bluuebunny/crossref_metadata_2025 huggingface dataset:
Prior information differentially affects discrimination decisions and subjective confidence reports
Authors: Constant Marika , Pereira Michael , Faivre Nathan , Filevich Elisa
Published: October 2022

According to Bayesian models, both decisions and confidence are based on the same precision-weighted integration of prior expectations (“priors”) and incoming information (“likelihoods”). This assumes that priors are integrated optimally and equally in decisions and confidence, which has not been tested. In two experiments, we quantitatively assessed how priors inform both decisions and confidence. With a gamified dual-decision task we controlled the strength of priors and likelihoods to create pairs of conditions that were matched in posterior information, but differed on whether the prior or likelihood was more informative. We found that priors were underweighted in discrimination decisions, but used to a greater extent in confidence about those decisions, and this was not due to differences in processing time. With a Bayesian model we quantified the weighting parameters for the prior at both levels, and confirmed that priors are more optimally used in explicit confidence, even when underused in decisions.
Genomic Changes During the Evolution of theCoxiellaGenus Along the Parasitism-Mutualism Continuum
Authors: Santos-Garcia Diego , Morel Olivier , Henri Hélène , Filali Adil El , Buysse Marie , Noël Valérie , McCoy Karen D. , Gottlieb Yuval , Klasson Lisa , Zenner Lionel , Duron Olivier , Vavre Fabrice
Published: October 2022

The Coxiellaceae family is composed of five genera showing lifestyles ranging from free-living to symbiosis. Among them,Coxiella burnetiiis a well-known pathogen causing Q fever in humans. This bacterium presents both intracellular (parasitic) and environmental (resistant) forms. Recently, several environmentalCoxiellagenomes have been reported, among which several have come from intracellular mutualistic symbionts of ticks, termedCoxiella-like endosymbionts. We sequenced two newCoxiella-LE genomes fromDermacentor marginatus(CLEDm) andOrnithodoros maritimus(CLEOmar) ticks, the latter belonging to theC. burnetiilineage. Using these newly sequencedCoxiella-LEs and 43 Coxiellaceae genomes, we conducted comparative genomic and phylogenomic analyses to increase our knowledge ofC. burnetiipathogenicity and the emergence ofCoxiella-LEs. Results highlight the probably parasitic nature of the common ancestor of the Coxiellaceae. Indeed, the virulence factor Dot/Icm T4 Secretion System is present in most, but not all, Coxiellaceae. Whereas it is part of a putative pathogenic island inC. burnetii, it has been entirely lost or inactivated inCoxiella-LEs, suggesting its importance in pathogenesis. Additionally, we found that a Sha/Mrp antiporter was laterally acquired in theC. burnetiilineage. This antiporter might be involved in alkali resistance and the development of the resistant form that is able to persist in the environment for long periods of time. The Sha operon is eroded or absent inCoxiella-LEs. Finally, we found that allCoxiellarepresentatives produce B vitamins and co-factors indicating a pre-adaptation ofCoxiellato mutualism with hematophagous arthropods. Accordingly, the ancestor ofC. burnetiiandCoxiella-LEs was likely a parasitic bacterium able to manipulate its host cell and to produce vitamins and co-factors for its own use.
A community genomics approach to natural hybridization
Authors: Zbinden Zachery D. , Douglas Marlis R. , Chafin Tyler K. , Douglas Michael E.
Published: October 2022

Hybridization is a complicated, oft-misunderstood process. Once deemed unnatural and uncommon, hybridization is now recognized as ubiquitous among species. But hybridization rates within and among communities are poorly understood despite the relevance to ecology, evolution, and conservation. To clarify, we examined hybridization across 75 freshwater fish communities within the Ozarks of the North American Interior Highlands (USA) by SNP genotyping 33 species (N=2,865 individuals; ddRAD). We found evidence of hybridization (70 putative hybrids; 2.4% of individuals) among 18 species-pairs involving 73% (24/33) of study species, with the majority being concentrated within one family (Leuciscidae/minnows; 15 species; 66 individuals). Interspecific genetic exchange— or introgression— was evident from 24 backcrossed individuals (10/18 species-pairs). Hybrids occurred within 42 of 75 communities (56%). Four selected environmental variables (species richness, protected area extent, precipitation [May and annually]) exhibited 73–78% accuracy in predicting hybrid occurrence via random forest classification. Our community-level assessment identified hybridization as spatially widespread and environmentally dependent (albeit predominantly within one large, diverse family). Our approach provides a more holistic survey of natural hybridization by testing a wide range of species-pairs, thus contrasting with more conventional evaluations.
Brain-inspired methods for achieving robust computation in heterogeneous mixed-signal neuromorphic processing systems
Authors: Zendrikov Dmitrii , Solinas Sergio , Indiveri Giacomo
Published: October 2022

Neuromorphic processing systems implementing spiking neural networks with mixed signal analog/digital electronic circuits and/or memristive devices represent a promising technology for edge computing applications that require low power, low latency, and that cannot connect to the cloud for off-line processing, either due to lack of connectivity or for privacy concerns. However these circuits are typically noisy and imprecise, because they are affected by device to device variability, and operate with extremely small currents. So achieving reliable computation and high accuracy following this approach is still an open challenge that has hampered progress on one hand and limited widespread adoption of this technology on the other. By construction, these hardware processing systems have many constraints that are biologically plausible, such as heterogeneity and non-negativity of parameters. More and more evidence is showing that applying such constraints to artificial neural networks, including those used in artificial intelligence, promotes robustness in learning and improves their reliability. Here we delve even more in neuroscience and present network-level brain-inspired strategies that further improve reliability and robustness in these neuromorphic systems: we quantify, with chip measurements, to what extent population averaging is effective in reducing variability in neural responses, we demonstrate experimentally how the neural coding strategies of cortical models allow silicon neurons to produce reliable signal representations, and show how to robustly implement essential computational primitives, such as selective amplification, signal restoration, working memory, and relational networks, exploiting such strategies. We argue that these strategies can be instrumental for guiding the design of robust and reliable ultra-low power electronic neural processing systems implemented using noisy and imprecise computing substrates such as subthreshold neuromorphic circuits and emerging memory technologies.
Riverscape community genomics: A comparative analytical approach to identify common drivers of spatial structure
Authors: Zbinden Zachery D. , Douglas Marlis R. , Chafin Tyler K. , Douglas Michael E.
Published: October 2022

Genetic differentiation among local groups of individuals, i.e., genetic β-diversity, is a key component of population persistence related to connectivity and isolation. However, most genetic investigations of natural populations focus on a single species, overlooking opportunities for multispecies conservation plans to benefit entire communities in an ecosystem. We present an approach to evaluate genetic β-diversity within and among many species and demonstrate how thisriverscape community genomicsapproach can be applied to identify common drivers of genetic structure. Our study evaluated genetic β-diversity in 31 co-distributed native stream fishes sampled from 75 sites across the White River Basin (Ozarks, USA) using SNP genotyping (ddRAD). Despite variance among species in the degree of genetic divergence, general spatial patterns were identified corresponding to river network architecture. Most species (N=24) were partitioned into discrete sub-populations (K=2–7). We used partial redundancy analysis to compare species-specific genetic β-diversity across four models of genetic structure: Isolation by distance (IBD), isolation by barrier (IBB), isolation by stream hierarchy (IBH), and isolation by environment (IBE). A significant proportion of intraspecific genetic variation was explained by IBH (x□ =62%), with the remaining models generally redundant. We found evidence for consistent spatial modularity in that gene flow is higher within rather than between hierarchical units (i.e., catchments, watersheds, basins), supporting the generalization of the Stream Hierarchy Model. We discuss our conclusions regarding conservation and management and identify the 8-digit Hydrologic Unit (HUC) as the most relevant spatial scale for managing genetic diversity across riverine networks.
Genome assembly of three AmazonianMorphobutterfly species reveals Z-chromosome rearrangements between closely-related species living in sympatry
Authors: Bastide Héloïse , López-Villavicencio Manuela , Ogereau David , Lledo Joanna , Dutrillaux Anne-Marie , Debat Vincent , Llaurens Violaine
Published: October 2022

The genomic processes enabling speciation and the coexistence of species in sympatry are still largely unknown. Here we describe the whole genome sequencing and assembly of three closely-related species from the butterfly genusMorpho:Morpho achilles(Linnaeus, 1758),M. helenor(Cramer, 1776) andM. deidamia(Hübner, 1819). These large blue butterflies are emblematic species of the Amazonian rainforest. They live in sympatry in a wide range of their geographical distribution and display parallel diversification of dorsal wing colour pattern, suggesting local mimicry. By sequencing, assembling and annotating their genomes, we aim at uncovering pre-zygotic barriers preventing gene flow between these sympatric species. We found a genome size of 480 Mb for the three species and a chromosomal number ranging from 2n = 54 forM. deidamiato 2n = 56 forM. achillesandM. helenor. We also detected inversions on the sex chromosome Z that were differentially fixed between species, suggesting that chromosomal rearrangements may contribute to their reproductive isolation. The annotation of their genomes allowed us to recover in each species at least 12,000 protein-coding genes and to discover duplications of genes potentially involved in pre-zygotic isolation like genes controlling colour discrimination (L-opsin). Altogether, the assembly and the annotation of these three new reference genomes open new research avenues into the genomic architecture of speciation and reinforcement in sympatry, establishingMorphobutterflies as a new eco-evolutionary model.
Novel EGFR-Mutant Mouse Models of Lung Adenocarcinoma Reveal Adaptive Immunity Requirement for Durable Osimertinib Response
Authors: Kleczko Emily K , Le Anh T , Hinz Trista K , Nguyen Teresa T , Navarro Andre , Hu Cheng-Jun , Clambey Eric T , Merrick Daniel T , Weiser-Evans Mary , Nemenoff Raphael A , Heasley Lynn E
Published: October 2022

Lung cancers bearing oncogenically-mutated EGFR represent a significant fraction of lung adenocarcinomas (LUADs) for which EGFR-targeting tyrosine kinase inhibitors (TKIs) provide a highly effective therapeutic approach. However, these lung cancers eventually acquire resistance and undergo progression within a characteristically broad treatment duration range. Our previous study of EGFR mutant lung cancer biopsies highlighted the positive association of a TKI-induced interferon γ transcriptional response with increased time to treatment progression. To test the hypothesis that host immunity contributes to the TKI response, we developed novel genetically-engineered mouse models of EGFR mutant lung cancer bearing exon 19 deletions (del19) or the L860R missense mutation. Both oncogenic EGFR mouse models developed multifocal LUADs from which transplantable cancer cell lines sensitive to the EGFR-specific TKIs, gefitinib and osimertinib, were derived. When propagated orthotopically in the left lungs of syngeneic C57BL/6 mice, deep and durable shrinkage of the cell line-derived tumors was observed in response to daily treatment with osimertinib. By contrast, orthotopic tumors propagated in immune deficientnu/numice exhibited modest tumor shrinkage followed by rapid progression on continuous osimertinib treatment. Importantly, osimertinib treatment significantly increased intratumoral CD3+ T cell content relative to diluent treatment. The findings provide strong evidence supporting the requirement for adaptive immunity in the durable therapeutic control of EGFR mutant lung cancer.
Re-examining supposed correlations between synonymous codon usage and protein bond angles inE. coli
Authors: Akeju Opetunde J. , Cope Alexander L.
Published: October 2022

A recent paper by Rosenberg et al. [2022] found a surprising correlation between synonymous codon usage and the dihedral bond angles of the resulting amino acid. However, their analysis did not account for the strongest known correlate of codon usage: gene expression. We applied the approach of Rosenberg et al. [2022] to simulated protein-coding sequences that (1) maintain the general relationship between codon usage and gene expression and (2) completely random codon usage. The analysis of the simulated data assuming a general relationship between gene expression and codon usage returned results remarkably similar to the real data. More concerning was the large number of significant results detected when sequences with random codon usage were analyzed. We believe that the specific results of Rosenberg et al. [2022] were confounded by the relationship between codon usage and gene expression, but also that their method is generally prone to detecting noise in protein bond angle distributions.
CXCL4 signaling and gene induction in human monocytes involve a TLR4 response divergent from LPS
Authors: Yang Chao , Yuan Ruoxi , Mishra Bikash , Bell Richard D. , Zhang Yaxia , Du Yong , Ah Kioon Marie Dominique , Barrat Franck J. , Ivashkiv Lionel B.
Published: October 2022

The chemokine CXCL4 activates myeloid cells and contributes to the pathogenesis of inflammatory and fibrotic diseases. One mechanism of CXCL4 action is binding of nucleic acids to promote their internalization and activation of endosomal TLRs. However, the signaling pathways and receptors that mediate myeloid cell responses to CXCL4 alone are not well characterized. Here, we report that in primary human monocytes, CXCL4 activated NF-κB and a TBK1-JNK signaling axis that drive the expression of inflammatory, fibrotic and neutrophil chemokine genes, and also RIPK3-dependent necroptosis. Surprisingly, six distinct lines of evidence targeting TLR4 expression and function suggested a role for TLR4 in CXCL4 responses. However, in contrast to the canonical TLR4 agonist LPS, CXCL4 did not effectively activate an autocrine IFN response or IL-12 family genes, even after IFN-γ priming of monocytes. In accord with its role in inducing chemokine and inflammatory gene expression, CXCL4 regulated neutrophil and macrophage infiltration into skin wounds, and promoted wound healing in a mouse model. Our findings suggest that CXCL4 modulates the profile of TLR4 responses to induce a macrophage phenotype divergent from LPS-activated cells, provide new insights into mechanisms by which CXCL4 activates human monocytes, and implicate CXCL4 in regulation of skin wound healing.
The effect of habitat loss and fragmentation on isolation-by-distance and time
Authors: Sgarlata Gabriele Maria , Maié Tiago , de Zoeten Tiago , Rasteiro Rita , Chikhi Lounès
Published: October 2022

Throughout Earth’s natural history, habitats have undergone drastic changes in quality and extent, influencing the distribution of species and their diversity. In the last few hundred years, human activities have destroyed natural habitats at an unprecedent rate, converting continuous habitat into fragmented and isolated patches. Recent global metanalyses suggest that habitat loss and fragmentation (HL&F) has negatively impacted the genetic diversity of many taxa across the world. These conclusions have been drawn by comparing present-day genetic patterns from populations occurring in continuous and fragmented landscapes. In this work, we attempted to go beyond ‘pattern’ and investigate through simulations some of the ‘processes’ that influence genetic variation in the context of HL&F. Since most species have a geographically restricted dispersal (known as “isolation-by-distance”, IBD), we studied the impact of HL&F on isolation-by-distance. We characterised the behaviour of IBD in the case of i) instantaneous HL&F, ii) gradual (two-steps) HL&F, and iii) instantaneous HL&F following range expansion. In addition, we propose a spatially-explicit theoretical framework by modifying the original theoretical results on isolation-by-distance (Slatkin, 1991; Slatkin, 1993) and apply them to a toroidal stepping-stone model in the context of HL&F. Our results suggest that isolation-by-distance can be maintained for relatively long time after HL&F, thus pointing to the long-term importance of spatial genetic structure in species genetic diversity. In addition, our results may explain why present-day fragmented population still show significant IBD pattern although being disconnected.
Survey of the Phytophthora species diversity revealsP. abietivoraas a potential Phytophthora root rot pathogen in Québec Christmas tree plantations
Authors: Charron Guillaume , Yergeau Julie , Van der Heyden Hervé , Bilodeau Guillaume J. , Beaulieu Carole , Tanguay Philippe
Published: October 2022

Christmas trees are an economically and culturally important ornamental plant in North America. Many microorganisms are pathogens of firs cultivated as Christmas trees. Among those,Phytophthoracauses millions of dollars in damage to plantations annually. In Canada, it is still not known which species are responsible for Phytophthora root rot (PRR) of cultivatedAbiesspecies. Between 2019 and 2021, soil and root samples were collected from 40 Christmas tree plantations in Québec province. We used soil baiting and direct root isolation to assess the diversity of culturablePhytophthoraspp. The obtained isolates were identified with a multi-locus sequencing approach, and we used the sequencing data to place them along thePhytophthoraphylogeny. A total of 44 isolates from six differentPhytophthoraspecies were identified, one fitting the provisional speciesP.sp.□kelmania□. A seventh taxa, represented by a group of 10 isolates, could not be assigned to any knownPhytophthoraspecies. Among the known species,Phytophthora abietivorawas the most prevalent isolated species associated with PRR. Pathogenicity trials confirmed the pathogenicity potential ofP. abietivoraon both Fraser and balsam fir seedlings. Our studies provide a first snapshot of the Phytophthora diversity in Québec’s Christmas tree productions and describe multiple potential first associations betweenPhytophthoraspecies andAbies balsameaandA. fraseri.
Phospholipase C6 Regulates HydroxyprolineO-arabinosyltransferase-mediated Pollen Tube Growth inArabidopsis
Authors: Beuder Steven , Hua Xuesi , Dorchak Alexandria , MacAlister Cora A.
Published: October 2022

HydroxyprolineO-arabinosylation is a highly-conserved and plant-specific post-translational modification found on extensins and other structural proteins in the cell wall, and is catalyzed by HydroxyprolineO-arabinosyltransferases (HPATs). InArabidopsis, loss ofHPAT1andHPAT3 (hpat1/3) causes reorganization of components in the pollen tube (PT) cell wall, which compromises cell wall structural integrity and decreases PT growth and fertility. We have previously shown that reduced secretion (caused by loss-of-function mutations in secretory genesEXO70A2, SEC15A, andSEC1A) suppressed cell wall defects and strongly rescued poor growth and fertility inhpat1/3PTs. Here, we show that a missense mutation inPHOSPHOLIPASE C6 (PLC6) also rescueshpat1/3PT growth and fertility. Transgenic insertion mutations that disruptPLC6expression did not improvehpat1/3pollen fertility, and did not affect PT growth or fertility in the wild type background. This data suggests that our missense allele (plc6-4) does not function like a true loss-of-function allele, and that PLC6 is not required for wild type PT growth. However, in the absence ofhpat1/3, plc6-4PTs have defects in transmission and polarized growth, as indicated by meandering growth paths and a resulting crooked appearance.plc6-4PT elongation and straightness are more sensitive to elevated levels of calcium than wild type. This may be due the nature of theplc6-4mutation, which causes an E569K amino acid substitution in the lipid-binding C2 domain. The 569 position is located among conserved residues that bind calcium. The resulting charge inversion caused by the E569K substitution may disrupt PLC6’s lipid binding and phospholipase activities. Here, we show thatPLC6influences polarized PT growth and HPAT-mediated PT growth and fertility, and future studies are necessary to better understand the relationship between calcium andPLC6in PT growth.
Weaker selection on genes with treatment-specific expression consistent with a limit on plasticity evolution inArabidopsis thaliana
Authors: Roberts Miles , Josephs Emily B
Published: October 2022

Differential gene expression between environments often underlies phenotypic plasticity. However, environment-specific expression patterns are hypothesized to relax selection on genes, and thus limit plasticity evolution. We collated over 27 terabases of RNA-sequencing data onArabidopsis thalianafrom over 300 peer-reviewed studies and 200 treatment conditions to investigate this hypothesis. Consistent with relaxed selection, genes with more treatment-specific expression have higher levels of nucleotide diversity and divergence at nonsynonymous sites but lack stronger signals of positive selection. This result persisted even after controlling for expression level, gene length, GC content, the tissue specificity of expression, and technical variation between studies. Overall, our investigation supports the existence of a hypothesized trade-off between the environment specificity of a gene’s expression and the strength of selection on said gene inA. thaliana. Future studies should leverage multiple genome-scale datasets to tease apart the contributions of many variables in limiting plasticity evolution.
Persistent lytic bacteriophage infection as a novel strategy for exploitation of nutrient-limited host bacteria
Authors: Dorling Jack , Nhiri Naima , Corral-Lugo Andrés , Jacquet Eric , Tavares Paulo
Published: October 2022

Wild bacteria, from the open ocean to the gut, experience persistent nutrient limitation. This fundamentally affects bacterial physiology and metabolism and has profound impacts on their infection by bacterial viruses (bacteriophages). For virulent bacteriophages, which cannot enter a lysogenic state, this poses a problem for environmental persistence. Here we demonstrate that virulent bacteriophage SPP1 productively infects nutrient-limited stationary phase cultures of the Gram-positive bacteriumBacillus subtilis. Slow production and release of low numbers of infective viral particles resulted from a prolonged infection of the host population. Extensive culture lysis was greatly delayed, releasing additional viral particles and promoting fresh infections of bacterial survivors. Induced overproduction of cell surface bacteriophage receptor YueB, compensating for its scarcity in stationary phase, expedited infection dynamics under nutrient-limiting conditions, but did not change overall infection productivity. The temporal program of SPP1 gene expression differed from exponential phase, consistent with a prolonged, persistent mode of infection. Reduced expression of genes coding viral structural proteins correlated with the low yield of infectious particles. Importantly, exogenous influx of the carbon source maltose enhanced viral particle production. Our results uncover a novel adaptive strategy of a lytic phage for productive infection of nutrient-limited bacterial populations through persistent, exhaustive infection.
Effects of sensorineural hearing loss on formant-frequency discrimination: Measurements and models
Authors: Carney Laurel H. , Cameron David A. , Kinast Kameron B. , Feld C. Evelyn , Schwarz Douglas M. , Leong U-Cheng , McDonough Joyce M.
Published: October 2022

This study concerns the effect of hearing loss on discrimination of formant frequencies in vowels. In the response of the healthy ear to a harmonic sound, auditory-nerve (AN) rate functions fluctuate at the fundamental frequency, F0. Responses of inner-hair-cells (IHCs) tuned near spectral peaks are captured (or dominated) by a single harmonic, resulting in lower fluctuation depths than responses of IHCs tuned between spectral peaks. Therefore, the depth of neural fluctuations (NFs) varies along the tonotopic axis and encodes spectral peaks, including formant frequencies of vowels. This NF code is robust across a wide range of sound levels and in background noise. The NF profile is converted into a rate-place representation in the auditory midbrain, wherein neurons are sensitive to low-frequency fluctuations. The NF code is vulnerable to sensorineural hearing loss (SNHL) because capture depends upon saturation of IHCs, and thus the interaction of cochlear gain with IHC transduction. In this study, formant-frequency discrimination limens (DLFFs) were estimated for listeners with normal hearing or mild to moderate SNHL. The F0 was fixed at 100 Hz, and formant peaks were either aligned with harmonic frequencies or placed between harmonics. Formant peak frequencies were 600 and 2000 Hz, in the range of first and second formants of several vowels. The difficulty of the task was varied by changing formant bandwidth to modulate the contrast in the NF profile. Results were compared to predictions from model auditory-nerve and inferior colliculus (IC) neurons, with listeners’ audiograms used to individualize the AN model. Correlations between DLFFs, audiometric thresholds near the formant frequencies, age, and scores on the Quick speech-in-noise test are reported. SNHL had a strong effect on DLFFfor the second formant frequency (F2), but relatively small effect on DLFFfor the first formant (F1). The IC model appropriately predicted substantial threshold elevations for changes in F2 as a function of SNHL and little effect of SNHL on thresholds for changes in F1.
Incorporating environmental time series into species distribution models
Authors: Smith Austin M , Capinha Cesar , Kramer Andrew M
Published: October 2022

Species distribution models (SDMs) are widely used to gain ecological understanding and guide conservation decisions. These models are developed with a wide variety of algorithms - from statistic-based approaches to machine learning approaches - but a requirement almost all share is the use of predictor variables that strongly simplify the temporal variability of driving factors. Conversely, novel architectures of deep learning neural networks allow dealing with fully explicit spatiotemporal dynamics and thus fitting SDMs without the need to simplify the temporal and spatial dimension of predictor data. We present and demonstrate a deep learning based SDM approach that uses time series of spatial data as predictors using distribution data for 74 species from a well-established benchmark dataset. The deep learning approach provided consistently accurate models, directly using time series of predictor data and thus avoiding the use of pre-processed predictor sets that can obscure relevant aspects of environmental variation.
Leveraging PDE solver for predicting transient space-use dynamics in ecological and epidemiological systems
Authors: Tao Yun
Published: October 2022

Model predictions of animal and human space-use patterns stemming from individual-level movement behaviors have not only contributed significantly to our understanding of population and community dynamics, but they could also inform the development of conservation, natural resource management, and disease control policies. The recent proliferation of high-resolution movement data has ushered in a paradigm shift in how space use is considered: instead of being defined narrowly as the stationary, long-term distribution of individual locations, there is a growing recognition of its transient dynamics, e.g.., how space-use pattern varies before it eventually stabilizes. However, movement models are slow to follow due to longstanding technical challenges in solving transient space-use dynamics. Here, we introduce a numerical framework that enables transient analysis of mechanistic movement models based on partial differential (Fokker-Planck) equations. We demonstrate its potential applications in the context of general research questions in movement ecology using classical and new case studies as illustrations. We demonstrate the framework’s applications and versatility in classical home range models, but also show how it may be extended to address new ecological questions.
Mechanisms of masking by Schroeder-phase harmonic tone complexes in the budgerigar (Melopsittacus undulatus)
Authors: Henry Kenneth S. , Wang Yingxuan , Abrams Kristina S. , Carney Laurel H
Published: October 2022

Schroeder-phase harmonic tone complexes can have a flat temporal envelope and either rising or falling instantaneous-frequency sweeps within periods of the fundamental frequency (F0), depending on the phase-scaling parameter C. Human thresholds for tone detection in a concurrent Schroeder masker are 10-15 dB lower for positive C values (rising frequency sweeps) compared to negative (falling sweeps), potentially due to the impulse response of cochlear filtering, though this hypothesis remains controversial. Birds provide an interesting animal model for studies of Schroeder masking because prior reports suggest less behavioral threshold difference between maskers with opposite C values. However, most behavioral studies focused on relatively low masker F0s, and neurophysiological mechanisms in birds have not been explored. We performed behavioral Schroeder-masking experiments in budgerigars (Melopsittacus undulatus) using a wide range of masker F0 and C values. The signal frequency was 2800 Hz. Neural recordings at the midbrain processing level characterized encoding of behavioral stimuli in awake animals. Behavioral thresholds increased with increasing masker F0 and showed minimal difference between opposite C values, consistent with prior studies. Neural recordings showed prominent temporal and rate-based encoding of Schroeder F0, and in many neurons, marked response asymmetry between Schroeder stimuli with opposite C values. Neural thresholds for Schroeder-masked tone detection were (1) in most cases based on a response decrement compared to the masker alone, consistent with prominent modulation tuning in midbrain neurons, and (2) generally similar between opposite masker C values. These results highlight the likely importance of envelope cues in behavioral studies of Schroeder masking.
Spike-phase coupling patterns reveal laminar identity in primate cortex
Authors: Davis Zachary W. , Dotson Nicholas M. , Franken Tom , Muller Lyle , Reynolds John
Published: October 2022

The cortical column is one of the fundamental computational circuits in the brain. In order to understand the role neurons in different layers of this circuit play in cortical function it is necessary to identify the boundaries that separate the laminar compartments. While histological approaches can reveal ground truth they are not a practical means of identifying cortical layersin vivo. The gold standard for identifying laminar compartments in electrophysiological recordings is current-source density (CSD) analysis. However, laminar CSD analysis requires averaging across reliably evoked responses that target the input layer in cortex, which may be difficult to generate in less well studied cortical regions. Further the analysis can be susceptible to noise on individual channels resulting in errors in assigning laminar boundaries. Here, we have analyzed linear array recordings in multiple cortical areas in both the common marmoset and the rhesus macaque. We describe a pattern of laminar spike-field phase relationships that reliably identifies the transition between input and deep layers in cortical recordings from multiple cortical areas in two different non-human primate species. This measure corresponds well to estimates of the location of the input layer using CSDs, but does not require averaging or specific evoked activity. Laminar identity can be estimated rapidly with as little as a minute of ongoing data and is invariant to many experimental parameters. This method may serve to validate CSD measurements that might otherwise be unreliable or to estimate laminar boundaries when other methods are not practical.
Taxonomic identification accuracy from BOLD and GenBank databases using over a thousand insect barcodes from Colombia
Authors: Baena-Bejarano Nathalie , Reina Catalina , Martínez-Revelo Diego Esteban , Medina Claudia A. , Tovar Eduardo , Uribe-Soto Sandra , Neita-Moreno Jhon Cesar , Gonzalez Mailyn A.
Published: October 2022

Recent declines of insect populations at high rates have resulted in the need to develop a quick method to determine their diversity and to process massive data for the identification of species of highly diverse groups. A short sequence of DNA from COI is widely used for insect identification by comparing it against sequences of known species. Repositories of sequences are available online with tools that facilitate matching of the sequences of interest to a known individual. However, the performance of these tools can differ. Here we aim to assess the accuracy in identification of insect taxonomic categories from two repositories, BOLD Systems, and GenBank. This was done by comparing the sequence matches between taxonomist identification and the suggested identification from the platforms. We used 1160 sequences in eight orders of insects from Colombia. After the comparison, we reanalyzed the results from a representative subset of the data from the subfamily Scarabaeinae (Coleoptera). Overall, BOLD systems outperformed GenBank, and the performance of both engines differed by orders and other taxonomic categories (species, genus and family). Higher rates of accurate identification were obtained at family and genus level. The accuracy was higher in BOLD for the orders Coleoptera at family, for Coleoptera and Lepidoptera at genus, and species level. The other orders performed similarly in both repositories. Moreover, the Scarabaeinae subset showed that in this group species were correctly identified when BOLD match percentage was above 93.4% and a total of 85% of the samples were correctly assigned to a taxonomic category. These results accentuate the great potential of the identification engines to place insects accurately into their respective taxonomic categories based on DNA barcodes and highlight the reliable use of BOLD Systems for insect identification in the absence of a large reference database for a highly diverse country.
Design and characterization of a protein fold switching network
Authors: Ruan Biao , He Yanan , Chen Yingwei , Choi Eun Jung , Chen Yihong , Motabar Dana , Solomon Tsega , Simmerman Richard , Kauffman Thomas , Gallagher D. Travis , Orban John , Bryan Philip N.
Published: October 2022

Protein sequences encoding three common small folds (3α, β–grasp, and α/β–plait) were connected in a network with high-identity intersections, termed nodes. The structures of proteins around nodes were determined using NMR spectroscopy and analyzed for stability and binding function. To generate nodes, the amino acid sequence encoding a shorter fold (3a or β–grasp) is embedded in the structure of the~50% longer α/β–plait fold and a new sequence is designed that satisfies two sets of native interactions. This leads to protein pairs with a 3a or β–grasp fold in the shorter form but an α/β–plait fold in the longer form. Further, embedding smaller antagonistic folds in longer folds creates critical states in the longer folds such that single amino acid substitutions can switch both their fold and function. This suggests that abrupt fold switching may be a mechanism of evolving new protein structures and functions.
Modification of Seurat v4 for the development of a phase assignment tool able to distinguish between G2 and Mitotic cells
Authors: Watson Steven , Porter Harry , Sudbery Ian , Thompson Ruth
Published: October 2022

Single cell RNA sequencing (scRNAseq) is a rapidly advancing field which allows for the characterization of the cellular heterogeneity of gene expression profiles within a population. Cell cycle phase is a major contributor to gene expression variance between cells and computational analysis tools have been developed to assign cell cycle phase to scRNAseq datasets. Whilst these tools can be extremely useful, all have the drawback that they classify cells as G1, S or G2/M. Discrete cell phase assignment tool are unable to differentiate between G2 and M and continuous phase assignments tools are unable to identify a region corresponding specifically to mitosis in a pseudo-timeline for continuous assignment along the cell cycle. Bulk RNA sequencing was used to identify differentially expressed genes between mitotic and interphase cells isolated based on phospho-histone H3 expression using fluorescence activated cell sorting. The gene lists were used to develop a Modified Seurat Mitotic Sort (MoSMiS) methodology which can distinguish G2 and M phase cells in single cell RNA sequencing data. The phase assignment tools present in Seurat were modified to allow for cell cycle phase assignment of all stages of the cell cycle identifying a mitotic specific cell population.
Zwitterionic versus neutral molecules of fluoroquinolones: crystal structure of danofloxacin dihydrate
Authors: Felczak Aleksandra , Kalinowska-Lis Urszula , Kusz Joachim , Chęcińska Lilianna
Published: October 2022

The crystal structure of danofloxacin (DFX) as a zwitterionic dihydrate [systematic name: (1S,4S)-5-(3-carboxylato-1-cyclopropyl-6-fluoro-4-oxo-1,4-dihydroquinolin-7-yl)-2-methyl-2,5-diazabicyclo[2.2.1]heptan-2-ium dihydrate], C19H20FN3O3·2H2O, has been determined for the first time. The stability of the crystal structure is ensured by N—H...O and O—H...O hydrogen bonds, some of which are assisted by charge. The zwitterionic molecules of DFX are packed in stacks and this structural motif can be defined as a basic one from a supramolecular and energetic point of view. Hirshfeld surface analysis was used for an additional interpretation of the close contacts. The nature of the intermolecular interactions was evaluated in a pairwise manner. Destabilizing interactions were also discussed. In the context of our study on danofloxacin, we addressed the question: how common is a zwitterionic form for fluoroquinolones (FQ) in the crystalline state? A survey of the Cambridge Structural Database limited to anhydrous/hydrated/solvated forms of the most typical FQs revealed that neutral molecules are preferred, while zwitterions are less common.
At the crossroad of digital and tourism entrepreneurship: mediating effect of digitalization in hospitality industry
Authors: Suder Marcin , Duda Joanna , Kusa Rafał , Mora-Cruz Alexandra
Published: October 2022

Purpose

This study aims to explore the role of digital technologies in tourism entrepreneurship. In particular, the main objective of this research is to examine the relationships among proactiveness, innovativeness, digitalization, and firm performance and growth in the hotel industry.

Design/methodology/approach

The data for this investigation were collected from 110 one- or two-star hotels that were operating in Poland during the time of this research. This study employs PLS-SEM to analyze the relationships among the examined variables.

Findings

The results show that digitalization has a significantly positive impact on a hotel’s performance. Moreover, digitalization mediates the impact of entrepreneurial behaviors on performance. In particular, digitization is a full mediator for the impact of proactiveness on firm growth and innovation on market performance. Additionally, there is a partial complementary mediation effect of digitalization in the case of impact of innovativeness on firm growth; digitization is not a mediator for the impact of proactiveness on firm growth.

Originality/value

Previous studies have not captured the relationships among entrepreneurship, digitalization, and performance; this study helps to fill the gap and examine these associations in the hospitality industry. The outcome of this study provides valuable insights for hoteliers for understanding the role (and importance) of digitalization in the context of proactiveness and innovativeness.
On the use of finite differences for vibration-based damage localization in laminated composite plates
Authors: Oliveira Tomás , Araújo dos Santos José V. , Lopes Hernâni
Published: October 2022

Purpose

Laminated composite materials are a staple of modern material development, with extremely strong fibers being combined with resins to form versatile and efficient engineering structures. However, the advancements in material development must be accompanied by equally advanced methods for damage detection, localization and quantification, as these materials develop inherently unique failure modes. This paper aims to further the study of the use of modal shapes and their spatial derivatives to localize damage in laminated composite rectangular plates. Exploring different damage scenarios and models, as well as different orders of mode shape derivatives of laminated plates.

Design/methodology/approach

ANSYS® Parametric Design Language (APDL) is used to perform finite element analysis of plates with several damage scenarios and damage mechanics models. MATLAB® is used to post-process these simulation results, namely by calculating the derivatives using finite differences, applying three distinct sets of damage indices, including one that is presently proposed. To mimic experimental conditions and test the resilience of the derivative orders, different noise levels are introduced into the results of the finite element analysis. A quality index is employed to quantitatively evaluate the solutions, mainly regarding the response to the introduced noise.

Findings

The results show that the applied damage localization methods have comparable results in terms of quality. These results also show that the quality of the damage localizations is higher when the damaged areas coincide with high displacement/curvature areas of the mode shapes and that higher noise levels have a more noticeable negative impact when employing higher-order derivatives.

Originality/value

Exploring different damage scenarios and models, as well as different orders of mode shape derivatives of laminated plates. The influence of a specific damage layer on the order of derivatives of modal response is evaluated, showing promising results concerning its identification.
How time pressure is associated with knowledge sharing: a dual-path mechanism study
Authors: Li Xianmiao , Xu Zhenting , Hu Yuqin
Published: October 2022

Purpose

This study aims to explore the dual-path effects of challenge (CTP) and hindrance time pressure (HTP) on knowledge sharing, which provides theoretical reference for knowledge teams to carry out knowledge sharing smoothly.

Design/methodology/approach

This study collected two waves of data and surveyed 416 employees in China. Regression analysis, bootstrapping and structure equitation modeling was adopted to test the hypotheses.

Findings

CTP has a positive impact on employee knowledge sharing, while HTP has a negative impact on employee knowledge sharing. Self-efficacy plays a mediating role between CTP and knowledge sharing, and emotional exhaustion plays a mediating role between HTP and knowledge sharing. The perceived organizational support can moderate the relationship between CTP and self-efficacy and between HTP and emotional exhaustion.

Originality/value

This study explains the reasons for the academic controversy about the effect of time pressure, enhances the scholars’ attention and understanding of the dual-path mechanism between time pressure and knowledge sharing and augments the theoretical research of time pressure and knowledge sharing.
Do adjustments bring auditors peace of mind? The effect of previous audit adjustments on current-year audit pricing
Authors: Chen Songsheng , Magnan Michel , Tian Zhili , Yao Li
Published: October 2022

Purpose

This paper aims to investigate the effect of prior years’ audit adjustments, a proxy for auditors’ private information regarding the persistence of their clients’ audit risk, on audit pricing in the current year.

Design/methodology/approach

The authors use unique data sets of audit adjustments and audit fieldwork days from China, and a regression approach, to test their hypothesis.

Findings

The authors find that larger previous audit adjustments are associated with higher current-year audit fees, which is partially attributed to increased audit effort. The authors further document that the results are more pronounced when audit adjustments are consistently made in the same direction or more recent; in these cases, a larger percentage of the total effect is also attributable to the risk premium, instead of audit effort. Finally, the authors find that the effect of previous audit adjustments on current-year audit fees is stronger for firms with younger chief executive officers and specialist auditors.

Originality/value

To the authors’ best knowledge, they are the first to test the implication of auditors’ private information in setting audit fees. In addition to demonstrating that audit fees consist of a risk premium and a component to cover related costs, the authors further show variations in the relative importance between costs and risk premium under various contexts.
Factors implementing sustainable circular economy in agro-produce supply chain: DEMATEL-DANP-based approach
Authors: Avikal Shwetank , Pant Rushali , Barthwal Anurag , Ram Mangey , Upadhyay Rajesh Kumar
Published: October 2022

Purpose

The sustainable and circular growth of agro-produce is crucial in today's era. The current paper focuses on identifying the drivers which promote sustainability as well as circularity in the agro-produce supply chain and favor its implementation in agro-produce supply chain.

Design/methodology/approach

Drivers are identified by carrying out a brief literature review and then short-listed based on the expert's opinion. The crucial drivers identified are then categorized into four groups, i.e. farms, social, government and organization. A DEMATEL-DANP approach is used to analyze the relation among subfactors and factors by deriving network relations map. Further, the weights of each subfactor are measured followed by calculating the ranks of the drivers in significance with successful implementation of sustainable circular economy.

Findings

This study has applied DEMATEL-DANP approach to analyze the relationship among four factors and twelve sub factors and their contribution towards adopting the culture of sustainable circular economy in agro-produce supply chain. The results show that “Integration of farmers” and “Updated infrastructure and tools of the farm to promote diverse farming” are primary drivers for implementing SCE in APSC.

Originality/value

The research explored the domains of sustainability and circularity separately. Drivers that could accelerate the implementation of circularity in agro-produce in a sustainable manner were identified. This will help in designing sustainable circular model for working of the agro-produce supply chain.