bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modulation of sleep-courtship balance by nutritional status inDrosophila
Authors: Duhart José M. , Baccini Victoria , Zhang Yanan , Machado Daniel R. , Koh Kyunghee 
Published: October 2020

AbstractSleep is essential but incompatible with other behaviors, and thus sleep drive competes with other motivations. We previously showedDrosophilamales balance sleep and courtship via octopaminergic neurons that act upstream of courtship-regulating P1 neurons (Machado et al., 2017). Here we show nutrition modulates the sleep-courtship balance and identify sleep-regulatory neurons downstream of P1 neurons. Yeast-deprived males exhibited attenuated female-induced nighttime sleep loss yet normal daytime courtship, which suggests male flies consider nutritional status in deciding whether the potential benefit of pursuing female partners outweighs the cost of losing sleep. Trans-synaptic tracing and calcium imaging identified dopaminergic neurons projecting to the protocerebral bridge (DA-PB) as postsynaptic partners of P1 neurons. Activation of DA-PB neurons led to reduced sleep in normally fed but not yeast-deprived males. Additional PB-projecting neurons regulated male sleep, suggesting several groups of PB-projecting neurons act downstream of P1 neurons to mediate nutritional modulation of the sleep-courtship balance.
idCOV: a pipeline for quick clade identification of SARS-CoV-2 isolates
Authors: Zhu Xun , Chang Ti-Cheng , Webby Richard , Wu Gang 
Published: October 2020

AbstractidCOV is a phylogenetic pipeline for quickly identifying the clades of SARS-CoV-2 virus isolates from raw sequencing data based on a selected clade-defining marker list. Using a public dataset, we show that idCOV can make equivalent calls as annotated by Nextstrain.org on all three common clade systems using user uploaded FastQ files directly. Web and equivalent command-line interfaces are available. It can be deployed on any Linux environment, including personal computer, HPC and the cloud. The source code is available athttps://github.com/xz-stjude/idcov. A documentation for installation can be found athttps://github.com/xz-stjude/idcov/blob/master/README.md.
A velocity plan with internal feedback control best explains modulation of saccade kinematics during eye-hand coordination
Authors: V Varsha , Gopal Atul , Jana Sumitash , Padhi Radhakant , Murthy Aditya 
Published: October 2020

ABSTRACTFast movements like saccadic eye movements that occur in the absence of sensory feedback are often thought to be under internal feedback control. In this framework, a desired input in the form of desired displacement signal is widely believed to be encoded in a spatial map of the superior colliculus (SC). This is then converted into a dynamic velocity signal that drives the oculomotor neurons. However, recent evidence has shown the presence of a dynamic signal within SC neurons, which correlates with saccade velocity. Hence, we used models based on optimal control theory to test whether saccadic execution could be achieved by a velocity based internal feedback controller. We compared the ability of a trajectory control model based on velocity to that of an endpoint control model based on final displacement to capture saccade behavior of modulation of peak saccade velocity by the hand movement, independent of the saccade amplitude. The trajectory control model tracking the desired velocity in optimal feedback control framework predicted this saccade velocity modulation better than an endpoint control model. These results suggest that the saccadic system has the flexibility to incorporate a velocity plan based internal feedback control that is imposed by task context.NEW & NOTEWORTHYWe show that the saccade generation system may use an explicit velocity tracking controller when demand arises. Modulation of peak saccade velocity due to modulation of the velocity of the accompanying hand movement was better captured using a velocity tracking stochastic optimal control model compared to an endpoint model of saccade control. This is the first evidence of trajectory planning and control for the saccadic system based on optimal control theory.
Picture naming yields highly consistent cortical activation patterns: test-retest reliability of magnetoencephalography recordings
Authors: Ala-Salomäki Heidi , Kujala Jan , Liljeström Mia , Salmelin Riitta 
Published: October 2020

AbstractReliable paradigms and imaging measures of individual-level brain activity are paramount when reaching from group-level research studies to clinical assessment of individual patients. Magnetoencephalography (MEG) provides a direct, non-invasive measure of cortical processing with high spatiotemporal accuracy, and is thus well suited for assessment of functional brain damage in patients with language difficulties. This MEG study aimed to identify, in a picture naming paradigm, source-localized evoked activity and modulations of cortical oscillations that show high test-retest reliability across measurement days in healthy individuals, demonstrating their applicability in clinical settings. For patients with a severe language disorder picture naming can be a challenging task. Therefore, we also determined whether a semantic judgement task (‘is this item living’) with a spoken response (‘yes’/’no’) would suffice to induce comparably consistent activity within brain regions related to language production. The MEG data was collected from 19 healthy participants on two separate days. In picture naming, evoked activity was consistent across measurement days (intraclass correlation coefficient (ICC)>0.4) in the left frontal (400–800 ms after image onset), sensorimotor (200–800 ms), parietal (200–600 ms), temporal (200–800 ms), occipital (400–800 ms) and cingulate (600–800 ms) regions, as well as the right temporal (600–800 ms) region. In the semantic judgement task, consistent evoked activity was spatially more limited, occurring in the left temporal (200–800 ms), sensorimotor (400–800 ms), occipital (400–600 ms) and subparietal (600–800 ms) regions, and the right supramarginal cortex (600–800 ms). The naming task showed typical beta oscillatory suppression in premotor and sensorimotor regions (800–1200 ms) but other consistent modulations of oscillatory activity were mostly observed in posterior cortical regions that have not typically been associated with language processing. The high test-retest consistency of MEG evoked activity in the picture naming task testifies to its applicability in clinical evaluations of language function, as well as in longitudinal MEG studies of language production in clinical and healthy populations.
A computational grid-to-place-cell transformation model indicates a synaptic driver of place cell impairment in early-stage Alzheimer’s Disease
Authors: Ness Natalie , Schultz Simon R. 
Published: October 2020

AbstractAlzheimer’s Disease (AD) is characterized by progressive neurodegeneration and cognitive impairment. Synaptic dysfunction is an established early symptom, which correlates strongly with cognitive decline, and is hypothesised to mediate the diverse neuronal network abnormalities observed in AD. However, how synaptic dysfunction contributes to network pathology and cognitive impairment in AD remains elusive. Here, we present a grid-cell-to-place-cell transformation model of long-term CA1 place cell dynamics to interrogate the effect of synaptic loss on network function and environmental representation. Synapse loss modelled after experimental observations in the APP/PS1 mouse model was found to induce firing rate alterations and place cell abnormalities that have previously been observed in AD mouse models, including enlarged place fields and lower across-session stability of place fields. Our results support the hypothesis that synaptic dysfunction underlies cognitive deficits, and demonstrate how impaired environmental representation may arise in the early stages of AD. We further propose that dysfunction of excitatory and inhibitory inputs to CA1 pyramidal cells may cause distinct impairments in place cell function, namely reduced stability and place map resolution.Author SummaryCognitive decline in Alzheimer’s Disease (AD) correlates most strongly with dysfunction and loss of synapses in affected brain regions. While synaptic dysfunction is a well-established early symptom of AD, how impaired synaptic transmission may lead to progressive cognitive decline, remains subject to active research. In this study, we examine the effect of synapse loss on neuronal network function using a computational model of place cells in the hippocampal network. Place cells encode a cognitive map of an animal’s environment, enabling navigation and spatial memory. This provides a useful indicator of cognitive function, as place cell function is well characterized and abnormalities in place cell firing have been shown to underlie navigational deficits in rodents. We find that synapse loss in our network is sufficient to produce progressive impairments in place cell function, which resemble those observed in mouse models of the disease, supporting the hypothesis that synaptic dysfunction may underlie the cognitive impairment in AD. Furthermore, we observe that loss of excitatory and inhibitory synapses produce distinct spatial impairments. Future experiments investigating the relative contribution of different synaptic inputs may thus allow new insights into the neuronal network alterations in AD and potentially enable the identification of new therapeutic targets.
Diets affect the age-dependent decline of associative learning inCaenorhabditis elegans
Authors: Higurashi Satoshi , Tsukada Sachio , Aleogho Binta Maria , Park Joo Hyun , Tanaka Masaru , Nakano Shunji , Mori Ikue , Noma Kentaro 
Published: October 2020

AbstractThe causality and mechanism of dietary effects on brain aging are still unclear due to the long time scales of aging. The nematodeCaenorhabditis eleganshas contributed to aging research because of its short lifespan and easy genetic manipulation. When fed the standard laboratory diet,Escherichia coli,C. elegansexperiences an age-dependent decline in temperature-food associative learning, called thermotaxis. To address if diet affects this decline, we screened 35 lactic acid bacteria as alternative diets and found that animals maintained high thermotaxis ability when fed a clade ofLactobacillienriched with heterofermentative bacteria. Among them,Lactobacillusreuterimaintained the thermotaxis of aged animals without affecting their lifespan and motility. The effect ofLb. reuteridepends on the DAF-16 transcription factor functioning in neurons. Furthermore, RNA sequencing analysis revealed that differentially expressed genes between aged animals fed different bacteria were enriched with DAF-16 targets. Our results demonstrate that diet can impact brain aging in adaf-16dependent manner without changing the lifespan.
Increased amphetamine-induced hyperactivity intranslin (Tsn)KO mice is driven by elevated adiposity
Authors: Fu Xiuping , Shah Aparna P. , Keighron Jacqueline , Mou Ta-Chung M. , Ladenheim Bruce , Alt Jesse , Fukudome Daisuke , Niwa Minae , Tamashiro Kellie , Tanda Gianluigi , Sawa Akira , Cadet Jean-Lud , Rais Rana , Baraban Jay M. 
Published: October 2020

AbstractThe translin/trax microRNA-degrading enzyme mediates activity-induced changes in translation that underlie several long-lasting forms of cellular plasticity. As translin and trax are expressed in dopaminergic and striatal neurons, we proceeded to investigate whether deletion ofTsnblocks amphetamine sensitization, a long-lasting, translation-dependent form of behavioral plasticity,Although we expected constitutiveTsndeletion to impair amphetamine sensitization, we found, instead, that it enhances the hyperlocomotion produced by the initial dose of amphetamine. Since these mice display elevated adiposity, which alters pharmacokinetics of many drugs, we measured brain amphetamine levels inTsnknockout mice and found that these are elevated. We also found that diet-induced increases in adiposity in WT mice correlate with elevated brain amphetamine levels. As amphetamine and its analogues are widely used to treat attention deficit disorder, which is associated with obesity, further studies are needed to assess the impact of adiposity on amphetamine levels in these patients.
Neuroinflammation alters the phenotype of lymphangiogenic vessels near the cribriform plate
Authors: Hsu Martin , Madrid Andy , Choi Yun Hwa , Laaker Collin , Herbath Melinda , Sandor Matyas , Fabry Zsuzsanna 
Published: October 2020

AbstractMeningeal lymphatic vessels residing in the dural layer surrounding the dorsal regions of the brain, basal regions, and near the cribriform plate have all been implicated in the management of neuroinflammation and edema. Interestingly, only the lymphatic vessels near the cribriform plate undergo functional lymphangiogenesis in a mouse model of Multiple Sclerosis, suggesting these particular lymphatics uniquely undergo dynamic changes in response to neuroinflammation and may have distinct access to pro-lymphangiogenic factors in the CNS. However, it is unknown if these newly formed lymphangiogenic vessels are functionally similar to steady-state or if they have any other functional changes during neuroinflammation. In this study, we generated a novel protocol to isolate lymphatic endothelial cells from the cribriform plate for single cell analysis. We demonstrate that neuroinflammation-induced lymphangiogenic vessels undergo unique changes, including the capture of CNS-derived antigens, upregulation of adhesion and immune-modulatory molecules to interact with dendritic cells, and display IFN-γ dependent changes in response to the microenvironment. Single-cell trajectory analysis showed that cribriform plate lymphangiogenic vessels are post-proliferative and not generated from trans-differentiation of myeloid cells. Additionally, we show that these lymphangiogenic vessels have access to a CSF reservoir, express the water pore Aquaporin-1, and may have direct access to the CSF due to gaps in the arachnoid epithelial layer separating the dura from the subarachnoid space. These data characterize cribriform plate lymphatics and demonstrate that these vessels are dynamic structures that engage in leukocyte interactions, antigen sampling, and undergo expansion to drain excess fluid during neuroinflammation. Neuroinflammation not only induces efficient drainage of CSF but also alters the functions of lymphatic vessels near the cribriform plate.
Postharvest handling induces changes in fruit DNA methylation status and is associated with alterations in fruit quality in tomato (Solanum lycopersicumL.)
Authors: Zhou Jiaqi , Chen Bixuan , Albornoz Karin , Beckles Diane M 
Published: October 2020

AbstractPostharvest handling of tomato (Solanum lycopersicumL.), specifically low-temperature storage and early harvest are used to extend shelf life, but often reduce fruit quality. Recent work suggests that DNA methylation dynamics influences fruit ripening through the demethylaseSlDML2gene. However, the influence of postharvest handling on DNA methylation in relation to fruit quality is unclear. This work aimed to clarify these issues by analyzing DNA methylation using methyl-sensitive amplification polymorphism (MSAP), semi-quantitative transcriptional analysis of marker genes for fruit quality (RIN;RIPENING INHIBITOR) and DNA methylation (SlDML2;Solanum lycopersicumL.DNA demethylase 2), and, fruit biochemical quality biomarkers. Multivariate analysis of these data supported the view that DNA methylation of fruit was influenced more by postharvest handling than ripening stage, however, fruit quality was influenced mainly by ripening. Fruit chilled postharvest were distinct in their DNA methylation state and quality characteristics, which implied that these three phenomena i.e., chilling, methylation, and quality are highly connected. In addition, different postharvest handling methods modulatedSlDML2transcript levels but had little effect on the level ofRINtranscripts in fruit that reached the Turning stage after early harvest, and cold storage. These data collectively helped to advance our interpretation of tomato fruit ripening. In conclusion, our findings revealed that postharvest-induced variation in fruit quality is in relation to DNA methylation. Long-term this work will help better connect physiological changes in tomato fruit to events happening at the molecular level.
Overcoming barriers to the registration of new varieties
Authors: Yang Chin Jian , Russell Joanne , Ramsay Luke , Thomas William , Powell Wayne , Mackay Ian 
Published: October 2020

AbstractDistinctness, Uniformity and Stability (DUS) is an intellectual property system introduced in 1961 by the International Union for the Protection of New Varieties of Plants (UPOV) for safeguarding the investment and rewarding innovation in developing new plant varieties. Despite the rapid advancement in our understanding of crop biology over the past 60 years, the DUS system has not changed and is still dependent upon a set of morphological traits for testing candidate varieties. As the demand for more plant varieties increases, the barriers to registration of new varieties become more acute and thus require urgent review to the system. To highlight the challenges and remedies in the current system, we evaluated a comprehensive panel of 805 UK barley varieties that span the entire history of DUS testing. Our findings reveal the system deficiencies and provide evidence for a shift towards a robust genomics enabled registration system for new crop varieties.
The coevolution of mammae number and litter size
Authors: Stewart Thomas A. , Yoo Ihna , Upham Nathan S. 
Published: October 2020

AbstractMammals are unique in provisioning their offspring with milk, lactiferous nourishment produced in glandular organs called mammae. Mammae number is hypothesized to coevolve with litter size, acting as a constraint on offspring survival. However, predicted canonical relations between mammae number and litter size (i.e., the ‘one-half’ and ‘identity’ rules) are untested across Mammalia. Here we analyze data for 2,301 species and show how these characters coevolve. In Mammalia, mammae number approximates the maximum reported litter size of a species, and mammae number explains more variation in litter size than other species-level traits (mass, gestation length, diet, and seasonality of contemporary geographic distribution). Clades show differences in these patterns, indicating that certain life history strategies might break the ‘rules’ of mammary evolution. Mammae number is an underappreciated constraint on fecundity that has influenced the radiation of mammals.
Batch-Corrected Distance Mitigates Temporal and Spatial Variability for Clustering and Visualization of Single-Cell Gene Expression Data
Authors: Liang Shaoheng , Dou Jinzhuang , Iqbal Ramiz , Chen Ken 
Published: October 2020

AbstractClustering and visualization are essential parts of single-cell gene expression data analysis. The Euclidean distance used in most distance-based methods is not optimal. Batch effect, i.e., the variability among samples gathered from different times, tissues, and patients, introduces large between-group distance and obscures the true identities of cells. To solve this problem, we introduce Batch-Corrected Distance (BCD), a metric using temporal/spatial locality of the batch effect to control for such factors. We validate BCD on a simulated data as well as applied it to a mouse retina development dataset and a lung dataset. We also found the utility of our approach in understanding the progression of the Coronavirus Disease 2019 (COVID-19). BCD achieves more accurate clusters and better visualizations than state-of-the-art batch correction methods on longitudinal datasets. BCD can be directly integrated with most clustering and visualization methods to enable more scientific findings.
Neural Network Organization for Courtship Song Feature Detection inDrosophila
Authors: Baker Christa A. , McKellar Claire , Nern Aljoscha , Dorkenwald Sven , Pacheco Diego A. , Pang Rich , Eckstein Nils , Funke Jan , Dickson Barry J. , Murthy Mala 
Published: October 2020

ABSTRACTAnimals communicate using sounds in a wide range of contexts, and auditory systems must encode behaviorally relevant acoustic features to drive appropriate reactions. How feature detection emerges along auditory pathways has been difficult to solve due to challenges in mapping the underlying circuits and characterizing responses to behaviorally relevant features. Here, we study auditory activity in theDrosophila melanogasterbrain and investigate feature selectivity for the two main modes of fly courtship song, sinusoids and pulse trains. We identify 24 new cell types of the intermediate layers of the auditory pathway, and using a new connectomic resource, FlyWire, we map all synaptic connections between these cell types, in addition to connections to known early and higher-order auditory neurons - this represents the first map of the auditory pathway. We additionally determine the sign (excitatory or inhibitory) of most synapses in this auditory connectome. We find that auditory neurons display a continuum of preferences for courtship song modes, and that neurons with different song mode preferences are highly interconnected in a network that lacks hierarchical structure. Among this network, frequency tuning is centered on the range of frequencies present in song, whereas pulse rate tuning extends to rates outside of song, suggesting that these neurons form a basis set for downstream processing. Our study provides new insights into the organization of auditory coding within theDrosophilabrain.
Graph-theoretical Analysis of EEG Functional Connectivity during Balance Perturbation in Traumatic Brain Injury: A Pilot Study
Authors: Handiru Vikram Shenoy , Alivar Alaleh , Hoxha Armand , Saleh Soha , Suviseshamuthu Easter S. , Yue Guang , Allexandre Didier 
Published: October 2020

AbstractTraumatic Brain Injury (TBI) often results in balance impairment, increasing the risk of falls, and the chances of further injuries. However, the underlying neurophysiological mechanisms of postural control after TBI are not well understood. To this end, we conducted a pilot study with a multimodal approach of EEG, MRI, and Diffusion Tensor Imaging (DTI) to explore the neural mechanisms of unpredictable balance perturbations in 17 chronic TBI participants and 15 matched Healthy Controls (HC). As quantitative measures of the functional integration and segregation of the brain networks during the postural task, we computed the global graph-theoretic network measures (global efficiency and modularity) of brain functional connectivity derived from source-space EEG in different frequency bands. We observed that the TBI group showed a lower balance performance as measured by the Center of Pressure (COP) displacement during the task, and the Berg Balance Scale. They also showed altered brain activation and connectivity during the balance task. In particular, the task modulation of brain network segregation in alpha-band was reduced in TBI. Moreover, the DTI findings revealed that the structural damage is associated with reduced network connectivity and integration. In terms of the neural correlates, we observed a distinct role played by different frequency bands; greater theta-band modularity during the task was strongly correlated with the BBS in TBI group; alpha-band and beta-band graph-theoretic measures were associated with the measures of white matter structural integrity. Our future studies will focus on how postural training will modulate the functional brain networks in TBI.