bluuebunny/crossref_metadata_2025_split huggingface dataset:
A D-2-hydroxyglutarate biosensor based on specific transcriptional regulator DhdR
Authors: Xiao Dan , Zhang Wen , Guo Xiaoting , Liu Yidong , Hu Chunxia , Guo Shiting , Kang Zhaoqi , Xu Xianzhi , Ma Cuiqing , Gao Chao , Xu Ping 
Published: February 2021

AbstractD-2-Hydroxyglutarate (D-2-HG) is a metabolite in many physiological metabolic processes. When D-2-HG is aberrantly accumulated due to mutations in isocitrate dehydrogenases or D-2-HG dehydrogenase, it functions in a pro-oncogenic manner and is thus considered a therapeutic target and biomarker in many cancers. In this study, DhdR fromAchromobacter denitrificansNBRC 15125 was identified as an allosteric transcription factor that negatively regulates D-2-HG dehydrogenase expression and responds to presence of D-2-HG. It is the first known transcription regulator specifically responding to D-2-HG across all domains of life. Based on the allosteric effect of DhdR, a D-2-HG biosensor was developed by combining DhdR with amplified luminescent proximity homogeneous assay technology. The biosensor was able to detect D-2-HG in serum, urine, and cell culture with high specificity and sensitivity. Additionally, this biosensor was also successfully used to identify the role of D-2-HG metabolism in lipopolysaccharide biosynthesis ofPseudomonas aeruginosa, demonstrating its broad usages.
Collective detection based on visual information in animal groups
Authors: Davidson Jacob D. , Sosna Matthew M. G. , Twomey Colin R. , Sridhar Vivek H. , Leblanc Simon P. , Couzin Iain D. 
Published: February 2021

AbstractThe spatio-temporal distribution of individuals within a group (i.e its internal structure) plays a defining role in how individuals interact with their environment, make decisions, and transmit information via social interactions. Group-living organisms across taxa, including many species of fish, birds, ungulates, and insects, use vision as the predominant modality to coordinate their collective behavior. Despite this importance, there have been few quantitative studies examining visual detection capabilities of individuals within groups. We investigate key principles underlying individual, and collective, visual detection of stimuli (which could include cryptic predators, potential food items, etc.) and how this relates to the internal structure of groups. While the individual and collective detection principles are generally applicable, we employ a model experimental system of schooling golden shiner fish (Notemigonus crysoleucas) to relate theory directly to empirical data, using computational reconstruction of the visual fields of all individuals to do so. Our integrative approach allows us to reveal how the external visual information available to each group member depends on the number of individuals in the group, the position within the group, and the location of the external visually-detectable stimulus. We find that in small groups, individuals have detection capability in nearly all directions, while in large groups, occlusion by neighbors causes detection capability to vary with position within the group. We then formulate a simple, and generally applicable, model that captures how visual detection properties emerge due to geometric scaling of the space occupied by the group and occlusion caused by neighbors. We employ these insights to discuss principles that extend beyond our specific system, such as how collective detection depends on individual body shape, and the size and structure of the group.
On the sensitivity analysis of porous finite element models for cerebral perfusion estimation
Authors: Józsa T. I. , Padmos R. M. , El-Bouri W. K. , Hoekstra A. G. , Payne S. J. 
Published: February 2021

AbstractComputational physiological models are promising tools to enhance the design of clinical trials and to assist in decision making. Organ-scale haemodynamic models are gaining popularity to evaluate perfusion in a virtual environment both in healthy and diseased patients. Recently, the principles of verification, validation, and uncertainty quantification of such physiological models have been laid down to ensure safe applications of engineering software in the medical device industry. The present study sets out to establish guidelines for the usage of a three-dimensional steady state porous cerebral perfusion model of the human brain following principles detailed in the verification and validation (V&V 40) standard of the American Society of Mechanical Engineers. The model relies on the finite element method and has been developed specifically to estimate how brain perfusion is altered in ischaemic stroke patients before, during, and after treatments. Simulations are compared with exact analytical solutions and a thorough sensitivity analysis is presented covering every numerical and physiological model parameter.The results suggest that such porous models can approximate blood pressure and perfusion distributions reliably even on a coarse grid with first order elements. On the other hand, higher order elements are essential to mitigate errors in volumetric blood flow rate estimation through cortical surface regions. Matching the volumetric flow rate corresponding to major cerebral arteries is identified as a validation milestone. It is found that inlet velocity boundary conditions are hard to obtain and that constant pressure inlet boundary conditions are feasible alternatives. A one-dimensional model is presented which can serve as a computationally inexpensive replacement of the three-dimensional brain model to ease parameter optimisation, sensitivity analyses and uncertainty quantification.The findings of the present study can be generalised to organ-scale porous perfusion models. The results increase the applicability of computational tools regarding treatment development for stroke and other cerebrovascular conditions.
Functional MRI of native and non-native speech production in sequential German-English bilinguals
Authors: Treutler Miriam , Sörös Peter 
Published: February 2021

AbstractBilingualism and multilingualism are highly prevalent. Non-invasive brain imaging has been used to study the neural correlates of native (L1) and non-native (L2) speech and language production, mainly on the lexical and syntactic level. Here, we acquired continuous fast event-related FMRI during visually cued overt production of exclusively German and English vowels and syllables. We analyzed data from 13 university students, native speakers of German and sequential English bilinguals. The production of non-native English sounds was associated with increased activity of the left primary sensori-motor cortex, bilateral cerebellar hemispheres (lobule VI), left inferior frontal gyrus, and left anterior insula compared to native German sounds. The contrast German > English sounds was not statistically significant. Our results emphasize that the production of non-native speech requires additional neural resources already on a basic phonological level in sequential bilinguals.
Recovering sedimentary ancient DNA of harmful dinoflagellates off Eastern Tasmania, Australia, over the last 9 000 years
Authors: Armbrecht Linda , Paine Bradley , Bolch Christopher J.S. , Cooper Alan , McMinn Andrew , Woodward Craig , Hallegraeff Gustaaf 
Published: February 2021

AbstractHarmful algal blooms (HABs) have significantly impacted the seafood industry along the Tasmanian east coast over the past four decades. To investigate the history of regional HABs, we applied sedimentary ancient DNA analyses (sedaDNA) to coastal sediments up to ∼9 000 years old collected inshore and offshore Maria Island, Tasmania. We used metagenomic shotgun sequencing combined with a hybridisation capture array (‘HABbaits1’) to target harmful dinoflagellates of the generaAlexandrium, Gymnodinium,andNoctiluca scintillans. Bioinformatic analyses were used to verifysedaDNA sequences and their presence in older layers, especially for microreticulate cyst forming species includingGymnodinium catenatumdue to its important role in shellfish toxicity. Our results show that theAlexandriumgenus (up to 854 and 20 reads per sample inshore and offshore, respectively, based on capture-data) has been present off eastern Tasmania within the last ∼8 307 years. ForG. catenatumwe detected a total of only 9 unambiguously verified reads sporadically between ∼7 638 years ago and the present in the offshore core. We recovered verifiedsedaDNA of the fragile, non-fossilising speciesN. scintillans, along with evidence of increased relative abundance from 2010, consistent with plankton surveys. This study identifies challenges regardingsedaDNA sequence validation of some species (in particular, forG. catenatum), and provides guidance for the development of tools to monitor past and present HAB species and events, and to improve future HAB event predictions.HighlightsMetagenomicsedaDNA and hybridisation capture enabled analyses of harmful dinoflagellates off TasmaniaSequence validation was used to confirm the presence ofAlexandriumspp.,Gymnodiniumspp. andNoctiluca scintillansAlexandriumandGymnodiniumhave been present in Tasmanian waters during the past ∼9 000 yearsNoctiluca scintillans sedaDNA derived relative abundance correlates with its recorded increase since 2010
Contribution of interneuron subtype-specific GABAergic signalling to emergent sensory processing in somatosensory whisker barrel cortex in mouse
Authors: Baruchin Liad J. , Kohl Michael M. , Butt Simon J.B 
Published: February 2021

AbstractMammalian neocortex is important for conscious processing of sensory information. Fundamental to this function is balanced glutamatergic and GABAergic signalling. Yet little is known about how this interaction arises in the developing forebrain despite increasing insight into early GABAergic interneuron (IN) circuits. To further study this, we assessed the contribution of specific INs to the development of sensory processing in the mouse whisker barrel cortex. Specifically we explored the role of INs in speed coding and sensory adaptation. In wild-type animals, both speed processing and adaptation were present as early as the layer 4 critical period of plasticity, and showed refinement over the period leading to active whisking onset. We then conditionally silenced action-potential-dependent GABA release in either somatostatin (SST) or vasoactive intestinal peptide (VIP) INs. These genetic manipulations influenced both spontaneous and sensory-evoked activity in an age and layer-dependent manner. Silencing SST+ INs reduced early spontaneous activity and abolished facilitation in sensory adaptation observed in control pups. In contrast, VIP+ IN silencing had an effect towards the onset of active whisking. Silencing either IN subtype had no effect on speed coding. Our results reveal how these IN subtypes differentially contribute to early sensory processing over the first few postnatal weeks.
Integration of differential gene expression with weighted gene correlation network analysis identifies genes whose expression is remodeled throughout physiological aging in mouse tissues
Authors: Ferreira Margarida , Francisco Stephany , Soares Ana R. , Nobre Ana , Pinheiro Miguel , Reis Andreia , Neto Sonya , Rodrigues Ana João , Sousa Nuno , Moura Gabriela , Santos Manuel A. S. 
Published: February 2021

AbstractGene expression alterations occur in all mouse tissues during aging, but recent works highlight minor rather than major dysregulation amplitude for most genes, questioning whether differentially expressed genes on their own provide deep insight into aging biology. To clarify this issue, we have combined differential gene expression with weighted gene correlation network analysis (WGCNA) to identify expression signatures accounting for the pairwise relations between gene expression profiles and the cumulative effect of genes with small fold- changes during aging in the brain, heart, liver, skeletal muscle, and pancreas of C57BL/6 mice. Functional enrichment analysis of the overlap of genes identified in both approaches showed that immunity-related responses, mitochondrial energy metabolism, tissue regeneration and detoxification are prominently altered in the brain, heart, muscle, and liver, respectively, reflecting an age-related global loss of tissue function. While data showed little overlap among the age-dysregulated genes between tissues, aging triggered common biological processes in distinct tissues, particularly proteostasis-related pathways, which we highlight as important features of murine tissue physiological aging.
MEG, myself, and I: individual identification from neurophysiological brain activity
Authors: Da Silva Castanheira Jason , Orozco Hector D , Misic Bratislav , Baillet Sylvain 
Published: February 2021

AbstractLarge, openly available datasets and current analytic tools promise the emergence of population neuroscience. The considerable diversity in personality traits and behaviour between individuals is reflected in the statistical variability of neural data collected in such repositories. This amount of variability challenges the sensitivity and specificity of analysis methods to capture the personal characteristics of a putative neural portrait. Recent studies with functional magnetic resonance imaging (fMRI) have concluded that patterns of resting-state functional connectivity can both successfully identify individuals within a cohort and predict some individual traits, yielding the notion of aneural fingerprint. Here, we aimed to clarify the neurophysiological foundations of individual differentiation from features of the rich and complex dynamics of resting-state brain activity using magnetoencephalography (MEG) in 158 participants. Akin to fMRI approaches, neurophysiological functional connectomes enabled the identification of individuals, with identifiability rates similar to fMRI’s. We also show that individual identification was equally successful from simpler measures of the spatial distribution of neurophysiological spectral signal power. Our data further indicate that identifiability can be achieved from brain recordings as short as 30 seconds, and that it is robust over time: individuals remain identifiable from recordings performed weeks after their baseline reference data was collected. Based on these results, we can anticipate a vast range of further research and practical applications of individual differentiation from neural electrophysiology in personalized, clinical, and basic neuroscience.
Identifying gene regulatory networks of senescence in postharvest broccoli (Brassica oleracea)
Authors: Ahlawat Yogesh , Li Song , Pliakoni Eleni D. , Brecht Jeffrey , Liu Tie 
Published: February 2021

ABSTRACTThe facts of postharvest food loss and waste and the resulting consequences affect us in many ways, ranging from important economic and social issues to lasting and detrimental environmental problems. We are using genomic tools to understand senescence in postharvest broccoli florets when stored at room temperature or 4 °C. The RNA-sequencing approaches provide key insights into the gradual changes in transcriptome profiling in broccoli during postharvest storage. Identification of those key factors could lead to a better understanding of gene regulation of postharvest senescence. Those genes could serve as ‘freshness-indicators’ that have the potential to mediate senescence and to generate germplasm for breeding new varieties with longer shelf-life in Brassica vegetables. Such a tool would also allow a new level of postharvest logistics based on physiological age, supporting improved availability of high-quality, nutritious, fresh vegetables and fruits.One sentence summaryA gene regulatory network modulates senescence in postharvest broccoli florets
Neoliberalism and management accounting: reconfiguring governmentality and extending territories
Authors: Wickramasinghe Danture , Cooper Christine , Alawattage Chandana 
Published: February 2021

PurposeThe purpose of this paper is to introduce the themes and aims of this Accounting, Auditing & Accountability (AAAJ) special issue and comments on the papers included in the issue. The paper provides a thematic outline along which the future researchers can undertake more empirical research examining how neoliberalism shapes, and shaped by, management accounting.Design/methodology/approachThis entails a brief review of the previous critical accounting works that refer to liberalism and neoliberalism to identify and highlight the specific themes and trajectories of neoliberal implications of management accounting has been and can be explored. This is followed by a brief commentary on the papers the authors have included in this special issue; these commentaries explain how these papers capture various dimensions of enabling and enacting neoliberal governmentality.FindingsThe authors found that management accounting is now entering new territories beyond its conventional disciplinary enclosures of confinement, reconfiguring its functionalities to enable and enact a circulatory mode of neoliberal governmentality. These new functionalities then produce and reproduce entrepreneurial selves in myriad forms of social connections, networks and platforms within and beyond formal organizational settings, amid plethora of conducts, counter-conducts and resistances and new forms of identities and subjectivities.Research limitations/implicationsThis review can be read in relation to the papers included in the special issue as the whole issue will inspire more ideas, frameworks and methodologies for further studies.Originality/valueThere is little research reviewing and commenting how management accounting now being enacted and enabled with new functionalities operating new territories and reconfiguring forms of governmentality. This paper inspires a new agenda on this project.
Inscriptions without boundaries: how action at a distance is enabled on social media
Authors: Gullberg Cecilia , Weinryb Noomi 
Published: February 2021

PurposeThe purpose of this paper is to explore the role of inscriptions on social media in enabling action at a distance. The purpose is addressed by investigating how and by what mechanisms inscriptions on social media can shape action at a distance.Design/methodology/approachWe conduct a qualitative analysis of the Facebook page of a crowdfunded grassroots initiative, where the founders and their stakeholders interact.FindingsWe identify two mechanisms by which inscriptions on social media can shape action at a distance: a flow of micro-level inscriptions and a joint stabilisation of inscriptions. By signalling achievement, creating a sense of closeness and highlighting powerful explanations, these mechanisms guide what action at a distance is taken and by whom. Action thereby becomes a mutual exercise between centres of calculation and distant peripheries, highly intertwined with the stability of inscriptions. The two mechanisms indicate the importance of the boundaryless nature of the inscriptions in shaping action at a distance.Originality/valueOur findings indicate new forms of inscriptions and, consequently, of novel conditions for action at a distance. These insights add to the literature on Web 2.0 and accounting, which has mainly revolved around the relationship between centres of calculation and distant peripheries that act upon each other rather than around the inscriptions that enable such action.
Triggering sustainability communication in a B2B context: combining action research and sensemaking
Authors: Apostol Oana , Mäkelä Marileena , Heikkilä Katariina , Höyssä Maria , Kalliomäki Helka , Jokinen Leena , Saarni Jouni 
Published: February 2021

PurposeThe paper explores processes associated with the adoption of corporate sustainability communication in a B2B context. It employs a combined action research and sensemaking approach to document moments that precede the initiation of external sustainability communication.Design/methodology/approachThe paper is the outcome of an action research project, where we examine the case of one industrial company that was silent on its multiple sustainability-related practices, but recently decided to become more transparent to the outside world. A processual approach to sensemaking is adopted to show how organisational and non-organisational members actively participated in meaning co-construction.FindingsCorporate silence can be disrupted by triggering events that cause moments of sudden realisation for organisational members, eventually leading to the initiation of sensemaking processes inside the organisation. Once this occurs, the possibility of externally communicating sustainability appears a feasible and strategic approach to pursue. We document how different actors are involved in meaning co-construction and how the entire process of sensemaking unfolds.Practical implicationsA sensemaking approach sheds light on the complexity of sustainability communication, where multiple actors are involved. This is a useful approach to consider in order to couple sustainability with other organisational practices. Moreover, sensemaking opens a window of opportunity for various societal actors' interventions to shape the role and content of sustainability communication.Originality/valueThe paper offers an original, theoretically informed methodological contribution to the literature on sustainability communication by coupling a sensemaking approach with action research. The approach is employed to examine the role of internal organisational actors in sustainability reporting processes, an area that has received scant attention.
How COVID-19 affects individuals' food consumption behaviour: a consumer survey on attitudes and habits in Turkey
Authors: Güney Osman Inanç , Sangün Levent 
Published: February 2021

PurposeAfter the novel coronavirus disease 2019 (COVID-19) was declared a pandemic by the World Health Organization in March 2020, its devastating effects began to be closely monitored all over the world. The new order that emerged due to the fight against the virus soon began to affect all our habits and behaviours. The fact that food consumption is vital for human well-being makes this an important area to investigate in terms of the impact of COVID-19. This research was carried out to investigate the changes in consumers' food consumption behaviour and habits during the COVID-19 pandemic and determine the factors that explain these changes.Design/methodology/approachIn line with the recommendations for social distancing under pandemic conditions, the empirical data were collected via computer-assisted telephone interviewing (CATI). The participants were 1,023 individuals living in the major cities of the seven regions of Turkey. An ordered probit regression model was used to estimate the attitudes related to the changes in food consumption behaviour and habits, and descriptive statistics are provided to show the current food consumption and purchase situation.FindingsThe results showed that the changes in food consumption behaviour and habits due to the pandemic were related to price increase concerns, stockpiling, awareness of food waste, safety and excessive, food access concerns, natural/organic food preferences and packaging of foods. Moreover, the participants tended to prepare food at home and preferred food that was popular with other consumers. Consumers mainly bought food from discount stores and local grocery stores and consumed fresh vegetables and fruits, animal-based products, cereals and pulses.Originality/valueThe current study contributes to knowledge regarding the effects of the coronavirus pandemic on food consumption behaviour by using a predictive model and provides behavioural estimations by using a countrywide questionnaire. The results show that the pandemic affects food consumption routines and food perspective of consumers in various ways.