bluuebunny/crossref_metadata_2025_split huggingface dataset:
Next-generation matrices for marine metapopulations: the case of sea lice on salmon farms*
Authors: Harrington Peter D. , Cantrell Danielle L. , Lewis Mark A. 
Published: May 2022

AbstractClassifying habitat patches as sources or sinks and determining metapopulation persistence requires coupling connectivity between habitat patches with local demographic rates. In this paper we show how next-generation matrices, originally popularized in epidemiology to calculate new infections after one generation, can be used in an ecological context to couple connectivity with local demography to calculate sources and sinks as well as metapopulation persistence in marine metapopulations. To demonstrate the utility of the method, we construct a next-generation matrix for a network of sea lice populations on salmon farms in the Broughton Archipelago, BC, an intensive salmon farming region on the west coast of Canada where certain salmon farms are currently being removed under an agreement between local First Nations and the provincial government. We identify the salmon farms which are acting as the largest sources of sea lice and show that in this region the most productive sea lice populations are also the most connected. We find that the farms which are the largest sources of sea lice have not yet been removed from the Broughton Archipelago, and that warming temperatures could lead to increased sea louse growth.
Community review: a robust and scalable selection system for resource allocation within open science and innovation communities
Authors: Graham Chris L. B. , Landrain Thomas E. , Vjestica Amber , Masselot Camille , Lawton Elliot , Blondel Leo , Haenel Luca , Tzovoras Bastian Greshake , Santolini Marc 
Published: May 2022

AbstractResource allocation is essential to the selection and implementation of innovative projects in science and technology. With large stakes involved in concentrating large fundings over a few promising projects, current “winner-take-all” models for grant applications are time-intensive endeavours that mobilise significant researcher time in writing extensive project proposals, and rely on the availability of a few time-saturated volunteer experts. Such processes usually carry over several months, resulting in high effective costs compared to expected benefits. Faced with the need for a rapid response to the Covid19 pandemic in 2020, we devised an agile “community review” system to allocate micro-grants for the fast prototyping of innovative solutions. Here we describe and evaluate the implementation of this community review across 147 projects from the “Just One Giant Lab’s OpenCOVID19 initiative” and “Helpful Engineering” open research communities. The community review process uses granular review forms and requires the participation of grant applicants in the review process. Within a year, we organised 7 rounds of review, resulting in 614 reviews from 201 reviewers, and the attribution of 48 micro-grants of up to 4,000 euros. We show that this system is fast, with a median process duration of 10 days, scalable, with a median of 4 reviewers per project independent of the total number of projects, and fair, with project rankings highly preserved after the synthetic removal of reviewers. We investigate the potential bias introduced by involving applicants in the process, and find that review scores from both applicants and non-applicants have a similar correlation of r=0.28 with other reviews within a project, matching previous observations using traditional approaches. Finally, we find that the ability of projects to apply to several rounds allows to both foster the further implementation of successful early prototypes, as well as provide a pathway to constructively improve an initially failing proposal in an agile manner. Overall, this study quantitatively highlights the benefits of a frugal, community review system acting as a due diligence for rapid and agile resource allocation in open research and innovation programs, with particular implications for decentralised communities.
Genetic and peripheral visual system changes underlie evolving butterfly mate preference
Authors: VanKuren Nicholas W. , Buerkle Nathan P. , Westerman Erica L. , Im Alexandria K. , Massardo Darli , Southcott Laura M. , Lu Wei , Palmer Stephanie E. , Kronforst Marcus R. 
Published: May 2022

Many studies have linked genetic variation to behavior, but less is known about how that variation alters the neural circuits that drive behavior. We investigated the genetic and neurobiological basis of courtship preference variation in Heliconius butterflies, which use vision to identify appropriate mates based on wing color patterns. We found that Heliconius cydno preference variation was strongly associated with genetic variation and differential expression of senseless-2, a gene predominantly expressed in the eye. Further measurements of photoreceptor sensitivities revealed differences in inter-photoreceptor inhibition of ultraviolet-sensitive cells corresponding to courtship preference variation. Our results reveal a genetic basis for preference/cue co-evolution, suggest a link between sens-2 and visual system variation, and support the idea that changing peripheral neural computations can significantly alter essential behaviors.SummaryGenetic and expression variation of senseless-2 and inter-photoreceptor inhibition predict visual mate preference in a clade of diverse butterflies.
Localization of chemical synapses and modulatory release sites in the cardiac ganglion of the crab, Cancer borealis
Authors: Rue Mara C.P. , Baas-Thomas Natasha , Iyenger Priya , Scaria Lara , Marder Eve 
Published: May 2022

AbstractThe crustacean cardiac ganglion (CG) comprises nine neurons that provide rhythmic drive to the heart. The CG is the direct target of multiple modulators. Synapsin-like immunoreactivity was found clustered around the somata of the large cells (LC) and in a neuropil at the anterior branch of the CG trunk. This implicates the soma as a key site of synaptic integration, an unusual configuration in invertebrates. Proctolin is an excitatory neuromodulator of the CG and proctolin-like immunoreactivity exhibited partial overlap with putative chemical synapses near the LCs and at the neuropil. A proctolin-like projection was also found in a pair of excitatory nerves entering the CG. GABA-like immunoreactivity was nearly completely colocalized with chemical synapses near the LCs but absent at the anterior branch neuropil. GABA-like projections were found in a pair of inhibitory nerves entering the CG. Cancer borealis Allatostatin B1 (CbAST-B1), red pigment concentrating hormone (RPCH) and FLMRFamide-like immunoreactivity each had a unique pattern of staining and co-localization with putative chemical synapses. These results provide morphological evidence that synaptic input is integrated at LC somata in the CG. Our findings provide a topographical organization for some of the multiple inhibitory and excitatory modulators that alter the rhythmic output of this semi-autonomous motor circuit.
High precision magnetoencephalography reveals increased right-inferior frontal gyrus beta power during response conflict
Authors: Daniel Pria L. , Bonaiuto James J. , Bestmann Sven , Aron Adam R. , Little Simon 
Published: May 2022

AbstractFlexibility of behavior and the ability to rapidly switch actions is critical for adaptive living in humans. It is well established that the right-inferior frontal gyrus (R-IFG) is recruited during outright action-stopping, relating to increased beta (12-30 Hz) power. Additionally, pre-supplementary motor area (pre-SMA) is plausibly recruited during response conflict/switching, relating to increased theta (4-8 Hz) power. It has been posited that inhibiting incorrect response tendencies is central to motor flexibility. However, it is not known if the commonly reported R-IFG beta signature of response inhibition in action-stopping is also recruited during response conflict, which would suggest overlapping networks for stopping and switching. In the current study, we analyzed high precision magnetoencephalography (hpMEG) data recorded with very high trial numbers (total n > 10,000) from 8 subjects during different levels of response conflict. We hypothesized that a R-IFG-triggered network for response inhibition is domain general and also involved in mediating response conflict. We therefore tested whether R-IFG showed increased beta power dependent on the level of response conflict. We also hypothesized that pre-SMA is an important node in response conflict processing, and tested whether pre-SMA theta power increased for response conflict trials. Using event-related spectral perturbations and linear mixed modeling, we found that both R-IFG beta and pre-SMA theta increased for response conflict trials, with the R-IFG beta increase specific to trials with strong response conflict. This result supports a more generalized role for R-IFG beta in response inhibition, beyond simple stopping behavior towards response switching.Significance StatementResponse inhibition is a core component of cognitive control. Neural mechanisms of response inhibition are typically studied using stopping paradigms. However, there is an unresolved debate regarding whether the response inhibition network is specific to stopping or generalizes to switching between tasks and overcoming conflict between competing response tendencies. Increased beta (12-30 Hz) in R-IFG has historically been interpreted as a marker of successful response inhibition in the stop-signal task. Here, we investigated the presence of this electrophysiological marker of response inhibition specifically during response conflict (switching). We found R-IFG beta power increased for trials with strong response conflict, and not for weak or no response conflict, thereby supporting a generalized role for R-IFG beta in response inhibition and switching.
Salivary Proinflammatory Cytokines IL-1β, IL-6 and TNF Decrease With Age
Authors: Costantino Evangelina , Castell Sofía Daiana , Harman María Florencia , Pistoresi- Palencia María Cristina , Actis Adriana Beatriz 
Published: May 2022

ABSTRACTObjectiveto analyze salivary concentrations interleukin-1β (IL-1β), 6 (IL-6) and tumor necrosis factor (TNF) according to age in healthy subjects to determine baseline inflammatory state of the oral mucosa in elderly subjects, who are at higher risk of developing inflammation-related diseases.Materials and methodssixty-four healthy volunteers were divided into groups according to age: 20-39 (G1; n=20); 40-59 (G2; n=24); 60-80 years (G3; n=20). Their stomatognathic system and periodontal status were assessed; consumption of food sources of fatty acids (FA) was evaluated using a validated food frequency questionnaire. IL-1β, IL-6, and TNF salivary levels were determined (ELISA) in mixed unstimulated saliva. Kruskal Wallis and Spearman’s correlation tests were applied (p<0.05).Resultssalivary IL-1β and TNF levels were lower in G2 (p=0.001) and G3 (p<0.001) than in G1; IL-6 levels were lower in G3 than in G2 and G1 (p= <0.001). IL-1β showed the highest concentration in all groups (p<0.001). No statistically significant differences in salivary cytokine levels were observed on sex in any of the groups. Associations were observed between salivary cytokines and consumption of some foods containing FA.Conclusionsalivary concentration of proinflammatory cytokines decreased with age. It could be influenced by ageing-related changes. In addtition, the baseline inflammatory state of the oral mucosa would appear to be influenced by dietary intake of sources of anti-inflammatory FA.Clinical relevancethe knowledge about inflammatory state of the oral mucosa, as determined by salivary cytokine concentrations, could be useful for understanding and prevention of developing inflammation-related diseases.
Boid Inclusion Body Disease (BIBD) Is Also a Disease of Wild Boa Constrictors
Authors: Alfaro-Alarcón Alejandro , Hetzel Udo , Smura Teemu , Baggio Francesca , Morales Juan Alberto , Kipar Anja , Hepojoki Jussi 
Published: May 2022

ABSTRACTReptarenaviruses cause Boid Inclusion Body Disease (BIBD), a potentially fatal disease, occurring in captive constrictor snakes boas and pythons worldwide. Classical BIBD, characterized by the formation of pathognomonic cytoplasmic inclusion bodies (IBs), occurs mainly in boas, whereas in pythons, for example, reptarenavirus infection most often manifests as central nervous system signs with limited IB formation. The natural hosts of reptarenaviruses are unknown, although wild constrictor snakes are among the suspects. Here, we report BIBD with reptarenavirus infection in indigenous captive and wild boid snakes in Costa Rica using histology, immunohistology, transmission electron microscopy, next-generation sequencing (NGS), and RT-PCR. The snakes studied represented diagnostic post mortem cases of captive and wild caught snakes since 1989. The results from NGS on archival paraffin blocks confirm that reptarenaviruses have been present in wild boa constrictors in Costa Rica already in the 1980s. Continuous sequences de novo assembled from the low-quality RNA obtained from paraffin embedded tissue allowed the identification of a distinct pair of reptrarenavirus S and L segments in all studied animals; in most cases reference assembly could recover almost complete segments. Sampling of three prospective cases in 2018 allowed examination of fresh blood or tissues, and resulted in identification of additional reptarenavirus segments and hartmanivirus co-infection. Our results show that BIBD is not only a disease of captive snakes, but also occurs in indigenous wild constrictor snakes in Costa Rica, suggesting boa constrictors to play a role in natural reptarenavirus circulation.IMPORTANCEThe literature describes cases of boid inclusion body disease (BIBD) in captive snakes since the 1970s, and in the 2010s, others and we identified reptarenaviruses as the causative agent. BIBD affects captive snakes globally, but the origin and the natural host of reptarenaviruses remains unknown. In this report, we show BIBD and reptarenavirus infections in two native Costa Rican constrictor snake species, and by studying archival samples, we show that both the viruses and the disease have been present in wild snakes in Costa Rica at least since the 1980s. The diagnosis of BIBD in wild boa constrictors suggests that this species plays a role in the circulation of reptarenaviruses. Additional sample collection and analysis would help to clarify this role further and the possibility of e.g. vector transmission from an arthropod host.
Pervasive transcription enhances the accessibility of H-NS-silenced promoters and generates bistability in Salmonella virulence gene expression
Authors: Figueroa-Bossi Nara , Sanchez-Romero María Antonia , Kerboriou Patricia , Naquin Delphine , Mendes Clara , Bouloc Philippe , Casadesús Josep , Bossi Lionello 
Published: May 2022

SummaryIn Escherichia coli and Salmonella, many genes silenced by the nucleoid structuring protein H-NS are activated upon inhibiting Rho-dependent transcription termination. This response is poorly understood and difficult to reconcile with the view that H-NS acts mainly by blocking transcription initiation. Here we have analysed the basis for the upregulation of H-NS-silenced Salmonella Pathogenicity Island 1 (SPI-1) in cells depleted of Rho-cofactor NusG. Evidence from genetic experiments, semi-quantitative 5’ RACE-Seq and ChiP-Seq shows that transcription originating from spurious antisense promoters, when not stopped by Rho, elongates into a H-NS-bound regulatory region of SPI-1, displacing H-NS and rendering the DNA accessible to the master regulator HilD. In turn, HilD’s ability to activate its own transcription triggers a positive feedback loop that results in transcriptional activation of the entire SPI-1. Significantly, single-cell analyses revealed that this mechanism is largely responsible for the coexistence of two subpopulations of cells that, although genetically identical, either express or don’t express SPI-1 genes. We propose that cell-to-cell differences produced by stochastic spurious transcription, combined with feedback loops that perpetuate the activated state, can generate bimodal gene expression patterns in bacterial populations.
Mobile Laser Scanner understory characterization: an exploratory study on hazel grouse in Italian Alps
Authors: Galluzzi Marta , Puletti Nicola , Armanini Marco , Chirichella Roberta , Mustoni Andrea 
Published: May 2022

AbstractForest vegetation structure assessment is a time expensive effort with traditional methods. The Mobile Laser Scanner (MLS) technology can greatly speed up field works, achieve detailed quantification of three-dimensional forest structure at detailed resolution and drive forest management to increase the conservation status of forests-specialist bird species. In this study, using Mobile hand-held Laser Scanner (MLS), we calculated a fine-scale vegetation density index (namely the Plant Density Index, PDI) to characterize the vertical structure of forest subcanopy (0-10 m). The collected MLS point clouds were used to estimate the abundance of Potential Hiding Refuges (PHR) for the hazel grouse (Tetrastes bonasia), a sedentary bird extremely sensitive to forest structure and composition. The study was carried out in 10 plots located in the Adamello Brenta Geopark (Southern Alps, Italy). The species was detected in 8 out of 18 transects in an uneven-aged spruce forest with a discontinuous tree cover. The PDI decreases as the height increases, showing greater value in the shrub and herbaceous layer while the upper values are represented by trees stems, and branches. Visibility analysis of lower understory, highlighted PHR mean value of 73.2% (sd = 9.2%). In our area, PDI and PHR revealed that the environmental factors for hazel grouse occurrence are forests with open habitats, understory vegetation, and good hiding opportunities. Our study is the first application that uses MLS derived parameters to describe the ecological niche of a grouse and we presented the surveyed area as “case report” of hazel grouse habitat.
Interpreting and de-noising genetically engineered barcodes in a DNA virus
Authors: Blois Sylvain , Goetz Benjamin M. , Bull James J. , Sullivan Christopher S. 
Published: May 2022

ABSTRACTThe concept of a nucleic acid barcode applied to pathogen genomes is easy to grasp and the many possible uses are straightforward. But implementation may not be easy, especially when growing through multiple generations or assaying the pathogen long-term. The potential problems include: the barcode might alter fitness, the barcode may accumulate mutations, and construction of the marked pathogens may result in unintended barcodes that are not as designed. Here, we generate approximately 5000 randomized barcodes in the genome of the prototypic small DNA virus murine polyomavirus. We describe the challenges faced with interpreting the barcode sequences obtained from the library. Our Illumina NextSeq sequencing recalled much greater variation in barcode sequencing reads than the expected 5000 barcodes – necessarily stemming from the Illumina library processing and sequencing error. Using data from defined control virus genomes cloned into plasmid backbones we develop a vetted post-sequencing method to cluster the erroneous reads around the true virus genome barcodes. These findings may foreshadow problems with randomized barcodes in other microbial systems and provide a useful approach for future work utilizing nucleic acid barcoded pathogens.
Allosteric links between the hydrophilic N-terminus and transmembrane core of human Na+/H+ antiporter NHA2
Authors: Velázquez Diego , Průša Vojtěch , Masrati Gal , Sychrova Hana , Ben-Tal Nir , Zimmermannova Olga 
Published: May 2022

AbstractThe human Na+/H+ antiporter NHA2 (SLC9B2) transports Na+ or Li+ across the plasma membrane in exchange for protons, and is implicated in various pathologies. It is a 537 amino acids protein with an 82 residues long hydrophilic cytoplasmic N-terminus followed by a transmembrane part comprising 14 transmembrane helices. We optimized the functional expression of HsNHA2 in the plasma membrane of a salt-sensitive Saccharomyces cerevisiae strain and characterized a set of mutated or truncated versions of HsNHA2 in terms of their substrate specificity, transport activity, localization and protein stability. We identified a highly conserved proline 246, located in the core of the protein, as being crucial for ion selectivity. The replacement of P246 with serine or threonine resulted in antiporters with altered substrate specificity and increased resistance to the HsNHA2-specific inhibitor phloretin that were not only highly active at an acidic pH of 4.0 (like the native antiporter), but also at neutral pH. We also experimentally confirmed the importance of a putative salt bridge between E215 and R432 for antiporter function and structural integrity. Truncations of the first 50 - 70 residues of the N-terminus doubled the transport activity of HsNHA2, whilst changes in the charge at positions E47, E56, K57, or K58 decreased the antiporter’s transport activity. Thus, the hydrophilic N-terminal part of the protein appears to allosterically autoinhibit its cation transport. Our data also show this in vivo approach to be useful for a rapid screening of SNP’s effect on HsNHA2 activity.
LaeA-dependent production of small molecules ofAspergillus nigerthat compete with specific antibodies that bind to human immune receptors
Authors: Escobar N. , Keizer E. M. , van Neer J. F. , Arentshorst M. , van Strijp J. A. G. , Haas P. J. A. , Ram A. F. J. , Punt P. J. , Wösten H. A. B. , de Cock H. 
Published: May 2022

AbstractMicroorganisms secrete a variety of compounds into their environment such as proteins, carbohydrates, and secondary metabolites. These molecules play diverse roles in the interaction of microbes with their abiotic and biotic environment. Little is known about secreted fungal molecules mediating immune evasion. Here we screened culture media of three Aspergilli to assess whether these fungi secrete molecules that can compete with specific antibodies that bind to human immune receptors. Culture media ofAspergillus fumigatusAf293,Aspergillus tubingensisCBS 133792 and the non-acidifying mutant strainAspergillus nigerD15#26 contained components that showed competition for binding to a total of 13 receptors, of which PSGL-1, CXCR1, and CXCR2, were shared between the three species. Filtration experiments showed that most, if not all, interacting components were ≤ 3 kDa. Production of the components that competed with antibodies to bind to CD88 and CXCR2 was shown to be regulated by LaeA. The component(s) that competed for binding to CXCR1 was not only produced in the non-acidifying strainAspergillus nigerD15#26 but also in the non-acidifyingoahAdeletion strain ofAspergillus niger. Together, these data show thatAspergillusspecies might produce small molecules that interact with human immune receptors.