bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neural correlates of state transitions elicited by a chemosensory danger cue
Authors: Jesuthasan Suresh , Krishnan Seetha , Cheng Ruey-Kuang , Mathuru Ajay 
Published: April 2020

AbstractBackgroundDetection of predator cues changes the brain state in prey species and helps them avoid danger. Dysfunctionality in changing the central state appropriately in stressful situations is proposed to be an underlying cause of multiple psychiatric disorders in humans.MethodsHere, we investigate the dynamics of neural circuits mediating response to a threat, to characterize these states and to identify potential control networks. We use resonant scanning 2-photon microscopy forin vivobrain-wide imaging and custom designed behavioral assays for the study.ResultsWe first show that 5-7 day old zebrafish larvae react to an alarm pheromone (Schreckstoff) with reduced mobility. They subsequently display heightened vigilance, as evidenced by increased dark avoidance. Calcium imaging indicates that exposure toSchreckstoffelicits stimulus-locked activity in olfactory sensory neurons innervating a lateral glomerulus and in telencephalic regions including the putative medial amygdala and entopeduncular nucleus. Sustained activity outlasting the stimulus delivery was detected in regions regulating neuromodulator release, including the lateral habenula, posterior tuberculum, superior raphe, and locus coeruleus.ConclusionWe propose that these latter regions contribute to the network that defines the “threatened” state, while neurons with transient activity serve as the trigger. Our study highlights the utility of the zebrafish larval alarm response system to examine neural circuits during stress dependent brain state transitions and to discover potential therapeutic agents when such transitions are disrupted.
Symbiotic and non-symbiotic members of the genusEnsifer(syn.Sinorhizobium) are separated into two clades based on comparative genomics and high-throughput phenotyping
Authors: Fagorzi Camilla , Ilie Alexandru , Decorosi Francesca , Cangioli Lisa , Viti Carlo , Mengoni Alessio , diCenzo George C 
Published: April 2020

ABSTRACTRhizobium – legume symbioses serve as a paradigmatic example for the study of mutualism evolution. The genusEnsifer(syn.Sinorhizobium) contains diverse plant-associated bacteria, a subset of which can fix nitrogen in symbiosis with legumes. To gain insights into the evolution of symbiotic nitrogen fixation (SNF), and inter-kingdom mutualisms more generally, we performed extensive phenotypic, genomic, and phylogenetic analyses of the genusEnsifer. The data suggest that SNF emerged several times within the genusEnsifer, likely through independent horizontal gene transfer events. Yet, the majority (105 of 106) of theEnsiferstrains with thenodABCandnifHDKnodulation and nitrogen fixation genes were found within a single, monophyletic clade. Comparative genomics highlighted several differences between the “symbiotic” and “non-symbiotic” clades, including divergences in their pangenome content. Additionally, strains of the symbiotic clade carried 325 fewer genes, on average, and appeared to have fewer rRNA operons than strains of the non-symbiotic clade. Characterizing a subset of tenEnsiferstrains identified several phenotypic differences between the clades. Strains of the non-symbiotic clade could catabolize 25% more carbon sources, on average, than strains of the symbiotic clade, and they were better able to grow in LB medium and tolerate alkaline conditions. On the other hand, strains of the symbiotic clade were better able to tolerate heat stress and acidic conditions. We suggest that these data support the division of the genusEnsiferinto two main subgroups, as well as the hypothesis that pre-existing genetic features are required to facilitate the evolution of SNF in bacteria.
FaDA: A Shiny web application to accelerate common lab data analyses
Authors: Feseha Yodit , Moiteaux Quentin , Geffard Estelle , Ramstein Gérard , Brouard Sophie , Danger Richard 
Published: April 2020

AbstractBackgroundWeb-based data analysis and visualization tools are mostly designed for specific purposes, such as data from whole transcriptome RNA sequencing or single-cell RNA sequencing. However, limited efforts have been made to develop tools designed for data of common laboratory data for non-computational scientists. The importance of such web-based tool is stressed by the current increased samples capacity of conventional laboratory tools such as quantitative PCR, flow cytometry or ELISA.ResultsWe provide a web-based application FaDA, developed with the R Shiny package providing users to perform statistical group comparisons, including parametric and non-parametric tests, with multiple testing corrections suitable for most of the standard wet-lab analyses. FaDA provides data visualization such as heatmap, principal component analysis (PCA) and receiver operating curve (ROC). Calculations are performed through the R language.ConclusionsFaDA application provides a free and intuitive interface allowing biologists without bioinformatic skills to easily and quickly perform common lab data analyses. The application is freely accessible athttps://shiny-bird.univ-nantes.fr/app/FadaAbbreviationsAUC: Area Under the Curve; FaDA: Fast Data Analysis; GEO: Gene Expression Omnibus; ELISA: enzyme-linked immunosorbent assay; PCA: Principal Component Analysis; qPCR: quantitative PCR; ROC: Receiver Operating Curve.
Maturation of lateral habenula and early-life experience-dependent alteration with behavioral disorders in adulthood
Authors: Nakamura Tomoya , Kurosaki Kohei , Kanemoto Munenori , Sasahara Masakiyo , Ichijo Hiroyuki 
Published: April 2020

AbstractThe lateral habenula (LHb) inhibits midbrain monoaminergic neurons, thereby regulating emotion/cognition. Abnormally high activity in the LHb causes behavioral disorders, but how stressful experiences affect neuronal circuits underlying emotion remains poorly understood. Here, we report the effects of chronic stress on the LHb in postnatal day (P)1-9, P10-20, and P36-45 mice in the pre-, early, and late stages of LHb maturation. At P60, only mice exposed during P10-20 exhibited LHb-specific changes: abnormally high-stress reactivity shown by the expression of the immediate-early gene product (Zif268/Egr1) with insufficient number of parvalbumin (PV) neurons containing GABA. Furthermore, these mice showed anxiety/depression-like behaviors in the light-dark box test/forced swim test. Thus, experiences in early-life are essential for the maturation of neuronal circuits underlying emotion. Early-life stress is thought to have caused anxiety/depression in adulthood by disrupting the maturation of inhibitory PV neurons in the LHb in a period-specific manner.
SARS-CoV-2 Isolation and Propagation from Turkish COVID-19 patients
Authors: Tastan Cihan , Yurtsever Bulut , Sir Gozde , Kancagi Derya Dilek , Demir Sevda , Abanuz Selen , Seyis Utku , Yildirim Mulazim , Kuzay Recai , Elibol Omer , Arbak Serap , Elmas Merve Acikel , Birdogan Selcuk , Sahin Eray , Ozcan Orhan , Sezerman Ugur , Ovali Ercument 
Published: April 2020

AbstractThe novel coronavirus pneumonia, which was named later as Coronavirus Disease 2019 (COVID-19), is caused by the Severe Acute Respiratory Syndrome Coronavirus 2, namely SARS-CoV-2. It is a positive-strand RNA virus that is the seventh coronavirus known to infect humans. The COVID-19 outbreak presents enormous challenges for global health behind the pandemic outbreak. The first diagnosed patient in Turkey has been reported by the Republic of Turkey Ministry of Health on March 11, 2020. Today, over ninety thousand cases in Turkey, and two million cases around the world have been declared. Due to the urgent need for vaccine and anti-viral drug, isolation of the virus is crucial. Here, we report one of the first isolation and characterization studies of SARS-CoV-2 from nasopharyngeal and oropharyngeal specimens of diagnosed patients in Turkey. This study provides an isolation and replication methodology, and cell culture tropism of the virus that will be available to the research communities.Article SummaryScientists have isolated virus from Turkish COVID-19 patients. The isolation, propagation, and plaque and immune response assays of the virus described here will serve in following drug discovery and vaccine testing.
Single-cell transcriptomic analysis identifies neocortical developmental differences between human and mouse
Authors: Zhou Ziheng , Wang Shuguang , Zhang Dengwei , Jiang Xiaosen , Li Jie , Gu Ying , Sun Hai-Xi 
Published: April 2020

AbstractBackgroundThe specification and differentiation of neocortical projection neurons is a complex process under precise molecular regulation; however, little is known about the similarities and differences in cerebral cortex development between human and mouse at single-cell resolution.ResultsHere, using single-cell RNA-seq (scRNA-seq) data we explore the divergence and conservation of human and mouse cerebral cortex development using 18,446 and 7,610 neocortical cells. Systematic cross-species comparison reveals that the overall transcriptome profile in human cerebral cortex is similar to that in mouse such as cell types and their markers genes. By single-cell trajectories analysis we find human and mouse excitatory neurons have different developmental trajectories of neocortical projection neurons, ligand-receptor interactions and gene expression patterns. Further analysis reveals a refinement of neuron differentiation that occurred in human but not in mouse, suggesting that excitatory neurons in human undergo refined transcriptional states in later development stage. By contrast, for glial cells and inhibitory neurons we detected conserved developmental trajectories in human and mouse.ConclusionsTaken together, our study integrates scRNA-seq data of cerebral cortex development in human and mouse, and uncovers distinct developing models in neocortical projection neurons. The earlier activation of cognition -related genes in human may explain the differences in behavior, learning or memory abilities between the two species.
Multi-day rTMS exerts site-specific effects on functional connectivity but does not influence associative memory performance
Authors: Hendrikse Joshua , Coxon James , Thompson Sarah , Suo Chao , Fornito Alex , Yücel Murat , Rogasch Nigel C 
Published: April 2020

AbstractTranscranial magnetic stimulation (TMS) is a non-invasive brain stimulation technique with the capacity to modulate brain network connectivity and cognitive function. Recent studies have demonstrated long-lasting improvements in associative memory and resting-state connectivity following multi-day repetitive TMS (rTMS) to individualised parietal-hippocampal networks. We aimed to assess the reproducibility and network- and cognitive-specificity of these effects following multi-day rTMS. Participants received four days of 20 Hz rTMS to a subject-specific region of left lateral parietal cortex exhibiting peak functional connectivity to the left hippocampus. In a separate week, the same stimulation protocol was applied to a subject-specific region of pre-supplementary motor area (pre-SMA) exhibiting peak functional connectivity to the left putamen. We assessed changes to associative memory before and after each week of stimulation (N = 39), and changes to resting-state functional connectivity before and after stimulation in week one (N = 36). We found no evidence of long-lasting enhancement of associative memory or increased parieto-hippocampal connectivity following multi-day rTMS to the parietal cortex, nor increased pre-SMA-putamen connectivity following multi-day rTMS to pre-SMA. Instead, we observed some evidence of site-specific modulations of functional connectivity lasting ∼24 hours, with reduced connectivity within targeted networks and increased connectivity across distinct non-targeted networks. Our findings suggest a complex interplay between multi-day rTMS and network connectivity. Further work is required to develop reliable rTMS paradigms for driving changes in functional connectivity between cortical and subcortical regions.
Wharton’s Jelly-derived mesenchymal stromal cells retain their immunophenotype and immunomodulating characteristics after transfection with polyethylenimine
Authors: Ramos-Murillo Ana Isabel , Rodríguez Elizabeth , Ricaurte Cristian , Beltrán Karl , Camacho Bernardo , Salguero Gustavo A. , Godoy-Silva Rubén Darío 
Published: April 2020

AbstractBackgroundWharton’s Jelly-derived mesenchymal stromal cells (WJ-MSCs) present several advantages over other sources of multipotent stem cells, not only because they are obtained from neonatal umbilical cord, which is considered a biological waste, but also display higher proliferation rate and low senescence at later passages compared to stromal cells obtained from other sources. In the field of tissue engineering, WJ-MSCs have a wide therapeutic potential, due to their multipotential capacity, which can be reinforced if cells are genetically modified to direct their differentiation towards a specific lineage; unfortunately, as primary cells, WJ-MSC are difficult to transfect. Therefore, the objective of the present work was to standardize a protocol for the transfection of WJ-MSCs using a cationic polymer. Such protocol is important for future developments that contemplate the genetic modification of WJ-MSCs for therapeutic purposes.MethodsIn this work, WJ-MSCs were genetically modified using polyethylenimine (PEI) and a lentiviral plasmid that encodes for green fluorescent protein (pGFP). To achieve WJ-MSCs transfection, complexes between PEI and pGFP, varying its composition (N/P ratio), were evaluated and characterized by size, zeta potential and cytotoxicity. At the N/P ratio condition where the highest transfection efficiencies were obtained, immunophenotype, immunomodulation properties and multipotential capacity of WJ-MSCs were evaluated.ResultsHere, we present the standardization of the transfection conditions of the WJ-MSCs in a monolayer culture with PEI. The concentrations of plasmid and PEI that have the best transfection efficiencies were establishedConclusionsTransfection with PEI doesn’t affect immunophenotype, immunomodulatory properties and differentiation capacity of WJ-MSCs.
Freely chosen cadence during cycling attenuates intracortical inhibition and increases intracortical facilitation compared to a similar fixed cadence
Authors: Sidhu Simranjit , Lauber Benedikt 
Published: April 2020

AbstractIn contrast to other rhythmic tasks such as running, the preferred movement rate in cycling does not minimize energy consumption. It is possible that neurophysiological mechanisms contribute to the choice of cadence, however this phenomenon is not well understood. Eleven participants cycled at a fixed workload of 125 W and different cadences including a freely chosen cadence (FCC, ∼72), and fixed cadences of 70, 80, 90 and 100 revolutions per minute (rpm) during which transcranial magnetic stimulation (TMS) was used to measure short interval intracortical inhibition (SICI) and intracortical facilitation (ICF). There was significant increase in SICI at 70 (P= 0.004), 80 (P= 0.008) and 100 rpm (P= 0.041) compared to FCC. ICF was significantly reduced at 70 rpm compared to FCC (P= 0.04). Inhibition-excitation ratio (SICI divided by ICF) declined (P= 0.014) with an increase in cadence. The results demonstrate that SICI is attenuated during FCC compared to fixed cadences. The outcomes suggest that the attenuation of intracortical inhibition and augmentation of ICF may be a contributing factor for FCC.
Structural and functional complexity of vocalizations in a cooperatively breeding passerine, Jungle Babbler
Authors: Yambem Soniya Devi , Chorol Sonam , Jain Manjari 
Published: April 2020

AbstractAnimal vocal communication ranges from simple to complex based on repertoire size, structure, and composition of calls and the information encoded in them. According to the social complexity hypothesis, communication complexity tends to increase with an increase in social complexity. While several studies on mammalian systems exist supporting this, evidence from avian systems is comparatively limited. Towards this, we present evidence for complex acoustic communication in a cooperatively breeding passerine, Jungle Babbler, based on three aspects of complexity: an extensive repertoire of acoustically-distinct calls, within-call structural complexity and the diverse behavioural contexts in which these calls are used. Jungle Babblers were found to possess a structurally and functionally diverse vocal repertoire comprising 15 different calls. Detailed acoustic analyses of multisyllabic calls revealed that these calls are composed of different notes. Further, despite a large number of notes present in the repertoire, the number of calls were limited to 15. This implies that there may be underlying rules that determine call composition to give rise to functional calls to which receivers respond. We also found that these calls were produced in a variety of affiliative and agonistic contexts and were employed towards coordination of diverse social behaviours including group movement, foraging, brood care, aggression and vigilance. Yet, 7 out of 15 vocalizations were produced in the context of vigilance. This disproportionate investment of vocalizations towards co-ordinated acoustic vigilance is characteristic of many cooperatively breeding birds. Our study extends support for the social complexity hypothesis and also lays the foundation for future investigations on combinatorial and syntactical rules underlying call structure and function in bird vocalizations.Significance statementStudies on vocal complexity in birds have focussed mainly on repertoire size, structure and function. However, fine temporal and spectral features of elements that constitute a call/song are rarely examined to evaluate vocal complexity. We examined complex communication in a cooperatively breeding social passerine, Jungle Babbler for which we assessed repertoire size, function, acoustic features of calls and of their constituent elements. Jungle Babblers were found to possess a structurally and functionally diverse vocal repertoire comprising of 15 calls, 46% of which were in the context of vigilance, thereby extending support to the social complexity hypothesis. We also found that several calls were composed of multiple, acoustically distinct notes. These findings will be foundational in understanding the interrelations between sociality and communicative complexity and underlying combinatorial rules that determine call structure and function.
Italian Odonates in the Pandora’s Box: A Comprehensive DNA Barcoding Inventory Shows Taxonomic Warnings at the Holarctic Scale
Authors: Galimberti Andrea , Assandri Giacomo , Maggioni Davide , Ramazzotti Fausto , Baroni Daniele , Bazzi Gaia , Chiandetti Ivan , Corso Andrea , Ferri Vincenzo , Galuppi Mirko , Ilahiane Luca , La Porta Gianandrea , Laddaga Lorenzo , Landi Federico , Mastropasqua Fabio , Ramellini Samuele , Santinelli Roberto , Soldato Giovanni , Surdo Salvatore , Casiraghi Maurizio 
Published: April 2020

AbstractThe Odonata are considered among the most endangered freshwater faunal taxa. Their DNA-based monitoring relies on validated reference datasets that are often lacking or do not cover important biogeographical centres of diversification. This study presents the results of a DNA barcoding campaign on Odonata, based on the standard 658 bp 5’ end region of the mitochondrial COI gene, involving the collection of 812 specimens (409 of which barcoded) from peninsular Italy and its main islands (328 localities), belonging to all the 88 species (31 Zygoptera and 57 Anisoptera) known from the country. Additional BOLD and GenBank data from Holarctic samples expanded the dataset to 1294 DNA barcodes. A multi-approach species delimitation analysis involving two distance (OT and ABGD) and four tree-based (PTP, MPTP, GMYC, bGMYC) methods were used to explore these data. Of the 88 investigated morphospecies, 75 (85%) unequivocally corresponded to distinct Molecular Operational Units, whereas the remaining ones were classified as ‘warnings’ (i.e., showing a mismatch between morphospecies assignment and DNA-based species delimitation). These results are in contrast with other DNA barcoding studies on Odonata showing up to 95% of identification success. The species causing warnings were grouped in three categories depending on if they showed low, high, or mixed genetic divergence patterns. The analysis of haplotype networks revealed unexpected intraspecific complexity at the Italian, Palearctic, and Holarctic scale, possibly indicating the occurrence of cryptic species. Overall, this study provides new insights into the taxonomy of odonates and a valuable basis for future DNA and eDNA-based monitoring studies.
Poly-dispersed-acid-functionalized-single-walled carbon nanotubes (AF-SWCNTs) are potent inhibitor of BCG induced inflammatory response in macrophage cell lines
Authors: Bhardwaj Deepika , Saxena Rajiv K. 
Published: April 2020

AbstractPresent study is focussed on the modulation ofMycobacterium bovisBCG induced inflammatory response by poly-dispersed acid-functionalized single-walled carbon nanotubes (AF-SWCNTs) in macrophages. Flow cytometric and confocal microscopy studies indicated that both BCG and AF-SWCNTs were efficiently internalized by RAW 264.7 and MH-S macrophage cell lines and were essentially localized in the cytoplasmic area. The results indicated strong antioxidant activity of AF-SWCNTs in mitigating BCG induced oxidative and nitrosative stress. We also found a marked decline in expression of BCG induced pro-inflammatory genes like COX-2, iNOS, TNF-α, IL-6 and IL-1β on treatment with AF-SWCNTs at transcriptional level. Decline in expression of BCG induced COX-2 by AF-SWCNTs was also confirmed at protein level using Western blotting. Anti-inflammatory activity of AF-SWCNTs was further validated by our results showing that AF-SWCNTs treatment induced a precipitous decline in BCG induced release of Matrix Metalloproteinases MMP-2 and MMP-9 by macrophage cell lines, by using Gelatin zymography. Taken together, our results demonstrate potent anti-inflammatory role of AF-SWCNTs in alleviating BCG induced inflammation.