bluuebunny/crossref_metadata_2025_split huggingface dataset:
Why Environmental Biomarkers Work: Transcriptome-Proteome Correlations and Modeling of Multi-Stressor Experiments in the Marine BacteriumTrichodesmium
Authors: Walworth Nathan G. , Saito Mak A. , Lee Michael D. , McIlvin Matthew R. , Moran Dawn M. , Kellogg Riss M. , Fu Fei-Xue , Hutchins David A. , Webb Eric A. 
Published: June 2021

AbstractOcean microbial communities are important contributors to the global biogeochemical reactions that sustain life on Earth. The factors controlling these communities are being increasingly explored through the use of metatranscriptomic and metaproteomic environmental biomarkers, despite ongoing uncertainty about the coherence between RNA and protein signals. Using published proteomes and transcriptomes from the abundant colony-forming cyanobacteriumTrichodesmium(strainT. erythraeumIMS101) grown under varying Fe and/or P limitation and/or co-limitation in low and high CO2, we observed robust correlations of stress induced proteins and RNAs (i.e., those involved in transport and homeostasis) that can yield useful information on nutrient status under low and/or high CO2. Conversely, transcriptional and translational correlations of many other central metabolism pathways exhibit broad discordance. A cellular RNA and protein production/degradation model demonstrates how biomolecules with small initial inventories, such as environmentally responsive proteins, can achieve large increases in fold-change units, as opposed to those with higher basal expression and inventory such as metabolic systems. Microbial cells, due to their close proximity to the environment, tend to show large adaptive responses to environmental stimuli in both RNA and protein that result in transcript-protein correlations. These observations and model results demonstrate a multi-omic coherence for environmental biomarkers and provide the underlying mechanism for those observations, supporting the promise for global application in detecting responses to environmental stimuli in a changing ocean.
nzffdr: an R package to import, clean and update data from the New Zealand Freshwater Fish Database
Authors: Lee Finnbar , Young Nick 
Published: June 2021

AbstractThe New Zealand Freshwater Fish Database (NZFFD) is a repository of more than 155,000 records of freshwater fish observations from around New Zealand, maintained by the National Institute of Water and Atmospheric Research (NIWA). Records from the NZFFD can be downloaded using a web interface. The statistical computing language R is now widely used for data wrangling, analysis, and visualisation. Here, we present nzffdr, an open source R software package that: i) allows users to query and download data from the New Zealand Freshwater Fish Database directly in R, ii) provides functions to clean imported data, iii) facilitates the addition of information such as species names and Department of Conservation threat classification status, and iv) a workflow for visualising information from the NZFFD. The nzffdr package aims to standardise, simplify, and speed up a workflow likely already used in anad hocmanner by scientists across New Zealand and abroad.
Transfer rate of enveloped and non-enveloped viruses between fingerpads and surfaces
Authors: Anderson Claire E. , Boehm Alexandria B. 
Published: June 2021

AbstractFomites can represent a reservoir for pathogens, which may be subsequently transferred from surfaces to skin. In this study we aim to understand how different factors (including virus type, surface type, time since last handwash, and direction of transfer) affect virus transfer rates, defined as the fraction of virus transferred, between fingerpads and fomites. To determine this, 360 transfer events were performed with 20 volunteers using Phi6 (a surrogate for enveloped viruses) and MS2 (a surrogate for non-enveloped viruses), and three clean surfaces (stainless steel, painted wood, and plastic). Considering all transfer events (all surfaces and both transfer directions combined), the mean transfer rates of Phi6 and MS2 were 0.17 and 0.26, respectively. Transfer of MS2 was significantly higher than Phi6 (P<0.05). Surface type was a significant factor that affected the transfer rate of Phi6: Phi6 is more easily transferred to and from stainless steel and plastic than to and from painted wood. Direction of transfer was a significant factor affecting MS2 transfer rates: MS2 is more easily transferred from surfaces to fingerpads than from fingerpads to surfaces. Data from these virus transfer events, and subsequent transfer rate distributions, provide information which can be used to refine quantitative microbial risk assessments. This study is the first to provide a large-scale data set of transfer events with a surrogate for enveloped viruses, which extends the reach of the study to the role of fomites in the transmission of human enveloped viruses like influenza and SARS-CoV-2.ImportanceThis study created the first large-scale data set for the transfer of enveloped viruses between skin and surfaces. The data set produced by this study provides information on modelling the distribution of enveloped and non-enveloped virus transfer rates, which can aid in the implementation of risk assessment models in the future. Additionally, enveloped and non enveloped viruses were applied to experimental surfaces in an equivalent matrix to avoid matrix effects, so results between different viral species can be directly compared without confounding effects of different matrices. Our results indicating how virus type, surface type, time since last handwash, and direction of transfer affect virus transfer rates can be used in decision-making processes to lower the risk of viral infection from transmission through fomites.
Regulation of GTPase function by autophosphorylation
Authors: Johnson Christian W. , Seo Hyuk-Soo , Terrell Elizabeth M. , KleinJan Fenneke , Gebregiworgis Teklab , Gasmi-Seabrook Genevieve M. C. , Geffken Ezekiel A. , Lakhani Jimit , Song Kijun , Popow Olesja , Paulo Joao A. , Liu Andrea , Mattos Carla , Marshall Christopher B. , Ikura Mitsuhiko , Morrison Deborah K. , Dhe-Paganon Sirano , Haigis Kevin M. 
Published: June 2021

SUMMARYA unifying feature of the RAS superfamily is a functionally conserved GTPase cycle that proteins use to transition between active and inactive states. Here, we demonstrate that active site autophosphorylation of some small GTPases is an intrinsic regulatory mechanism that reduces nucleotide hydrolysis and enhances nucleotide exchange, thus altering the on/off switch that forms the basis for their signaling functions. Using x-ray crystallography, nuclear magnetic resonance spectroscopy, biolayer interferometry binding assays, and molecular dynamics on autophosphorylated mutants of H-RAS and K-RAS, we show that phosphoryl transfer from GTP requires dynamic movement of the switch II domain and that autophosphorylation promotes nucleotide exchange by opening of the active site and extraction of the stabilizing Mg. Finally, we demonstrate that autophosphorylated K-RAS exhibits altered effector interactions, including a reduced affinity for RAF proteins. Thus, autophosphorylation leads to altered active site dynamics and effector interaction properties, creating a pool of GTPases that are functionally distinct from the non-phosphorylated counterpart.
Bacterial response to spatial gradients of algal-derived nutrients in a porous microplate
Authors: Kim Hyungseok , Kimbrel Jeffrey A. , Vaiana Christopher A. , Wollard Jessica R. , Mayali Xavier , Buie Cullen R. 
Published: June 2021

AbstractPhotosynthetic microalgae are responsible for 50% of the global atmospheric CO2 fixation into organic matter and hold potential as a renewable bioenergy source. Their metabolic interactions with the surrounding microbial community (the algal microbiome) play critical roles in carbon cycling, but due to methodological limitations, it has been challenging to examine how community is developed by spatial proximity to their algal host. Here we introduce a hydrogel-based porous microplate to co-culture algae and bacteria, where metabolites are constantly exchanged between the microorganisms while maintaining physical separation. In the microplate we found that the diatom Phaeodactylum tricornutum accumulated to cell abundances ~20 folds higher than under normal batch conditions due to constant replenishment of nutrients through the hydrogel. We also demonstrate that algal-associated bacteria, both single isolates and complex communities, responded to inorganic nutrients away from their host as well as organic nutrients originating from the algae in a spatially predictable manner. These experimental findings coupled with a mathematical model suggest that host proximity and algal culture growth phase impact bacterial community development in a taxon-specific manner through organic and inorganic nutrient availability. Our novel system presents a useful tool to investigate universal metabolic interactions between microbes in aquatic ecosystems.
INTRINSIC MOTOR NEURONE EXCITABILITY IS REDUCED IN SOLEUS AND TIBIALIS ANTERIOR OF OLDER ADULTS
Authors: Orssatto Lucas B. R. , Borg David N. , Blazevich Anthony J. , Sakugawa Raphael L. , Shield Anthony J. , Trajano Gabriel S. 
Published: June 2021

ABSTRACTAge-related deterioration within both motor neurones and monoaminergic systems should theoretically reduce neuromodulation by weakening motor neuronal persistent inward current (PIC) amplitude. However, this assumption remains untested. Surface electromyographic signals were collected using two 32-channel electrode matrices placed on soleus and tibialis anterior of 25 older adults (70±4years) and 17 young adults (29±5 years) to investigate motor unit discharge behaviours. Participants performed triangular-shaped plantar and dorsiflexion contractions to 20% of maximum torque at a rise-decline rate of 2%/s of each participant’s maximal torque. Pairwise and composite paired-motor unit analyses were adopted to calculate delta frequency (ΔF), which has been used to differentiate between the effects of synaptic excitation and intrinsic motor neuronal properties and is assumed to be proportional to PIC amplitude. Soleus and tibialis anterior motor units in older adults had lower ΔFs calculated with either the pairwise [−0.99 and −1.46 pps; −35.4 and − 33.5%, respectively] or composite (−1.18 and −2.28 pps; −32.1 and −45.2%, respectively) methods. Their motor units also had lower peak discharge rates (−2.14 and −2.03 pps; −19.7 and −13.9%, respectively) and recruitment thresholds (−1.50 and −2.06% of maximum, respectively) than young adults. These results demonstrate reduced intrinsic motor neurone excitability during low-force contractions in older adults, likely mediated by decreases in the amplitude of persistent inward currents. Our findings might be explained by deterioration in the motor neurones or monoaminergic systems and could contribute to the decline in motor function during ageing; these assumptions should be explicitly tested in future investigations.
Model sharing in the human medial temporal lobe
Authors: Glitz Leonie , Juechems Keno , Summerfield Christopher , Garrett Neil 
Published: June 2021

AbstractEffective planning involves knowing where different actions will take us. However natural environments are rich and complex, leading to an exponential increase in memory demand as a plan grows in depth. One potential solution to this problem is to share the neural state transition functions used for planning between similar contexts. Here, we asked human participants to perform a sequential decision making task designed so that knowledge could be shared between some contexts but not others. Computational modelling showed that participants shared a model of state transitions between contexts where appropriate. fMRI data identified the medial temporal lobe as a locus for learning of state transitions, and within the same region, correlated BOLD patterns were observed in contexts where state transition information were shared. Finally, we show that the transition model is updated more strongly following the receipt of positive compared to negative outcomes, a finding that challenges conventional theories of planning which assume knowledge about our environment is updated independently of outcomes received. Together, these findings propose a computational and neural account of how information relevant for planning can be shared between contexts.
Sacrificing mackerel for sustainability: case study of a local cultural festival in northeastern Taiwan
Authors: Wu Ying-Ching 
Published: June 2021

PurposeThe purpose of this paper is to describe how people in a coastal community act upon anxieties about overexploitation of a shared resource and their attempts to ease the moral tension caused by the rapid industrialization of their fishery. This anthropological study contributes to the cross-disciplinary discussion of community-based resource management.Design/methodology/approachThe study is based on ethnographic fieldwork done at the Nanfang'ao port located in northeastern Taiwan. This port has several prosperous offshore fisheries including a mackerel fishery. The mackerel fishery has undergone important transformations in recent decades. The first was a total transformation of fishing methods in 2013. The second was the government's formulation of the “Regulations for Fishing Vessels Catching Mackerels and Jacks,” implemented in 2014. This research illustrates how people in a community take various approaches to pursue sustainability for the human beings and the more-than-human world.FindingsIn Nanfang'ao port, local people have developed a meaningful cultural festival through the integration of various symbols and rituals from different contexts in an effort to call attention to moral issues associated with the mackerel fishery.Originality/valueThis research contributes to the discussion on community resource management of marine fishery.
Integration of TQM and ERP to enhance organizational performance and excellence: empirical evidence from public sector using SEM
Authors: Al-Dhaafri Hassan , Alosani Mohammed 
Published: June 2021

PurposeThe study aims to examine the joint effect of total quality management (TQM), enterprise resource planning (ERP) and organizational performance on organizational excellence.Design/methodology/approachTo achieve the goal of this study through the hypothesized model, a survey questionnaire research design was employed. The data were collected from a Dubai Police organization. Out of 550 questionnaires, 320 questionnaires were returned. The structural equation modelling (SEM) partial least squares approach was used to analyze the data for measurement and structural models.FindingsThe statistical results confirmed the positive and significant effects of TQM, ERP and organizational performance on organizational excellence. The mediation role of organizational performance between TQM, ERP and organizational excellence also was confirmed.Practical implicationsThroughout this study, further details and valuable implications have been discussed. Findings provide several practical implications. Findings also help practitioners and managers make proper decisions when implementing TQM, ERP and excellence practices in their organizations. With the joint effect of TQM, ERP and organizational performance, organizations can achieve maximum strong excellence and remain in a competitive market. This current study presents potential to be used in didactical initiatives.Originality/valueThis study is a unique empirical research that examines the joint effect of TQM, ERP and performance on excellence relationships. In other words, the current study is one of the few studies that investigate the mediating role of organizational performance beside the organizational excellence as the ultimate variable in developing country, specifically in UAE.
Scale‐dependent shifts in functional and phylogenetic structure of Mediterranean island plant communities over two centuries
Authors: Zhang Chunhui , Cadotte Marc W. , Chiarucci Alessandro , Loreau Michel , Willis Charles G. , Si Xingfeng , Li Lanping , Cianciaruso Marcus V. 
Published: June 2021

Abstract

Since the Industrial Revolution, the rapid global population and economic expansion have had tremendous impacts on biodiversity across spatial scales, especially for islands. While changes in species richness are easily inferred, the impact of human activity on the underlying community assembly processes has been difficult to ascertain because of lack of long‐term community data.

Here, we document how the manifestations of plant community assembly have changed over time and space in a Mediterranean archipelago, using a long‐term dataset of plant species composition on 16 Tuscan islands sampled across two centuries. The community structure of Mediterranean island plant communities was assessed by integrating species' trait and evolutionary distances.

We found that, with increasing island area, the functional and phylogenetic structure of plant communities shifted from clustered early (1830–1950) to overdispersed more recently (1951–2015). On large islands, extirpated species were generally more phylogenetically or functionally similar to remaining residents than expected by chance, while colonists were generally more distantly related to residents. The extinction of similar species and the colonization of dissimilar species drove plant communities towards overdispersion.

Synthesis. We provide evidence that plant community assembly on islands has dramatically changed following increased human impacts during the last two centuries, and that this change is shaped by the scale dependency of species extinctions and colonizations. Our results reveal accelerated species replacements of closely related residents by distant colonists on large islands over time, reflecting changes in community assembly and which could alter the functioning of island ecosystems in the future.
Personal narratives of learning self‐management: Lessons for practice based on experiences of people with serious mental illness
Authors: Strong Susan , Letts Lori 
Published: June 2021

AbstractIntroductionClinicians are challenged to deliver self‐management interventions in recovery‐oriented services for individuals living with serious mental illnesses. Little is known about how people learn self‐management skills and questions remain about how best to deliver support. To offer insights for delivery, this research describes the lived experiences of learning self‐management and the meaning of those experiences within recovery journeys and the context of health‐care delivery.MethodsDesign followed van Manen's approach of phenomenology through an occupational therapist's lens. Using purposeful criterion sampling until saturation, 25 adults with psychosis experiences (8–40 years) from six community‐based specialised mental health programs were interviewed. Conceptual maps were cocreated depicting key learning experiences, intersections with services, and recommendations. Data reduction, reconstruction and explication of meaning occurred concurrently, and multiple strategies were used to transparently support an open, iterative, reflexive process.FindingsParticipants described eight essential tasks to live well, learned often serendipitously, taking up to 15–30 years to find the right combination of supports and self‐management strategies to achieve what they felt was a life of quality. Self‐management needs were not routinely addressed by services and extended beyond illness or crisis management while participants grappled with emotions, self‐concept, relationships, and occupational issues. Participants asked providers to “teach us to teach ourselves”; “invite clients” to the decision table; and deal directly with emotions of fear, shame, and trust with respect to self and relationships. Findings challenge conventional conceptualisations of self‐management to consider clients living interdependent lives with tasks performed in context, dynamically influenced by complex personal, socio‐ecological relationships.ConclusionsParticipants' narratives compel increasing access to strategic personalised self‐management learning opportunities as an effort to shorten the prolonged recovery paths. Findings offer ways providers can understand and address eight self‐management learning tasks from the perspective of lived experiences. Self‐management was enmeshed with recovery, health, and building a life.
The Structure and Financing of Health Care Systems Affected How Providers Coped With COVID‐19
Authors: WAITZBERG RUTH , QUENTIN WILM , WEBB ERIN , GLIED SHERRY 
Published: June 2021

Policy Points
We compared the structure of health care systems and the financial effects of the COVID‐19 pandemic on health care providers in the United States, England, Germany, and Israel: systems incorporating both public and private insurers and providers.
The negative financial effects on health care providers have been more severe in the United States than elsewhere, owing to the prevalence of activity‐based payment systems, limited direct governmental control over available provider capacity, and the structure of governmental financial relief.
In a pandemic, activity‐based payment reverses the conventional financial positions of payers and providers and may prevent providers from prioritizing public health because of the desire to avoid revenue loss caused by declines in patient visits.
Issue politicization and social class: How the electoral supply activates class divides in political preferences
Authors: ARES MACARENA 
Published: June 2021

AbstractAgainst premature claims about the declining political relevance of social class in post‐industrial democracies, recent research indicates that class continues to be a relevant determinant of political preferences. In post‐industrial societies ‘old’ class divides on economic issues coexist with ‘new’ class alignments on cultural topics. While there is cumulated evidence of social classes’ distinct placement on these issues, this paper argues that the strength of class divides depends on the extent to which these issues are politicized by political parties. Studying preferences on economic and cultural issues (attitudes towards redistribution, immigration, gay rights and European integration), this study shows that class divides in preferences are context dependent. The multilevel analyses drawing on data from the European Social Survey and the Chapel Hill Expert Survey for 27 European democracies demonstrate that classes’ differences in preferences are accentuated on issues strongly contested and emphasized by parties, and mitigated on issues where party conflict is weaker. Adding to recent literature on parties and class conflict, this study identifies another stage at which parties can affect the strength of class voting. The varying strength of class divides across contexts also has implications for parties’ ability to garner support beyond a single class. This becomes increasingly unlikely in contexts of high issue politicization.