bluuebunny/crossref_metadata_2025_split huggingface dataset:
Constructing the hierarchy of predictive auditory sequences in the marmoset brain
Authors: Jiang Yuwei , Komatsu Misako , Chen Yuyan , Xie Ruoying , Zhang Kaiwei , Xia Ying , Gui Peng , Liang Zhifeng , Wang Liping 
Published: October 2021

AbstractOur brains constantly generate predictions of sensory input that are compared with actual inputs, propagate the prediction-errors through a hierarchy of brain regions, and subsequently update the internal predictions of the world. However, the essential feature of predictive coding, the notion of hierarchical depth and its neural mechanisms, remains largely unexplored. Here, we investigated the hierarchical depth of predictive auditory processing by combining functional magnetic resonance imaging (fMRI) and high-density whole-brain electrocorticography (ECoG) in marmoset monkeys during an auditory local-global paradigm in which the temporal regularities of the stimuli were designed at two hierarchical levels. The prediction-errors and prediction updates were examined as neural responses to auditory mismatches and omissions. Using fMRI, we identified a hierarchical gradient along the auditory pathway: midbrain and sensory regions represented local, short-time-scale predictive processing followed by associative auditory regions, whereas anterior temporal and prefrontal areas represented global, long-time-scale sequence processing. The complementary ECoG recordings confirmed the activations at cortical surface areas and further differentiated the signals of prediction-error and update, which were transmitted via putatively bottom-up γ and top-down β oscillations, respectively. Furthermore, omission responses caused by absence of input, reflecting solely the two levels of prediction signals that are unique to the hierarchical predictive coding framework, demonstrated the hierarchical predictions in the auditory, temporal, and prefrontal areas. Thus, our findings support the hierarchical predictive coding framework, and outline how neural circuits and spatiotemporal dynamics are used to represent and arrange a hierarchical structure of auditory sequences in the marmoset brain.
Internally Generated Time in the Rodent Hippocampus is Logarithmically Compressed
Authors: Cao Rui , Bladon John H. , Charczynski Stephen J. , Hasselmo Michael E. , Howard Marc W. 
Published: October 2021

AbstractThe Weber-Fechner law proposes that our perceived sensory input increases with physical input on a logarithmic scale. Hippocampal “time cells” carry a record of recent experience by firing sequentially during a circumscribed period of time after a triggering stimulus. Different cells have “time fields” at different delays up to at least tens of seconds. Past studies suggest that time cells represent a compressed timeline by demonstrating that fewer time cells fire late in the delay and their time fields are wider. This paper asks whether the compression of time cells obeys the Weber-Fechner Law. Time cells were studied with a hierarchical Bayesian model that simultaneously accounts for the firing pattern at the trial level, cell level, and population level. This procedure allows separate estimates of the within-trial receptive field width and the across-trial variability. After isolating across-trial variability, time field width increased linearly with delay. Further, the time cell population was distributed evenly along a logarithmic time axis. These findings provide strong quantitative evidence that the neural temporal representation in rodent hippocampus is logarithmically compressed and obeys a neural Weber-Fechner Law.
Comparative analysis reveals the long-term co-evolutionary history of parvoviruses and vertebrates
Authors: Campbell Matthew A. , Loncar Shannon , Kotin Robert , Gifford Robert J. 
Published: October 2021

ABSTRACTParvoviruses (familyParvoviridae) are small DNA viruses that cause numerous diseases of medical, veterinary, and agricultural significance and have important applications in gene and anticancer therapy. DNA sequences derived from ancient parvoviruses are common in animal genomes and analysis of theseendogenous parvoviral elements(EPVs) has demonstrated that the family, which includes twelve vertebrate-specific genera, arose in the distant evolutionary past. So far, however, such ‘paleovirological’ analysis has only provided glimpses into biology of parvoviruses and their long-term evolutionary interactions with hosts. Here, we comprehensively map EPV diversity in 752 published vertebrate genomes, revealing defining aspects of ecology and evolution within individual parvovirus genera. We identify 364 distinct EPV sequences and show these represent ∼200 unique germline incorporation events, involving at least five distinct parvovirus genera, that took place at points throughout the Cenozoic Era. We use the spatiotemporal and host range calibrations provided by these sequences to infer defining aspects of long-term evolution within individual parvovirus genera, including mammalian vicariance for genusProtoparvovirus, and inter-class transmission for genusDependoparvovirus. Moreover, our findings support a model of virus evolution in which the long-term co-circulation of multiple parvovirus genera in vertebrates reflects the adaptation of each viral genus to fill a distinct ecological niche. Our discovery that parvovirus diversity can be understood in terms of genus-specific adaptations acquired over millions of years has important implications for their development as therapeutic tools - we show that these endeavours can now be approached from a rational foundation based on comparative evolutionary analysis. To support this, we published our data in the form of an open, extensible, and cross-platform database designed to facilitate the wider utilisation of evolution-related domain knowledge in parvovirus research.
Genome-wide association identifies candidate genes for drought tolerance in coast redwood and giant sequoia
Authors: De La Torre Amanda R. , Sekhwal Manoj K. , Puiu Daniela , Salzberg Steven L. , Scott Alison Dawn , Allen Brian , Neale David B. , Chin Alana R.O. , Buckley Thomas N. 
Published: October 2021

SUMMARYDrought is a major limitation for survival and growth in plants. With more frequent and severe drought episodes occurring due to climate change, it is imperative to understand the genomic and physiological basis of drought tolerance to be able to predict how species will respond in the future. In this study, univariate and multitrait multivariate GWAS methods were used to identify candidate genes in two iconic and ecosystem-dominating species of the western US – coast redwood and giant sequoia – using ten drought-related physiological and anatomical traits and genome-wide sequence-capture SNPs. Population level phenotypic variation was found in carbon isotope discrimination, osmotic pressure at full turgor, xylem hydraulic diameter and total area of transporting fibers in both species. Our study identified new 78 new marker × trait associations in coast redwood and six in giant sequoia, with genes involved in a range of metabolic, stress and signaling pathways, among other functions. This study contributes to a better understanding of the genomic basis of drought tolerance in long-generation conifers and helps guide current and future conservation efforts in the species.Significance StatementClimate change brings more frequent and severe drought events that challenge the survival of natural populations of plants. While most of our knowledge about drought tolerance comes from annual and domesticated plants, the genomic basis of drought tolerance in long-generation trees is poorly understood. Here, we aim to fill this gap by identifying candidate genes in two conifer species, coast redwood and giant sequoia.
Toll-like receptor signalling via IRAK4 confers epithelial integrity and tightness through regulation of junctional tension
Authors: Peterson Jesse , Sivars Kinga Balogh , Bianco Ambra , Röper Katja 
Published: October 2021

AbstractToll-like receptors (TLRs) in mammalian systems are well characterised for their role in innate immunity. In addition, TLRs also fulfil crucial functions outside immunity, including the dorso-ventral patterning function of the original Toll receptor in Drosophila and neurogenesis in mice. Recent discoveries in flies suggested key roles for TLRs in epithelial cells in patterning of cytoskeletal activity near epithelial junctions. Here we address the function of TLRs and the downstream key signal transduction component IRAK4 (interleukin-1 receptor associated kinase 4) in human epithelial cells. Using differentiated human Caco-2 cells as a model for the intestinal epithelium, we show that these cells exhibit baseline TLR signalling as revealed by p-IRAK4 and that blocking IRAK4 function leads to a loss of epithelial tightness involving key changes at tight junctions and adherens junctions. These changes correlate with a loss of epithelial tension and changes in junctional actomyosin. Knock-down of IRAK4 and certain TLRs phenocopies the inhibitor treatment. These data suggest a model whereby TLR receptors near epithelial junctions might be involved in a continuous sensing of the epithelial state to promote epithelial tightness and integrity.
Analysis of the Streptococcus mutans proteome during acid and oxidative stress reveals modules of co-expression and an expanded role for the TreR transcriptional regulator
Authors: Tinder Elizabeth L. , Faustoferri Roberta C. , Buckley Andrew A. , Quivey Robert G. , Baker Jonathon L. 
Published: October 2021

AbstractStreptococcus mutans promotes a tooth-damaging dysbiosis in the oral microbiota because it can form biofilms and survive acid stress better than most of its ecological competitors, which are typically health-associated. Many of these commensals produce hydrogen peroxide, therefore S. mutans must manage both oxidative stress and acid stress with coordinated and complex physiological responses. In this study, the proteome of S. mutans was examined during regulated growth in acid and oxidative stresses, as well as in deletion mutants with impaired oxidative stress phenotypes, Δnox and ΔtreR. 607 proteins exhibited significantly different abundance levels across the conditions tested, and correlation network analysis identified modules of co-expressed proteins that were responsive to the deletion of nox and/or treR, as well as acid and oxidative stress. The data provided evidence explaining the ROS-sensitive and mutacin-deficient phenotypes exhibited by the ΔtreR strain. SMU.1069-1070, a poorly understood LytTR system, had elevated abundance in the ΔtreR strain. S. mutans LytTR systems regulate mutacin production and competence, which may explain how TreR affects mutacin production. Furthermore, the gene cluster that produces mutanobactin, a lipopeptide important in ROS tolerance, displayed reduced abundance in the ΔtreR strain. The role of Nox as a keystone in the oxidative stress response was also emphasized. Crucially, this dataset provides oral health researchers with a proteome atlas that will enable a more complete understanding of the S. mutans stress responses that are required for pathogenesis, and facilitate the development of new and improved therapeutic approaches for dental caries.ImportanceDental caries is the most common chronic infectious disease worldwide, and disproportionally affects marginalized socioeconomic groups. Streptococcus mutans is a considered a primary etiologic agent of caries, with its pathogenicity dependent on coordinated physiologic stress responses that mitigate the damage caused by the oxidative and acid stress common within dental plaque. In this study, the proteome of S. mutans was examined during growth in acidic and oxidative stresses, as well in nox and treR deletion mutants. 607 proteins were differentially expressed across the strains/growth conditions, and modules of co-expressed proteins were identified, which enabled mapping the acid and oxidative stress responses across S. mutans metabolism. The presence of TreR was linked to mutacin production via LytTR system signaling and to oxidative stress via mutanobactin production. The data provided by this study will guide future research elucidating S. mutans pathogenesis and developing improved preventative and treatment modalities for dental caries.
Molecular connectivity between extra-cytoplasmic sigma factors and PhoP accounts for integrated mycobacterial stress response
Authors: Goar Harsh , Paul Partha , Khan Hina , Sarkar Dibyendu 
Published: October 2021

AbstractThe main purpose of this study is to understand how mycobacteria can sense numerous stress conditions and mount an appropriate stress response. Recent studies suggest that at low pH M. tuberculosis encounters reductive stress, and in response, modulates redox homeostasis by utilizing the phoPR regulatory system. However, the mechanism of integrated regulation of stress response remains unknown. To probe how PhoP contributes to redox stress response, we find that a PhoP-depleted M. tuberculosis shows a significantly enhanced susceptibility to redox stress relative to the WT bacilli. In keeping with these results, PhoP was shown to contribute to mycothiol redox state. Because SigH, one of the alternative sigma factors of mycobacteria, is known to control expression of redox inducible genes, we probed whether previously-reported PhoP-SigH interaction accounts for mycobacterial redox stress response. We had shown that under acidic conditions PhoP functions in maintaining pH homeostasis via its interaction with SigE. In striking contrast, here we show that under redox stress, direct recruitment of SigH, but not PhoP-SigH interaction, controls expression of mycobacterial thioredoxin genes, a major mycobacterial anti-oxidant system. Together, these unexpected results uncover novel stress-specific enhanced or reduced interaction events of sigma factors and PhoP, as the underlying mechanisms of an adaptive programme, which couples low pH conditions and mycobacterial thiol redox homeostasis.SignificanceM. tuberculosis encounters reductive stress under acidic pH. To investigate the mechanism of integrated stress response, we show that PhoP plays a major role in mycobacterial redox stress response. We observed a significant correlation between phoP-dependent and redox-active expression of thioredoxin genes, a major mycobacterial antioxidant system. Further probing on functioning of regulators reveals that while PhoP controls pH homeostasis via its interaction with SigE, direct recruitment of SigH, but not PhoP-SigH interaction, controls expression of thioredoxin genes. These strikingly contrasting results showing enhanced PhoP-SigE interaction under acidic pH and reduced PhoP-SigH interaction under redox conditions, uncover the underlying novel mechanism of mycobacterial adaptive program, coupling low pH with maintenance of redox homeostasis.
Accounting articles on developing countries in ranked English language journals: a meta-review
Authors: Moses Olayinka , Hopper Trevor 
Published: October 2021

PurposeThe paper conducts a metadata analysis of articles on developing countries in highly ranked “international” accounting journals, the topics covered, research methods employed, their authorship and impact, across countries and continents.Design/methodology/approachA database of the publications of accounting journals ranked A*, A and B in the Australian Business Dean Council (ABDC) journal rankings from 2009 to 2018 was constructed. A structured literature review, partly using NVivo and Leximancer, analysed the 1,317 articles on developing countries. A parallel online repository contains the research data.FindingsArticles on accounting in developing countries increased by 36% over the ten years but remained a small proportion of all published articles (i.e. 1,317 of 13,805 representing 9.5%). They have concentrated on quantitative market-based studies of financial reporting and auditing, especially in larger and relatively richer developing countries in Asia and Africa, with developed capital markets. Broader topics deemed important in recent reviews of the area, for instance, on achieving Sustainable Development Goals (SDGs) and on smaller, poorer countries, which have been neglected, albeit less so in qualitative studies. The research identifies important jurisdictional differences. Many authors held positions in British Commonwealth universities. The most cited articles overall, all quantitative, were in highly ranked North American journals, whereas most qualitative studies came from journals located in richer British Commonwealth countries.Research limitations/implicationsThe study only covers English language journals. Journals in other languages and lesser ranked journals, especially those based in developing countries, may be important sources too.Practical implicationsMore research on a broader range of accounting issues, especially in smaller and poorer developing countries, is needed. Although quantitative work is valuable, more recognition of the value of qualitative studies is needed, especially given the disappointing results of market-based policies prescribed by foreign institutions and their shift to advocating good governance reforms and achieving SDGs.Originality/valueTo the best of the authors’ knowledge, this is the most exhaustive analysis of recent accounting research on developing countries. It traces which journals have published such research, when, on which countries, on what topics and by whom. This is of interest to journal editors, course designers and researchers in the area. The authors hope that making the raw data and detailed analyses available online, consistent with protocols adopted in science disciplines, will encourage accounting researchers to do likewise to enable further testing of results and claims and build knowledge cumulatively.
Toward an omniopticon: the potential of blockchain technology toward influencing vulnerable populations in contested markets
Authors: Carrasco Heather , Romi Andrea M. 
Published: October 2021

PurposeThe purpose of this paper is to explore the use of blockchain technology in contested markets. The authors specifically consider the development and utilization of this accounting system as a device that might democratize contested markets for vulnerable populations, supporting contested entrepreneurs while “cooling” the moral contestation to the market.Design/methodology/approachThis study analyzes the relationship between vulnerable populations and contested market activities, the inclusive development and potential trust created by a blockchain accounting information system and how this interaction potentially creates support for economic and social systems.FindingsThis paper demonstrates that, in an era of decreased trust especially as it relates to a digital, globalized marketplace, blockchain has the potential to create democracies of access, trust and agency. This system overcomes many of the deficiencies associated with transparency and accountability and connects market participants with society, strengthening its potential to bridge two opposing vulnerable population viewpoints necessary for possible contested market development.Research limitations/implicationsThe authors contribute to a deeper understanding of the role of emerging technologies in the interconnectedness between vulnerable populations in a contested market. Recognizing that blockchain is an imperfect version of its ideal intention, the authors also discuss the limitations of the system with respect to corruption, collusion and potential issues of adoption, and how this reduces the influence of blockchain as a “cooling” device within contested markets.Practical implicationsThe authors provide an illustrative example whereby an entire industry might be persuaded from avoidance to promotion of new traceability devices and supported in the development of an accessible market.Social implicationsGlobal government's economic support for social systems continues to experience significant declines. With ever-degrading healthcare, infrastructure, public education, childcare, etc., new sources of economic influx are often desired. One potential source of additional funds is from the tax revenues derived from contested market transactions, those stigmatized industries often operating illegally. With substantial public distrust, blockchain potentially provides such industries with democratization and the trust necessary to transition the industry into a legal environment, with tax revenues benefiting various social systems.Originality/valueThis study goes beyond the preliminary discussions of the benefits and consequences of blockchain. Instead, the authors focus on the use of blockchain within contested markets and its ability to influence vulnerable populations. The authors also consider the use of blockchain-based accounting information systems to provide a holistic and more democratic platform from a regulatory, market participant and societal standpoint.
A carbon dioxide detector fabrication with screen printing technique for use in airplanes
Authors: Masat Mehmet , Ertuğrul Mehmet , Korul Hakan 
Published: October 2021

Purpose
From the beginning of aviation history, fire has been a serious problem for aircrafts. The purpose of this study is to provide a reference document on current risks and proposed reductions for smoke and fire incidents in commercial transport aircrafts. For this purpose, metal oxide carbon dioxide (CO2) detector was produced with the screen printing technique to detect CO2 and carbon monoxide gases from the sensors required to observe the occurrence of fire that may occur in the aircraft and to take the necessary steps to control it.

Design/methodology/approach
The screen printing technique was used as the gas sensor production technique for the produced sensor and tin oxide was used as the metal oxide in the produced samples. The samples produced were examined under the gases with specified gas detecting properties, and it was concluded that they can be used simultaneously with smoke detectors to increase the detection reliability and decrease the alarm time with the smoke detectors currently used in today's passenger aircrafts.

Findings
When the electrical characteristics of the sensor made were examined, it was observed that it meets the requirements of the Federal Aviation Administration and European Aviation Safety Agency standards (the fire should be detected within 1 min), and the false alarm situation experienced in the smoke sensors used today can be eliminated.

Originality/value
There is no other sensor than the smoke detectors that are used for fire detection in cargo section, lavatories and avionic compartment on aircrafts. With this study, the gas detecting feature of the produced samples was examined under the specified gases, and it was concluded that they can be used simultaneously with smoke detectors to increase detection reliability and decrease alarm time as compared to with the smoke detectors currently used in today's passenger aircrafts.