays did not point at a quantitative shift. MiSeq-based characterization of the belowground effects of giant goldenrod revealed a local increase of mainly Cladosporiaceae and Glomeraceae. This asymmetric boost in the fungal community was reflected in a specific shift in the fungivorous nematode community. Our findings provide insight in the potential impact of invasive plants on local fungal communities.
A torsion-based rheometer for measuring viscoelastic material properties
Authors: Jutzeler Elise , Asp Merrill , Kerr Katherine , Song Dawei , Patteson Alison 
Published: September 2020

ABSTRACTRheology and the study of viscoelastic materials is an integral part of engineering and the study of biophysical systems however the cost of a rheometer is only feasible for colleges, universities and research laboratories. Even if a rheometer can be purchased it is bulky and delicately calibrated limiting its usefulness to the laboratory itself. The design presented here is less than a tenth of the cost of a professional rheometer and portable making it the ideal solution for high school students as a way to introduce viscoelasticity at a younger age as well as for use in the field for obtaining preliminary rheological data.
Mean-field modeling of brain-scale dynamics for the evaluation of EEG source-space networks
Authors: Allouch Sahar , Yochum Maxime , Kabbara Aya , Duprez Joan , Khalil Mohamad , Wendling Fabrice , Hassan Mahmoud , Modolo Julien 
Published: September 2020

AbstractUnderstanding the dynamics of brain-scale functional networks at rest and during cognitive tasks is the subject of intense research efforts to unveil fundamental principles of brain functions. To estimate these large-scale brain networks, the emergent method called “electroencephalography (EEG) source connectivity” has generated increasing interest in the network neuroscience community, due to its ability to identify cortical brain networks with satisfactory spatio-temporal resolution, while reducing mixing and volume conduction effects. However, no consensus has been reached yet regarding a unified EEG source connectivity pipeline, and several methodological issues have to be carefully accounted for to avoid pitfalls. Thus, a validation toolbox that provides flexible “ground truth” models is needed for an objective methods/parameters evaluation and, thereby an optimization of the EEG source connectivity pipeline. In this paper, we show how a recently developed large-scale model of brain-scale activity, named COALIA, can provide to some extent such ground truth by providing realistic simulations of source-level and scalp-level activity. Using a bottom-up approach, the model bridges cortical micro-circuitry and large-scale network dynamics. Here, we provide an example of the potential use of COALIA to analyze, in the context of epileptiform activity, the effect of three key factors involved in the “EEG source connectivity” pipeline: (i) EEG sensors density, (ii) algorithm used to solve the inverse problem, and (iii) functional connectivity measure. Results showed that a high electrode density (at least 64 channels) is required to accurately estimate cortical networks. Regarding the inverse solution/connectivity measure combination, the best performance at high electrode density was obtained using the weighted minimum norm estimate (wMNE) combined with the weighted phase lag index (wPLI). Although those results are specific to the considered aforementioned context (epileptiform activity), we believe that this model-based approach can be successfully applied to other experimental questions/contexts. We aim at presenting a proof-of-concept of the interest of COALIA in the network neuroscience field, and its potential use in optimizing the EEG source-space network estimation pipeline.
Mimicry is associated with procedural learning, not social bonding, neural systems in autism
Authors: Tunçgenç Bahar , Koch Carolyn , Herstic Amira , Eigsti Inge-Marie , Mostofsky Stewart 
Published: September 2020

AbstractMimicry facilitates social bonding throughout the lifespan. Mimicry impairments in autism spectrum conditions (ASC) are widely reported, including differentiation of the brain networks associated with its social bonding and learning functions. This study examined associations between volumes of brain regions associated withsocial bondingversusprocedural skill learning, and mimicry of gestures during a naturalistic interaction in ASC and neurotypical (NT) children. Consistent with predictions, results revealed reduced mimicry in ASC relative to the NT children. Mimicry frequency was negatively associated with autism symptom severity. Mimicry was predicted predominantly by the volume of procedural skill learning regions in ASC, and by bonding regions in NT. Further, bonding regions contributed significantly less to mimicry in ASC than in NT, while the contribution of learning regions was not different across groups. These findings suggest that associating mimicry with skill learning, rather than social bonding, may partially explain observed communication difficulties in ASC.
Wing Geometry and Genetic Analyses Reveal Contrasting Spatial Structures between Male and FemaleAedes aegyptiPopulations in Metropolitan Manila, Philippines
Authors: Carvajal Thaddeus M. , Amalin Divina M. , Watanabe Kozo 
Published: September 2020

AbstractBackgroundMany important arboviral diseases (e.g. dengue, chikungunya) are transmitted by the bite of a female mosquito vector,Aedes aegypti. Hence, the population genetic structure of the mosquito has been studied in order to understand its role as an efficient vector. Several studies utilized an integrative approach; to combine genetic and phenotypic data to determine the population structure ofAe. aegyptibut these studies have only focused on female populations. To address this particular gap, our study compared the population variability and structuring between male and femaleAe. aegyptipopulations using phenotypic (wing geometry) and genetic (microsatellites) data from a highly-urbanized and dengue-endemic region of the Philippines, Metropolitan Manila.MethodsFive mosquito populations comprised of female (n = 137) and male (n = 49) adultAe. aegyptimosquitoes were used in this study. All mosquito individuals underwent geometric morphometric (26 landmarks), and genetic (11 microsatellite loci) analyses.ResultsResults revealed thatFSTestimates (genetic) were 0.055 and 0.009 whileQSTestimates (phenotypic) were 0.318 and 0.309 in in male and female populations, respectively. Wing shape variation plots showed that male populations were distinctly separated from each other while female populations overlapped. Similarly, discriminant analysis of principal components using genetic data revealed that male populations were also distinctly separated from each other while female populations showed near-overlapping populations. Genetic and phenetic dendrograms showed the formation of two groups in male populations but no groups in female populations. Further analysis indicated a significant correlation(r= 0.68,p= 0.02) between the genetic and phenetic distances of male populations. Bayesian analysis using genetic data also detected multiple clusters in male (K = 3) and female (K = 2) populations, while no clusters were detected using the phenotypic data from both sexes.ConclusionsOur results revealed contrasting phenotypic and genetic patterns between male and femaleAe. aegypti, indicating that male populations were more spatially structured than female populations. Although genetic markers demonstrated higher sensitivity in detecting population structures than phenotypic markers, correlating patterns of population structure were still observed between the two markers.
Scarcity of scale-free topology is universal across biochemical networks
Authors: Smith Harrison B. , Kim Hyunju , Walker Sara I. 
Published: September 2020

AbstractBiochemical reactions underlie all living processes. Like many biological and technological systems, their complex web of interactions is difficult to fully capture and quantify with simple mathematical objects. Nonetheless, a huge volume of research has suggested many real-world biological and technological systems – including biochemical systems – can be described rather simply as ‘scale-free’ networks, characterized by a power-law degree distribution. More recently, rigorous statistical analyses across a variety of systems have upended this view, suggesting truly scale-free networks may be rare. We provide a first application of these newer methods across two distinct levels of biological organization: analyzing a large ensemble of biochemical networks generated from the reactions encoded in 785 ecosystem-level metagenomes and 1082 individual-level genomes (representing all three domains of life). Our results confirm only a few percent of individual and ecosystem-level biochemical networks meet the criteria necessary to be anything more than super-weakly scale-free. Leveraging the simultaneous analysis of the multiple coarse-grained projections of biochemistry, we perform distinguishability tests across properties of individual and ecosystem-level biochemical networks to determine whether or not they share common structure, indicative of common generative mechanisms across levels. Our results indicate there is no sharp transition in the organization of biochemistry across distinct levels of the biological hierarchy - a result that holds across different network projections. This suggests the existence of common organizing principles operating across different levels of organization in biochemical networks, independent of the project chosen.Author SummaryFully characterizing living systems requires rigorous analysis of the complex webs of interactions governing living processes. Here we apply statistical approaches to analyze a large data set of biochemical networks across two levels of organization: individuals and ecosystems. We find that independent of level of organization, the standard ‘scale-free’ model is not a good description of the data. Interestingly, there is no sharp transition in the shape of degree distributions for biochemical networks when comparing those of individuals to ecosystems. This suggests the existence of common organizing principles operating across different levels of biochemical organization that are revealed across different network projections.
Privacy preserving storage of sequenced genomic data
Authors: Hekel Rastislav , Budis Jaroslav , Kucharik Marcel , Radvanszky Jan , Pös Zuzana , Szemes Tomas 
Published: September 2020

AbstractIntroductionCurrent and future applications of genomic data may raise ethical and privacy concerns. Processing and storing these data introduces a risk of abuse by a potential adversary since a human genome contains sensitive personal information. For this reason, we developed a privacy preserving method, called Varlock, for secure storage of sequenced genomic data.Materials and methodsWe used a public set of population allele frequencies to mask personal alleles detected in genomic reads. Each personal allele described by the public set is masked by a randomly selected population allele with respect to its frequency. Masked alleles are preserved in an encrypted confidential file that can be shared, in whole or in part, using public-key cryptography.ResultsOur method masked personal variants and introduced new variants detected in a personal masked genome. Alternative alleles with lower population frequency were masked and introduced more often. We performed a joint PCA analysis of personal and masked VCFs, showing that the VCFs between the two groups can not be trivially mapped. Moreover, the method is reversible and personal alleles can be unmasked in specific genomic regions on demand.ConclusionOur method masks personal alleles within genomic reads while preserving valuable non-sensitive properties of sequenced DNA fragments for further research. Personal alleles may be restored in desired genomic regions and shared with patients, clinics, and researchers. We suggest that the method can provide an additional layer of security for storing and sharing the raw aligned reads.
Recessive effects in cancer predisposition exposed by genome-wide and proteome-wide association studies
Authors: Brandes Nadav , Linial Nathan , Linial Michal 
Published: September 2020

AbstractThe characterization of germline genetic variation affecting cancer risk, known as cancer predisposition, is fundamental to preventive and personalized medicine. Current attempts to detect cancer predisposition genomic regions are typically based on small-scale familial studies or genome-wide association studies (GWAS) over dedicated case-control cohorts. In this study, we utilized the UK Biobank as a large-scale prospective cohort to conduct a comprehensive analysis of cancer predisposition using both GWAS and proteome-wide association study (PWAS), a method that highlights genetic associations mediated by functional alterations to protein-coding genes. We discovered 137 unique genomic loci implicated with cancer risk in the white British population across nine cancer types and pan-cancer. While most of these genomic regions are supported by external evidence, our results highlight novel loci as well. We performed a comparative analysis of cancer predisposition between cancer types, finding that most of the implicated regions are cancer-type specific. We further analyzed the role of recessive genetic effects in cancer predisposition. We found that 30 of the 137 cancer regions were recovered only by a recessive model, highlighting the importance of recessive inheritance outside of familial studies. Finally, we show that many of the cancer associations exert substantial cancer risk in the studied cohort, suggesting their clinical relevance.
A DNA Methylation Reader–Chaperone Regulator–Transcription Factor Complex Activates OsHKT1;5 Expression during Salinity Stress
Authors: Wang Jie , Nan Nan , Li Ning , Liu Yutong , Wang Tian-Jing , Hwang Inhwan , Liu Bao , Xu Zheng-Yi 
Published: September 2020

Abstract
Irrigated lands are increasingly salinized, which adversely affects agricultural productivity. To respond to high sodium (Na+) concentrations, plants harbor multiple Na+ transport systems. Rice (Oryza sativa) HIGH-AFFINITY POTASSIUM (K+) TRANSPORTER1;5 (OsHKT1;5), a Na+-selective transporter, maintains K+/Na+ homeostasis under salt stress. However, the mechanism regulating OsHKT1;5 expression remains unknown. Here, we present evidence that a protein complex consisting of rice BCL-2-ASSOCIATED ATHANOGENE4 (OsBAG4), OsMYB106, and OsSUVH7 regulates OsHKT1;5 expression in response to salt stress. We isolated a salt stress–sensitive mutant, osbag4-1, that showed significantly reduced OsHKT1;5 expression and reduced K+ and elevated Na+ levels in shoots. Using comparative interactomics, we isolate0d two OsBAG4-interacting proteins, OsMYB106 (a MYB transcription factor) and OsSUVH7 (a DNA methylation reader), that were crucial for OsHKT1;5 expression. OsMYB106 and OsSUVH7 bound to the MYB binding cis-element (MYBE) and the miniature inverted-repeat transposable element (MITE) upstream of the MYBE, respectively, in the OsHKT1;5 promoter. OsBAG4 functioned as a bridge between OsSUVH7 and OsMYB106 to facilitate OsMYB106 binding to the consensus MYBE in the OsHKT1;5 promoter, thereby activating the OsHKT1;5 expression. Elimination of the MITE or knockout of OsMYB106 or OsSUVH7 decreased OsHKT1;5 expression and increased salt sensitivity. Our findings reveal a transcriptional complex, consisting of a DNA methylation reader, a chaperone regulator, and a transcription factor, that collaboratively regulate OsHKT1;5 expression during salinity stress.
Vascular Bundles Mediate Systemic Reactive Oxygen Signaling during Light Stress
Authors: Zandalinas Sara I. , Fichman Yosef , Mittler Ron 
Published: September 2020

Abstract
Systemic signaling and systemic acquired acclimation (SAA) are essential for plant survival during episodes of environmental stress. Recent studies highlighted a key role for reactive oxygen species (ROS) signaling in mediating systemic responses and SAA during light stress in Arabidopsis (Arabidopsis thaliana). These studies further identified the RESPIRATORY BURST OXIDASE HOMOLOG D (RBOHD) protein as a key player in mediating rapid systemic ROS responses. Here, we report that tissue-specific expression of RBOHD in phloem or xylem parenchyma cells of the rbohD mutant restores systemic ROS signaling, systemic stress-response transcript expression, and SAA to a local treatment of light stress. We further demonstrate that RBOHD and RBOHF are both required for local and systemic ROS signaling at the vascular bundles of Arabidopsis. Taken together, our findings highlight a key role for RBOHD-driven ROS production at the vascular bundles of Arabidopsis in mediating light stress–induced systemic signaling and SAA. In addition, they suggest that the integration of ROS, calcium, electric, and hydraulic signals, during systemic signaling, occurs at the vascular bundles.
Trust me, I am the social media manager! Public sector communication's trust work in municipality social media channels
Authors: Lovari Alessandro , Materassi Letizia 
Published: September 2020

PurposeThe study aims at investigating the role of social media managers (SMMs) as trust mediators and access points in the context of local government. Little empirical work is devoted to this issue and the purpose of the paper is to provide a better understanding of the trust work routines.Design/methodology/approachThis paper presents the results of a pilot study. Authors adopt a qualitative approach, using semi-structured in-depth interviews with a selected panel of PR professionals, managing social media channels on behalf of eleven Italian municipalities.FindingsSMMs are aware of having a key-role in nurturing trust, and trust is a design value of their work. This article shows many “signs of trust” that SMMs perceive as important to foster trust in the digital environment and in relations with citizens within the municipal context.Research limitations/implicationsThis pilot study draws upon a small sample and a single country-focus.Practical implicationsThe detected “signs of trust” can be useful for further investigations and provide SMMs with practical suggestions to integrate into their strategies.Originality/valueTwo main fields – the use of social media and the impact on public sector communication and the institution/citizen trust relationships – are connected to the specific role played by SMMs: an emerging figure as yet little analyzed by scholars.
Smart factories for single-family wooden houses – a practitioner’s perspective
Authors: Vestin Alexander , Säfsten Kristina , Löfving Malin 
Published: September 2020

PurposeThe meaning of Industry 4.0 has started to be outlined for the construction industry, but there is still limited knowledge on the implications for the single-family wooden house building industry. The purpose of this paper is to expand the understanding of what the fourth industrial revolution implies for the single-family wooden house industry. The paper contributes with practitioners’ view of the content and meaning of a smart single-family wooden house factory.Design/methodology/approachAn exploratory multiple case study was carried out at two Swedish single-family wooden house builders, combined with a traditional literature review.FindingsAs a result of a multiple case studies, the content and meaning of a smart single-family wooden house factory was elaborated on. In total, 15 components of a smart single-family wooden house factory were identified, of which 8 corresponded to the components of Industry 4.0 as described in other sectors.Research limitations/implicationsThe study can be expanded to also include multi-family wooden house builders and other branches of the offsite wooden building industry.Practical implicationsManagers in the house-building industry who want to improve and strive for a smart single-family wooden house factory can learn from this study, get an insight of what other companies consider as important and how it relates to Industry 4.0.Originality/valueTo the best of the authors’ knowledge, this study is a first attempt to understand what Industry 4.0 mean and how it can be accomplished for the single-family wooden house offsite manufacturing industry.
An extended car-following model integrating average speed and electronic throttle dynamics of multiple preceding vehicles
Authors: Li Shihao , Cheng Rongjun , Ge Hongxia , Zheng Pengjun 
Published: September 2020

Purpose
The purpose of this study is to explore the influence of the electronic throttle (ET) dynamics and the average speed of multiple preceding vehicles on the stability of traffic flow.

Design/methodology/approach
An extended car-following model integrating the ET dynamics and the average speed of multiple preceding vehicles is presented in this paper. The novel model’s stability conditions are obtained by using the thought of control theory, and the modified Korteweg–de Vries equation is inferred in terms of the nonlinear analysis method. In addition, some simulation experiments are implemented to explore the properties of traffic flow, and the results of these experiments confirm the correctness of theoretical analysis.

Findings
In view of the results of theoretical analysis and numerical simulation, traffic flow will become more stable when the average speed and ET dynamics of multiple preceding vehicles are considered, and the stability of traffic flow will also be enhanced by increasing the number of preceding vehicles considered.

Research limitations/implications
This study leaves the factors such as the mixed traffic flow, the multilane and so on out of account in real road environment, which more or less influences the traffic flow’s stability, so the real traffic environment is not fully reflected.

Originality/value
There is little research integrating ET dynamics and the average velocity of multiple preceding vehicles to study the properties of traffic flow. The enhanced model constructed in this study can better reflect the real traffic, which can also give some theoretical reference for the development of connected and autonomous vehicles.