bluuebunny/crossref_metadata_2025_split huggingface dataset:
Homeostasis as a fundamental principle for a coherent theory of brains
Authors: Turner J. Scott 
Published: April 2019

‘Brains’ may be considered to be computation engines, with neurons and synapses analogized to electronic components wired into networks that process information, learn and evolve. Alternatively, ‘brains’ are cognitive systems, which contain elements of intentionality, purposefulness and creativity that do not fit comfortably into a brain-as-computer metaphor. I address the question of how we may think most constructively about brains in their various forms—solid, liquid or fluid—and whether there is a coherent theory that unites them all. In this essay, I explore cognitive systems in the context of new understanding of life's distinctive nature, in particular the core concept of homeostasis, and how this new understanding lays a sound conceptual foundation for an expansive theory of brains.This article is part of the theme issue ‘Liquid brains, solid brains: How distributed cognitive architectures process information'.
How does mobility help distributed systems compute?
Authors: Vining William F. , Esponda Fernando , Moses Melanie E. , Forrest Stephanie 
Published: April 2019

Brains are composed of connected neurons that compute by transmitting signals. The neurons are generally fixed in space, but the communication patterns that enable information processing change rapidly. By contrast, other biological systems, such as ant colonies, bacterial colonies, slime moulds and immune systems, process information using agents that communicate locally while moving through physical space. We refer to systems in which agents are strongly connected and immobile assolid, and to systems in which agents are not hardwired to each other and can move freely asliquid. We ask how collective computation depends on agent movement. A liquid cellular automaton (LCA) demonstrates the effect of movement and communication locality on consensus problems. A simple mathematical model predicts how these properties of the LCA affect how quickly information propagates through the system. While solid brains allow complex network structures to move information over long distances, mobility provides an alternative way for agents to transport information when long-range connectivity is expensive or infeasible. Our results show how simple mobile agents solve global information processing tasks more effectively than similar systems that are stationary.This article is part of the theme issue ‘Liquid brains, solid brains: How distributed cognitive architectures process information’.
Evolutionary aspects of reservoir computing
Authors: Seoane Luís F. 
Published: April 2019

Reservoir computing (RC) is a powerful computational paradigm that allows high versatility with cheap learning. While other artificial intelligence approaches need exhaustive resources to specify their inner workings, RC is based on a reservoir with highly nonlinear dynamics that does not require a fine tuning of its parts. These dynamics project input signals into high-dimensional spaces, where training linear readouts to extract input features is vastly simplified. Thus, inexpensive learning provides very powerful tools for decision-making, controlling dynamical systems, classification, etc. RC also facilitates solving multiple tasks in parallel, resulting in a high throughput. Existing literature focuses on applications in artificial intelligence and neuroscience. We review this literature from an evolutionary perspective. RC’s versatility makes it a great candidate to solve outstanding problems in biology, which raises relevant questions. Is RC as abundant in nature as its advantages should imply? Has it evolved? Once evolved, can it be easily sustained? Under what circumstances? (In other words, is RC an evolutionarily stable computing paradigm?) To tackle these issues, we introduce a conceptual morphospace that would map computational selective pressures that could select for or against RC and other computing paradigms. This guides a speculative discussion about the questions above and allows us to propose a solid research line that brings together computation and evolution with RC as test model of the proposed hypotheses.This article is part of the theme issue ‘Liquid brains, solid brains: How distributed cognitive architectures process information’.
Liquid brains, solid brains
Authors: Solé Ricard , Moses Melanie , Forrest Stephanie 
Published: April 2019

Cognitive networks have evolved a broad range of solutions to the problem of gathering, storing and responding to information. Some of these networks are describable as static sets of neurons linked in an adaptive web of connections. These are ‘solid’ networks, with a well-defined and physically persistent architecture. Other systems are formed by sets of agents that exchange, store and process information but without persistent connections or move relative to each other in physical space. We refer to these networks that lack stable connections and static elements as ‘liquid’ brains, a category that includes ant and termite colonies, immune systems and some microbiomes and slime moulds. What are the key differences between solid and liquid brains, particularly in their cognitive potential, ability to solve particular problems and environments, and information-processing strategies? To answer this question requires a new, integrative framework.
This article is part of the theme issue ‘Liquid brains, solid brains: How distributed cognitive architectures process information’.
Modeling of Yield Losses and Risk Analysis of Fungicide Profitability for Managing Fusarium Head Blight in Brazilian Spring Wheat
Authors: Rodrigues Duffeck Maíra , dos Santos Alves Kaique , Jackson Machado Franklin , David Esker Paul , Medeiros Del Ponte Emerson 
Published: April 2019

AbstractFusarium head blight (FHB), caused by theFusarium graminearumspecies complex, is a serious disease of wheat in Brazil. A review of literature on fungicide efficacy for field trials evaluated in Brazil was conducted to obtain FHB-yield data and explore their relationship. Thirty-seven studies (9 years and 11 locations) met the criteria for inclusion (FHB index ≥ 5% and max-min range ≥ 4 percent points [p.p.]). Studies were group into two production situations: low (Yl≤ 3,631 kg ha−1) or high (Yh> 3,631 kg ha−1) yield, based on the median of maximum yields across trials. Population-average intercepts, but not the slopes, from fitting a random-coefficients model, differed significantly betweenYl(2,883.6 kg ha−1) andYh(4,419.5 kg ha−1). The calculated damage coefficient was 1.05 %−1and 1.60 %−1forYhandYl, respectively. A crop model simulated attainable wheat yields for 10 planting dates within each year during a 28-year period, including prior (1980-1989) and after (1990-2007) FHB resurgence. Simulated losses using disease predictions to penalize yield were in general agreement in magnitude with literature reports, for both periods. Economic analysis for scenarios of variable fungicide costs and wheat prices, and one versus two sprays of tebuconazole, showed that the probability of not-offsetting the costs was higher (> 0.75) prior to FHB resurgence than after the 1990. Our approach may be useful for designing of longlasting, yet profitable, contingency tactics to management FHB in wheat. Currently one spray of triazole fungicide during flowering is more likely a profitable decision than applying two sprays, for which there is greater uncertainty.
Advantages of Multi-shell Diffusion for Studies of Brain Development in Youth
Authors: Pines Adam R. , Cieslak Matthew , Baum Graham L. , Cook Philip A. , Adebimpe Azeez , Dávila Diego G. , Elliott Mark A. , Jirsaraie Robert , Murtha Kristin , Oathes Desmond J. , Piiwaa Kayla , Rosen Adon F. G. , Rush Sage , Shinohara Russell T. , Bassett Danielle S. , Roalf David R. , Satterthwaite Theodore D. 
Published: April 2019

ABSTRACTDiffusion tensor imaging (DTI) has advanced our understanding of how brain microstructure evolves over development. However, the proliferation of multi-shell diffusion imaging sequences has coincided with notable advances in the modeling of neuronal diffusion patterns, such as Neurite Orientation Dispersion and Density Imaging (NODDI) and Laplacian-regularized Mean Apparent Propagator MRI (MAPL). The relative utility of these newer diffusion models for understanding brain maturation remains sparsely investigated. Additionally, despite evidence that motion artifact is a major confound for studies of development, the relative vulnerability of these models to in-scanner motion has not been described. Accordingly, in a sample of 123 youth (ages 12-30) we evaluated DTI, NODDI, and MAPL for associations with age and in-scanner head motion at multiple scales, including mean white matter values, voxelwise analyses, and tractography-based structural brain networks. Our results reveal that multi-shell diffusion imaging sequences can be leveraged to robustly characterize neurodevelopment, even within the framework of DTI. However, these metrics of diffusion are variably impacted by motion, highlighting the importance of modeling choices for studies of movement-prone populations. Our findings suggest that while traditional DTI is sensitive to neurodevelopmental trends, contemporary modeling techniques confer key advantages for neurodevelopmental inquiries.
Regulation of HMGB2 integrates ribosome biogenesis and innate immune responses to DNA
Authors: Bianco Christopher , Mohr Ian 
Published: April 2019

SUMMARYRibosomes are universally important in biology and their production is dysregulated by developmental disorders, cancer, and virus infection. Although presumed required for protein synthesis, how ribosome biogenesis impacts virus reproduction and cell-intrinsic immune responses remains untested. Surprisingly, we find that restricting ribosome biogenesis stimulated human cytomegalovirus (HCMV) replication without suppressing translation. Interfering with ribosomal RNA (rRNA) accumulation triggered nucleolar stress and repressed expression of High Mobility Group Box 2 (HMGB2), a chromatin-associated protein that facilitates cytoplasmic double-stranded (ds) DNA-sensing by cGAS. Furthermore, it reduced cytoplasmic HMGB2 abundance and impaired induction of interferon beta (IFNB1) mRNA, which encodes a critical anti-proliferative, proinflammatory cytokine, in response to HCMV or dsDNA in uninfected cells. This establishes that rRNA accumulation regulates innate immune responses to dsDNA by controlling HMGB2 abundance. Moreover, it reveals that rRNA accumulation and/or nucleolar activity unexpectedly regulate dsDNA-sensing to restrict virus reproduction and regulate inflammation.
Can immunosuppressed mice control oral infection by the opportunistic pathogenEncephalitozoon intestinalis?
Authors: da Costa Moura Maria Lucia , Alvares-Saraiva Anuska Marcelino , Pérez Elizabeth Cristina , Xavier José Guilherme , Spadacci-Morena Diva Denelle , Moysés Carla Renata Serantoni , Dell’Armelina Rocha Paulo Ricardo , Lallo Maria Anete 
Published: April 2019

AbstractIntestinal mucosa (IM), or the outer surface of the intestine, serves at the primary site for the interaction of various pathogens that cause infection via the oral route. Thus, IM is crucial for developing an efficient adaptive immune response against pathogenic micro-organisms, thereby preventing their colonization and subsequent infection. In the present study, we investigated the immune response toEncephalitozoon intestinalis-caused infection in the IM and gut-associated lymphoid tissue (GALT) in C57BL/6 female mice. To mimic an immunosuppressive condition, the mice were treated with cyclophosphamide (Cy). Histopathology revealed lymphoplasmacytic enteritis at 7 and 14 days-post-infection (dpi) in all infected groups; however, inflammation diminished at 21 and 28 dpi. Cy treatment also led to a higher number ofE. intestinalisspores and lesions, which reduced at 28 dpi. In addition, flow cytometry analysis demonstrated CD4+and CD8+T cells to be predominant immune cells, with a significant increase in both Th1 and Th2 cytokines at 7 and 14 dpi, as demonstrated by histopathology. In conclusion, Cy treatment reduced GALT (Peyer’s plaques and mesenteric lymph nodes) and peritoneum populations but increased the T-cell population in the intestinal mucosa and the production of pro-inflammatory cytokines, which were able to eliminate this opportunistic fungus and reduced the infection.
Retinal and callosal activity-dependent chandelier cell elimination shapes binocularity in primary visual cortex
Authors: Wang Bor-Shuen , Bernardez Sarria Maria Sol , He Miao , Crair Michael C , Huang Z. Josh 
Published: April 2019

AbstractIn mammalian primary visual cortex (V1), integration of the left and right visual scene into a binocular percept derives from convergent ipsi- and contralateral geniculocortical inputs and trans-callosal projections between the two hemispheres. However, the underlying developmental mechanisms remain incompletely understood. Using genetic methods in mice we found that during the days before eye-opening, retinal and callosal activity drives massive apoptosis of GABAergic chandelier cells (ChCs) in the binocular region of V1. Blockade of ChC elimination resulted in a contralateral-dominated V1 and deficient binocular vision. As activity patterns within and between retinas prior to vision convey organization of the visual field, their regulation of ChC density through the trans-callosal pathway may prime a nascent binocular territory for subsequent experience-driven tuning during the post-vision critical period.One Sentence SummaryPrior to eye opening the developing retina primes the visual cortex for binocular vision by adjusting the density of a cortical inhibitory neuron type.
Vicarious reward unblocks associative learning about novel cues in male rats
Authors: van Gurp Sander , Hoog Jochen , Kalenscher Tobias , van Wingerden Marijn 
Published: April 2019

AbstractMany species, including humans, are sensitive to social signals and their valuation is important in social learning. When social cues indicate that another is experiencing reward, they could convey vicarious reward value and prompt social learning. Here, we introduce a task that investigates if vicarious reward delivery in male rats can drive reinforcement learning in a formal associative learning paradigm. Using the blocking/unblocking paradigm, we found that when actor rats have fully learned a stimulus-self reward association, adding a cue that predicted additional partner reward unblocked associative learning about this cue. In contrast, additional cues that did not predict partner reward remained blocked from acquiring associative value. Preventing social signal exchange between the partners resulted in cues signaling partner reward remaining blocked. Taken together, these results suggest that vicarious rewards can drive reinforcement learning in rats, and that the transmission of social cues is necessary for this learning to occur.
Integration of a Computational Pipeline for Dynamic Inference of Gene Regulatory Networks in Single Cells
Authors: Ko Kyung Dae , Dell’Orso Stefania , Juan Aster H. , Sartorelli Vittorio 
Published: April 2019

SUMMARYSingle-cell RNA-seq permits the characterization of the molecular expression states of individual cells. Several methods have been developed to spatially and temporally resolve individual cell populations. However, these methods are not always integrated and some of them are constrained by prior knowledge. Here, we present an integrated pipeline for inference of gene regulatory networks. The pipeline does not rely on prior knowledge, it improves inference accuracy by integrating signatures from different data dimensions and facilitates tracing variation of gene expression by visualizing gene-interacting patterns of co-expressed gene regulatory networks at distinct developmental stages.
Dynamic response in the larval geoduck clam proteome to elevated pCO2
Authors: Timmins-Schiffman Emma , Guzmán José M. , Elliott Rhonda , Vadopalas Brent , Roberts Steven B. 
Published: April 2019

AbstractPacific geoduck clams (Panopea generosa) are found along the Northeast Pacific coast where they are significant components of coastal and estuarine ecosystems and the basis of a growing and highly profitable aquaculture industry. The Pacific coastline, however, is also the sight of rapidly changing ocean habitat, including significant reductions in pH. The impacts of ocean acidification on invertebrate bivalve larvae have been widely documented and it is well established that many species experience growth and developmental deficiencies when exposed to low pH. As a native of environments that have historically lower pH than the open ocean, it is possible that geoduck larvae are less impacted by these effects than other species. Over two weeks in larval development (days 6-19 post-fertilization) geoduck larvae were reared at pH 7.5 or 7.1 in a commercial shellfish hatchery. Larvae were sampled at six time points throughout the period for a in-depth proteomics analysis of developmental molecular physiology. Larvae reared at low pH were smaller than those reared at ambient pH, especially in the prodissoconch II phase of development. Competency for settlement was also delayed in larvae from the low pH conditions. A comparison of proteomic profiles over the course of development reveal that these differing phenotypic outcomes are likely due to environmental disruptions to the timing of molecular physiological events as suites of proteins showed differing profiles of abundance between the two pH environments. Ocean acidification likely caused an energetic stress on the larvae at pH 7.1, causing a shift in physiological prioritization with resulting loss of fitness.
Neural Selectivity, Efficiency, and Dose Equivalence in Deep Brain Stimulation through Pulse Width Tuning and Segmented Electrodes
Authors: Anderson Collin J. , Anderson Daria Nesterovich , Pulst Stefan M. , Butson Christopher R. , Dorval Alan D. 
Published: April 2019

AbstractBackgroundAchieving deep brain stimulation (DBS) dose equivalence is challenging, especially with pulse width tuning and directional contacts. Further, the precise effects of pulse width tuning are unknown.MethodsWe created multicompartment neuron models for two axon diameters and used finite element modeling to determine extracellular influence from standard and segmented electrodes. We analyzed axon activation profiles and calculated volumes of tissue activated.ResultsLong pulse widths focus the stimulation effect on small, nearby fibers, suppressing white matter tract activation (responsible for some DBS side effects) and improving battery utilization. Directional leads enable similar benefits to a greater degree. We derive equations for equivalent activation with pulse width tuning and segmented contacts.InterpretationsWe find agreement with classic studies and reinterpret recent articles concluding that short pulse widths focus the stimulation effect on small, nearby fibers, decrease side effects, and improve power consumption. Our field should reconsider shortened pulse widths.
Individual structural features constrain the mouse functional connectome
Authors: Melozzi Francesca , Bergmann Eyal , Harris Julie A. , Kahn Itamar , Jirsa Viktor , Bernard Christophe 
Published: April 2019

ABSTRACTWhole brain dynamics intuitively depends upon the internal wiring of the brain; but to which extent the individual structural connectome constrains the corresponding functional connectome is unknown, even though its importance is uncontested. After acquiring structural data from individual mice, we virtualized their brain networks and simulatedin silicofunctional MRI data. Theoretical results were validated against empirical awake functional MRI data obtained from the same mice. We demonstrate that individual structural connectomes predict the functional organization of individual brains. Using a virtual mouse brain derived from the Allen Mouse Brain Connectivity Atlas, we further show that the dominant predictors of individual structure-function relations are the asymmetry and the weights of the structural links. Model predictions were validated experimentally using tracer injections, identifying which missing connections (not measurable with diffusion MRI) are important for whole brain dynamics in the mouse. Individual variations thus define a specific structural fingerprint with direct impact upon the functional organization of individual brains, a key feature for personalized medicine.SIGNIFICANCE STATEMENTThe structural connectome is a key determinant of brain function and dysfunction. The connectome-based model approach aims to understand the functional organization of the brain by modeling the brain as a dynamical system and then studying how the functional architecture rises from the underlying structural skeleton. Here, taking advantage of mice studies, we systematically investigated the informative content of different structural features in explaining the emergence of the functional ones. We demonstrate that individual variations define a specific structural fingerprint with a direct impact upon the functional organization of individual brains stressing the importance of using individualized models to understand brain function. We show how limitations of connectome reconstruction with the diffusion-MRI method restrict our comprehension of the structural-functional relation.
Conformational Heterogeneity in Human Interphase Chromosome Organization Reconciles the FISH and Hi-C Paradox
Authors: Shi Guang , Thirumalai D. 
Published: April 2019

AbstractHi-C experiments are used to infer the contact probabilities between loci separated by varying genome lengths. Contact probability should decrease as the spatial distance between two loci increases. However, studies comparing Hi-C and FISH data show that in some cases the distance between one pair of loci, with larger Hi-C readout, is paradoxically larger compared to another pair with a smaller value of the contact probability. Here, we show that the FISH-Hi-C paradox can be resolved using a theory based on a Generalized Rouse Model for Chromosomes (GRMC). The FISH-Hi-C paradox arises because the cell population is highly heterogeneous, which means that a given contact is present in only a fraction of cells. Insights from the GRMC is used to construct a theory, without any adjustable parameters, to extract the distribution of subpopulations from the FISH data, which quantitatively reproduces the Hi-C data. Our results show that heterogeneity is pervasive in genome organization at all length scales, reflecting large cell-to-cell variations.