bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogenetic analysis by SNP and development of SSR marker inPassiflora
Authors: Wu Yanyan , Tian Qinglan , Huang Weihua , Liu Jieyun , Xia Xiuzhong , Yang Xinghai , Mou Haifei 
Published: July 2020

AbstractInformation of thePassifloragenome is still very limited. Understand the evolutionary relationship between different species ofPassiflora, and develop a large number of SSR markers to provide a basis for the genetic improvement ofPassiflora. Applying restriction site associated DNA sequencing (RAD-Seq) technology, we studied the phylogeny, simple sequence repeat (SSR) and marker transferability of 10 accessions of 6 species ofPassiflora. Taking the partial assembly sequence of accessions P4 as the reference genome, we constructed the phylogenetic tree using the detected 46,451 high-quality single nucleotide polymorphisms (SNPs), showing that P6, P7, P8 and P9 were a single one while P5 and P10 were clustered together, and P1, P2, P3 and P4 were closer in genetic relationship. Using P8 as the reference genome, a total of 12,452 high-quality SNPs were used to construct phylogenetic tree. P3, P4, P7, P8, P9 and P10 were all single branch while P1 and P2 were clustered together, and P5 and P6 were clustered into one branch. A principal component analysis (PCA) revealed a similar population structure, which four cultivated passion fruits forming a tight cluster. A total of 2,614 SSRs were identified in the genome of 10Passifloraaccessions. The core motifs were AT, GA, AAG etc., 2-6 bases, 4-16 repeats, and 2,515 pairs of SSR primer were successfully developed.Tthe SSR transferability in cultivated passion fruits is the best. These results will contribute to the study of genomics and molecular genetics in passion fruit.
Systematic Engineering of Artificial Metalloenzymes for New-to-Nature Reactions
Authors: Vornholt Tobias , Christoffel Fadri , Pellizzoni Michela M. , Panke Sven , Ward Thomas R. , Jeschek Markus 
Published: July 2020

AbstractArtificial metalloenzymes (ArMs) catalyzing new-to-nature reactions under mild conditions could play an important role in the transition to a sustainable, circular economy. While ArMs have been created for a variety of bioorthogonal transformations, attempts at optimizing their performance by enzyme engineering have been case-specific and resulted only in modest improvements. To realize the full potential of ArMs, methods that enable the rapid discovery of highly active ArM variants for any reaction of interest are required. Here, we introduce a broadly applicable, automation-compatible ArM engineering platform, which relies on periplasmic compartmentalization inEscherichia colito rapidly and reliably identify improved ArM variants based on the biotin-streptavidin technology. We systematically assess 400 ArM mutants for five bioorthogonal transformations involving different metal cofactors, reaction mechanisms and substrate-product pairs, including novel ArMs for gold-catalyzed hydroamination and hydroarylation. The achieved activity enhancements of up to fifteen-fold over wild type highlight the potential of the systematic approach to ArM engineering. We further capitalize on the sequence-activity data to suggest and validate smart strategies for future screening campaigns. This systematic, multi-reaction study has important implications for the development of highly active ArMs for novel applications in biocatalysis and synthetic biology.
The genetic architecture underlying ecological adaptation in Atlantic herring is not consistent with the infinitesimal model
Authors: Han Fan , Jamsandekar Minal , Pettersson Mats E. , Su Leyi , Fuentes-Pardo Angela , Davis Brian , Bekkevold Dorte , Berg Florian , Cassini Michele , Dahle Geir , Farell Edward D. , Folkvord Arild , Andersson Leif 
Published: July 2020

AbstractAtlantic herring is widespread in North Atlantic and adjacent waters and is one of the most abundant vertebrates on earth. This species is well suited to explore genetic adaptation due to minute genetic differentiation at selectively neutral loci. Here we report hundreds of loci underlying ecological adaptation to different geographic areas and spawning conditions. Four of these represent megabase inversions confirmed by long read sequencing. The genetic architecture underlying ecological adaptation in the herring is in conflict with the infinitesimal model for complex traits because of the large shifts in allele frequencies at hundreds of loci under selection.
GAF is essential for zygotic genome activation and chromatin accessibility in the earlyDrosophilaembryo
Authors: Gaskill Marissa M. , Gibson Tyler J. , Larson Elizabeth D. , Harrison Melissa M. 
Published: July 2020

AbstractFollowing fertilization, the genomes of the germ cells are reprogrammed to form the totipotent embryo. Pioneer transcription factors are essential for remodeling the chromatin and driving the initial wave of zygotic gene expression. InDrosophila melanogaster, the pioneer factor Zelda is essential for development through this dramatic period of reprogramming, known as the maternal- to-zygotic transition (MZT). However, it was unknown whether additional pioneer factors were required for this transition. We identified an additional maternally encoded factor required for development through the MZT, GAGA Factor (GAF). GAF is necessary to activate widespread zygotic transcription and to remodel the chromatin accessibility landscape. We demonstrated that Zelda preferentially controls expression of the earliest transcribed genes, while genes expressed during widespread activation are predominantly dependent on GAF. Thus, progression through the MZT requires coordination of multiple pioneer-like factors, and we propose that as development proceeds control is gradually transferred from Zelda to GAF.
Dissociating breathlessness symptoms from mood in asthma
Authors: Harrison Olivia K. , Marlow Lucy , Finnegan Sarah , Ainsworth Ben , Pattinson Kyle T. S. 
Published: July 2020

AbstractAsthma is one of many chronic diseases in which discordance between objectively measured pathophysiology and symptom burden is well recognised. Understanding the influences on symptom burden beyond pathophysiology could improve our ability to treat symptoms. While co-morbidities such as anxiety and depression may play a role, the impact of this relationship with symptoms on our ability to perceive bodily sensations (termed ‘interoception’), or even our general and symptom-specific attention is not yet understood. Here we studied 63 individuals with asthma and 30 healthy controls. Alongside physiological tests including spirometry, bronchodilator responsiveness, expired nitric oxide and blood eosinophils, we collected self-reported questionnaires covering affective factors such as anxiety and depression, as well as asthma symptoms and asthma-related quality of life (individuals with asthma only). Participants additionally completed a breathing-related interoception task and two attention tasks designed to measure responsiveness to general temporal/spatial cues and specific asthma-related threatening words. We conducted an exploratory factor analysis across the questionnaires which gave rise to key components of ‘Mood’ and ‘Symptoms’, and compared these to physiological, interoceptive and attention measures. While no relationships were found between symptoms and physiological measures in asthma alone, negative mood was related to both decreased interoceptive metacognitive sensitivity (‘insight’ into interoceptive performance) and metacognitive bias (confidence in interoceptive decisions), as well as increased effects of spatial orienting cues in both asthma and controls. Furthermore, the relationship between the extent of symptoms and negative mood revealed potential sub-groups within asthma, with those who displayed the most severe symptoms without concurrent negative mood also demonstrating altered physiological, interoceptive and attention measures. Our findings are a step towards understanding how both symptoms and mood are related to our ability to interpret bodily symptoms, and to explore how the balance between mood and symptoms may help us understand the heterogeneity in conditions such as asthma.
The planning horizon for movement sequences
Authors: Ariani Giacomo , Kordjazi Neda , Pruszynski J. Andrew , Diedrichsen Jörn 
Published: July 2020

AbstractWhen performing a long chain of actions in rapid sequence, future movements need to be planned concurrently with ongoing action. However, how far ahead we plan, and whether this ability improves with practice, is currently unknown. Here we designed an experiment in which healthy volunteers produced sequences of 14 finger presses quickly and accurately on a keyboard in response to numerical stimuli. On every trial, participants were only shown a fixed number of stimuli ahead of the current keypress. The size of this viewing window varied between 1 (next digit revealed with the pressing of the current key) and 14 (full view of the sequence). Participants practiced the task for five days and their performance was continuously assessed on random sequences. Our results indicate that participants used the available visual information to plan multiple actions into the future, but that the planning horizon was limited: receiving information about more than 3 movements ahead did not result in faster sequence production. Over the course of practice, we found larger performance improvements for larger viewing windows and an expansion of the planning horizon. These findings suggest that the ability to plan future responses during ongoing movement constitutes an important aspect of skillful movement. Based on the results, we propose a framework to investigate the neuronal processes underlying simultaneous planning and execution.Significance StatementAlthough skill learning has typically focused on the training of specific movement sequences, practice improves performance even for random sequences. Here we hypothesize that a fundamental aspect of skilled sequential behavior is the ability to plan multiple actions into the future, both before and during execution. By controlling the amount of visual information available for motor planning, we show that people plan at least three movements beyond current action and that this planning horizon expands with practice. Our findings suggest that coordinating ongoing movement and planning of future actions is an essential component of skilled sequential behavior and offer testable predictions for the neural implementation of online motor planning.
Quantitative proteomics reveals the protective effects of ESD against osteoarthritis via attenuating inflammation and modulating immune response
Authors: Hao Ying , Wu Yang , Wang Shanglong , Wang Chungguo , Qu Sihao , Li Li , Yu Guohua , Liu Zimin , Zhao Zhen , Fan Pengcheng , Zhang Zengliang , Shi Yuanyuan 
Published: July 2020

AbstractEpimedium, Salvia miltiorrhiza, andDioscorea nipponicaMakino (ESD) have been combined to treat osteoarthritis (OA) for a long time. In this study we used quantitative proteomics to find the protective effects of ESD against OA and possible mechanism. After papain-induced rats’ OA model established ESD was intragastrically administrated to rats for four weeks. Label-free quantitative proteomics was used to screen the comprehensive protein profiling changes in both OA and ESD groups. After stringent filtering, 62 proteins were found to be significantly up-regulated and 208 proteins were down-regulated in OA model compared with sham-operated control. Functional analysis revealed that these OA up-regulated proteins were enriched in the activation of humoral immunity response, complement activation, leukocyte mediated immunity, acute inflammatory, endocytosis regulation, and proteolysis regulation. ESD partially recovered the protein profiling changes in OA model. The effects of ESD were also assessed by measurement of behavioral activity and pathologic changes in the joints. ESD showed protective effects in suppressing inflammation, releasing joint pain, and attenuating cartilage degradation. Our study presented that ESD as a potential candidate to alleviate OA damage by reducing inflammation and modulating of immune system.
Graphein - a Python Library for Geometric Deep Learning and Network Analysis on Protein Structures and Interaction Networks
Authors: Jamasb Arian R. , Viñas Ramon , Ma Eric J. , Harris Charlie , Huang Kexin , Hall Dominic , Lió Pietro , Blundell Tom L. 
Published: July 2020

AbstractGeometric deep learning has well-motivated applications in the context of biology, a domain where relational structure in datasets can be meaningfully leveraged. Currently, efforts in both geometric deep learning and, more broadly, deep learning applied to biomolecular tasks have been hampered by a scarcity of appropriate datasets accessible to domain specialists and machine learning researchers alike. However, there has been little exploration of how to best to integrate and construct geometric representations of these datatypes. To address this, we introduce Graphein as a turn-key tool for transforming raw data from widely-used bioinformatics databases into machine learning-ready datasets in a high-throughput and flexible manner. Graphein is a Python library for constructing graph and surface-mesh representations of protein structures and biological interaction networks for computational analysis. Graphein provides utilities for data retrieval from widely-used bioinformatics databases for structural data, including the Protein Data Bank, the recently-released AlphaFold Structure Database, and for biomolecular interaction networks from STRINGdb, BioGrid, TRRUST and RegNetwork. The library interfaces with popular geometric deep learning libraries: DGL, PyTorch Geometric and PyTorch3D though remains framework agnostic as it is built on top of the PyData ecosystem to enable inter-operability with scientific computing tools and libraries. Graphein is designed to be highly flexible, allowing the user to specify each step of the data preparation, scalable to facilitate working with large protein complexes and interaction graphs, and contains useful pre-processing tools for preparing experimental files. Graphein facilitates network-based, graph-theoretic and topological analyses of structural and interaction datasets in a high-throughput manner. As example workflows, we make available two new protein structure-related datasets, previously unused by the geometric deep learning community. We envision that Graphein will facilitate developments in computational biology, graph representation learning and drug discovery.Availability and implementationGraphein is written in Python. Source code, example usage and tutorials, datasets, and documentation are made freely available under the MIT License at the following URL: graphein.ai
Global transcriptional regulation by cell-free supernatant ofSalmonellaTyphimurium peptide transporter mutant leads to inhibition of intra-species biofilm initiation
Authors: Chandra Kasturi , Muralidhara Prerana , Kamanna Sathisha , Tatu Utpal S. , Chakravortty Dipshikha 
Published: July 2020

AbstractSalmonellais a genus of widely spread Gram negative, facultative anaerobic bacteria, which is known to cause ¼th of diarrheal morbidity and mortality globally. It causes typhoid fever and gastroenteritis by gaining access to the host gut through contaminated food and water.Salmonellautilizes its biofilm lifestyle to strongly resist antibiotics and persist in the host. Although biofilm removal or dispersal has been studied widely, the inhibition of the initiation ofSalmonellabiofilm remains elusive. This study was conducted to determine the anti-biofilm property of the cell-free supernatant obtained from a carbon-starvation inducible proline peptide transporter mutant (ΔyjiY)strain. Our study shows thatSalmonellaΔyjiYculture supernatant primarily inhibits biofilm initiation by regulating biofilm-associated transcriptional network. This work demonstrates that highly abundant proteases such as HslV and GrpE cleave the protein aggregates, whereas global transcription regulators H-NS, FlgM regulate expression of SPIs and flagellar genes. Relatively low abundances of flavoredoxin, glutaredoxin, thiol peroxidase etc. leads to accumulation of ROS within the biofilm, and subsequent toxicity. This work further suggests that targeting these oxidative stress relieving proteins might be a good druggable choice to reduceSalmonellabiofilm.ImportanceThe enteric pathogenSalmonellaforms biofilm in the internal organs of asymptomatic carriers, and on abiotic surfaces that leads to contamination of food and water. Biofilms are highly drug-resistant life forms that also helps in host immune evasion. Therefore, recent insurgence of drug tolerant strains necessitates development of biofilm inhibitory strategies, and finding novel druggable targets. In this study we investigated the bioactive molecules present in the cell-free supernatant of a biofilm deficient strain ofSalmonellaTyphimurium that inhibit biofilm initiation by the wildtype strain. Further we showed that the supernatant treatment leads to virulence defectin vivo. Collectively, our results suggest a comprehensive view of virulence regulation inSalmonellaby the cell-free supernatant of the biofilm deficient strain.
Leading in an Amish Paradise: humanistic leadership in the Old Order Amish
Authors: Keim Charles , Shadnam Masoud 
Published: July 2020

PurposeThe authors examined the traditional leadership practiced by the Old Order Amish located in the Holmes and Wayne counties of America. Despite popular stereotypes, this community is remarkably innovative and resilient. Amish leadership aligns with the central tenets of humanistic leadership and provides a rich illustration of how such a leadership paradigm can foster a vibrant, inclusive and sustainable community. Unlike current leadership models that focus on instrumental values like wealth, profit and growth, Amish leadership is concerned with faith, community and living a simple life with purpose and dignity.Design/methodology/approachThe primary data required for this paper were collected by the lead author during a six-month ethnographic study on several Amish communities located in Ohio. The authors also consulted a large set of archival data, including think tank reports, census data, biographies, magazine features and academic publications, which helped in placing the primary data in perspective and reminding of the particularities of the contexts from which the primary data were collected. For the data analysis, the authors used a thematic analysis approach to allow the salient themes of Amish humanistic leadership emerge from the data.FindingsA total offour themes emerged from this study: (1) leadership as local identity and practice; (2) leaders without benefits, chosen by the lot; (3) leaders present matters, followers discuss and decide; (4) community welfare as the yardstick for evaluation. These themes highlighted some of the key aspects of humanistic leadership eclipsed in the mainstream theories of management and leadership. They showed how the Amish respond to the encroachment of technology, which holds critical clues for how humanistic leaders can place the needs of their people before the demands of their shareholders. By examining Amish leadership in detail, this study demonstrated the potential of humanistic leadership for creating a strong and sustainable community while also contributing to the empirical foundation of humanistic management.Originality/valueGiven the closed nature of the Amish, only few academic studies exist, which examined their leadership style. Furthermore, the traditional and conservative nature of the Amish community has prevented critics from investigating their leadership as a model for revitalizing other communities.
Does national culture influence management's accounting behaviour and strategy? – an empirical analysis of European IFRS adopters
Authors: Reisch Lucas 
Published: July 2020

PurposeThis study examines, in a European context, whether a management-induced International Financial Reporting Standards (IFRS) accounting strategy is affected by national culture. It analyses the association between management's accounting strategy and Hofstede's cultural dimensions of individualism and uncertainty avoidance, as well as institutional and firm-specific factors.Design/methodology/approachUsing hand-collected accounting decisions from 301 annual reports of firms from 14 European countries in 2017, a model is developed to identify two ordinally scaled accounting strategy variables, each representing the aggregated effect of the decisions on earnings and equity ratio. Afterwards, the effect of the cultural dimensions on these accounting-strategy variables is analysed by an ordered logistic regression.FindingsThe results do not support an association between management's accounting strategy and national culture, complementing the previous critical literature on values-based theories of culture. However, there is evidence that national legal enforcement, disclosure requirements and firm size explain differences in management's accounting strategy across countries.Research limitations/implicationsUsing the cultural value dimensions of the Global Leadership and Organizational Behavior Effectiveness (GLOBE) project, the findings are robust and stable. However, the study is limited to a European data set and the sample year.Practical implicationsThis study contributes to the discussion on the transparency and comparability of IFRS accounting. The results imply that these issues are not affected by cultural differences but rather by differences in institutional and firm-specific factors. In order to bring about improvements, regulators should establish a uniform institutional setting, while the standard setter should reduce the number of implicit and explicit accounting choices embodied in the IFRS.Originality/valueThe paper advances the understanding of cultural influences on management's IFRS accounting behaviour by providing an alternative to the existing accruals approach.
Transient performance of a magnetically geared induction machine
Authors: Bidouche Badr-El-Boudour , Lubin Thierry , Mezani Smaïl 
Published: July 2020

Purpose
The purpose of this paper is to investigate the transient performance of an induction machine coupled with a magnetic gear for industrial applications with low speed and high torque requirements. This new solution increases mechanical reliability and does not require maintenance and lubrication. The main objective is to study the direct-on-line starting ability of the electrical machine and its stability regarding a sudden change for the load torque.

Design/methodology/approach
A nonlinear analytical model for the induction machine and the magnetic gear is first developed. The model is then linearized around an operating point to obtain the transfer function between the load angle and the electromagnetic torque from which an analytical expression for the mechanical resonant frequency is obtained.

Findings
It is shown that the direct on-line starting is possible, if the moment of inertia of the load is not greater than a maximum value. Moreover, it is demonstrated that this new system present inherent overload protection.

Originality/value
A new high-performance direct-on-line starting electrical machine is proposed to achieve high torque at low speed without mechanical gear to improve reliability and reduce maintenance.