bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of vestibular stimulation on gait stability when walking at different step widths
Authors: Magnani Rina M. , van Dieën Jaap H. , Bruijn Sjoerd M. 
Published: September 2021

AbstractVestibular information modulates muscle activity during gait, presumably to contribute to stability. If this is the case, stronger effects of perturbing vestibular information on local dynamic stability of gait, a measure of the locomotor system’s response to small, naturally occurring perturbations, can be expected for narrow-base walking (which needs more control) than for normal walking and smaller effects for wide-base walking (which needs less control). An important mechanism to stabilize gait is to coordinate foot placement to center of mass (CoM) state. Vestibular information most likely contributes to sensing this CoM state. We, therefore, expected that stochastic electrical vestibular stimulation (EVS) would decrease the correlation between foot placement and CoM state during the preceding swing phase. In fourteen healthy participants, we measured the kinematics of the trunk (as a proxy of the CoM), and feet, while they walked on a treadmill in six conditions: control (usual step width), narrow-base, and wide-base, each with and without stochastic EVS (peak amplitude of 5 mA; RMS of ~ 1.2 mA; frequency band from 0 to 25 Hz). Stochastic EVS decreased local dynamic stability irrespective of step width. Foot placement correlated stronger with trunk motion during walking with EVS than without in the control condition. However, residual variance in foot placement was increased when walking with EVS, indicating less precise foot placement. Thus, a vestibular error signal leads to a decrease in gait stability and precision of foot placement but these effects are not consistently modulated by step width.
Structured random receptive fields enable informative sensory encodings
Authors: Pandey Biraj , Pachitariu Marius , Brunton Bingni W. , Harris Kameron Decker 
Published: September 2021

AbstractBrains must represent the outside world so that animals survive and thrive. In early sensory systems, neural populations have diverse receptive fields structured to detect important features in inputs, yet significant variability has been ignored in classical models of sensory neurons. We model neuronal receptive fields as random, variable samples from parameterized distributions and demonstrate this model in two sensory modalities using data from insect mechanosensors and mammalian primary visual cortex. Our approach leads to a significant theoretical connection between the foundational concepts of receptive fields and random features, a leading theory for understanding artificial neural networks. The modeled neurons perform a randomized wavelet transform on inputs, which removes high frequency noise and boosts the signal. Further, these random feature neurons enable learning from fewer training samples and with smaller networks in artificial tasks. This structured random model of receptive fields provides a unifying, mathematically tractable framework to understand sensory encodings across both spatial and temporal domains.
A linear neural circuit for light avoidance in Drosophila larvae
Authors: Sorkaç Altar , Savva Yiannis A. , Savaş Doruk , Talay Mustafa , Barnea Gilad 
Published: September 2021

AbstractUnderstanding how neural circuits underlie behaviour is challenging even in the era of the connectome because it requires a combined approach encompassing anatomical and functional analyses. This is exemplified in studying the circuit underlying the light-avoidance behaviour displayed by the larvae of the fruit fly Drosophila melanogaster. While this behaviour is robust and the nervous system relatively simple, only bits and pieces of the circuit have been delineated1. Indeed, some studies resulted in contradicting conclusions regarding the contributions of various neuronal types to this behaviour2,3. Here we devise trans-Tango MkII, a new version of the transsynaptic circuit tracing and manipulation tool trans-Tango4. We implement trans-Tango MkII in anatomical tracing and combine it with circuit epistasis analysis. We use neuronal inhibition to test necessity of particular neuronal types for light-avoidance. We complement these experiments by selective neuronal activation to examine sufficiency in rescuing light-avoidance deficiencies exhibited by photoreceptor mutants. Together, our studies reveal a four-order, linear circuit for light-avoidance behaviour connecting the light-detecting photoreceptors with a pair of neuroendocrine cells via two types of clock neurons. Our combined approach could be readily expanded to other larval circuits. Further, this strategy provides the framework for studying more complex nervous systems and behaviours.
Chromosome-scale genome assembly of Eustoma grandiflorum, the first complete genome sequence in family Gentianaceae
Authors: Shirasawa Kenta , Arimoto Ryohei , Hirakawa Hideki , Ishimorai Motoyuki , Ghelfi Andrea , Miyasaka Masami , Endo Makoto , Kawabata Saneyuki , Isobe Sachiko 
Published: September 2021

AbstractEustoma grandiflorum (Raf.) Shinn., is an annual herbaceous plant native to the southern United States, Mexico, and the Greater Antilles. It has a large flower with a variety of colors and an important flower crop. In this study, we established a chromosome-scale de novo assembly of E. grandiflorum by integrating four genomic and genetic approaches: (1) Pacific Biosciences (PacBio) Sequel deep sequencing, (2) error correction of the assembly by Illumina short reads, (3) scaffolding by chromatin conformation capture sequencing (Hi-C), and (4) genetic linkage maps derived from an F2 mapping population. The 36 pseudomolecules and unplaced 64 scaffolds were created with total length of 1,324.8 Mb. Full-length transcript sequencing was obtained by PacBio Iso-Seq sequencing for gene prediction on the assembled genome, Egra_v1. A total of 36,619 genes were predicted on the genome as high confidence HC) genes. Of the 36,619, 25,936 were annotated functions by ZenAnnotation. Genetic diversity analysis was also performed for nine commercial E. grandiflorum varieties bred in Japan, and 254,205 variants were identified. This is the first report of the construction of reference genome sequences in E. grandiflorum as well as in the family Gentianaceae.
Local neuronal excitation and global inhibition during epileptic fast ripples in humans
Authors: Curot Jonathan , Barbeau Emmanuel , Despouy Elodie , Denuelle Marie , Sol Jean Christophe , Lotterie Jean-Albert , Valton Luc , Peyrache Adrien 
Published: September 2021

AbstractUnderstanding the neuronal basis of epileptiform activity is a major challenge in neurology. Interictal epileptiform discharges are associated with fast ripples (FRs, >200 Hz) in the local field potential (LFP) and are a promising marker of the epileptogenic zone. Here, by using a novel hybrid macro-micro depth electrode, combining classic depth recording of LFP and two or three tetrodes enabling up to 15 neurons in local circuits to be recorded simultaneously, we have characterized neuronal responses to FRs on the same hybrid and other electrodes targeting other brain regions. While FRs were associated with increased neuronal activity in local circuits only, they were followed by inhibition in large-scale networks. Neuronal responses to FRs were homogeneous in local networks but differed across brain areas. Similarly, post-FR inhibition varied across recording locations and subjects and was shorter than typical inter-FR intervals, suggesting that this inhibition is a fundamental refractory process for the networks. These findings demonstrate that FRs engage local and global networks and point to network features that pave the way for new diagnostic and therapeutic strategies.
Comparative Genome Analysis of ‘Candidatus Phytoplasma luffae’ Reveals the Influential Roles of Potential Mobile Units in Phytoplasma Evolution
Authors: Huang Ching-Ting , Cho Shu-Ting , Lin Yu-Chen , Tan Choon-Meng , Chiu Yi-Ching , Yang Jun-Yi , Kuo Chih-Horng 
Published: September 2021

AbstractPhytoplasmas are insect-transmitted plant pathogens that cause substantial losses in agriculture. In addition to economic impact, phytoplasmas induce distinct disease symptoms in infected plants, thus attracting attention for research on molecular plant-microbe interactions and plant developmental processes. Due to the difficulty of establishing an axenic culture of these bacteria, culture-independent genome characterization is a crucial tool for phytoplasma research. However, phytoplasma genomes have strong nucleotide composition biases and are repetitive, which make it challenging to produce complete assemblies. In this study, we utilized Illumina and Oxford Nanopore sequencing technologies to obtain the complete genome sequence of ‘Candidatus Phytoplasma luffae’ strain NCHU2019 that is associated with witches’ broom disease of loofah (Luffa aegyptiaca) in Taiwan. The fully assembled circular chromosome is 769 kb in size and is the first representative genome sequence of group 16SrVIII phytoplasmas. Comparative analysis with other phytoplasmas revealed that NCHU2019 has an exceptionally repetitive genome, possessing a pair of 75 kb repeats and at least 13 potential mobile units (PMUs) that account for ~25% of its chromosome. This level of genome repetitiveness is exceptional for bacteria, particularly among obligate pathogens with reduced genomes. Our genus-level analysis of PMUs demonstrated that these phytoplasma-specific mobile genetic elements can be classified into three major types that differ in gene organization and phylogenetic distribution. Notably, PMU abundance explains nearly 80% of the variance in phytoplasma genome sizes, a finding that provides a quantitative estimate for the importance of PMUs in phytoplasma genome variability. Finally, our investigation found that in addition to horizontal gene transfer, PMUs also contribute to intra-genomic duplications of effector genes, which may provide redundancy for neofunctionalization or subfunctionalization. Taken together, this work improves the taxon sampling for phytoplasma genome research and provides novel information regarding the roles of mobile genetic elements in phytoplasma evolution.
De-novo chromosome level assembly of plant genomes from long read sequence data
Authors: Sharma Priyanka , Masouleh Ardashir Kharabian , Topp Bruce , Furtado Agnelo , Henry Robert J. 
Published: September 2021

SummaryRecent advances in the sequencing and assembly of plant genomes have allowed the generation of genomes with increasing contiguity and sequence accuracy. The chromosome level assembly of the contigs generated from long read sequencing has involved the use of proximity analysis (Hi-C) or traditional genetic maps to guide the placement of sequence contigs within chromosomes. The development of highly accurate long reads by repeated sequencing of circularized DNA (PacBio HiFi) has greatly increased the size of contigs. We now report the use of HiFiasm to assemble the genome of Macadamia jansenii. a genome that has been used as model to test sequencing and assembly. This achieved almost complete chromosome level assembly from the sequence data alone without the need for higher level chromosome map information. Eight of the 14 chromosomes were represented by a single large contig and the other 6 assembled into 2-4 main contigs. The small number of chromosome breaks appear to be due to highly repetitive regions of ribosomal genes that cannot be assembled by these approaches. De novo assembly of near complete chromosome level plant genomes now seems possible using these sequencing and assembly tools. Further targeted strategies might allow these remaining gaps to be closed.Significance statement (of up to two sentences)De novo assembly of near complete chromosome level plant genomes is now possible using current long read sequencing and assembly tools.
Distinct and diverse chromatin-proteomes of ageing mouse organs reveal protein signatures that correlate with physiological functions
Authors: Oliviero Giorgio , Kovalchuk Sergey , Rogowska-Wrzesinska Adelina , Schwämmle Veit , Jensen Ole N. 
Published: September 2021

SUMMARYTemporal molecular changes in ageing mammalian organs are of relevance to disease etiology because many age-related diseases are linked to changes in the transcriptional and epigenetic machinery that regulate gene expression. We performed quantitative proteome analysis of chromatin-enriched protein extracts to investigate the dynamics of the chromatin-proteomes of the mouse brain, heart, lung, kidney, liver, and spleen at 3, 5, 10, and 15 months of age. Each organ exhibited a distinct chromatin-proteome and sets of unique proteins. The brain and spleen chromatin-proteomes were the most extensive, diverse, and heterogenous among the six organs. The spleen chromatin proteome appeared static during the lifespan, presenting a young phenotype that reflects the permanent alertness state and important role of this organ in physiological defense and immunity. We identified a total of 5928 proteins, including 2472 nuclear or chromatin associated proteins across the six mouse organs. Up to 3125 proteins were quantified in each organ demonstrating distinct and organ-specific temporal protein expression timelines and regulation at the post-translational level. Bioinformatics meta- analysis of these chromatin proteomes revealed distinct physiological and ageing- related features for each organ. Our results demonstrate the efficiency of organelle specific proteomics for in vivo studies of a model organism and consolidate the hypothesis that chromatin-associated proteins are involved in distinct and specific physiological functions in ageing organs.HIGHLIGHTSQuantitative chromatin-proteome analysis during mouse lifespan;Chromatin analysis in vitro and in vivo mouse models;Distinct chromatin proteomes of six organs during mouse lifespan;Correlations between ageing and chromatin regulation in mammalian lifespan.
Deep Learning-based Prediction of Early Cerebrovascular Events after Transcatheter Aortic Valve Replacement
Authors: Okuno Taishi , Overtchouk Pavel , Asami Masahiko , Tomii Daijiro , Stortecky Stefan , Praz Fabien , Lanz Jonas , Siontis George CM , Gräni Christoph , Windecker Stephan , Pilgrim Thomas 
Published: September 2021

ABSTRACTBackgroundCerebrovascular events (CVE) are one of the most feared complications of transcatheter aortic valve replacement (TAVR). CVE appear difficult to predict due to their multifactorial origin incompletely explained by clinical predictors. We aimed to build a deep learning-based predictive tool for TAVR-related CVE.MethodsIntegrated clinical and imaging characteristics from consecutive patients enrolled into a prospective TAVR registry were analysed. CVE comprised any strokes and transient ischemic attacks. Predictive variables were selected by recursive feature reduction to train an autoencoder predictive model. Area under the curve (AUC) represented the model’s performance to predict 30-day CVE.ResultsAmong 2,279 patients included between 2007 and 2019, both clinical and imaging data were available in 1,492 patients. Median age was 83 years and STS score was 4.6%. Acute (<24 hours) and subacute (day 2-30) CVE occurred in 19 (1.3%) and 36 (2.4%) patients, respectively. The occurrence of CVE was associated with an increased risk of death (HR [95%CI]: 2.62 [1.82-3.78]). The constructed predictive model uses less than 107 clinical and imaging variables and has an AUC of 0.79 (0.65-0.93).ConclusionsTAVR-related CVE can be estimated using a deep learning-based predictive algorithm. The model was implemented online for broad usage. (https://www.welcome.alviss.ai/#/cvecalculator).
TerraFlow, A New High Parameter Data Analysis Tool, Reveals Systemic T-cell Exhaustion and Dysfunctional Cytokine Production in Classical Hodgkin Lymphoma
Authors: Freeman Daniel , Diefenbach Catherine , Lam Linda , Le Tri , Alexandre Jason , Raphael Bruce , Grossbard Michael , Kaminetzky David , Ruan Jia , Chattopadhyay Pratip K. 
Published: September 2021

AbstractThe incredible variety of proteins associated with immune responses presents a major challenge in immune monitoring. When combinations of these proteins are measured, cell types that influence disease can be precisely identified. Here, we introduce TerraFlow, a novel data analysis tool that performs an exhaustive search of disease-associated cell populations from high-parameter flow cytometry experiments. Using a newly generated dataset, from 24-color immune checkpoint-focused and 18-color immune function-focused experiments, we apply TerraFlow to classical Hodgkin lymphoma (cHL), where systemic T-cell immunity has not been investigated in detail. We reveal novel immune perturbations in newly diagnosed cHL, as well as persistent immune perturbations after treatment. Newly diagnosed patients have elevated levels of activated (CD278+), exhausted (e.g., CD366+ and CD152+ phenotypes), and IL17-expressing cells, along with diminished levels of naïve and central memory (CD127+) T-cells and fewer IFNγ+ and TNF+ T-cells. Exhaustion signatures are reduced with treatment, but compared to healthy individuals, treated patients still exhibit more activated (CD278+ phenotypes), exhausted (CD366+), and IL17-expressing cells. Notably, TerraFlow identifies more phenotypic differences between patient groups than FlowSOM and CellCNN, often with better predictive power. Finally, we introduce a new non-gating approach for data analysis that obviates the need for time-consuming and subjective setting of fluorescence thresholds. Our results benchmark TerraFlow against common methods, provide mechanistic support for past reports of immune deficiency in cHL, and provide a roadmap for future immunotherapy and biomarker studies.
Reproduction in deep-sea vent shrimps is shaped by diet and phylogeny, with rhythms unlinked to surface production
Authors: Methou Pierre , Chen Chong , Watanabe Hiromi K. , Cambon-Bonavita Marie-Anne , Pradillon Florence 
Published: September 2021

AbstractVariations in offspring production according to feeding strategies or food supply have been recognized in many animals from various ecosystems. Despite an unusual trophic structure based on non-photosynthetic primary production, these relationships remain largely under-studied in chemosynthetic ecosystems. Here, we useRimicarisshrimps from deep-sea hydrothermal vents as a study case to explore relations between reproduction, diets and food supply in these environments. For that, we compared reproductive outputs of three congeneric shrimps differing by their diets. They inhabit vents located under oligotrophic waters of tropical gyres with opposed latitudes, allowing us to also examine the prevalence of phylogenetic vs environmental drivers in their reproductive rhythms. For this we used both our original data and a compilation of published observations on the presence of ovigerous females covering various seasons over the past 35 years. We report distinct egg production trends betweenRimicarisspecies relying solely on chemosymbiosis –R. exoculataandR. kairei– and those relying on mixotrophy –R. chacei– whereR. chaceiproduces broods with higher numbers of smaller eggs. Besides, our data and historical records suggest a reproductive period with substantial proportions of brooding females mostly between January and early April for all examined species whatever the region. Intriguingly, this periodicity does not correspond to seasonal variations in surface production with presence of brooding females during either boreal winter or austral summer. These observations contrast with the long-standing paradigm in deep-sea species for which periodic reproductive patterns have always been attributed to seasonal variations of photosynthetic production sinking from surface. Our results suggest the presence of intrinsic basis for biological rhythms in the deep sea, and bring to light the importance of having year-round observations in order to understand life history of vent animals.
Induction of transposable element expression is central to innate sensing
Authors: Rookhuizen Derek C. , Bonte Pierre-Emmanuel , Ye Mengliang , Hoyler Thomas , Gentili Matteo , Burgdorf Nina , Durand Sylvère , Aprahamian Fanny , Kroemer Guido , Manel Nicolas , Waterfall Joshua J , Milne Richard , Goudot Christel , Towers Greg J. , Amigorena Sebastian 
Published: September 2021

SUMMARYEvidence indicates that transposable elements (TEs) stimulate innate sensing pathways in various pathologies but it is not clear whether they are sensed during normal physiological responses. Here we show that, during activation with an exogenous pathogen associated molecular pattern (PAMP), dendritic cells (DCs) epigenetically remodel heterochromatin at TEs by depleting the methyltransferase Suv39h1 and reducing histone-3 lysine-9 trimethylation (H3K9me3). TLR4 signaling activates TE expression to enhance innate responses through the DNA sensor cGAS. Cytosolic cGAS-bound DNA comprised LINE1 TEs as the predominant endogenous ligands. Concordantly, LINE1 inhibition attenuated the type-I IFN response to LPS and rescued influenza virus infection. We propose that in healthy cells, exogenous PAMPs epigenetically activate self-derived PAMPs (LINE1) that engage cGAS to enhance responses. These data explain why pathogens employ redundant and broad innate immune countermeasures, to suppress activation of host PAMPs and illustrate a hitherto unappreciated role for host genome-derived PAMPs in response to pathogens.
Environmental niche and demographic modeling of American chestnut near its southwestern range limit
Authors: Laport Robert G. , Brookover Zoe S. , Christman Brian D. , Ng Julienne , Philley Kevin , Craddock J. Hill 
Published: September 2021

AbstractThe inadvertent introduction and rapid spread of chestnut blight (caused byCryphonectria parasitica(Murr.) Barr) in the early 20th century resulted in the demise of American chestnut (Castanea dentata(Marsh.) Borkh.; Fagaceae) as a major component of forest canopies and had negative impacts on eastern forest communities. Research efforts over the last century have documented the persistence of occasional trees and root crown/stump sprouts throughout much of the species’ historic range providing the basis for ongoing breeding of blight-resistant stock and restoration efforts. Unfortunately, it remains unclear how much of the historic range remains climatically suitable for remnant trees that may harbor unique genetic variation for successful reintroduction efforts. Here we investigate whether the southwestern portion of the historical range remains environmentally suitable for undiscovered remnant populations ofC. dentatausing environmental niche modeling. We also use stage-structured matrix projection models to investigate the potential demographic future ofC. dentatain W Tennessee, N Mississippi, SW Kentucky, and NW Alabama based upon observations of American chestnut in these areas over the last several decades. We found that suitable habitat associated with higher elevations and areas of high forest canopy cover occurs throughout much of the southwestern portion of the historical range and that populations of American chestnut in these areas are predicted to drastically decline over the next ~100-200 years without conservation interventions to mitigate the negative consequences of chestnut blight.