bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novelty detection in early olfactory processing of the honey bee, Apis mellifera
Authors: Lei H. , Haney S. , Jernigan C. , Guo X.J. , Cook C.N. , Bazhenov M. , Smith B.H. 
Published: October 2021

AbstractAnimals are constantly bombarded with stimuli, which presents a fundamental problem of sorting among pervasive uninformative stimuli and novel, possibly meaningful stimuli. We evaluated novelty detection behaviorally in honey bees as they position their antennae differentially in an air stream carrying familiar or novel odors. We then characterized neuronal responses to familiar and novel odors in the first synaptic integration center in the brain – the antennal lobes. We found that the neurons that exhibited stronger initial responses to the odor that was to be familiarized are the same units that later distinguish familiar and novel odors, independently of chemical identities. These units, including both projection neurons and local neurons, showed a decreased response to the familiar odor but an increased response to the novel odor. Our results suggest that the antennal lobe may assign a category of familiarity or novelty to an odor stimulus in addition to its chemical identity code. Therefore, the mechanisms for novelty detection may be present in early sensory processing, either as a result of local synaptic interaction or via feedback from higher brain centers.
In silico analysis for potential proteins and microRNAs in Glioblastoma and Parkinsonism
Authors: Banerjee Sayak , Chakraborty Souvik , Maiti Tarasankar , Bisawas Sristi 
Published: October 2021

AbstractIn today’s world, neurodegenerative diseases such as Alzheimer’s disease, Parkinson’s Disease, Huntington’s Disease as well as brain cancers such as astrocytomas, ependymomas, glioblastomas have become a great threat to us. In this study, we are trying to find a probable molecular connection associated with two very much different diseases, Glioblastoma, also known as Glioblastoma Multiforme (cancers of microglial cells of our brain) and Parkinson’s disease. We at first downloaded the microarray datasets of these two diseases from Gene Expression Omnibus (GEO) and then analyzed them by the GEO2R tool. After analysis, we found 249 common upregulated differential expressed genes and 135 common downregulated differential expressed genes of these two diseases. Therefore the common differentially expressed genes, both upregulated and downregulated, were imported into STRING online tool to find out the protein-protein interactions. Now, this whole network was subjected to Cytoscape and the top ten hub genes were found by Cyto-Hubba plug-in. The top then hub genes are EGFR, CCNB1, CDK1, CCNA2, CHEK1, RAD51, MAD2L1, KIF20A, BUB1, and CCNB2. These all genes are upregulated in both diseases. To find out the biological processes, molecular functions, cellular components, and pathways associated with these hub genes Enrichr online software was used. We used miRNet software to determine the interactions of hub genes with microRNAs. This study will be useful in the future for drug targets discovery for these diseases.
Aberrant Functional Connectivity between Reward and Inhibitory Control Networks in Pre-Adolescent Binge Eating Disorder
Authors: Murray Stuart B. , Alba Celina , Duval Christina J. , Nagata Jason M. , Cabeen Ryan P. , Lee Darrin J. , Toga Arthur W. , Siegel Steven J. , Jann Kay 
Published: October 2021

AbstractBackgroundBehavioral features of binge eating disorder (BED) suggest abnormalities in reward and inhibitory control. Studies of adult populations suggest functional abnormalities in reward and inhibitory control networks. Despite behavioral markers often developing in children, the neurobiology of pediatric BED remains unstudied.Methods58 pre-adolescent children (aged 9-10-years) with BED and 66 age, BMI and developmentally-matched control children were extracted from the 3.0 baseline (Year 0) release of the Adolescent Brain Cognitive Development (ABCD) Study. We investigated group differences in resting-state functional MRI (rs-fMRI) functional connectivity (FC) within and between reward and inhibitory control networks. A seed-based approach was employed to assess nodes in the reward (orbitofrontal cortex, nucleus accumbens, amygdala) and inhibitory control (dorsolateral prefrontal cortex, anterior cingulate cortex) networks via hypothesis-driven seed-to- seed analyses, and secondary seed-to-voxel analyses.ResultsOur findings revealed reduced FC between the dlPFC and amygdala, and between the anterior cingulate cortex and orbitofrontal cortex in pre-adolescent children with BED, relative to age, gender, BMI and developmentally matched controls. These findings indicating aberrant connectivity between nodes of inhibitory control and reward networks were corroborated by the whole-brain FC analyses.ConclusionsEarly-onset BED may be characterized by diffuse abnormalities in the functional synergy between reward and cognitive control networks, without perturbations within reward and inhibitory control networks, respectively. The decreased capacity to regulate a reward-driven pursuit of hedonic foods, which is characteristic of BED, may in part, rest on this dysconnectivity between reward and inhibitory control networks.
The long-term effects of repeated heroin vapor inhalation during adolescence on measures of nociception and anxiety-like behavior in adult Wistar rats
Authors: Gutierrez Arnold , Harvey Eric L. , Creehan Kevin M. , Taffe Michael A. 
Published: October 2021

AbstractRationaleAdolescents represent a vulnerable group due to increased experimentation with illicit substances that is often associated with the adolescent period, and because adolescent drug use can result in long-term effects that differ from those caused by drug use initiated during adulthood.ObjectivesThe purpose of the present study was to determine the effects of repeated heroin vapor inhalation during adolescence on measures of nociception, and anxiety-like behavior during adulthood in female and male Wistar rats.MethodsRats were exposed twice daily to 30-minutes of heroin vapor from post-natal day (PND) 36 to PND 45. At 12 weeks of age, baseline thermal nociception was assessed across a range of temperatures with a warm-water tail-withdrawal assay. Anxiety-like behavior was assessed in an elevated plus-maze (EPM) and activity was measured in an open field arena. Starting at 23 weeks of age, baseline thermal nociception was re-assessed, nociception was determined after acute heroin or naloxone injection, and anxiety-like behavior was redetermined in the EPM.ResultsAdolescent heroin inhalation altered baseline thermal nociception in female rats at 12 weeks of age and in both female and male rats at ∼23 weeks. Heroin-treated animals exhibited anxiety-like behavior when tested in the elevated plus-maze, showed blunted heroin-induced analgesia, but exhibited no effect on naloxone-induced hyperalgesia.ConclusionsThe present study demonstrates that heroin vapor inhalation during adolescence produces behavioral and physiological consequences in rats that persist well into adulthood.
Amplification and attenuation of noisy expression by export processes
Authors: Smith Madeline , Soltani Mohammad , Kulkarni Rahul , Singh Abhyudai 
Published: October 2021

AbstractInside mammalian cells, single genes are known to be transcribed in stochastic bursts leading to the synthesis of nuclear RNAs that are subsequently exported to the cytoplasm to create mRNAs. We systematically characterize the role of export processes in shaping the extent of random fluctuations (i.e. noise) in the mRNA level of a given gene. Using the method of Partitioning of Poisson arrivals, we derive an exact analytical expression for the noise in mRNA level assuming that the nuclear retention time of each RNA is an independent and identically distributed random variable following an arbitrary distribution. These results confirm recent experimental/theoretical findings that decreasing the nuclear export rate buffers the noise in mRNA level, and counterintuitively, decreasing the noise in the nuclear retention time enhances the noise in the mRNA level. Next, we further generalize the model to consider a dynamic extrinsic disturbance that affects the nuclear-to-cytoplasm export. Our results show that noise in the mRNA level varies non-monotonically with the disturbance timescale. More specifically, high- and low-frequency external disturbances have little impact on the mRNA noise level, while noise is amplified at intermediate frequencies. In summary, our results systematically uncover how the coupling of bursty transcription with nuclear export can both attenuate or amplify noise in mRNA levels depending on the nuclear retention time distribution and the presence of extrinsic fluctuations.
MetaScore: A novel machine-learning based approach to improve traditional scoring functions for scoring protein-protein docking conformations
Authors: Jung Yong , Geng Cunliang , Bonvin Alexandre M. J. J. , Xue Li C. , Honavar Vasant G. 
Published: October 2021

AbstractProtein-protein interactions play a ubiquitous role in biological function. Knowledge of the three-dimensional (3D) structures of the complexes they form is essential for understanding the structural basis of those interactions and how they orchestrate key cellular processes. Computational docking has become an indispensable alternative to the expensive and timeconsuming experimental approaches for determining 3D structures of protein complexes. Despite recent progress, identifying near-native models from a large set of conformations sampled by docking - the so-called scoring problem - still has considerable room for improvement.We present here MetaScore, a new machine-learning based approach to improve the scoring of docked conformations. MetaScore utilizes a random forest (RF) classifier trained to distinguish near-native from non-native conformations using a rich set of features extracted from the respective protein-protein interfaces. These include physico-chemical properties, energy terms, interaction propensity-based features, geometric properties, interface topology features, evolutionary conservation and also scores produced by traditional scoring functions (SFs). MetaScore scores docked conformations by simply averaging of the score produced by the RF classifier with that produced by any traditional SF. We demonstrate that (i) MetaScore consistently outperforms each of nine traditional SFs included in this work in terms of success rate and hit rate evaluated over the top 10 predicted conformations; (ii) An ensemble method, MetaScore-Ensemble, that combines 10 variants of MetaScore obtained by combining the RF score with each of the traditional SFs outperforms each of the MetaScore variants. We conclude that the performance of traditional SFs can be improved upon by judiciously leveraging machine-learning.
Computational modelling of trans-synaptic nanocolumns, a modulator of synaptic transmission
Authors: Li Xiaoting , Hémond Gabriel , Godin Antoine G. , Doyon Nicolas 
Published: October 2021

AbstractNanocolumns are trans-synaptic structures which align presynaptic vesicles release sites and postsynaptic receptors. However, how these nano structures shape synaptic signaling remains little understood. Given the difficulty to probe submicroscopic structures experimentally, computer modelling is a usefull approach to investigate the possible functional impacts of nanocolumns. In our in silico model, as has been experimentally observed, a nanocolumn is characterized by a tight distribution of postsynaptic receptors aligned with the presynaptic vesicle release site and by the presence of trans-synaptic molecules which can modulate neurotransmitter diffusion. We found that nanocolumns can play an important role in reinforcing synaptic current mostly when the presynaptic vesicle contains a small number of neurotransmitters. We also show that synapses with and without nanocolumns could have differentiated responses to spontaneous or evoked events. Our work provides a new methodology to investigate in silico the role of the submicroscopic organization of the synapse.Author summaryNeurotransmitter release, diffusion, and binding to postsynaptic receptors are key steps in synaptic transmission. However, the submicroscopic arrangement of receptors and presynaptic sites of neurotransmitter release remains little investigated. Experimental observations revealed the presence of trans-synaptic nanocolumns which span both the pre and post synaptic sites and fine tune the position of the post synaptic receptors. The functional impact of these nanocolumns (i.e. their influence on synaptic current) is both little understood and difficult to investigate experimentally. Here we construct a novel in silico model to investigate the functional impact of nanocolumns and show that they could play a functional role in reinforcing weak synapses.
Kinetic interplay between droplet maturation and coalescence modulates shape of aged protein condensates
Authors: Garaizar Adiran , Espinosa Jorge R. , Joseph Jerelle A. , Collepardo-Guevara Rosana 
Published: October 2021

ABSTRACTBiomolecular condensates formed by the process of liquid–liquid phase separation (LLPS) play diverse roles inside cells, from spatiotemporal compartmentalisation to speeding up chemical reactions. Upon maturation, the liquid-like properties of condensates, which underpin their functions, are gradually lost, eventually giving rise to solid-like states with potential pathological implications. Enhancement of inter-protein interactions is one of the main mechanisms suggested to trigger the formation of solid-like condensates. To gain a molecular-level understanding of how the accumulation of stronger interactions among proteins inside condensates affect the kinetic and thermodynamic properties of biomolecular condensates, and their shapes over time, we develop a tailored coarse-grained model of proteins that transition from establishing weak to stronger inter-protein interactions inside condensates. Our simulations reveal that the fast accumulation of strongly binding proteins during the nucleation and growth stages of condensate formation results in aspherical solid-like condensates. In contrast, when strong inter-protein interactions appear only after the equilibrium condensate has been formed, or when they accumulate slowly over time, with respect to the time needed for droplets to fuse and grow, spherical solid-like droplets emerge. By conducting atomistic potential-of-mean-force simulations of NUP-98 peptides—prone to forming inter-protein β-sheets—we observe that formation of inter-peptide β-sheets increases the strength of the interactions consistently with the loss of liquid-like condensate properties we observe at the coarse-grained level. Overall, our work aids in elucidating fundamental molecular, kinetic, and thermodynamic mechanisms linking the rate of change in protein interaction strength to condensate shape and maturation during ageing.
Nine-month presence of SARS-CoV-2 in saliva: a case report
Authors: Jansen Gijsbert J. , Wiersma Marit 
Published: October 2021

AbstractSARS-CoV-2 is a novel coronavirus that mainly affects the upper airways. Approximately one third of all detected cases is asymptomatic. We report an asymptomatic individual who tested positive for SARS-CoV-2 over a period of nine months. Of this individual, whole mouth saliva was tested by a novel fluorescence in situ hybridization-based assay which detects only the ‘active’ form of the virus. During the observation period of nine months, there was a possible co-infection with a second SARS-CoV-2 variant accompanied by none or very low antibody production until the possible co-infection. We suspect that the SARS-CoV-2 infection in this individual is limited to the salivary glands and does not spread (much) throughout the systemic compartment(s) of the body.
Estimate of the rate of unreported COVID-19 cases during the first outbreak in Rio de Janeiro
Authors: Aronna M.S. , Guglielmi R. , Moschen L.M. 
Published: October 2021

AbstractIn this work we fit an epidemiological model SEIAQR (Susceptible - Exposed - Infectious - Asymptomatic - Quarantined - Removed) to the data of the first COVID-19 outbreak in Rio de Janeiro, Brazil. Particular emphasis is given to the unreported rate, that is, the proportion of infected individuals that is not detected by the health system. The evaluation of the parameters of the model is based on a combination of error-weighted least squares method and appropriate B-splines. The structural and practical identifiability is analyzed to support the feasibility and robustness of the parameters’ estimation. We use the bootstrap method to quantify the uncertainty of the estimates. For the outbreak of March-July 2020 in Rio de Janeiro, we estimate about 90% of unreported cases, with a 95% confidence interval (85%, 93%).
Expression dynamics of ARGONAUTE proteins during meiosis in Arabidopsis
Authors: Oliver Cecilia , Martinez German 
Published: October 2021

AbstractMeiosis is a specialized cell division that is key for reproduction and genetic diversity in sexually reproducing plants. Recently, different RNA silencing pathways have been proposed to carry a specific activity during meiosis, but the pathways involved during this process remain unclear. Here, we explored the subcellular localization of different ARGONAUTE (AGO) proteins, the main effectors of RNA silencing, during male meiosis in Arabidopsis thaliana using immunolocalizations with commercially available antibodies. We detected the presence of AGO proteins associated with posttranscriptional gene silencing (AGO1, 2 and 5) in the cytoplasm or the nucleus, while AGOs associated with transcriptional gene silencing (AGO4 and 9) localized exclusively in the nucleus. These results indicate that the localization of different AGOs correlates with their predicted roles at the transcriptional and posttranscriptional levels and provide an overview of their timing and potential role during meiosis.
Kv1 channels regulate variations in spike patterning and temporal reliability in the avian cochlear nucleus angularis
Authors: Baldassano James F. , MacLeod Katrina M. 
Published: October 2021

AbstractDiverse physiological phenotypes in a neuronal population can broaden the range of computational capabilities within a brain region. The avian cochlear nucleus angularis (NA) contains a heterogeneous population of neurons whose variation in intrinsic properties results in electrophysiological phenotypes with a range of sensitivities to temporally modulated input. The low-threshold potassium conductance (GKLT) is a key feature of neurons involved in fine temporal structure coding for sound localization but a role for these channels in intensity or spectrotemporal coding has not been established. To determine whether GKLT affects the phenotypical variation and temporal properties of NA neurons, we applied dendrotoxin (DTX), a potent antagonist of Kv1-type potassium channels, to chick brain stem slices in vitro during whole-cell patch clamp recordings. We found a cell-type specific subset of NA neurons were sensitive to DTX: single-spiking NA neurons were most profoundly affected, as well as a subset of tonic firing neurons. Both tonic I (phasic onset bursting) and tonic II (delayed firing) neurons showed DTX sensitivity in their firing rate and phenotypical firing pattern. Tonic III neurons were unaffected. Spike time reliability and fluctuation sensitivity measured in DTX-sensitive NA neurons was also reduced with DTX. Finally, DTX reduced spike threshold adaptation in these neurons, suggesting that GKLT contributes to the temporal properties that allow coding of rapid changes in the inputs to NA neurons. These results suggest that variation in Kv1 channel expression may be a key factor in functional diversity in the avian cochlear nucleus.New and noteworthyThe dendrotoxin-sensitive voltage-gated potassium conductance typically associated with neuronal coincidence detection the timing pathway for sound localization is demonstrated to affect spiking patterns and temporal input sensitivity in the intensity pathway in the avian auditory brain stem. The Kv1-family channels appear to be present in a subset of cochlear nucleus angularis neurons, regulate spike threshold dynamics underlying high-pass membrane filtering, and contribute to intrinsic firing diversity.
Vpr shapes the proviral landscape and polyclonal HIV-1 reactivation patterns in cultured cells
Authors: Atindaana Edmond , Emery Sarah , Burnett Cleo , Pitcher Jake , Kidd Jeffrey M. , Telesnitsky Alice 
Published: October 2021

AbstractCell culture models suggest that the HIV-1 viral protein R (Vpr) is dispensable for latency establishment. However, whether Vpr affects the persistent proviral landscape and responsiveness to latency reversing agents (LRAs) is unclear. Here, integration site landscape, clonal dynamics, and latency reversal effects of Vpr were studied by comparing barcoded vpr+ and vpr- populations arising after infection of Jurkat cells in vitro. The results showed that individual integrant clones differed in fractions of LTR-active daughter cells: some clones gave rise to few to no LTR-active cells while for others almost all daughter cells were LTR-active. Integrant clones with at least 60% LTR-active cells (high LTR-active clones) contained proviruses positioned closer to preexisting enhancers (H3K27ac) and promoters (H3K4me3) than clones with <30% LTR-active cells (low LTR-active clones). Comparing vpr+ and vpr- populations revealed that the vpr+ population was depleted of high LTR-active clones. Complementing vpr-defective proviruses by transduction with vpr 16 days after infection led to rapid loss of high LTR-active clones, indicating that the effect of Vpr on proviral populations occurs post-integration. Comparing vpr+ and vpr- integration sites revealed that predominant vpr+ proviruses were farther from enhancers and promoters. Correspondingly, distances to these marks among previously reported intact HIV proviruses in ART-suppressed patients were more similar to those in the vpr+ pool than to vpr- integrants. To compare latency reactivation agent (LRA) responsiveness, the LRAs prostratin and JQ1 were applied separately or in combination. vpr+ and vpr- population-wide trends were similar, but combination treatment reduced virion release in a subset of vpr- clones relative to when JQ1 was applied separately, an effect not observed in vpr+ pools. Together, these observations highlight the importance of Vpr to proviral population dynamics, integration site landscapes, and responsiveness to latency reversing agents.One Sentence SummaryExpression properties and responsiveness to latency reactivation agents of individual HIV-1 proviral clones within polyclonal populations are masked by dominant clones and influenced by proviral proximity to certain epigenetic marks and by Vpr, a viral factor not previously known to affect latency and reactivation.
Effects of cryo-EM cooling on structural ensembles
Authors: Bock Lars V. , Grubmüller Helmut 
Published: October 2021

AbstractStructure determination by cryo electron microscopy (cryo-EM) provides information on structural heterogeneity and ensembles at atomic resolution. To obtain cryo-EM images of macromolecules, the samples are first rapidly cooled down to cryogenic temperatures. To what extent the structural ensemble is perturbed during cooling is currently unknown. Here, to quantify the effects of cooling, we combined continuum model calculations of the temperature drop, molecular dynamics simulations of a ribosome complex before and during cooling with kinetic models. Our results suggest that three effects markedly contribute to the narrowing of the structural ensembles: thermal contraction, reduced thermal motion within local potential wells, and the equilibration into lower free-energy conformations by overcoming separating free-energy barriers. During cooling, barrier heights below 10 kJ/mol were found to be over-come, which is expected to reduce B-factors in ensembles imaged by cryo-EM. Our approach now enables the quantification of the heterogeneity of room-temperature ensembles from cryo-EM structures.