bluuebunny/crossref_metadata_2025_split huggingface dataset:
Path integration in large-scale space and with novel geometries: Comparing Vector Addition and Encoding-Error Models
Authors: Harootonian S. K. , Wilson R. C. , Hejtmánek L. , Ziskin E. M. , Ekstrom A. D. 
Published: October 2019

AbstractPath integration is thought to rely on vestibular and proprioceptive cues yet most studies in humans involve primarily visual input, providing limited insight into their contributions. We developed a paradigm involving walking in an omnidirectional treadmill in which participants were guided on two legs of a triangle and then found their back way to origin. In Experiment 1, we tested a range of different triangle types while keeping distance relatively constant to determine the influence of spatial geometry. Participants overshot the angle they needed to turn and undershot the distance they needed to walk, with no consistent effect of triangle type. In Experiment 2, we manipulated distance while keeping angle relatively constant to determine how path integration operated over both shorter and longer distances. Participants underestimated the distance they needed to walk to the origin, with error increasing as a function of the walked distance. To attempt to account for our findings, we developed computational models involving vector addition, the second of which included terms for the influence of past trials on the current one. We compared against a previously developed model of human path integration, the Encoding Error model. We found that the vector addition models captured the tendency of participants to under-encode guided legs of the triangles and an influence of past trials on current trials. Together, our findings expand our understanding of body-based contributions to human path integration, further suggesting the value of vector addition models in understanding these important components of human navigation.Author SummaryHow do we remember where we have been? One important mechanism for doing so is called path integration, which refers to the ability to track one’s position in space with only self-motion cues. By tracking the direction and distance we have walked, we can create a mental arrow from the current location to the origin, termed the homing vector. Previous studies have shown that the homing vector is subject to systematic distortions depending on previously experienced paths, yet what influences these patterns of errors, particularly in humans, remains uncertain. In this study, we compare two models of path integration based on participants walking two legs of a triangle without vision and then completing the third leg based on their estimate of the homing vector. We found no effect of triangle shape on systematic errors, while path length scaled the systematic errors logarithmically, similar to Weber-Fechner law. While we show that both models captured participant’s behavior, a model based on vector addition best captured the patterns of error in the homing vector. Our study therefore has important implications for how humans track their location, suggesting that vector-based models provide a reasonable and simple explanation for how we do so.
Fine human genetic map based on UK10K data set
Authors: Hao Ziqian , Du Pengyuan , Pan Yi-Hsuan , Li Haipeng 
Published: October 2019

AbstractRecombination is a major force that shapes genetic diversity. Determination of recombination rate is important and can theoretically be improved by increasing the sample size. However, it is challenging to estimate recombination rates when the sample size is extraordinarily large because of computational burden. In this study, we used a refined artificial intelligence approach to estimate the recombination rate of the human genome using the UK10K human genomic dataset with 7,562 genomic sequences and its three subsets with 200, 400 and 2,000 genomic sequences under the Out-of-Africa demography model. We not only obtained an accurate human genetic map, but also found that the fluctuation of estimated recombination rate is reduced along the human genome when the sample size is increased. UK10K recombination activity is less concentrated than its subsets. Our results demonstrate how the sample size affects the estimated recombination rate, and analyses of a larger number of genomes result in a more precise estimation of recombination rate.
Evaluating spatiotemporal integration of shape cues
Authors: Burchfield Taylor , Greene Ernest 
Published: October 2019

ABSTRACTPrior work has shown that humans can successfully identify letters that are constructed with a sparse array of dots, wherein the dot pattern reflects the strokes that would normally be used to fashion a given letter. In the present work the dots were briefly displayed, one at a time in sequence, varying the spatial order in which they were shown. A forward sequence was spatially ordered as though one were passing a stroke across the dots to connect them. Experiments compared this baseline condition to the following three conditions: a) the dot sequence was spatially ordered, but in the reverse direction from how letter strokes might normally be written; b) the dots in each stroke of the letter were displayed in a random order; c) the sequence of displayed dots were chosen for display from any location in the letter. Significant differences were found between the baseline condition and all three of the comparison conditions, with letter recognition being far worse for the random conditions than for conditions that provided consistent spatial ordering of dot sequences. These findings show that spatial order is critical for integration of shape cues that have been sequentially displayed.
Temporal signatures of criticality in human cortical excitability as probed by early somatosensory responses
Authors: Stephani T. , Waterstraat G. , Haufe S. , Curio G. , Villringer A. , Nikulin V. V. 
Published: October 2019

AbstractBrain responses vary considerably from moment to moment, even to identical sensory stimuli. This has been attributed to changes in instantaneous neuronal states determining the system’s excitability. Yet the spatio-temporal organization of these dynamics remains poorly understood. Here we test whether variability in stimulus-evoked activity can be interpreted within the framework of criticality, which postulates dynamics of neural systems to be tuned towards the phase transition between stability and instability as is reflected in scale-free fluctuations in spontaneous neural activity. Using a novel non-invasive approach in 33 male participants, we tracked instantaneous cortical excitability by inferring the magnitude of excitatory post-synaptic currents from the N20 component of the somatosensory evoked potential. Fluctuations of cortical excitability demonstrated long-range temporal dependencies decaying according to a power law across trials – a hallmark of systems at critical states. As these dynamics covaried with changes in pre-stimulus oscillatory activity in the alpha band (8–13 Hz), we establish a mechanistic link between ongoing and evoked activity through cortical excitability and argue that the co-emergence of common temporal power laws may indeed originate from neural networks poised close to a critical state. In contrast, no signatures of criticality were found in subcortical or peripheral nerve activity. Thus, criticality may represent a parsimonious organizing principle of variability in stimulus-related brain processes on a cortical level, possibly reflecting a delicate equilibrium between robustness and flexibility of neural responses to external stimuli.Significance StatementVariability of neural responses in primary sensory areas is puzzling, as it is detrimental to the exact mapping between stimulus features and neural activity. However, such variability can be beneficial for information processing in neural networks if it is of a specific nature, namely if dynamics are poised at a so-called critical state characterized by a scale-free spatio-temporal structure. Here, we demonstrate the existence of a link between signatures of criticality in ongoing and evoked activity through cortical excitability, which fills the long-standing gap between two major directions of research on neural variability: The impact of instantaneous brain states on stimulus processing on the one hand and the scale-free organization of spatio-temporal network dynamics of spontaneous activity on the other.
A Wirelessly Powered Implantable CMOS Neural Recording Sensor Array using Pulse-based Neural Amplifier
Authors: Mulberry Geoffrey , White Kevin A. , Kim Brian N. 
Published: October 2019

AbstractThe most important organ in the human body is unquestionably the brain. Yet, despite its importance, it is one of the least well understood organs. One reason for this lack of understanding of the brain is the lack of data available to researchers from in vivo studies. Historically, collecting measurements from the brain has been difficult due to the high risk to the patient. Recently technology has been developed to allow electrical measurements to be taken from the brain directly, however most systems involve non-permanent sensors because of the requirement for transcranial wiring for power and data. Developments in the field of CMOS circuit design, wireless power transmission, and wireless data transmission have enabled the creation of implantable neural recording devices as a combination of these technologies. The implant designed in this paper is ∼15 mm in diameter and 2 mm at its thickest point on a flexible polyamide PCB. The flexible nature of the implant allows for the implant to conform to the surface of the brain. The implant requires no transcranial orifice since it is powered wirelessly and transmits data wirelessly via Bluetooth low energy. The CMOS neural amplifier chip on the implant utilizes an enhanced form of delta modulation to remove the requirement for large ADCs to be present on the die, saving space and enabling 1024 amplifiers and electrodes to be present on the chip. The implant is capable of measuring, modulating, and wirelessly transmitting a millivolt order signal to a PC for demodulation and analysis.
Aspirin-mediated DKK-1 increase rescues Wnt-driven stem-like phenotype in human intestinal organoids
Authors: Dunbar Karen , Valanciute Asta , Rajasekaran Vidya , Jamieson Thomas , Vinuela Paz Freile , Lima Ana , Blackmur James , Ochocka-Fox Anna-Maria , Arends Mark J. , Sansom Owen J. , Myant Kevin B , Farrington Susan M. , Dunlop Malcolm G. , Din Farhat V.N. 
Published: October 2019

ABSTRACTAspirin reduces the incidence and mortality of colorectal cancer (CRC). Wnt signalling drives CRC development from initiation to progression through regulation of epithelial-mesenchymal transition (EMT) and cancer stem cell populations (CSC). Here, we investigated whether aspirin can rescue these pro-invasive phenotypes associated with CRC progression in Wnt-driven human and mouse intestinal organoids. Aspirin rescues the Wnt-driven cystic organoid phenotype by promoting budding in mouse and human Apc deficient organoids, which is paralleled by decreased stem cell marker expression. Aspirin-mediated Wnt inhibition in ApcMin/+mice is associated with EMT inhibition and decreased cell migration, invasion and motility in CRC cell lines. Chemical Wnt activation induces EMT and stem-like alterations in CRC cells, which are rescued by aspirin. Aspirin increases expression of the Wnt antagonist Dickkopf-1 (DKK-1) in CRC cells and organoids derived from FAP patients. We provide evidence of phenotypic biomarkers of aspirin response with an increased epithelial and reduced stem-like state mediated by an increase in DKK-1. Thus we highlight a novel mechanism of aspirin-mediated Wnt inhibition and potential phenotypic and molecular biomarkers for trials.
Sample size evolution in neuroimaging research: an evaluation of highly-cited studies (1990-2012) and of latest practices (2017-2018) in high-impact journals
Authors: Szucs Denes , Ioannidis John PA 
Published: October 2019

AbstractWe evaluated 1038 of the most cited structural and functional (fMRI) magnetic resonance brain imaging papers (1161 studies) published during 1990-2012 and 273 papers (302 studies) published in top neuroimaging journals in 2017 and 2018. 96% of highly cited experimental fMRI studies had a single group of participants and these studies had median sample size of 12, highly cited clinical fMRI studies (with patient participants) had median sample size of 14.5, and clinical structural MRI studies had median sample size of 50. The sample size of highly cited experimental fMRI studies increased at a rate of 0.74 participant/year and this rate of increase was commensurate with the median sample sizes of neuroimaging studies published in top neuroimaging journals in 2017 (23 participants) and 2018 (24 participants). Only 4 of 131 papers in 2017 and 5 of 142 papers in 2018 had pre-study power calculations, most for single t-tests and correlations. Only 14% of highly cited papers reported the number of excluded participants whereas about 45% of papers in 2017 and 2018 reported excluded participants. Targeted interventions from publishers and funders could facilitate increase in sample sizes and adherence to better standards.
Epistasis, inbreeding depression and the evolution of self-fertilization
Authors: Awad Diala Abu , Roze Denis 
Published: October 2019

ABSTRACTInbreeding depression resulting from partially recessive deleterious alleles is thought to be the main genetic factor preventing self-fertilizing mutants from spreading in outcrossing hermaphroditic populations. However, deleterious alleles may also generate an advantage to selfers in terms of more efficient purging, while the effects of epistasis among those alleles on inbreeding depression and mating system evolution remain little explored. In this paper, we use a general model of selection to disentangle the effects of different forms of epistasis (additive-by-additive, additive-by-dominance and dominance-by-dominance) on inbreeding depression and on the strength of selection for selfing. Models with fixed epistasis across loci, and models of stabilizing selection acting on quantitative traits (generating distributions of epistasis) are considered as special cases. Besides its effects on inbreeding depression, epistasis may increase the purging advantage associated with selfing (when it is negative on average), while the variance in epistasis favors selfing through the generation of linkage disequilibria that increase mean fitness. Approximations for the strengths of these effects are derived, and compared with individual-based simulation results.
Age-related Structural and Functional Variations in 5967 Individuals across the Adult Lifespan
Authors: Luo Na , Sui Jing , Abrol Anees , Lin Dongdong , Chen Jiayu , Vergara Victor M. , Fu Zening , Du Yuhui , Damaraju Eswar , Xu Yong , Turner Jessica A. , Calhoun Vince D. 
Published: October 2019

ABSTRACTExploring brain changes across the human lifespan is becoming an important topic in neuroscience. Though there are multiple studies which investigated the relationship between age and brain imaging data, the results are heterogeneous due to small sample sizes and relatively narrow age ranges. Here, based on year-wise estimation of 5967 subjects from 13 to 72 years old, we aimed to provide a more precise description of adult lifespan variation trajectories of gray matter volume (GMV), structural network correlation (SNC) and functional network connectivity (FNC) using independent component analysis and multivariate linear regression model. Our results revealed the following relationships: 1)GMV linearly declined with age in most regions, while parahippocampus showed an inverted U-shape quadratic relationship with age; SNC presented a U-shape quadratic relationship with age within cerebellum, and inverted U-shape relationship primarily in the default mode network (DMN) and frontoparietal (FP) related correlation. 2) FNC tended to linearly decrease within resting-state networks (RSNs), especially in visual network and DMN. Early increase was revealed between RSNs, primarily in FP and DMN, which experienced decrease at older ages. U-shape relationship was also revealed to compensate for the cognition deficit in attention and subcortical related connectivity at late years. 3) The link between middle occipital gyrus and insula, as well as precuneus and cerebellum, exhibited similar changing trends between SNC and FNC across the adult lifespan. Collectively, these results highlight the benefit of lifespan study and provide a precise description of age-related regional variation and SNC/FNC changes based on a large dataset.
Revealing α oscillatory activity using voltage-sensitive dye imaging in monkey V1
Authors: Chemla Sandrine , Roux Sebastien , Reynaud Alexandre , Chavane Frédéric , VanRullen Rufin 
Published: October 2019

AbstractThe relevance of α oscillations (7-12Hz) in neural processing, although recognized long ago, remains a major research question in the field. While intensively studied in humans, α oscillations appear much less often investigated (and observed) in monkeys. Here we wish to provide data from non-human primates on stimulus-related α rhythm. Indeed, in humans, EEG α is enhanced in response to non-periodic dynamic visual stimulation (“perceptual echoes” or to a static stimulus (“flickering wheel illusion”). Do the same visual patterns induce an oscillatory response in monkey V1? We record voltage-sensitive dye signals from three anesthetized monkeys to investigate the population-based oscillatory neural response that is not resulting from attention-related feedback signals. We revealed α oscillations in monkey V1 which, when they occur, react in a manner comparable to human studies.
Monitoring of group mates in relation to their activity in mandrills
Authors: Schino Gabriele , Scerbo Martina 
Published: October 2019

ABSTRACTPrimates are known to have considerable knowledge about the social relationships that link their group mates, and are likely to derive this information from observing the social interactions that occur in their social group. They may therefore be hypothesized to pay particular attention to the social interactions involving group mates. In this study, we evaluated how the attention captive mandrills (Mandrillus sphinx) devote to their group mates was modulated by the behavior of the latter. Mandrills looked most frequently at foraging individuals and least frequently at sleeping invividuals. Mandrills also looked at grooming individuals more than at individuals that were simply sitting in contact. Grooming dyads were looked at regardless of the social rank and kinship of the individuals involved. These results contribute to our understanding of how primates obtain their social knowledge.
Investigating the Central Dogma of Molecular Biology in the Context of Nuclear Architecture and Cell Cycle
Authors: Dhuppar Shivnarayan , Mazumder Aprotim 
Published: October 2019

AbstractNuclear architecture is the organization of the genome within a cell nucleus with respect to different nuclear landmarks such as nuclear lamina, matrix or nucleoli. Lately it has emerged as a major regulator of gene expression in mammalian cells. The studies connecting nuclear architecture with gene expression are largely population-averaged and do not report on the heterogeneity in genome organization or in gene expression within a population. In this report we present a method for combining 3D DNA Fluorescencein situHybridization (FISH) with single molecule RNA FISH (smFISH) and immunofluorescence to study nuclear architecture-dependent gene regulation on a cell-by-cell basis. We further combine it with an imaging-based cell cycle staging to correlate nuclear architecture with gene expression across the cell cycle. We present this in the context ofCyclin A2 (CCNA2)gene for its known cell cycle-dependent expression. We show that, across the cell cycle, the expression of aCCNA2gene copy is stochastic and depends neither on its sub-nuclear position—which usually lies close to nuclear lamina—nor on the expression from the other copies.
Experimental and field data support habitat expansion of the allopolyploidArabidopsis kamchaticaowing to parental legacy of heavy metal hyperaccumulation
Authors: Paape Timothy , Akiyma Reiko , Cereghetti Teo , Onda Yoshihiko , Hirao Akira , Kenta Tanaka , Shimizu Kentaro K. 
Published: October 2019

AbstractLittle empirical evidence is available whether allopolyploid species combine or merge adaptations of parental species. The allopolyploid speciesArabidopsis kamchaticais a natural hybrid of the diploid parentsA. halleri, a heavy metal hyperaccumulator, andA. lyrata, a non-hyperaccumulating species. Zinc and cadmium were measured in native soils and leaf tissues in natural populations, and in hydroponic cultures ofA. kamchaticaandA. halleri. Pyrosequencing was used to estimate homeolog expression ratios. Soils from human modified sites showed significantly higher Zn concentrations than non-modified sites. Leaf samples ofA. kamchaticacollected from 40 field localities had > 1,000 µg g-1Zn in over half of the populations, with significantly higher amounts of Zn concentrations in plants from human modified sites. In addition, serpentine soils were found in two populations. Most genotypes accumulated >3000 µg g-1of Zn in hydroponic culture with high variability among them. Genes involved in hyperaccumulation showed a bias in thehalleri-derived homeolog.A. kamchaticahas retained constitutive hyperaccumulation ability inherited fromA. halleri. Our field and experimental data provides a compelling example in which the inheritance of genetic toolkits for soil adaptations likely contributed to the habitat expansion of an allopolyploid species.