bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of dim-light vision in the nocturnal coral reef fish family, Holocentridae
Authors: Fogg Lily G. , Cortesi Fabio , Lecchini David , Gache Camille , Marshall N. Justin , de Busserolles Fanny 
Published: May 2022

AbstractDevelopmental changes to the visual systems of animals are often associated with ecological shifts. Reef fishes experience a change in habitat between larval life in the shallow open ocean to juvenile and adult life on the reef. Some species also change their lifestyle over this period and become largely nocturnal. While these ecological transitions are well documented, little is known about the ontogeny of nocturnal reef fish vision. Here, we used histology and transcriptomics to investigate visual development in 12 representative species from both subfamilies, Holocentrinae (squirrelfishes) and Myripristinae (soldierfishes), in the nocturnal coral reef fish family, Holocentridae. Results revealed that the visual systems of holocentrids are initially well-adapted to photopic conditions with pre-settlement larvae having high cone densities, high cone opsin gene expression, a broad cone opsin gene repertoire (8 genes) and a multibank retina (i.e., stacked layers of rods) comprising up to two rod banks. At reef settlement, holocentrids started to invest more in their scotopic visual system and upregulated genes involved in cell differentiation/proliferation. By adulthood, they had well-developed scotopic vision with a rod-dominated multibank retina comprising 5-17 rod banks, increased summation of rods onto ganglion cells, high rod opsin gene expression, reduced cone opsin gene expression and repertoire (1-4 genes) and upregulated phototransduction genes. Finally, although the two subfamilies shared similar ecologies across development, their visual systems diverged after settlement, with Myripristinae investing more in scotopic vision than Holocentrinae. Hence, both ecology and phylogeny likely determine the development of the holocentrid visual system.Summary statementCoral reef fishes in the family Holocentridae remodel their retina at the cellular and molecular levels to adapt to a nocturnal lifestyle during development.
Insomnia symptoms and risk of bloodstream infections: prospective data from the prospective population-based HUNT Study, Norway
Authors: Thorkildsen Marianne S. , Laugsand Lars E. , Nilsen Tom I.L. , Mohus Randi M. , Høvik Lise H. , Rogne Tormod , Solligård Erik , Damås Jan K. , Gustad Lise T. 
Published: May 2022

AbstractObjectivePrevious research suggest decreased immune function and increased risk of infections in persons with insomnia. We examined the effect of insomnia symptoms on risk of bloodstream infections (BSI) and BSI-related mortality in a population-based prospective study.MethodsA total of 53,536 participants in the Norwegian HUNT2 study (1995–97) were linked to prospective data on clinically relevant BSIs until 2011. In Cox regression, we estimated hazard ratios (HRs) with 95% confidence interval (CI) for a first-time BSI and for BSI related mortality (BSI registered ≤30 days prior to death) associated with insomnia symptoms.ResultsCompared with participants who reported “no symptoms of insomnia”, participants reporting having “difficulty initiating sleep” often/almost every night had a HR for a first-time BSI of 1.14 (95% CI 0.96–1.34). Participants reporting “difficulties maintaining sleep” often/almost every night had a HR of 1.19 (95% CI 1.01–1.40), whereas those having a “feeling of non-restorative sleep” once a week or more had a HR of 1.23 (95% CI 1.04–1.46). Participants experiencing all three above insomnia symptoms frequently had a HR of 1.39 (1.04–1.87) and being troubled by insomnia to a degree that affected work performance was associated with a HR of 1.41 (95% CI 1.08–1.84). The HRs for BSI related mortality suggest an increased risk with increasing insomnia symptoms, but confidence intervals are wide and inconclusive.ConclusionsWe found that frequent insomnia symptoms and insomnia symptoms that affected work performance was associated with a weak positive increased risk of BSI.
Socioeconomic inequality in SARS-CoV-2 testing and COVID-19 outcomes in UK Biobank over the first year of the pandemic: can inequalities be explained by selection bias?
Authors: Carter Alice R , Clayton Gemma L , Borges M Carolina , Howe Laura D , Hughes Rachael A , Davey Smith George , Lawlor Deborah A , Tilling Kate , Griffith Gareth J 
Published: May 2022

AbstractBackgroundStructural barriers to testing may introduce selection bias in COVID-19 research. We explore whether changes to testing and lockdown restrictions introduce time-specific selection bias into analyses of socioeconomic position (SEP) and SARS-CoV-2 infection.MethodsUsing UK Biobank (N = 420 231; 55 % female; mean age = 56·3 [SD=8·01]) we estimated the association between SEP and i) being tested for SARS-CoV-2 infection versus not being tested ii) testing positive for SARS-CoV-2 infection versus testing negative and iii) testing negative for SARS-CoV-2 infection versus not being tested, at four distinct time-periods between March 2020 and March 2021. We explored potential selection bias by examining the same associations with hypothesised positive (ABO blood type) and negative (hair colour) control exposures. Finally, we conducted a hypothesis-free phenome-wide association study to investigate how individual characteristics associated with testing changed over time.FindingsThe association between low SEP and SARS-CoV-2 testing attenuated across time-periods. Compared to individuals with a degree, individuals who left school with GCSEs or less had an OR of 1·05 (95% CI: 0·95 to 1·16) in March-May 2020 and 0·98 (95% CI: 0·94 to 1·02) in January-March 2021. The magnitude of the association between low SEP and testing positive for SARS-CoV-2 infection increased over the same time-period. For the same comparisons, the OR for testing positive increased from 1·27 (95% CI: 1·08 to 1·50), to 1·73 (95% CI: 1·59 to 1·87). We found little evidence of an association between both control exposures and all outcomes considered. Our phenome-wide analysis highlighted a broad range of individual traits were associated with testing, which were distinct across time-periods.InterpretationThe association between SEP (and indeed many individual traits) and SARS-CoV-2 testing changed over time, indicating time-specific selection pressures in COVID-19. However, positive, and negative control analyses suggest that changes in the magnitude of the association between SEP and SARS-CoV-2 infection over time were unlikely to be explained by selection bias and reflect true increases in socioeconomic inequalities.FundingUniversity of Bristol; UK Medical Research Council; British Heart Foundation; European Union Horizon 2020; Wellcome Trust and The Royal Society; National Institute of Health Research; UK Economic and Social Research Council
A parallel channel of state-dependent sensory signaling from the cholinergic basal forebrain to the auditory cortex
Authors: Zhu Fangchen , Elnozahy Sarah E. , Lawlor Jennifer , Kuchibhotla Kishore V. 
Published: May 2022

AbstractCholinergic basal forebrain (CBF) signaling exhibits multiple timescales of activity with classic, slow signals related to brain and behavioral states and faster, phasic signals reflecting behavioral events, including movement and reinforcement. Recent evidence suggests that the CBF may also exhibit fast, sensory-evoked responses. It remains unknown, however, whether such sensory signals target the sensory cortex and how they relate to local functional topography. Moreover, the extent to which fast and slow CBF activity interact has been largely unexplored. Here, we used simultaneous two-channel, two-photon imaging of CBF axons and auditory cortical (AC) neurons to reveal that CBF axons project a robust, non-habituating, and stimulus-specific sensory signal to the AC. Individual axon segments exhibited heterogeneous but stable tuning to auditory stimuli allowing stimulus identity to be decoded from the population. However, CBF axons displayed no tonotopy and their frequency tuning was uncoupled from that of nearby cortical neurons. Chemogenetic suppression revealed the auditory thalamus as a principal source of auditory information to the CBF. Finally, slow fluctuations in cholinergic activity modulated the fast, sensory-evoked signals in the same axons, suggesting that a multiplexed combination of fast and slow signals is projected from the CBF to the AC. Taken together, our work demonstrates a novel, non-canonical function of the CBF as a parallel channel of state-dependent sensory signaling to the sensory cortex that provides repeated representations of a broad range of sound stimuli at all points on the tonotopic map.
Microbial paracetamol degradation involves a high diversity of novel amidase enzyme candidates
Authors: Rios-Miguel Ana B. , Smith Garrett J. , Cremers Geert , van Alen Theo , Jetten Mike S.M. , Op den Camp Huub J. M. , Welte Cornelia U. 
Published: May 2022

AbstractPharmaceuticals are relatively new to nature and often not completely removed in wastewater treatment plants (WWTPs). Consequently, these micropollutants end up in water bodies all around the world posing a great environmental risk. One exception to this recalcitrant conversion is paracetamol, whose full degradation has been linked to several microorganisms. However, the genes and corresponding proteins involved in microbial paracetamol degradation are still elusive. In order to improve our knowledge of the microbial paracetamol degradation pathway, we inoculated a bioreactor with sludge of a hospital WWTP (Pharmafilter, Delft, NL) and fed it with paracetamol as the sole carbon source. Paracetamol was fully degraded without any lag phase and the enriched microbial community was investigated by metagenomic and metatranscriptomic analyses, which demonstrated that the microbial community was very diverse. Dilution and plating on paracetamol-amended agar plates yielded twoPseudomonassp. isolates: a fast-growingPseudomonassp. that degraded 200 mg/L of paracetamol in approximately 10 hours while excreting a dark brown component to the medium, and a slow-growingPseudomonassp. that degraded paracetamol without obvious intermediates in more than 90 days. EachPseudomonassp. contained a different highly-expressed amidase (31% identity to each other). These amidase genes were not detected in the bioreactor metagenome suggesting that other as-yet uncharacterized amidases may be responsible for the first biodegradation step of paracetamol. Uncharacterized deaminase genes and genes encoding dioxygenase enzymes involved in the catabolism of aromatic compounds and amino acids were the most likely candidates responsible for the degradation of paracetamol intermediates based on their high expression levels in the bioreactor metagenome and thePseudomonasspp. genomes. Furthermore, cross-feeding between different community members might have occurred to efficiently degrade paracetamol and its intermediates in the bioreactor. This study increases our knowledge about the ongoing microbial evolution towards biodegradation of pharmaceuticals and points to a large diversity of (amidase) enzymes that are likely involved in paracetamol metabolism in WWTPs.HighlightsParacetamol was fully degraded by activated sludge from hospital wastewater.Low paracetamol concentrations were removed by a diverse microbial community.Pseudomonassp. dominated cultures with high paracetamol concentration.Uncharacterized amidases are probably involved in degrading paracetamol in WWTPs.Deaminases and dioxygenases might be degrading paracetamol transformation products.
Microglial expression of the Wnt signalling modulator DKK2 differs between human Alzheimer’s disease brains and mouse neurodegeneration models
Authors: Aghaizu Nozie D. , Jolly Sarah , Samra Satinder K. , Kalmar Bernadett , Craessaerts Katleen , Greensmith Linda , Salinas Patricia C. , Strooper Bart De , Whiting Paul J. 
Published: May 2022

AbstractWnt signalling is crucial for synapse and cognitive function. Indeed, deficient Wnt signalling is causally related to increased expression of DKK1, an endogenous negative Wnt regulator, and synapse loss, both of which likely contribute to cognitive decline in Alzheimer’s disease (AD). Increasingly, AD research efforts have probed the neuroinflammatory role of microglia, the resident immune cells of the central nervous system (CNS), which have furthermore been shown to be modulated by Wnt signalling.The DKK1 homologue DKK2 has been previously identified as an activated response and/or disease-associated microglia (DAM/ARM) gene in a mouse model of AD. Here we performed a detailed analysis of DKK2 in mouse models of neurodegeneration, and in human AD brain. In APP/PS1 and APPNL-G-F AD mouse model brains as well as in SOD1G93A ALS mouse model spinal cords, but not in control littermates, we demonstrated significant microgliosis and microglial Dkk2 mRNA upregulation in a disease-stage dependent manner. In the AD models, these DAM/ARM Dkk2+ microglia preferentially accumulated close to βAmyloid plaques. Furthermore, recombinant DKK2 treatment of rat hippocampal primary neurons blocked WNT7a-induced dendritic spine and synapse formation, indicative of an anti-synaptic effect similar to that of DKK1. In stark contrast, no such microglial DKK2 upregulation was detected in the post-mortem human frontal cortex from individuals diagnosed with AD or pathological ageing.In summary, the difference in microglial expression of the DAM/ARM gene DKK2 between mouse models and human AD brain highlights the increasingly recognised limitations of using mouse models to recapitulate facets of human neurodegenerative disease.Significance statementThe endogenous negative Wnt regulator Dkk2 is significantly upregulated at the mRNA level in microglia of AD mouse models, implying that microglia derived Dkk2 protein may detrimentally contribute to a reduced Wnt signalling tone in the AD brain, a known pathophysiological manifestation. Indeed, recombinant DKK2 prevented Wnt- dependent synapse formation in cultured neurons. However, DKK2 upregulation was not recapitulated in post-mortem human AD brains.The success of neurodegeneration animal models has relied on pathophysiology that for the most part correctly modelled human disease. Increasingly however, limitations to the validity of mouse models to recapitulate human neurodegenerative disease have become apparent, as evidenced by the present study by the difference in microglial DKK2 expression between AD mouse models and human AD brain.
An Entropy Approach for Choosing Gene Expression Cutoff
Authors: Vuong Hy , Nguyen Tung , Nguyen Huy , Truong Thao , Pham Son 
Published: May 2022

AbstractAnnotating cell types using single-cell transcriptome data usually requires binarizing the expression data to distinguish between the background noise vs. real expression or low expression vs. high expression cases. A common approach is choosing a “reasonable” cutoff value, but it remains unclear how to choose it. In this work, we describe a simple yet effective approach for finding this threshold value.
VanRS and CroRS cross-talk revealed by coevolutionary modeling regulates antibiotic resistance in VanA-type vancomycin-resistant Enterococcus faecalis
Authors: Jiang Xian-Li , Nguyen Uyen Thy , Ziegler Cheyenne , Goel Deepshikha , Palmer Kelli , Morcos Faruck 
Published: May 2022

AbstractEnterococcus faecalis is an opportunistic pathogen that can cause bacteremia and endocarditis. Previous studies have shown that concurrent treatment with cephalosporin and vancomycin antibiotics exhibit synergy in vancomycin-resistant E. faecalis to render the bacterium susceptible to antibiotic treatment whereas treatment with each antibiotic separately was not successful. Proteins responsible for mediating vancomycin and cephalosporin resistance are classified as two-component systems (TCS). TCS consist of a histidine kinase that phosphorylates a response regulator after environmental activation. These signaling networks have been shown to exhibit cross-talk interactions, and through direct coupling analysis, we identify encoded specificity between vancomycin resistance TCS, which are horizontally acquired, and cephalosporin resistance TCS, which are endogenous to E. faecalis. To verify cross-talk between these pathways is responsible for vancomycin and cephalosporin synergy, we use RNA-Seq to identify differentially expressed genes in VanA- and VanB-type vancomycin resistant enterococci after treatment with the cephalosporin antibiotic, ceftriaxone, and also with vancomycin. We find that cross-talk between VanSA and CroR in strain HIP11704 may be responsible for synergy, demonstrating that horizontally acquired TCS can have large impacts on pre-existing signaling networks. The presence of encoded specificity between exogenous TCS and endogenous TCS show that the systems co-evolve, and cross-talk between these systems may be exploited to engineer genetic elements that disrupt antibiotic resistance TCS pathways.Author SummaryBacteria may transmit genetic elements to other bacteria through the process known as horizontal gene transfer. In some enterococci, vancomycin resistance genes are acquired this way. Proteins encoded within the bacterial genome can interact with proteins acquired through horizontal gene transfer. The interaction that occurs between proteins VanSA and VanRA is known to mediate vancomycin antibiotic resistance in VanA-type vancomycin resistant enterococci (VRE), and the interaction between proteins CroS and CroR is an important pathway in cephalosporin antibiotic resistance. We show that the VanSA, which is obtained through horizontal gene transfer, inhibits CroR under treatment with antibiotics vancomycin and ceftriaxone. This interaction is responsible for the observed synergy between vancomycin and ceftriaxone in VanA-type VREs. These findings demonstrate how horizontally acquired genes may produce proteins that interrupt known protein interactions, including antibiotic resistance signaling pathways in bacteria. Furthermore, the specific mechanism found for VanA-type VREs provides a basis for engineering of horizontally acquired proteins that disrupt antibiotic resistance pathways.
Reconstructing the decline of Atlantic Cod with the help of environmental variability in the Scotian Shelf of Canada
Authors: Choi Jae S. 
Published: May 2022

AbstractIgnoring environmental variability can lead to imprecise and inaccurate estimates of abundance and their spatial distribution of organisms. Fully embracing environmental variability can improve precision and accuracy of estimates of abundance and distribution, especially when they can often be measured with lower costs. Using the example of Atlantic cod in the Scotian Shelf of the northwest Atlantic Ocean, we demonstrate the improved clarity of their historical population trends when such informative features are included. Further, the use of Bayesian spatiotemporal Conditional auto-regressive models substantially improves our ability to understand the role of ecosystem variability upon cod, even when samples are incomplete or missing. Finally, by decomposing biomass into number, weight and a Hurdle process to estimate habitat conditions, we can extract much more information on what has occurred in the past and make reasoned inference on processes.One-Sentence SummaryDeconstructing and reconstructing cod with environmental variability
Organic food market segmentation based on the neobehavioristic theory of consumer behavior
Authors: Tohidi Amirhossein , Mousavi Seyedehmona , Dourandish Arash , Alizadeh Parisa 
Published: May 2022

PurposeAlthough Iran is one of the largest producers and exporters of saffron in the world, the organic saffron market in Iran is still in its early stages, and there is scarce empirical evidence in this regard. Therefore, the study's primary purpose is to segment the organic saffron market in Mashhad, Iran using neobehavioristic theory and machine learning methods.Design/methodology/approachConsidering the neobehavioristic theory of consumer behavior, the organic saffron market was segmented using crisp and fuzzy clustering algorithms. Also, to assess the relative importance of the factors affecting the intention to buy organic saffron in each market segment, a sensitivity analysis was performed on the output of the artificial neural network (ANN). A total of 400 questionnaires were collected in Mashhad, Iran in January and February 2020.FindingsIn contrast to the belief that psychological factors are more important in market segmentation than demographic characteristics, findings showed that the demographic characteristics of consumers, especially education and income, are the dominant variables in the segmentation of the organic food market. Among the 4 A’s marketing mix elements, the results showed that a low level of awareness and accessibility are obstacles to organic saffron market development. Advertising, distribution channel improvement, package downsizing and online business development are suggested strategies for expanding the organic saffron market in Iran.Practical implicationsThe results of the present study will help policymakers and suppliers of organic saffron to identify their target markets and design short- and long-term marketing strategies to develop the organic saffron market.Originality/valueMachine learning methods and the neobehavioristic theory of consumer behavior were used to segment the organic food market.
The nature of innovation in hospital building design: a mixed grounded theory study
Authors: Sal Moslehian Anahita , Kocaturk Tuba , Andrews Fiona , Tucker Richard 
Published: May 2022

Purpose
Despite the undeniable need for innovation in hospital building design, the literature highlights the disconnect between research and practice as the primary knowledge gap hindering such innovation. This study shows this focus to be an oversimplification, for the complex processes that trigger design innovations and impact their ecosystems need to be examined from a systemic perspective. This paper aims to conceptualise the evolution of hospital building design and identify and explain the main factors triggering design and construction innovations over the past 100 years.

Design/methodology/approach
A novel hybrid research design to mixed grounded theory (MGT) methodology, with Charmaz constructivist paradigm, is developed as a new systematic way of constructing and interpreting the concepts and interconnections among them that triggered design innovation.

Findings
This study represents a taxonomy of concepts and an explanatory innovation framework, containing 617 interconnections between 146 factors classified across 14 categories. The complex innovation ecosystem comprises multi-faceted processes between heterogenous factors with both individual and collective impacts on design innovations.

Originality/value
This research highlights the main components of the innovation ecosystem and its overall behaviour in this field, and the most influential and interrelated contextual factors, as well as representing and mapping generative interactions that support innovation processes. This knowledge can help hospital researchers, designers, policymakers and stakeholders adopt a multidimensional outlook to analyse the strength of all influential factors, introduce potential novel ways of collaborating, conceptualise an organisational approach, re-formulate research questions through transdisciplinary methods and introduce interdisciplinary courses and programs in architecture schools, thereby contributing to timely design innovation.