bluuebunny/crossref_metadata_2025_split huggingface dataset:
Electroencephalogram Data Collection for Student Engagement Analysis with Audio-Visual Content
Authors: Singh Mansi , Mishra Shreya , Mehta Jayantika , Bansal Anusha , Baranwal Manoj , Upadhyay Rahul , Kumar Vinay 
Published: September 2022

AbstractRecognizing and monitoring students’ attention during learning is crucial to successful knowledge acquisition since it influences cognitive function. As a result, gaining a precise picture of a learner’s mental state may enable interactive learning systems to alter tutoring content, devise effective help tactics, and improve learning outcomes. In computer-based learning environments, keeping track of students’ mental states is vital. Investigating the feasibility of utilizing active learning in enhancing student engagement index when exposed to various visual stimuli is the genesis of this work. The research includes collecting EEG data from 20 participants (ten males, ten females) while resting and being subjected to various virtual infotainment/educational content. The EEG data were collected using the Allengers Neuro PLOT, a 40-channel wet electrode system. The work includes raw and pre-processed EEG data under quiescent and audio-visual continuous cues. The recorded data is accommodated by a sophisticated EEG data pre-processing pipeline and will be available to the research community for usage.Specifications Table
Choice seeking is motivated by the intrinsic need for personal control
Authors: Munuera Jérôme , Agost Marta Ribes , Bendetowicz David , Kerebel Adrien , Chambon Valérian , Lau Brian 
Published: September 2022

AbstractWhen deciding between options that do or do not lead to future choices, humans often choose to choose. We studied choice seeking by asking subjects to decide between a choice opportunity or performing a computer-selected action. Subjects preferred choice when these options were equally rewarded, even deterministically, and were willing to trade extrinsic rewards for the opportunity to choose. We explained individual variability in choice seeking using reinforcement learning models incorporating risk sensitivity and overvaluation of rewards obtained through choice. Degrading perceived controllability diminished choice preference, although willingness to repeat selection of choice opportunities remained unchanged. In choices following these repeats, subjects were sensitive to rewards following freely chosen actions, but ignored environmental information in a manner consistent with a desire to maintain personal control. Choice seeking appears to reflect the intrinsic need for personal control, which competes with extrinsic reward properties and external information to motivate behavior.Author summaryHuman decisions can often be explained by the balancing of potential rewards and punishments. However, some research suggests that humans also prefer opportunities to choose, even when these have no impact on future rewards or punishments. Thus, opportunities to choose may be intrinsically motivating, although this has never been experimentally tested against alternative explanations such as cognitive dissonance or exploration. We conducted behavioral experiments and used computational modelling to provide compelling evidence that choice opportunities are indeed intrinsically rewarding. Moreover, we found that human choice preference varied according to individual risk attitudes, and expressed a need for personal control that competes with maximizing reward intake.
Ventral striatal dopamine encodes unique properties of visual stimuli in mice
Authors: Gonzalez L. Sofia , Fisher Austen A. , D’Souza Shane P. , Cotella Evelin M. , Lang Richard A. , Robinson J. Elliott 
Published: September 2022

ABSTRACTThe mesolimbic dopamine system is an evolutionarily conserved set of brain circuits that plays a role in attention, appetitive behavior, and reward processing. In this circuitry, ascending dopaminergic projections from the ventral midbrain innervate targets throughout the limbic forebrain, such as the ventral striatum/nucleus accumbens (NAc). Dopaminergic signaling in the NAc has been widely studied for its role in behavioral reinforcement, reward prediction error encoding, and motivational salience. Less well characterized is the role of dopaminergic neurotransmission in the response to surprising or alerting sensory events. To address this, we used the genetically encoded dopamine sensor dLight1 and fiber photometry to explore the ability of striatal dopamine release in to encode the properties of salient sensory stimuli in mice, such as threatening looming discs. Here, we report that NAc lateral shell (LNAc) dopamine release encodes the rate and magnitude of environmental luminance changes rather than visual stimulus threat level. This encoding is highly sensitive, as LNAc dopamine could be evoked by light intensities that were imperceptible to human experimenters. We also found that light-evoked dopamine responses are wavelength-dependent at low irradiances, independent of the circadian cycle, robust to previous exposure history, and involve multiple phototransduction pathways. Thus, we have further elaborated the mesolimbic dopamine system’s ability to encode visual information in mice, which is likely relevant to a wide body of scientists employing light sources or optical methods in behavioral research involving rodents.
Hyperthermia elevates brain temperature and improves behavioural signs in animal models of Autism spectrum disorder
Authors: Lopez-Rodriguez Ana Belen , Murray Carol , Kealy John , Towns Clodagh , Nazmi Arshed , Arnold Logan , Doran Michelle , Lowry John , Cunningham Colm 
Published: September 2022

AbstractAutism Spectrum Disorders (ASD) are predominantly developmental in nature and largely genetically determined. There are some human data supporting the idea that fever can improve symptoms in some individuals but the human data for this are limited and there are almost no data to support this from animal models. In the current study we used a whole body hyperthermia (WBH) protocol and systemic inflammation induced by bacterial endotoxin (LPS) to dissociate temperature and inflammatory elements of fever in order to examine the impact of these environmental stressors on behavioural signs in two animal models relevant to ASD: C58BL/6 and Shank3B- mice. While only LPS induced inflammatory signatures in the brain, WBH and LPS induced both overlapping and distinct neuronal cFos activation in several brain regions and modest effects on heat shock gene expression. In behavioural experiments LPS significantly suppressed most activities over 24-48 hours while WBH reduced repetitive behaviours and improved social interaction in C58BL/6 mice. In Shank3B- mice WBH significantly reduced compulsive grooming. The data are the first, to our knowledge, to demonstrate that elevated body temperature, in the absence of underpinning inflammation, can improve some behavioural signs in two distinct animal models of ASD. Given the developmental and genetic nature of ASD, evidence that symptoms may be ameliorated by environmental perturbations indicates that there are possibilities for improving function in these individuals.
Adolescent ethanol exposure promotes mechanical allodynia and alters dopamine transmission in the nucleus accumbens shell
Authors: Kelley Abigail M. , Del Valle Eric J. , Zaman Samin , Karkhanis Anushree N. 
Published: September 2022

ABSTRACTExcessive alcohol consumption in adolescence can disrupt neural development and may augment pain perception. Recent studies have shown that the nucleus accumbens (NAc) shell is involved in mediating pain sensitivity after peripheral inflammation in rodent models of chronic pain and alcohol use disorder (AUD). Interestingly, there have been very few studies examining the impact of chronic ethanol exposure during adolescence on pain sensitivity in adulthood. Therefore, in this project we investigated the impact of adolescent chronic intermittent ethanol (aCIE) exposure on mechanical allodynia and thermal hyperalgesia. Furthermore, given the involvement of the NAc shell in pain processing and chronic ethanol mediated changes, we measured changes in accumbal dopamine kinetics during protracted withdrawal. We found that both male and female aCIE rats show mechanical allodynia during withdrawal; however, only male rats exhibit thermal hyperalgesia during protracted withdrawal. Furthermore, male and female aCIE rats show greater evoked tonic dopamine release, maximal rate of dopamine reuptake, and dopamine affinity to the dopamine transporter in the NAc shell compared to controls. With phasic stimulation, aCIE rats also showed greater dopamine release compared to air exposed rats. These data suggest that aCIE exposure exacerbates pain sensitivity during withdrawal. Furthermore, based on prior literature, it is possible that the increased pain sensitivity may be driven, at least in part, by augmented dopamine kinetics in the NAc shell observed in the current study.
Combined DiI and antibody labeling reveals complex dysgenesis of hippocampal spine synapses in a mouse model of Fragile X Syndrome
Authors: Speranza Luisa , Filiz Kardelen Dalım , Goebel Sarah , Perrone-Capano Carla , Pulcrano Salvatore , Volpicelli Floriana , Francesconi Anna 
Published: September 2022

AbstractStructural, functional, and molecular alterations in excitatory spine synapses are a common hall-mark of many neurodevelopmental disorders including intellectual disability and autism. Here, we describe an optimized methodology, based on combined use of DiI and immunofluorescence, for rapid and sensitive characterization of the structure and composition of spine synapses in native brain tissue. We successfully demonstrate the applicability of this approach by examining the properties of hippocampal spine synapses in juvenile Fmr1 KO mice, a mouse model of Fragile X Syndrome. We find that mutant mice display pervasive dysgenesis of spine synapses evidenced by an overabundance of both abnormally elongated thin spines and cup-shaped spines, in combination with reduced density of mushroom spines. We further find that mushroom spines expressing the actin-binding protein Synaptopodin – a marker for spine apparatus - are more prevalent in mutant mice. Previous work identified spines with Synaptopodin/spine apparatus as the locus of mGluR-LTD, which is abnormally elevated in Fmr1 KO mice. Altogether, our data suggest this enhancement may be linked to the preponderance of this subset of spines in the mutant. Overall, these findings demonstrate the sensitivity and versatility of the optimized methodology by uncovering a novel facet of spine dysgenesis in Fmr1 KO mice.
Prediction of RNA secondary structures in SARS-CoV-2 and comparison with contemporary predictions
Authors: Ziesel Alison , Jabbari Hosna 
Published: September 2022

AbstractSARS-CoV-2, the causative agent of covid-19, is known to exhibit secondary structure in its 5’ and 3’ untranslated regions, along with the frameshifting stimulatory element situated between ORF1a and 1b. To identify further regions containing conserved structure, multiple sequence alignment with related coronaviruses was used as a starting point from which to apply a modified computational pipeline developed to identify non-coding RNA elements in vertebrate eukaryotes. Three different RNA structural prediction approaches were employed in this modified pipeline. Forty genomic regions deemed likely to harbour structure were identified, ten of which exhibited three-way consensus substructure predictions amongst our predictive utilities. Intracomparison of the pipeline’s predictive utilities, along with intercomparison with three previously published SARS-CoV-2 structural datasets, were performed. Limited agreement as to precise structure was observed, although different approaches appear to agree upon regions likely to contain structure in the viral genome.
Modeling Breast Cancer Proliferation, Drug Synergies, and Alternating Therapies
Authors: He Wei , Demas Diane M. , Shajahan-Haq Ayesha N. , Baumann William T. 
Published: September 2022

SUMMARYEstrogen receptor positive (ER+) breast cancer is responsive to a number of targeted therapies used clinically. Unfortunately, the continuous application of targeted therapy often results in resistance. Mathematical modeling of the dynamics of cancer cell drug responses can help find better therapies that not only hold proliferation in check but also potentially stave off resistance. Toward this end, we developed a mathematical model that can simulate various mono, combination and alternating therapies for ER+ breast cancer cells at different doses over long time scales. The model is used to look for optimal drug combinations and predicts a significant synergism between Cdk4/6 inhibitors in combination with the anti-estrogen fulvestrant, which may help explain the clinical success of adding CDK4/6 inhibitors to anti-estrogen therapy. Lastly, the model is used to optimize an alternating treatment protocol that works as well as monotherapy while using less total drug dose.
A unified framework of realistic in silico data generation and statistical model inference for single-cell and spatial omics
Authors: Song Dongyuan , Wang Qingyang , Yan Guanao , Liu Tianyang , Li Jingyi Jessica 
Published: September 2022

AbstractIn the single-cell and spatial omics field, computational challenges include method benchmarking, data interpretation, and in silico data generation. To address these challenges, we propose an all-in-one statistical simulator, scDesign3, to generate realistic single-cell and spatial omics data, including various cell states, experimental designs, and feature modalities, by learning interpretable parameters from real datasets. Furthermore, using a unified probabilistic model for single-cell and spatial omics data, scDesign3 can infer biologically meaningful parameters, assess the goodness-of-fit of inferred cell clusters, trajectories, and spatial locations, and generate in silico negative and positive controls for benchmarking computational tools.
Complete loss of RelA and SpoT homologs in Arabidopsis reveals the importance of the plastidial stringent response in the interplay between chloroplast metabolism and plant defense response
Authors: Inazu Masataka , Nemoto Takanari , Suzuki Sae , Ono Sumire , Kanno Yuri , Seo Mitsunori , Oikawa Akira , Masuda Shinji 
Published: September 2022

AbstractThe highly phosphorylated nucleotide, guanosine tetraphosphate (ppGpp), functions as a secondary messenger in bacteria and chloroplasts. The accumulation of ppGpp alters plastidial gene expression and metabolism, which are required for proper photosynthetic regulation and robust plant growth. However, because four plastid-localized ppGpp synthases/hydrolases function redundantly, the impact of the loss of ppGpp-dependent stringent response on plant physiology remains unclear. We used the CRISPR/Cas9 technology to generate an Arabidopsis thaliana mutant lacking all four ppGpp synthases/hydrolases, and characterized its phenotype. The mutant showed 20-fold less ppGpp levels than the wild type (WT) under normal growth conditions, and exhibited leaf chlorosis and increased expression of defense-related genes as well as salicylic acid and jasmonate levels upon transition to nitrogen-starvation conditions. These results demonstrate that proper levels of ppGpp in plastids are required for controlling not only plastid metabolism but also phytohormone signaling, which is essential for plant defense.
“Um…, it’s really difficult to… um… speak fluently”: Neural tracking of spontaneous speech
Authors: Agmon Galit , Jaeger Manuela , Tsarfaty Reut , Bleichner Martin G , Golumbic Elana Zion 
Published: September 2022

AbstractSpontaneous real-life speech is imperfect in many ways. It contains disfluencies and ill-formed utterances and has a highly variable rate. When listening to spontaneous speech, the brain needs to contend with these features in order to extract the speaker’s meaning. Here, we studied how the neural response is affected by four specific factors that are prevalent in spontaneous colloquial speech: (1) the presence of non-lexical fillers, (2) the need to detect syntactic boundaries in disfluent speech, and (3) variability in speech rate. Neural activity (EEG) was recorded from individuals as they listened to an unscripted, spontaneous narrative, which was analyzed in a time-resolved fashion to identify fillers and detect syntactic boundaries. When considering these factors in a speech-tracking analysis, which estimates a temporal response function (TRF) to describe the relationship between the stimulus and the neural response it generates, we found that the TRF was affected by both of them. This response was observed for lexical words but not for fillers, and it had an earlier onset for opening words vs. closing words of a clause and for clauses with slower speech rates. These findings broaden ongoing efforts to understand neural processing of speech under increasingly realistic conditions. They highlight the importance of considering the imperfect nature of real-life spoken language, linking past research on linguistically well-formed and meticulously controlled speech to the type of speech that the brain actually deals with on a daily basis.
Long-read direct RNA sequencing reveals epigenetic regulation of chimeric gene-transposon transcripts in Arabidopsis thaliana
Authors: Berthelier Jérémy , Furci Leonardo , Asai Shuta , Sadykova Munissa , Shimazaki Tomoe , Shirasu Ken , Saze Hidetoshi 
Published: September 2022

AbstractTransposable elements (TEs) are accumulated in both intergenic and intragenic regions in plant genomes. Intragenic TEs often act as regulatory elements of associated genes and are also co-transcribed with genes, generating chimeric TE-gene transcripts. Despite the potential impact on mRNA regulation and gene function, the prevalence and transcriptional regulation of TE-gene transcripts are poorly understood. By long-read direct RNA sequencing and a dedicated bioinformatics pipeline, “ParasiTE”, we investigated the transcription and RNA processing of TE-gene transcripts in Arabidopsis thaliana. We identified a global production of TE-gene transcripts in thousands of A. thaliana gene loci, with TE sequences often being associated with alternative transcription start sites or transcription termination sites. The epigenetic state of intragenic TEs affects RNAPII elongation and usage of alternative poly(A) signals within TE sequences, regulating alternative TE-gene isoform production. Co-transcription and inclusion of TE-derived sequences into gene transcripts impact regulation of RNA stability and environmental responses of some loci. Our study provides novel insights into TE-gene interactions that contributes to mRNA regulation, transcriptome diversity, and environmental responses in plants.
PLANAtools - an interactive gene expression repository for the planarian Schmidtea mediterranea
Authors: Hoffman Michael , Wurtzel Omri 
Published: September 2022

AbstractMotivationPlanarians are a widespread model for studying regeneration. Major efforts for studying gene function in planarian regeneration produced massive datasets, including transcriptome-wide gene expression analyses from hundreds of conditions. However, the accessibility of gene expression datasets to investigators is limited because of the need for expertise in gene expression analysis in this model, the requirement for computational resources, and the lack of a curated planarian gene expression metadata resource associating samples and their controls.ResultsWe implemented a computational resource, PLANAtools, that is available online and provides a portal to the analysis of over 160 gene expression analyses. Planarian gene expression datasets from the last decade were processed using a standardized pipeline based on curated planarian metadata. PLANAtools generates plots, annotations, and analyses of gene expression data, based on user parameters.AvailabilityPLANAtools is implemented using the R/Shiny framework and is accessible from https://wurtzellab.org/planatools
Co-stimulatory molecules decide T cell fate through regulations of their invigoration and impairment
Authors: Ichikawa Kenji , Ichikawa Kazuhisa 
Published: September 2022

AbstractT cell invigoration is an essential step for eliminating pathogens and cancer cells. Co-stimulatory molecules, such as CD80, CD86, and ICOSLG reinforce TCR stimuli for T cell activations. Despite identifying multiple co-stimulatory molecules, the differences of those in downstream signaling have remained unclear. Here, we unravel the differences in avidity of co-stimulatory molecules with T cells cause distinct T cell fates. Specially, CD80 + TCR stimulus promotes induction of multiple T cell effector genes based on prolonged and magnified activation of ERK and AKT compared with other combined stimuli. Long-term and robust activation of these signaling pathways leads to T cell impairment by induction of PD1, and exhausted T cells are vulnerable to disrupt effector functions by interactions with PDL1. Collectively, we reveal the quantitative differences in binding activities of co-stimulatory molecules to T cells cause qualitative differences in downstream signals and gene expressions, thereby branching T cell fates.
Association of polymorphisms of IL-6 pathway genes (IL6, IL6R and IL6ST) with COVID-19 severity in an Amazonian population
Authors: Rodrigues Fabíola Brasil Barbosa , da Silva Rosilene , dos Santos Erika Ferreira , de Brito Mioni Thieli Figueiredo Magalhães , da Silva Andréa Luciana Soares , de Meira Leite Mauro , da Costa Flavia Póvoa , de Almeida Viana Maria de Nazaré do Socorro , de Sarges Kevin Matheus Lima , Cantanhede Marcos Henrique Damasceno , de Oliveira Lameira Veríssimo Adriana , da Silva Carvalho Mayara , Henriques Daniele Freitas , da Silva Carla Pinheiro , Nunes Juliana Abreu Lima , Costa Iran Barros , Viana Giselle Maria Rachid , Queiroz Maria Alice Freitas , Lima Sandra Souza , da Costa Lopes Jeferson , da Silva Torres Maria Karoliny , Bichara Carlos David Araújo , Vallinoto Izaura Maria Vieira Cayres , Vallinoto Antonio Carlos Rosario , dos Santos Eduardo José Melo 
Published: September 2022

AbstractInterleukin-6 have been recognized as a major role player in COVID-19 severity, being an important regulator of cytokine storm. Hence, the evaluation of the influence of polymorphisms in key genes of IL-6 pathway, namely IL6, IL6R and IL6ST, may provide valuable prognostic/predictive biomarkers on COVID-19. The present cross-sectional study genotyped three Single Nucleotide Polymorphisms - SNPs (rs1800795, rs2228145 and rs7730934) at IL6, IL6R and IL6ST genes, respectively, in 227 COVID-19 patients (132 hospitalized and 95 non-hospitalized). Genotype frequencies were compared between these groups. As control group, published data on gene and genotype frequencies was gathered from published studies from before the pandemic started. Our major results point to an association of IL6 C allele with COVID-19 severity. Moreover, IL-6 plasmatic levels were higher among IL6 CC genotype carriers. Additionally, the frequency of symptoms was higher at IL6 CC and IL6R CC genotypes. In conclusion the data suggest an important role of IL6 C allele and IL6R CC genotype on COVID-19 severity, in agreement with indirect evidences from literature about association of these genotypes with mortality rates, pneumonia, heightening of protein plasmatic levels proinflammatory driven effects.