bluuebunny/crossref_metadata_2025_split huggingface dataset:
Topological exploration of artificial neuronal network dynamics
Authors: Bardin Jean-Baptiste , Spreemann Gard , Hess Kathryn 
Published: September 2018

AbstractOne of the paramount challenges in neuroscience is to understand the dynamics of individual neurons and how they give rise to network dynamics when interconnected. Historically, researchers have resorted to graph theory, statistics, and statistical mechanics to describe the spatiotemporal structure of such network dynamics. Our novel approach employs tools from algebraic topology to characterize the global properties of network structure and dynamics.We propose a method based on persistent homology to automatically classify network dynamics using topological features of spaces built from various spike-train distances. We investigate the efficacy of our method by simulating activity in three small artificial neural networks with different sets of parameters, giving rise to dynamics that can be classified into four regimes. We then compute three measures of spike train similarity and use persistent homology to extract topological features that are fundamentally different from those used in traditional methods. Our results show that a machine learning classifier trained on these features can accurately predict the regime of the network it was trained on and also generalize to other networks that were not presented during training. Moreover, we demonstrate that using features extracted from multiple spike-train distances systematically improves the performance of our method.
Vertical transmission of sponge microbiota is inconsistent and unfaithful
Authors: Björk Johannes R. , Diéz-Vives Cristina , Astudillo-García Carmen , Archie Elizabeth A. , Montoya José M. 
Published: September 2018

AbstractClassic coevolutionary theory predicts that if beneficial microbial symbionts improve host fitness, they should be faithfully transmitted to offspring. More recently, the hologenome theory of evolution predicts resemblance between parent and offspring microbiomes and high partner fidelity between host species and their vertically transmitted microbes. Here, we test these ideas for the first time in multiple coexisting host species with highly diverse microbiota, leveraging known parent-offspring pairs sampled from eight species of wild marine sponges (Porifera). We found that the processes governing vertical transmission were both neutral and selective. A neutral model explained 66% of the variance in larval microbiota, which was higher than the variance this model explained for adult sponge microbiota (R2= 27%). However, microbes that are enriched above neutral expectations in adults were disproportionately transferred to offspring. Patterns of vertical transmission were, however, incomplete: larval sponges shared, on average, 44.8% of microbes with their parents, which was not higher than the fraction they shared with nearby non-parental adults. Vertical transmission was also inconsistent across siblings, as larval sponges from the same parent only shared 17% of microbes. Finally, we found no evidence that vertically transmitted microbes are faithful to a single sponge host species. Surprisingly, larvae were just as likely to share vertically transmitted microbes with larvae from other sponge species as they were with their own species. Our study demonstrates that common predictions of vertical transmission that stem from species-poor systems are not necessarily true when scaling up to diverse and complex microbiomes.
Reinforcement targets sexual or postmating prezygotic reproductive barriers depending on species abundance and population history
Authors: Poikela Noora , Kinnunen Johanna , Wurdack Mareike , Kauranen Hannele , Schmitt Thomas , Kankare Maaria , Snook Rhonda R. , Hoikkala Anneli 
Published: September 2018

AbstractThe impact of different reproductive barriers on species or population isolation may vary in different stages of speciation depending on evolutionary forces acting within species and through species’ interactions. Genetic incompatibilities between interacting species are expected to reinforce prezygotic barriers in sympatric populations and create character displacement between conspecific populations living within and outside the area of sympatry. The outcome of reinforcement has been suggested to be affected by the strength of postzygotic barriers, the history of species coexistence, and the impact of species abundancies on females’ discrimination against heterospecific males. We tested these predictions inDrosophila montanaandDrosophila flavomontanapopulations from different geographic regimes. All barriers betweenD. montanafemales andD. flavomontanamales were extremely strong, while in the reciprocal cross postzygotic isolation was less effective and the target of reinforcement varied according to population type. In long-established sympatric populations, whereD. flavomontanais abundant, reinforcement targeted sexual isolation, and in populations, where this species is a new invader and rare, reinforcement targeted postmating prezygotic barriers. Reinforcement of these barriers also created respective barriers between differentD. flavomontanapopulations. These findings show that interspecies interactions have far-reaching effects on strengthening species barriers and promoting speciation.
Amygdala neuronal ensembles dynamically encode behavioral states
Authors: Gründemann Jan , Bitterman Yael , Lu Tingjia , Krabbe Sabine , Grewe Benjamin F. , Schnitzer Mark J. , Lüthi Andreas 
Published: September 2018

AbstractInternal states, including affective or homeostatic states, are important behavioral motivators. The amygdala is a key brain region involved in the regulation of motivated behaviors, yet how distinct internal states are represented in amygdala circuits is unknown. Here, by imaging somatic neural calcium dynamics in freely moving mice, we identify changes in the relative activity levels of two major, non-overlapping populations of principal neurons in the basal nucleus of the amygdala (BA) that predict switches between exploratory and non-exploratory (defensive, anxiety-like) behavioral states across different environments. Moreover, the amygdala widely broadcasts internal state information via several output pathways to larger brain networks, and sensory responses in BA occur independently of behavioral state encoding. Thus, the brain processes external stimuli and internal states in an orthogonal manner, which may facilitate rapid and flexible selection of appropriate, state-dependent behavioral responses.
A screen for genes that regulate synaptic growth reveals mechanisms that stabilize synaptic strength
Authors: Goel Pragya , Khan Mehak , Howard Samantha , Kiragasi Beril , Kikuma Koto , Dickman Dion 
Published: September 2018

ABSTRACTSynapses grow, prune, and remodel throughout development, experience, and disease. This structural plasticity can destabilize information transfer in the nervous system. However, neural activity remains remarkably stable throughout life, implying that adaptive countermeasures exist to stabilize neurotransmission. Aberrant synaptic structure and function has been associated with a variety of neural diseases including Fragile X syndrome, autism, and intellectual disability. We have screened disruptions in over 300 genes in Drosophila for defects in synaptic growth at the neuromuscular junction. This effort identified 12 mutants with severe reductions or enhancements in synaptic growth. Remarkably, electrophysiological recordings revealed synaptic strength in all but one of these mutants was unchanged compared to wild type. We utilized a combination of genetic, anatomical, and electrophysiological analyses to illuminate three mechanisms that stabilize synaptic strength in the face of alterations in synaptic growth. These include compensatory changes in 1) postsynaptic receptor abundance; 2) presynaptic morphology; and 3) active zone structure. Together, this analysis identifies new genes that regulate synaptic growth and the adaptive strategies that synapses employ to homeostatically stabilize synaptic strength in response.AUTHOR SUMMARYThroughout development, maturation, experience, and disease, synapses undergo dramatic changes in growth and remodeling. Although these processes are necessary for learning and memory, they pose major challenges to stable function in the nervous system. However, neurotransmission is typically constrained within narrow physiological ranges, implying the existence of homeostatic mechanisms that maintain stable functionality despite drastic alterations in synapse number. In this study we investigate the relationship between synaptic growth and function across a variety of mutations in neural and synaptic genes in the fruitfly Drosophila melanogaster. Using the neuromuscular junction as a model system, we reveal three adaptive mechanisms that stabilize synaptic strength when synapses are dramatically under- or over-grown. Together, these findings provide insights into the strategies employed at both pre- and post-synaptic compartments to ensure stable functionality while allowing considerable flexibility in overall synapse number.
Repeated evolution of a morphological novelty: a phylogenetic analysis of the inflated fruiting calyx in the Physalideae tribe (Solanaceae)
Authors: Deanna Rocío , Larter Maximilien D. , Barboza Gloria E. , Smith Stacey D. 
Published: September 2018

PREMISE OF THE STUDYThe evolution of novel fruit morphologies has been integral to the success of angiosperms. The inflated fruiting calyx, in which the balloon-like calyx swells to completely surround the fruit, has evolved repeatedly across angiosperms and is postulated to aid in protection and dispersal. Here we investigate the evolution of this trait in the tomatillos and their allies (Physalideae, Solanaceae), using a newly estimated phylogeny and a suite of comparative methods to infer evolutionary gains and losses.METHODSThe Physalideae phylogeny was estimated using DNA sequences from four regions (ITS, LEAFY, trnL-F, waxy) using maximum likelihood and Bayesian Inference. Maximum likelihood model selection was used to determine the best fitting model of trait evolution. Using this model, we estimated ancestral states along with the numbers of gains and losses of fruiting calyx accrescence and inflation with Bayesian stochastic mapping. Also, phylogenetic signal in calyx morphology was examined with two metrics (parsimony score and Fritz and Purvis’ D).KEY RESULTSThe well resolved phylogeny points to multiple taxa in need of revision, including the eight genera that are non-monophyletic as presently circumscribed. Model fitting indicated that calyx evolution has proceeded in stepwise fashion, from non-accrescent, to accrescent, to inflated. Moreover, these transitions appear to be largely irreversible. Among the 215 sampled Physalideae, we inferred 24 gains of fruiting calyx accrescence, 24 subsequent transitions to a fully inflated calyx and only two reversals. A median of 50 shifts were estimated in total across the clade from the ancestral non-accrescent calyx. Nonetheless, fruiting calyx accrescence and inflation show strong phylogenetic signal.CONCLUSIONSOur phylogeny greatly improves the resolution of Physalideae and highlights the need for taxonomic work. The analyses of trait evolution reveal that the inflated fruiting calyx has evolved many times and that the trajectory towards this phenotype is generally stepwise and directional. These results provide a strong foundation for studying the genetic and developmental mechanisms responsible for the repeated origins of this charismatic fruit trait.
Derivation of a simple postoperative delirium incidence and severity prediction model
Authors: H. Lindroth , L. Bratzke , S. Twadell , P. Rowley , J. Kildow , M. Danner , L. Turner , B. Hernandez , W. Chang , R. Brown , R.D. Sanders 
Published: September 2018

SummaryBackgroundDelirium is an important postoperative complication, yet a simple and effective delirium prediction model remains elusive. We hypothesized that the combination of the National Surgical Quality Improvement Program (NSQIP) risk calculator for serious complications (NSQIP-SC) or risk of death (NSQIP-D), and cognitive tests of executive function (Trail Making Test A and B [TMTA, TMTB]), could provide a parsimonious model to predict postoperative delirium incidence or severity.MethodsData were collected from 100 adults (≥65yo) undergoing major non-cardiac surgery. In addition to NSQIP-SC, NSQIP-D, TMTA and TMTB, we collected participant age, sex, ASA score, tobacco use, type of surgery, depression, Framingham risk score, and preoperative blood pressure. Delirium was diagnosed with the Confusion Assessment Method (CAM), and the Delirium Rating Scale-R-98 (DRS) was used to assess symptom severity. LASSO and Best Subsets logistic and linear regression were employed in line with TRIPOD guidelines.ResultsThree participants were excluded due to intraoperative deaths (2) and alcohol withdrawal (1). Ninety-seven participants with a mean age of 71.68±4.55, 55% male (31/97 CAM+, 32%) and a mean Peak DRS of 21.5±6.40 were analyzed. Of the variables included, only NSQIP-SC and TMTB were identified to be predictors of postoperative delirium incidence (p<0.001, AUROC 0.81, 95% CI: 0.72, 0.90) and severity (p<0.001, Adj. R2: 0.30).ConclusionsIn this cohort, preoperative NSQIP-SC and TMTB were identified as predictors of postoperative delirium incidence and severity. Future studies should verify whether this two-factor model could be used for accurate delirium prediction.
Imaging tissues and cells beyond the diffraction limit with structured illumination microscopy and Bayesian image reconstruction
Authors: Pospíšil Jakub , Lukeš Tomáš , Bendesky Justin , Fliegel Karel , Spendier Kathrin , Hagen Guy M. 
Published: September 2018

AbstractBackgroundStructured illumination microscopy (SIM) is a family of methods in optical fluorescence microscopy that can achieve both optical sectioning and super-resolution effects. SIM is a valuable method for high resolution imaging of fixed cells or tissues labeled with conventional fluorophores, as well as for imaging the dynamics of live cells expressing fluorescent protein constructs. In SIM, one acquires a set of images with shifting illumination patterns. This set of images is subsequently treated with image analysis algorithms to produce an image with reduced out-of-focus light (optical sectioning) and/or with improved resolution (super-resolution).FindingsFive complete and freely available SIM datasets are presented including raw and analyzed data. We report methods for image acquisition and analysis using open source software along with examples of the resulting images when processed with different methods. We processed the data using established optical sectioning SIM and super-resolution SIM methods, and with newer Bayesian restoration approaches which we are developing.ConclusionVarious methods for SIM data acquisition and processing are actively being developed, but complete raw data from SIM experiments is not typically published. Publicly available, high quality raw data with examples of processed results will aid researchers when developing new methods in SIM. Biologists will also find interest in the high-resolution images of animal tissues and cells we acquired. All of the data was processed with SIMToolbox, an open source and freely available software solution for SIM.
A cost effective high-resolution climbing assay applied to Drosophila Parkinson’s and proprioception mutants reveal novel behavioural phenotypes
Authors: Aggarwal Aman , Reichert Heinrich , VijayRaghavan K. 
Published: September 2018

AbstractSevere locomotor impairment is a common phenotype of neurodegenerative disorders such as Parkinson’s disease (PD). Drosophila models of PD, studied from more than a decade, have helped in understanding the interaction between various genetic factors, such as parkin and PINK1, in this disease. To characterize locomotor behavioural phenotypes for these genes, fly climbing assays have been widely used. While these simple current assays for locomotor defects in Drosophila mutants measure some locomotor phenotypes well, it is possible that detection of subtle changes in behaviour is important to understand the early manifestation of locomotor disorders. We introduce a novel climbing behaviour assay which provides such fine-scale behavioural data and tests this proposition for the Drosophila model. We use this inexpensive, fully automated, high resolution assay to quantitatively characterize the parameters of climbing behaviour in three contexts. First, we characterize wild type flies and uncover a hitherto unknown sexual dimorphism in climbing behaviour. Second, we study climbing behaviour of heterozygous mutants of genes implicated in the fly PD model and reveal previously unreported prominent locomotor defects in some of these heterozygous fly lines. Finally, we study locomotor defects in a homozygous proprioceptory mutation (Trp-γ1) known to affect fine motor control in Drosophila. Moreover, we identify aberrant geotactic behaviour in Trp-γ1 mutants, thereby opening up a finer assay for geotaxis and its genetic basis. Our assay is therefore a cost-effective, general tool for measuring locomotor behaviours of wild type and mutant flies in fine detail and can reveal mild motor defects.Significance statementFine control of neuronal activity is required for proper motor output. Severe locomotor impairment is a common result of neurodegenerative disorders such as Parkinson’s disease (PD). The fruitfly, Drosophila, has been widely used as a model system to study the genetics of these disorders and simple climbing assays have been used to study the behavioural phenotypes of mutations in these genes. Here we introduce a novel, fully automated, high resolution climbing behaviour assay and use this assay to characterize climbing behaviour in wild type flies and in various fly mutant lines related to PD and defects in proprioception. Our assay is a general tool for measuring locomotor behaviours of flies in fine detail and can reveal very mild motor defects.
Influence of Arm Swing on Cost of Transport during Walking
Authors: de Graaf Myriam L. , Hubert Juul , Houdijk Han , Bruijn Sjoerd M. 
Published: September 2018

ABSTRACTNormal arm swing plays a role in decreasing the cost of transport during walking. However, whether excessive arm swing can reduce the cost of transport even further is unknown. Therefore, we tested the effects of normal and exaggerated arm swing on the cost of transport in the current study. Healthy participants (n=12) walked on a treadmill (1.25 m/s) in seven trials with different arm swing amplitudes (in-phase, passive restricted, active restricted, normal, three gradations of extra arm swing), while metabolic energy cost and the vertical angular momentum (VAM) and ground reaction moment (GRM) were measured.In general, VAM and GRM decreased as arm swing amplitude was increased, except for in the largest arm swing amplitude condition. The decreases in VAM and GRM were accompanied by a decrease in cost of transport from in-phase walking (negative amplitude) up to a slightly increased arm swing (non-significant difference compared to normal arm swing). The most excessive arm swings led to an increase in the cost of transport, most likely due to the cost of swinging the arms. In conclusion, increasing arm swing amplitude leads to a reduction in vertical angular moment and ground reaction moments, but it does not lead to a reduction in cost of transport for the most excessive arm swing amplitudes. Normal or slightly increased arm swing amplitude appears to be optimal in terms of cost of transport in young and healthy individuals.SUMMARY STATEMENTExcessive arm swing reduces the vertical angular momentum and ground reaction moment, but not necessarily the energetic cost of transport.
The spatial chronnectome reveals a dynamic interplay between functional segregation and integration
Authors: Iraji A. , DeRamus T.P. , Lewis N. , Yaesoubi M. , Stephen J.M. , Erhardt E. , Belger A. , Ford J.M. , McEwen S. , Mathalon D.H. , Mueller B.A. , Pearlson G.D. , Potkin S.G. , Preda A. , Turner J.A. , Vaidya J.G. , van Erp T.G.M. , Calhoun V.D. 
Published: September 2018

AbstractThe brain is highly dynamic, reorganizing its activity at different interacting spatial and temporal scales including variation within and between brain networks. The chronnectome is a model of the brain in which nodal activity and connectivity patterns are changing in fundamental and recurring ways through time. Most previous work has assumed fixed spatial nodes/networks, ignoring the possibility that spatial nodes or networks may vary in time, particularly at the level of the voxel. Here, we introduce an approach allowing for a spatially fluid chronnectome (called the spatial chronnectome for clarity), which focuses on the variation in spatiotemporal coupling at the voxel level within each network. We identify a novel set of spatially dynamic features which can be obtained and evaluated under different conditions. Results reveal transient spatially fluid interactions between intra- and inter-network relationships in which brain networks transiently merge and then separate again, emphasizing the dynamic interplay between segregation and integration. We also show that brain networks exhibit distinct spatial patterns with unique temporal characteristics, potentially explaining a broad spectrum of inconsistencies in previous studies which assumed static networks. Moreover, we show for the first time that anticorrelative connections to the default mode network, are transient as opposed to constant across the entire scan. Preliminary assessments of the approach using a multi-site dataset collected from 160 healthy subjects and 149 patients with schizophrenia (SZ) revealed the ability of the approach to obtain new information and nuanced alterations of brain networks that remain undetected during static analysis. For example, patients with SZ display transient decreases in voxel-wise network coupling including within visual and auditory networks that are not detectable in a spatially static analysis. Our approach also enabled calculation of a novel parameter, the intra-domain coupling variability which was higher within patients with SZ. The significant association between spatiotemporal uniformity and attention/vigilance cognitive domain highlights the cognitive relevance of the spatial chronnectome. In summary, the spatial chronnectome represents a new direction of research enabling the study of functional networks that are transient at the voxel level and identification of mechanisms for within and between-subject spatial variability to study functional brain homeostasis.