bluuebunny/crossref_metadata_2025_split huggingface dataset:
Boosting innate immunity:Asaiabacteria expressing a protein fromWolbachiadetermine macrophage activation and killing ofLeishmania
Authors: Varotto-Boccazzi Ilaria , Epis Sara , Arnoldi Irene , Corbett Yolanda , Gabrieli Paolo , Paroni Moira , Nodari Riccardo , Basilico Nicoletta , Sacchi Luciano , Gramiccia Marina , Gradoni Luigi , Tranquillo Vito , Bandi Claudio 
Published: June 2020

AbstractLeishmaniases are severe vector-borne diseases affecting humans and animals, caused byLeishmaniaprotozoans. Immune polarization plays a major role in determining the outcome ofLeishmaniainfections: hosts displaying M1-polarized macrophages are protected, while those biased on the M2 side acquire a chronic infection, that could develop into an overt and potentially deadly disease. The identification of the factors involved in M1 polarization is essential for the design of therapeutic and prophylactic interventions, including vaccines. Infection by the filarial nematodeDirofilaria immitiscould be one of the factors that interfere with leishmaniasis in dogs. Indeed, filarial nematodes induce a partial skew of the immune response towards M1, likely caused by their bacterial endosymbionts,Wolbachia. Here we have examined the potential ofAsaiaWSP, a bacterium engineered for the expression of theWolbachiasurface protein (WSP), as an inductor of M1 macrophage activation andLeishmaniakilling. Macrophages stimulated withAsaiaWSPdisplayed a strong leishmanicidal activity, comparable to that determined by the choice-drug amphotericin B. Additionally,AsaiaWSPdetermined the expression of markers of classical macrophage activation, including M1 cytokines, ROS and NO, and an increase in phagocytosis activity.Asaianot expressing WSP also induced macrophage activation, although at a lower extent compared toAsaiaWSP. In summary, our study, while providing a strong evidence for the immune-stimulating properties ofWolbachia, highlights the translational potential ofAsaiaWSPin the areas of the immune-prophylaxis and therapy of leishmaniases, as well as of other diseases that could be subverted by M1 macrophage activation.
Application of dielectric spectroscopy in the dynamically changing biological system – case ofNeocaridina davidishrimp starvation
Authors: Wlodarczyk Agnieszka , Wlodarczyk Patryk 
Published: June 2020

AbstractIn this work, dielectric studies onNeocaridina davidishrimps have been presented. The effect of starvation on dielectric properties such as conductivity or permittivity have been shown. It was found that the onset frequency of electrode polarization depends on starvation period, which is probably related to the cytoplasm viscosity. In the dielectric spectra of shrimps two relaxation processes have been identified i.e. α and β process. The α process is probably related to the counter ion polarization while β process to the mobility of macromolecules present in the body of a shrimp, mainly to the amount of lipids. It was also found that there is a difference in dielectric response between control group and the group regenerated after 14 day starvation period. Basing on dielectric response, one can conclude that the viscosity of cytoplasm of regenerated shrimps is higher and the cells are rich in the lipid droplets when compared to control group.
Role for both myeloid and plasmacytoid DC in driving primary T helper cell response toBurkholderia pseudomalleiin healthy individuals
Authors: Reddi Durga , Durant Lydia , Bernardo David , Noble Alistair , English Nicholas R. , Hendy Philip , Clark Graeme C. , Prior Joann L. , Williamson E. Diane , Knight Stella C. 
Published: June 2020

AbstractBurkholderia pseudomalleiis a Gram-negative bacterium that causes melioidosis, an infectious disease endemic to south-east Asia. AsB. pseudomalleiis antibiotic-resistant, the need for cell-based vaccines and therapies is crucial to managing melioidosis. Dendritic cells (DC) provide the first line of defense to infection and direct downstream immune responses. Using practical volumes of fresh healthy donor blood, we show that heat-killedB. pseudomalleiactivated and stimulated expression of pro-inflammatory cytokines TNF-α, IL-1β and IL-6 from both myeloid and plasmacytoid DC. Furthermore,B. pseudomallei-pulsed DC induced activation and proliferation of CD4+T-cells. Thus, both DC subsets are important for driving primary T helper cell responses toB. pseudomalleiin healthy individuals and have the potential to be targeted for future therapies and vaccines.Author SummaryMelioidosis is an infectious disease endemic to south-east Asia and northern Australia caused by the bacteriumBurkholderia pseudomallei. Melioidosis presents a significant public health threat because it has no effective vaccine or cure, leading to a high mortality rate of between 10-50%. We highlight the possibility of immune-based strategies targetingBurkholderia pseudomalleito better treat and prevent melioidosis. Specifically, we show that dendritic cells-the sentinel cells of the immune system-respond toB. pseudomalleiin healthy individuals and in turn can orchestrate downstream protective immune responses. Thus, dendritic cells may be key players in the development of both vaccines and therapeutics for melioidosis as well as other bacteria-driven diseases.
Crosstalk between Nitric Oxide and Retinoic Acid pathways is essential for amphioxus pharynx development
Authors: Caccavale F , Annona G , Subirana L , Escriva H , Bertrand S , D’Aniello S 
Published: June 2020

AbstractDuring animal ontogenesis, body axis patterning is finely regulated by complex interactions between several signaling pathways. Nitric Oxide (NO) and Retinoic Acid (RA) are potent morphogens that play a pivotal role in vertebrate development. Their involvement in axial patterning of head and pharynx shows conserved features in the chordate phylum. Indeed, in the cephalochordate amphioxus NO and RA are crucial for the correct development of pharyngeal structures. Here we demonstrate the functional cooperation between NO and RA occurring in amphioxus embryogenesis. During neurulation, NO modulates RA production through the transcriptional regulation of Aldh1a.2 that irreversibly converts retinaldehyde into RA. On the other hand, RA regulates the transcription of Nos genes, probably through RA Response Elements found in their regulatory regions. The reciprocal regulation of NO and RA pathways results to be essential for the normal pharyngeal development in amphioxus and suggests that this regulatory crosstalk could be conserved in vertebrates.
Chemogenetics reveal an anterior cingulate-thalamic pathway for attending to task-relevant information
Authors: Bubb Emma J. , Aggleton John P. , O’Mara Shane M. , Nelson Andrew J.D. 
Published: June 2020

AbstractIn a changing environment, we need to decide when to select items that resemble previously rewarded stimuli and when it is best to switch to other stimulus types. Here, we used chemogenetic techniques to provide causal evidence that activity in the rodent anterior cingulate cortex and its efferents to the anterior thalamic nuclei modulate the ability to attend to reliable predictors of important outcomes. Rats were tested on an attentional set-shifting paradigm that first measures the ability to master serial discriminations involving a constant stimulus dimension that reliably predicts reinforcement (intradimensional-shift), followed by the ability to shift attention to a previously irrelevant class of stimuli when reinforcement contingencies change (extradimensional-shift). Chemogenetic silencing of the anterior cingulate cortex (Experiment 1) as well as selective inactivation of anterior cingulate efferents to the anterior thalamic nuclei (Experiment 2) impaired intradimensional learning but, facilitated two sets of extradimensional-shifts. This pattern of results signals the loss of a cortico-thalamic system for cognitive control that preferentially processes stimuli resembling those previously associated with reward. Previous studies highlight a separate prefrontal system that promotes switching to hitherto inconsistent predictors of reward when contingencies change. Competition between these two systems regulates cognitive flexibility and choice.
Twist regulates Yorkie to guide lineage reprogramming of syncytial alary muscles
Authors: Rose Marcel , Bartle-Schultheis Jakob , Domsch Katrin , Reim Ingolf , Schaub Christoph 
Published: June 2020

SummaryThe genesis of syncytial muscles is typically considered as a paradigm for an irreversible developmental process. Notably, transdifferentiation of syncytial muscles is naturally occurring duringDrosophiladevelopment. The ventral longitudinal heart-associated musculature (VLM) arises by a unique mechanism that revokes the differentiated fate from the so-called alary muscles and comprises at least two distinct steps: syncytial muscle cell fragmentation into single myoblasts and direct reprogramming into founder cells of the VLM lineage. Here we provide evidence that the mesodermal master regulatortwistplays a key role during this reprogramming process. Acting downstream ofDrosophilaTbx1 (Org-1) in the alary muscle lineage, Twist is crucially required for the derepression of the Hippo pathway effector Yki and thus for the initiation of syncytial muscle dedifferentiation and fragmentation. Subsequently, cell-autonomous FGFR-Ras-MAPK signaling in the resulting mono-nucleated myoblasts is maintaining Twist expression, thereby stabilizing nuclear Yki activity and inducing their lineage switch into the founder cells of the VLM.
An expanding manifold in transmodal regions characterizes adolescent reconfiguration of structural connectome organization
Authors: Park Bo-yong , Bethlehem Richard A. I. , Paquola Casey , Larivière Sara , Cruces Raul R. , de Wael Reinder Vos ,   Neuroscience in Psychiatry Network (NSPN) Consortium, Bullmore Edward T. , Bernhardt Boris C. 
Published: June 2020

AbstractAdolescence is a critical time for the continued maturation of brain networks. Here, we assessed structural connectome development in a large longitudinal sample ranging from childhood to young adulthood. By projecting high-dimensional connectomes into compact manifold spaces, we identified a marked expansion of structural connectomes with the strongest effects in transmodal regions during adolescence. Findings reflected increased within-module connectivity together with increased segregation, indicating increasing differentiation of higher-order association networks from the rest of the brain. Projection of subcortico-cortical connectivity patterns into these manifolds showed parallel alterations in pathways centered on the caudate and thalamus. Connectome findings were contextualized via spatial transcriptome association analysis, highlighting genes enriched in cortex, thalamus, and striatum. Statistical learning of cortical and subcortical manifold features at baseline and their maturational change predicted measures of intelligence at follow-up. Our findings demonstrate that connectome manifold learning can bridge the conceptual and empirical gaps between macroscale network reconfigurations, microscale processes, and cognitive outcomes in adolescent development.ImpactManifold learning of longitudinal brain network data provides novel insights into adolescent structural connectome maturation, and how multiple scales of cortical and subcortical organization interact in typical neurodevelopment.
Probing machine-learning classifiers using noise, bubbles, and reverse correlation
Authors: Thoret Etienne , Andrillon Thomas , Léger Damien , Pressnitzer Daniel 
Published: June 2020

AbstractBackgroundMany scientific fields now use machine-learning tools to assist with complex classification tasks. In neuroscience, automatic classifiers may be useful to diagnose medical images, monitor electrophysiological signals, or decode perceptual and cognitive states from neural signals. However, such tools often remain black-boxes: they lack interpretability. A lack of interpretability has obvious ethical implications for clinical applications, but it also limits the usefulness of these tools to formulate new theoretical hypotheses.New methodWe propose a simple and versatile method to help characterize the information used by a classifier to perform its task. Specifically, noisy versions of training samples or, when the training set is unavailable, custom-generated noisy samples, are fed to the classifier. Multiplicative noise, so-called “bubbles”, or additive noise are applied to the input representation. Reverse correlation techniques are then adapted to extract either the discriminative information, defined as the parts of the input dataset that have the most weight in the classification decision, and represented information, which correspond to the input features most representative of each category.ResultsThe method is illustrated for the classification of written numbers by a convolutional deep neural network; for the classification of speech versus music by a support vector machine; and for the classification of sleep stages from neurophysiological recordings by a random forest classifier. In all cases, the features extracted are readily interpretable.Comparison with Existing MethodsQuantitative comparisons show that the present method can match state-of-the art interpretation methods for convolutional neural networks. Moreover, our method uses an intuitive and well-established framework in neuroscience, reverse correlation. It is also generic: it can be applied to any kind of classifier and any kind of input data.ConclusionsWe suggest that the method could provide an intuitive and versatile interface between neuroscientists and machine-learning tools.HighlightsThe heuristics of black-box classifiers can be probed with noisy inputsThe relevant features can be visualised in the input representation spaceThe method applies to any kind of data such as 2D images or 1D time seriesIt applies to any classifier such as deep neural networks, support vector machines, random forests
Moderate adolescent chronic intermittent ethanol exposure sex-dependently disrupts synaptic transmission and kappa opioid receptor function in the basolateral amygdala of adult rats
Authors: Przybysz Kathryn R. , Gamble Meredith E. , Diaz Marvin R. 
Published: June 2020

AbstractAdolescent alcohol exposure is associated with many negative outcomes that persist into adulthood, including altered affective and reward-related behaviors. However, the long-term neurological disruptions underlying these behavioral states are not fully understood. The basolateral amygdala (BLA) plays a critical role in many of these behaviors, and shifts in the excitatory/inhibitory balance in this area are capable of directly modulating their expression. While changes to BLA physiology have been demonstrated during the acute withdrawal phase following adolescent ethanol exposure, no studies to date have examined whether these persist long-term. The kappa opioid receptor (KOR) system is a neuromodulatory system that acts as a prominent mediator of negative affective behaviors, and alterations of this system have been implicated in the behavioral profile caused by chronic alcohol exposure in adulthood. Notably, in the BLA, the KOR system undergoes functional changes between adolescence and adulthood, but whether BLA KORs are functionally disrupted by adolescent ethanol exposure has not been examined. In this study, we exposed male and female Sprague-Dawley rats to a vapor inhalation model of moderate adolescent chronic intermittent ethanol (aCIE) and examined the long-term effects on GABAergic and glutamatergic neurotransmission within the adult BLA using whole-cell patch-clamp electrophysiology. We also assessed how KOR activation modulated these neurotransmitter systems in aCIE versus control rats using the selective KOR agonist, U69593. This investigation revealed that aCIE exposure disrupted basal glutamate transmission in females by increasing spontaneous excitatory postsynaptic current (sEPSC) frequency, while having no effects on glutamate transmission in males or GABA transmission in either sex. Interestingly, we also found that aCIE exposure unmasked a KOR-mediated suppression of spontaneous inhibitory postsynaptic current (sIPSC) frequency and sEPSC amplitude only in males, with no effects of aCIE exposure on KOR function in females. Together, these data suggest that moderate-level adolescent ethanol exposure produces long-term changes to BLA physiology and BLA KOR function, and that these changes are sex-dependent. This is the first study to examine persistent adaptations to both BLA physiology and KOR function following adolescent alcohol exposure, and opens a broad avenue for future investigation into other neurobiological and behavioral consequences of adolescent ethanol exposure-induced disruptions of these systems.
Marine Dadabacteria exhibit genome streamlining and phototrophy-driven niche partitioning
Authors: Graham Elaina D. , Tully Benjamin J. 
Published: June 2020

AbstractThe remineralization of organic material via heterotrophy in the marine environment is performed by a diverse and varied group of microorganisms that can specialize in the type of organic material degraded and the niche they occupy. The marineDadabacteriaare cosmopolitan in the marine environment and belong to a candidate phylum for which there has not been a comprehensive assessment of the available genomic data to date. Here in, we assess the functional potential of the oligotrophic, marineDadabacteriain comparison to terrestrial, coastal, and subsurface members of the phylum. Our analysis reveals that the marineDadabacteriahave undergone a genome streamlining event, reducing their genome size and the nitrogen content of their DNA and predicted proteome, relative to their terrestrial counterparts. Collectively, theDadabacteriahave the potential to degrade microbial particulate organic matter, specifically peptidoglycan and phospholipids. The marineDadabacteriabelong to two clades with distinct ecological niches in global metagenomic data: a shallow clade with the potential for photoheterotrophy through the use of proteorhodopsin, present predominantly in surface waters up to 100m depth; and a deep clade lacking the potential for photoheterotrophy that is more abundant in the deep photic zone.
openPFGE: An open source and low cost pulsed-field gel electrophoresis equipment
Authors: Lagos-Susaeta Diego , Salazar Oriana , Asenjo Juan A. 
Published: June 2020

AbstractDNA electrophoresis is a fundamental technique in molecular biology that allows the separation of DNA molecules up to ~50 Kbp. Pulsed-field gel electrophoresis [PFGE] is a variation of the conventional DNA electrophoresis technique that allows the separation of very large DNA molecules up to ~10 Mbp. PFGE equipment is very expensive and it becomes an access barrier to many laboratories. Also, just a few privative designs of the equipment are available and it becomes difficult for the community to improve or customize their functioning. Here, we provide an open source PFGE equipment capable of the separation of DNA molecules up to, at least, ~2 Mbp and at low cost: USD$850, about 3% of the price of typical commercial equipment.Specifications table
Impact of data-driven online financial consumption on supply chain services
Authors: Li Lei , Dai Yaxuan , Sun Yudong 
Published: June 2020

PurposeEmploying big data analysis tools, this study examines the significance of supply chain integration affecting online financial consumption, analyzes the online financial consumption demand of mobile phone consumers, promotes the optimization of supply chain services with consumers as the focus and proposes full integration of a mobile phone supply chain in terms of product, logistics and marketing, in order to improve the supply and demand relationship between consumers and suppliers; the overall objective is to promote further development of online financial consumption.Design/methodology/approachIn this study, TF-IDF (term frequency–inverse document frequency) and cosine similarity text analysis are used for analyzing online demand for mobile phone products, studying the influence of supply chain services on consumption demand and identifying strategies for promoting overall optimization of the supply chain to meet online financial consumption demands of consumers; the study analyzes online reviews on mobile phone topics from the JingDong (JD) platform and Weibo platform.FindingsResearch results show that online demand for mobile phone products is greatly influenced by supply chain links such as product design, logistics transportation and marketing promotion. The consumption demand for different mobile phone products has different emphases, but the differences are not significant. The overall improvement of the supply chain should focus on product research and development, logistics layout optimization and marketing promotion, in order to meet and guide the online financial demand of consumers and improve the effectiveness of supply chain management.Research limitations/implicationsThis study only considered data from China's largest online mobile phone sales platform and Weibo text data owing to the data sensitivity involved.Originality/valueThere are few supply chain optimization studies based on online financial consumption reviews from customers. Therefore, this study integrates online consumption trends into a supply chain analysis framework to explore strategies for promoting supply chain optimization according to customer demands, improving the benign interaction of participants in the supply chain and promoting the development of online financial consumption.
DNA barcoding of the South Korean Tettigoniidae (Orthoptera) using collection specimens reveals three potential species complexes
Authors: Kim Seon Yi , Kang Tae Hwa , Kim Tae Woo , Seo Hong Yul 
Published: June 2020

AbstractWe carried out DNA barcoding on 24 Korean tettigonid species of 19 genera deposited in the National Institute of Biological Resources to reevaluate the preliminary identification of each specimen. Sequence divergence of DNA barcodes obtained from 113 samples of the 24 species ranged from 0 to 30.4%, the intraspecific variation was 0–7.3%, and the interspecific divergence was 1.1–30.4%; we could not examine the barcoding gap. In the neighbor‐joining tree, the branch length among individuals of Tettigonia ussuriana, Paratlanticus ussuriensis, and Hexacentrus japonicus were relatively longer than those in other species. The detailed analysis of the morphological characters and DNA barcodes of the above three species revealed that these three species represent species complexes. The T. ussuriana complex comprised T. jungi, T. uvarovi, and T. ussuriana. Paratlanticus ussuriensis cluster contained four species; one cluster was identified as P. palgongensis based on morphological characteristics, but the other three clusters, including the P. ussuriensis cluster, require further detailed taxonomic analysis. Lastly, two species clusters were identified within the Hexacentrus japonicus clade. Based on the 99% sequence similarity obtained by blast search of the NCBI GenBank database, one of the clusters was identified as H. unicolor. Thus, the DNA barcoding revealed the presence of at least three cryptic species in Korean Tettigoniidae, although more detailed taxonomic analyses are required to establish their status. Therefore, we suggest that DNA barcoding is a very useful tool for increasing the identification accuracy of insect collections.