bluuebunny/crossref_metadata_2025_split huggingface dataset:
REACT-1 round 12 report: resurgence of SARS-CoV-2 infections in England associated with increased frequency of the Delta variant
Authors: Riley Steven , Wang Haowei , Eales Oliver , Haw David , Walters Caroline E. , Ainslie Kylie E. C. , Atchison Christina , Fronterre Claudio , Diggle Peter J. , Page Andrew J. , Prosolek Sophie J. , Trotter Alexander J. , Le Viet Thanh , Alikhan Nabil-Fareed , Jackson Leigh M , Ludden Catherine ,   The COVID-19 Genomics UK (COG-UK) Consortium, Ashby Deborah , Donnelly Christl A. , Cooke Graham , Barclay Wendy , Ward Helen , Darzi Ara , Elliott Paul 
Published: June 2021

AbstractBackgroundEngland entered a third national lockdown from 6 January 2021 due to the COVID-19 pandemic. Despite a successful vaccine rollout during the first half of 2021, cases and hospitalisations have started to increase since the end of May as the SARS-CoV-2 Delta (B.1.617.2) variant increases in frequency. The final step of relaxation of COVID-19 restrictions in England has been delayed from 21 June to 19 July 2021.MethodsThe REal-time Assessment of Community Transmision-1 (REACT-1) study measures the prevalence of swab-positivity among random samples of the population of England. Round 12 of REACT-1 obtained self-administered swab collections from participants from 20 May 2021 to 7 June 2021; results are compared with those for round 11, in which swabs were collected from 15 April to 3 May 2021.ResultsBetween rounds 11 and 12, national prevalence increased from 0.10% (0.08%, 0.13%) to 0.15% (0.12%, 0.18%). During round 12, we detected exponential growth with a doubling time of 11 (7.1, 23) days and an R number of 1.44 (1.20, 1.73). The highest prevalence was found in the North West at 0.26% (0.16%, 0.41%) compared to 0.05% (0.02%, 0.12%) in the South West. In the North West, the locations of positive samples suggested a cluster in Greater Manchester and the east Lancashire area. Prevalence in those aged 5-49 was 2.5 times higher at 0.20% (0.16%, 0.26%) compared with those aged 50 years and above at 0.08% (0.06%, 0.11%). At the beginning of February 2021, the link between infection rates and hospitalisations and deaths started to weaken, although in late April 2021, infection rates and hospital admissions started to reconverge. When split by age, the weakened link between infection rates and hospitalisations at ages 65 years and above was maintained, while the trends converged below the age of 65 years. The majority of the infections in the younger group occurred in the unvaccinated population or those without a stated vaccine history. We observed the rapid replacement of the Alpha (B.1.1.7) variant of SARS-CoV-2 with the Delta variant during the period covered by rounds 11 and 12 of the study.DiscussionThe extent to which exponential growth continues, or slows down as a consequence of the continued rapid roll-out of the vaccination programme, including to young adults, requires close monitoring. Data on community prevalence are vital to track the course of the epidemic and inform ongoing decisions about the timing of further lifting of restrictions in England.
Large-scale screening of asymptomatic for SARS-CoV-2 variants of concern and rapid P.1 takeover, Curitiba, Brazil
Authors: Adamoski Douglas , de Oliveira Jaqueline Carvalho , Bonatto Ana Claudia , Wassem Roseli , Nogueira Meri Bordignon , Raboni Sonia Mara , Trindade Edvaldo da Silva , Souza Emanuel Maltempi ,   SCB-UFPR COVID-19 team, Gradia Daniela Fiori 
Published: June 2021

AbstractTo provide a safer environment for individuals working on-site at the Federal University of Paraná, Curitiba, Brazil, we performed a large-scale mass testing SARS-CoV-2 program coupled with variant genotyping using two PCR-based approaches. We observed a fast dominance of the Gamma variant, displacing other variants in less than three months.Article Summary LineCoronavirus variants of concern may use asymptomatic population as silent spreaders to perform a fast displacement of previous established strains.
Gaze-Related Activity in Primate Frontal Cortex Predicts and Mitigates Spatial Uncertainty
Authors: Bharmauria Vishal , Schütz Adrian , Khoozani Parisa Abedi , Yan Xiaogang , Wang Hongying , Bremmer Frank , Crawford J. Douglas 
Published: June 2021

ABSTRACTA remarkable feature of primate behavior is the ability to predict future events based on past experience and current sensory cues. To understand how the brain plans movements in the presence of unstable cues, we recorded gaze-related activity in the frontal cortex of two monkeys engaged in a quasi-predictable cue-conflict task. Animals were trained to look toward remembered visual targets in the presence of a landmark that shifted with fixed amplitude but randomized direction. As simulated by a probabilistic model based on known physiology/behavior, gaze end points assumed a circular distribution around the target, mirroring the possible directions of the landmark shift. This predictive strategy was reflected in frontal cortex activity (especially supplementary eye fields), which anticipated future gaze distributions before the actual landmark shift. In general, these results implicate prefrontal cortex in the predictive integration of environmental cues and their learned statistical properties to mitigate spatial uncertainty.
G Protein-Coupled Receptor-Ligand Dissociation Rates and Mechanisms from τRAMD Simulations
Authors: Kokh Daria B. , Wade Rebecca C. 
Published: June 2021

ABSTRACTThere is a growing appreciation of the importance of drug-target binding kinetics for lead optimization. For G protein-coupled receptors (GPCRs), which mediate signaling over a wide range of timescales, the drug dissociation rate is often a better predictor of in vivo efficacy than binding affinity, although it is more challenging to compute. Here, we assess the ability of the τ-Random Acceleration Molecular Dynamics (τRAMD) approach to reproduce relative residence times and reveal dissociation mechanisms and the effects of allosteric modulation for two important membrane-embedded drug targets: the β2-adrenergic receptor and the muscarinic acetylcholine receptor M2. The dissociation mechanisms observed in the relatively short RAMD simulations (in which molecular dynamics (MD) simulations are performed using an additional force with an adaptively assigned random orientation applied to the ligand) are in general agreement with much more computationally intensive conventional MD and metadynamics simulations. Remarkably, although decreasing the magnitude of the random force generally reduces the number of egress routes observed, the ranking of ligands by dissociation rate is hardly affected and agrees well with experiment. The simulations also reproduce changes in residence time due to allosteric modulation and reveal associated changes in ligand dissociation pathways.TABLE OF CONTENTS GRAPHIC
High-accuracy alignment ensembles enable unbiased assessments of sequence homology and phylogeny
Authors: Edgar Robert C. 
Published: June 2021

AbstractMultiple sequence alignments (MSAs) are widely used to infer evolutionary relationships, enabling inferences of structure, function, and phylogeny. Standard practice is to construct one MSA by some preferred method and use it in further analysis; however, undetected MSA bias can be problematic. I describe Muscle5, a novel algorithm which constructs an ensemble of high-accuracy MSAs with diverse biases by perturbing a hidden Markov model and permuting its guide tree. Confidence in an inference is assessed as the fraction of the ensemble which supports it. Applied to phylogenetic tree estimation, I show that ensembles can confidently resolve topologies with low bootstrap according to standard methods, and conversely that some topologies with high bootstraps are incorrect. Applied to the phylogeny of RNA viruses, ensemble analysis shows that recently adopted taxonomic phyla are probably polyphyletic. Ensemble analysis can improve confidence assessment in any inference from an MSA.
easyFulcrum: An R package to process and analyze ecological sampling data generated using the Fulcrum mobile application
Authors: Di Bernardo Matteo , Crombie Timothy A. , Cook Daniel E. , Andersen Erik C. 
Published: June 2021

AbstractLarge-scale ecological sampling can be difficult and costly, especially for organisms that are too small to be easily identified in a natural environment by eye. Typically, these microscopic floral and fauna are sampled by collecting substrates from nature and then separating organisms from substrates in the laboratory. In many cases, diverse organisms can be identified to the species-level using molecular barcodes. To facilitate large-scale ecological sampling of microscopic organisms, we used a geographic data-collection platform for mobile devices called Fulcrum that streamlines the organization of geospatial sampling data, substrate photographs, and environmental data at natural sampling sites. These sampling data are then linked to organism isolation data from the laboratory. Here, we describe the easyFulcrum R package, which can be used to clean, process, and visualize ecological field sampling and isolation data exported from the Fulcrum mobile application. We developed this package for wild nematode sampling, but it is extensible to other organisms. The advantages of using Fulcrum combined with easyFulcrum are (1) the elimination of transcription errors by replacing manual data entry and/or spreadsheets with a mobile application, (2) the ability to clean, process, and visualize sampling data using a standardized set of functions in the R software environment, and (3) the ability to join disparate data to each other, including environmental data from the field and the molecularly defined identities of individual specimens isolated from samples.
Opioid antagonism reduces wanting by strengthening frontostriatal connectivity
Authors: Soutschek Alexander , Weber Susanna C. , Kahnt Thorsten , Quednow Boris B. , Tobler Philippe N. 
Published: June 2021

AbstractGoal-directed behavior depends on both motivational (“wanting”) and hedonic (“liking”) dimensions of rewards. Previous animal and human research linked wanting and liking to anatomically and neurochemically distinct brain mechanisms, but it remains unknown as to how the different brain regions and neurotransmitter systems interact in processing distinct reward dimensions. Here, we assessed how pharmacological manipulations of opioid and dopamine receptor activation modulate the neural processing of wanting and liking in humans in a randomized, placebo-controlled, double-blind clinical trial. Blocking opioid receptor activation with naltrexone selectively reduced wanting of rewards, which on a neural level was reflected by stronger coupling between dorsolateral prefrontal cortex and the striatum under naltrexone compared with placebo. Our findings thus provide insights into how opioid receptors mediate frontostriatal gating of specifically motivational, not hedonic, aspects of rewards.
Luminosity thresholds of colored surfaces are determined by their upper-limit luminances empirically internalized in the visual system
Authors: Morimoto Takuma , Numata Ai , Fukuda Kazuho , Uchikawa Keiji 
Published: June 2021

AbstractWe typically have a fairly good idea whether a given object is self-luminous or illuminated, but it is not fully understood how we make this judgement. This study aimed to identify determinants of the luminosity threshold, a luminance level at which a surface begins to appear self-luminous. We specifically tested a hypothesis that our visual system knows the maximum luminance level that a surface can reach under the physical constraint that a surface cannot reflect more light than any incident light and applies this prior to determine the luminosity thresholds. Observers were presented with a 2-degree circular test field surrounded by numerous overlapping colored circles and luminosity thresholds were measured as a function of (i) the chromaticity of the test field, (ii) the shape of surrounding color distribution and (iii) the color of the illuminant of the surrounding colors. We found that the luminosity thresholds peaked around the chromaticity of test illuminants and decreased as the purity of the test chromaticity increased. However, the loci of luminosity thresholds across chromaticities were nearly invariant to the shape of the surrounding color distribution and generally resembled the loci drawn from theoretical upper-limit luminances and upper-limit luminance boundaries of real objects. These trends were particularly evident for illuminants on the black-body locus and did not hold well under atypical illuminants such as magenta or green. These results support the idea that our visual system empirically internalizes the gamut of surface colors under natural illuminants and a given object appears self-luminous when its luminance exceeds this internalized upper-limit luminance.
Reprogramming and redifferentiation of mucosal-associated invariant T cells reveals tumor inhibitory activity
Authors: Sugimoto Chie , Murakami Yukie , Ishi Eisuke , Fujita Hiroyoshi , Wakao Hiroshi 
Published: June 2021

AbstractMucosal-associated invariant T (MAIT) cells belong to a family of innate-like T cells that bridge innate and adaptive immunities. Although MAIT cells have been implicated in tumor immunity, it currently remains unclear whether they function as tumor promoting or inhibitory cells. Therefore, we herein used induced pluripotent cell (iPSC) technology to investigate this issue. Murine MAIT cells were reprogrammed into iPSCs and redifferentiated towards MAIT-like cells (m-reMAIT cells). m-reMAIT cells were activated by an agonist and MR1-tetramer, a reagent to detect MAIT cells, in the presence and absence of antigen-presenting cells. This activation accompanied protein tyrosine phosphorylation and the production of T helper (Th)1-, Th2-, and Th17-cytokines and inflammatory chemokines. Upon adoptive transfer, m-reMAIT cells migrated to different organs with maturation in mice. Furthermore, m-reMAIT cells prolonged mouse survival upon tumor inoculation through the NK cell-mediated reinforcement of cytolytic activity. Collectively, the present results demonstrated the utility and role of m-reMAIT cells in tumor immunity, and will contribute to insights into the function of MAIT cells in immunity.
“What a wonderful world!”: human relatedness, social space and accountability through action in a top-level amateur choir
Authors: De Loo Ivo , Kamminga Pieter 
Published: June 2021

PurposeDuring choir rehearsals, a conductor continuously holds choir members accountable for what they do and how they sing. Hence, members are held accountable through action. This allows a conductor to emphasize his/her expertise and underline his/her authority. Choir members typically respond in certain ways when this is done, for instance by commenting on the feedback they receive or by trying to improve their singing. The interplay between these accounts, how they develop over time, and what they (do not) accomplish in terms of human relatedness are the focus of this study. We use Bauman's (1993) conceptualization of social space to investigate these issues.Design/methodology/approachBy providing reasons for their conduct and behaving in a certain way, a conductor and choir members, but also a choir's management, can alter their position in social space. Thereby, they solidify or change how they relate to other individuals in the choir. Bauman assumes that processes of social spacing require so-called “misunderstandings”. We examine seven misunderstandings that occurred in a particular rehearsal of a top-level amateur choir, analyzing their impact on human relatedness. Video analysis methods, interviews and photo-elicitation are the main research methods used.FindingsWe find both short-term and long-term effects of misunderstandings on human relatedness, and offer two extensions of Bauman's (1993) conception of social space. Firstly, we assert that there is a reflective side to processes of social spacing that needs to be taken into account when changes in human relatedness are discussed. Secondly, we find that the emotional impact of accountability on how individuals behave ought not to be underestimated, as this can have lasting effects on how people relate to one another.Originality/valueThis research makes two contributions to the extant literature. It is shown how accountability through action unfolds when people engage in leisurely activity, and how this affects the way they relate to one another – in sometimes unintentional and unpredictable ways. It also extends a well-known theoretical framework on social space that has seen little application in the accounting literature. This framework is adapted so that it may be used more fruitfully in future accounting studies.
What is good work in a hybrid organization? On the efforts of sequencing registers of valuation
Authors: Schrøder Ida , Cederberg Emilia , Hauge Amalie M. 
Published: June 2021

PurposeThis paper investigates how different and sometimes conflicting approaches to performance evaluations are hybridized in the day-to-day activities of a disciplined hybrid organization–i.e. a public child protection agency at the intersection between the market and the public sector.Design/methodology/approachThe paper is based on a one-year ethnography of how employees achieve to qualify their work as “good work” in situations with several and sometimes conflicting ideals of what “good work” is. Fieldwork material was collected by following casework activities across organizational boundaries. By combining accounting literature on hybridization with literature on practices of valuation, the paper develops a novel theoretical framework which allows for analyses of the various practices of valuation, when and where they clash and how they persist over time in everyday work.FindingsThroughout the study, four distinct registers of valuation were identified: feeling, theorizing, formalizing and costing. To denote the meticulous efforts of pursuing good work in all four registers of valuation, the authors propose the notion of sequencing. Sequencing is an ongoing process of moving conflicting registers away from each other and bringing them back together again. Correspondingly, at the operational level of a hybrid organization, temporary compartmentalization is a means of avoiding clashes, and in doing so, making it possible for different and sometimes conflicting ways of achieving good results to continuously hybridize and persist together.Research limitations/implicationsThe single-case approach allows for analytical depth, but limits the findings to theoretical, rather than empirical, generalizability. The framework the authors propose, however, is well-suited for mobilization and potential elaboration in further empirical contexts.Originality/valueThe paper provides a novel theoretical framework as well as rich empirical material from the highly political field of child protection work, which has seldomly been studied within accounting research.
Evaluating farm and export competitiveness of the Irish dairy industry: post-quota analysis
Authors: Cele Lungelo Prince , Hennessy Thia , Thorne Fiona 
Published: June 2021

Purpose
This paper aims to examine the competitiveness trends and rankings of the Irish dairy sector at the farm and trade levels, relative to selected European Union (EU) Member States, in the context of the removal of the EU milk quota in 2015.

Design/methodology/approach
Competitiveness indicators including partial productivity measures and accountancy-based indicators were used for farm competitiveness, and net export market share and normalised revealed comparative advantage (NRCA) were used for export competitiveness.

Findings
Amongst the countries examined, Ireland had the highest growth in partial productivity indicators and was ranked first with the lowest total costs and cash costs per kg of milk solids post-quota. However, the total economic cost sub-components showed that Irish dairy farmers had high opportunity costs for owned land and labour. While Irish dairy products such as butter and powders have demonstrated growth potential in competitiveness post-quota with Irish butter and whey ranked in top three relative to other countries, other products, i.e. cheese and liquid milk have declined in competitiveness according to key export competitiveness indicators used.

Practical implications
The challenge for Irish dairy farmers is how to mitigate relatively high land and labour costs, which can limit farm competitiveness in the long run. The key players in the Irish dairy industry can now better position themselves in the global dairy market, recognizing the competitiveness dynamics of the different dairy products and their competitors. Policy implications and further areas of research have been identified to help improve the overall competitiveness position. It is surprising that Irish butter is a leader in the EU, yet not much research has been done to understand the market dynamics of this sector.

Originality/value
To the best of the authors’ knowledge, this study is the first of its kind to use both farm and export competitiveness measures to analyse the Irish dairy industry relative to other countries in the context of quota abolition. Unlike previous studies on dairy export competitiveness, this study has disaggregated the processed dairy products, which allowed for the ranking of countries and comparability across countries using NRCA.