bluuebunny/crossref_metadata_2025_split huggingface dataset:
Laying Hens Affected By Newcastle Virus And Laryngotracheitis Virus Show Rapid Recovery After Treatment With Ivermectin
Authors: Fernandez-Díaz Manolo , Guevara Luis , Icochea Eliana , Montalván Angela , Villanueva-Pérez Doris , Fernandez-Sánchez Manolo , Ticona Julio , Zimic Mirko ,   COVID-19 Working Group in Perú
Published: July 2020

SUMMARYThis is an anecdotal observation of an intervention study involving laying hens from a commercial farm in the city of Chincha, Peru, who suffered an outbreak caused by Newcastle disease virus (NDV) and infectious laryngotracheitis virus (ILTV), confirmed by clinical observations, serological and molecular tests (PCR).In addition to receiving standard treatment appropriate to the state of health at the time of the operation, a group of birds were treated with a single dose of ivermectin administered subcutaneously (0.2 mL of a 1% solution equivalent to 200 µg/kg body weight), with a group of control birds not receiving the treatment being reserved.The results showed a remarkable recovery of symptoms after 24 hours of treatment among the birds that received ivermectin. At 4 days after treatment, the birds that received ivermectin showed visibly greater mobility and vivacity, as well as a recovery in egg production. PCR tests after 4 days of treatment with ivermectin were negative for NDV and ILTV.These results are interesting and suggest a possible effect of ivermectin against NDV and ILTV in birds. More controlled studies are needed to confirm this hypothesis.
Defending as a unit: sex- and context-specific territorial defence in a duetting bird
Authors: Mentesana Lucia , Moiron Maria , Guedes Ernesto , Cavalli Enzo , Tassino Bettina , Adreani Nicolas M. 
Published: July 2020

AbstractBehaviours such as territorial defence represent functionally integrated traits that underlie multiple behavioural variables such as physical and acoustic responses. Characterizing the multivariate structure of such traits is fundamental to understand their evolution. In bird species that form stable pair bonds and are territorial year-round, both sexes are expected to defend their territory; however, the role that each sex plays in defending their shared territory remains largely unknown. Evidence for the sex-roles during territorial defence is mixed and sex- and context-specific characterizations of territorial defence embracing the multivariate nature of the trait are currently lacking. Here we investigated sex- and context-specific variation in a hypothesised latent variable called “territorial defence” and tested whether duets were part of territorial defence in a wild population of rufous hornero (Furnarius rufus). To do so, we combined a simulated territorial intrusion approach during nest building and provisioning contexts with a structural equation modelling approach. Our results showed that, in males and females, the six measured behavioural variables were linked by a single latent trait, territorial defence, in both contexts. Flights over the decoy and duet songs were equally good proxies of territorial defence. Although males were defending more the territory than females, pair members showed a positive correlation in their behaviour. The structural equation modelling framework enabled us to capture a complex correlation pattern among behavioural variables, expanding upon a classic body of research on territorial defence. Thus, the combination of classical behavioural approaches with sophisticated statistical analyses brings new exciting possibilities to the field of behavioural ecology.Significance statementTerritorial defence is a key behaviour in territorial species as it plays a major role in an individual’s reproductive success and survival. Additionally, territorial defence has been proposed as one possible evolutionary driver of duetting behaviour, one of the most fascinating vocal behaviours in birds. As behaviours are evolutionary characters, they must be studied in a multivariate framework. In this study we focused on characterizing territorial defence during a simulated territorial intrusion in an integrative manner using a classical territorial intrusion framework. We did so in male and female rufous horneros (Aves:Furnaridae) across two breeding contexts, while simultaneously testing theoretical predictions about the role of duetting behaviour as key part of territorial defence. Overall, our study provides for the first time a sex- and context-comparison of the multivariate, latent variable “territorial defence” in duetting birds, while highlighting the potential of combining field behavioural approaches with structural equation modelling.
Metabolic effects of aripiprazole and olanzapine multiple-dose treatment in healthy volunteers. Association with pharmacogenetics
Authors: Koller Dora , Almenara Susana , Mejía Gina , Saiz-Rodríguez Miriam , Zubiaur Pablo , Román Manuel , Ochoa Dolores , Navares-Gómez Marcos , Santos-Molina Elena , Pintos-Sánchez Elena , Abad-Santos Francisco 
Published: July 2020

AbstractBackgroundAripiprazole and olanzapine are atypical antipsychotics. Both drugs can induce metabolic changes, however, the metabolic side effects produced by aripiprazole are more benign.ObjectivesTo evaluate if aripiprazole and olanzapine alter prolactin levels, lipid and glucose metabolism and hepatic, hematological, thyroid and renal function.MethodsTwenty-four healthy volunteers received 5 daily oral doses of 10 mg aripiprazole and 5 mg olanzapine in a crossover randomized clinical trial and were genotyped for 51 polymorphisms in 17 genes by qPCR. Drug plasma concentrations were measured by LC-MS. The biochemical and hematological analyses were performed by enzymatic methods.ResultsOlanzapine induced hyperprolactinemia but not aripiprazole.DRD3Ser/Gly andABCB1rs10280101, rs12720067 and rs11983225 polymorphisms and CYP3A phenotype had an impact on plasma prolactin levels. C-peptide concentrations were higher after aripiprazole administration and were influenced byCOMTrs4680 and rs13306278 polymorphisms. Olanzapine and theUGT1A1rs887829 polymorphism were associated with elevated glucose levels. CYP3A poor metabolizers had increased insulin levels. Triglyceride concentrations were decreased due to olanzapine and aripiprazole treatment and were variable based on CYP3A phenotypes and theAPOC3rs4520 genotype. Cholesterol levels were also decreased and depended onHTR2Ars6314 polymorphism. All hepatic enzymes, platelet and albumin levels and prothrombin time were altered during both treatments. Additionally, olanzapine reduced the leucocyte count, aripiprazole increased free T4 and both decreased uric acid concentrations.ConclusionsShort term treatment with aripiprazole and olanzapine had a significant influence on the metabolic parameters. However, it seems that aripiprazole provokes less severe metabolic changes.
Impact Analysis of SARS-CoV2 on Signaling Pathways during COVID19 Pathogenesis using Codon Usage Assisted Host-Viral Protein Interactions
Authors: Das Jayanta Kumar , Chakraborty Subhadip , Roy Swarup 
Published: July 2020

AbstractUnderstanding the molecular mechanism of COVID19 disease pathogenesis helps in the rapid development of therapeutic targets. Usually, viral protein targets host proteins in an organized fashion. The pathogen may target cell signaling pathways to disrupt the pathway genes’ regular activities, resulting in disease. Understanding the interaction mechanism of viral and host proteins involved in different signaling pathways may help decipher the attacking mechanism on the signal transmission during diseases, followed by discovering appropriate therapeutic solutions.The expression of any viral gene depends mostly on the host translational machinery. Recent studies report the great significance of codon usage biases in establishing host-viral protein-protein interactions (PPI). Exploiting the codon usage patterns between a pair of co-evolved host and viral proteins may present novel insight into the host-viral protein interactomes during disease pathogenesis. Leveraging the codon usage pattern similarity (and dissimilarity), we propose a computational scheme to recreate the hostviral protein interaction network (HVPPI). We use seventeen (17) essential signaling pathways for our current work and study the possible targeting mechanism of SARS-CoV2 viral proteins on such pathway proteins. We infer both negatively and positively interacting edges in the network. We can find a relationship where one host protein may target by more than one viral protein.Extensive analysis performed to understand the network topologically and the attacking behavior of the viral proteins. Our study reveals that viral proteins, mostly utilize codons, rare in the targeted host proteins (negatively correlated interaction). Among non-structural proteins, NSP3 and structural protein, Spike (S) protein, are the most influential proteins in interacting multiple host proteins. In ranking the most affected pathways, MAPK pathways observe to be worst affected during the COVID-19 disease. A good number of targeted proteins are highly central in host protein interaction networks. Proteins participating in multiple pathways are also highly connected in their own PPI and mostly targeted by multiple viral proteins.
Transcription inhibitors with XRE DNA-binding and cupin signal-sensing domains drive metabolic diversification in Pseudomonas
Authors: Trouillon Julian , Ragno Michel , Simon Victor , Attrée Ina , Elsen Sylvie 
Published: July 2020

ABSTRACTTranscription factors (TFs) are instrumental in the bacterial response to new environmental conditions. They can act as direct signal sensors and subsequently induce changes in gene expression leading to physiological adaptation. Here, by combining RNA-seq and DAP-seq, we studied a family of eight TFs in Pseudomonas aeruginosa. This family, encompassing TFs with XRE-like DNA-binding and cupin signal-sensing domains, includes the metabolic regulators ErfA, PsdR and PauR and five so far unstudied TFs. The genome-wide delineation of their regulons identified 39 regulatory interactions with genes mostly involved in metabolism. We found that the XRE-cupin TFs are inhibitors of their neighboring genes, forming local, functional units encoding proteins with functions in condition-specific metabolic pathways. The phylogenetic analysis of this family of regulators across the Pseudomonas genus revealed a wide diversity of such metabolic regulatory modules and identified species with potentially higher metabolic versatility. Numerous uncharacterized XRE-cupin TFs were found near metabolism-related genes, illustrating the need of further systematic characterization of transcriptional regulatory networks in order to better understand the mechanisms of bacterial adaptation to new environments.IMPORTANCEBacteria of the Pseudomonas genus, including the major human pathogen P. aeruginosa, are known for their complex regulatory networks and high number of transcription factors, which contribute to their impressive adaptive ability. However, even in the most studied species, most of the regulators are still uncharacterized. With the recent advances in high-throughput sequencing methods, it is now possible to fill this knowledge gap and help understanding how bacteria adapt and thrive in new environments. By leveraging these methods, we provide an example of a comprehensive analysis of an entire family of transcription factors and bring new insights into metabolic and regulatory adaptation in the Pseudomonas genus.
Visual field reconstruction using fMRI-based techniques
Authors: Carvalho Joana , Invernizzi Azzurra , Martins Joana , Jansonius Nomdo M. , Renken Remco J. , Cornelissen Frans W. 
Published: July 2020

AbstractPurposeTo evaluate the accuracy and reliability of functional magnetic resonance imaging (fMRI)-based techniques to assess the integrity of the visual field (VF).MethodsWe combined fMRI and neurocomputational models, i.e conventional population receptive field (pRF) mapping and a new advanced pRF framework “micro-probing” (MP), to reconstruct the visual field representations of different cortical areas. To demonstrate their scope, both approaches were applied in healthy participants with simulated scotomas (SS) and participants with glaucoma. For the latter group we compared the VFs obtained with standard automated perimetry (SAP) and via fMRI.ResultsUsing SS, we found that the fMRI-based techniques can detect absolute defects in VFs that are larger than 3 deg, in single participants, and based on 12 minutes of fMRI scan time. Moreover, we found that MP results in a less biased estimation of the preserved VF. In participants with glaucoma, we found that fMRI-based VF reconstruction detected VF defects with a correspondence to SAP that was decent, reflected by the positive correlation between fMRI-based sampling density and SAP-based contrast sensitivity loss (SAP) r2=0.44, p=0.0002.This correlation was higher for our new approach (MP) compared to that for the conventional pRF analysis.ConclusionsfMRI-based reconstruction of the VF enables the evaluation of vision loss and provides useful details on the properties of the visual cortex.Translational RelevancefMRI-based VF reconstruction provides an objective alternative to detect VF defects. It may either complement SAP, or could provide VF information in patients unable to perform SAP.
Neuroligin affects metastatic performance of CD66+ cells: Theoretical analysis of Multi-tissue RNA expressions through System modeling based Network mapping underin-vitroconstraints
Authors: Prakash Om 
Published: July 2020

ABSTRACTPresent study deals with theoretical analysis of multi-tissue RNA expressions through system model based network mapping under the constraints ofin-vitroexperiments. Here, effect of Neuroligin was evaluated on the performance of metastatic behavior of CD66+ cells of human female reproductive cell lines. Total 10 genes and 14 cell lines were considered in the study. Clustering of cell lines was done on the basis of network mapping under the same homeostatic constraints. Neuroligin was found to affect metastatic performance of CD66+ cells. Two CD66+ cell lines hTERT-HME1 and SK-BR-3 were found to most effective, in similar manner as brain cell lines as U-138MG & U-87MG.
Optimized gene expression from bacterial chromosome by high-throughput integration and screening
Authors: Saleski Tatyana E. , Chung Meng Ting , Carruthers David N. , Khasbaatar Azzaya , Kurabayashi Katsuo , Lin Xiaoxia Nina 
Published: July 2020

AbstractChromosomal integration of recombinant genes is desirable compared to expression from plasmids due to increased stability, reduced cell-to-cell variability, and the elimination of antibiotics for plasmid maintenance. Here, we present a new approach for tuning pathway gene expression levels via random integrations and high-throughput screening. We demonstrate multiplexed gene integration and expression-level optimization for isobutanol production inEscherichia coli. The integrated strains could, with significantly lower expression levels than plasmid-based expression, produce high titers (10.0 ± 0.9 g/L isobutanol in 48 h) and yields (69 % of the theoretical maximum). Close examination of pathway expression in the top-performing, as well as other isolates, reveals the complexity of cellular metabolism and regulation, underscoring the need for precise optimization while integrating pathway genes into the chromosome. This new method for multiplexed pathway gene integration and expression optimization could be readily extended to a wide range of pathways and chassis to create robust and efficient production strains.
Single molecule dynamics at a bacterial replication fork after nutritional downshift
Authors: Hernández-Tamayo Rogelio , Schmitz Hannah , Graumann Peter L. 
Published: July 2020

ABSTRACTReplication forks must respond to changes in nutrient conditions, especially in bacterial cells. By investigating the single molecule dynamics of replicative helicase DnaC, DNA primase DnaG, and of lagging strand polymerase DnaE in the model bacteriumBacillus subtilisin response to transient replication blocks due to DNA damage, to inhibition of the replicative polymerase, or to downshift of serine availability, we show that proteins react differentially to the stress conditions. DnaG appears to be recruited to the forks by a diffusion and capture mechanism, becomes more statically associated after arrest of polymerase PolC, but binds much less often after fork blocks due to DNA damage or to nutritional downshift. These results indicate that binding of the alarmone ppGpp due to the stringent response prevents DnaG from binding to forks rather than blocking bound primase. Dissimilar behaviour of DnaG and of DnaE suggest that both proteins are recruited independently to the forks, rather than jointly. Turnover of all three proteins was increased during replication block after nutritional downshift, different from the situation due to DNA damage or polymerase inhibition, showing high plasticity of forks in response to different stress conditions. Forks persisted during all stress conditions, apparently ensuring rapid return to replication extension.
Pulsations and flows in tissues: two collective dynamics with simple cellular rules
Authors: Thiagarajan Raghavan , Bhat Alka , Salbreux Guillaume , Inamdar Mandar M. , Riveline Daniel 
Published: July 2020

AbstractCollective motions of epithelial cellsin vivoare essential for morphogenesis in developmental biology. Tissues elongate, contract, flow, and oscillate, thus sculpting embryos. These tissue level dynamics are known, but the physical mechanisms at the cellular level are unclear, with various behaviors depending on the tissues and species. Moreover, investigations onin vitrotissue behavior usually focus on only one type of cell dynamics and use diverse theoretical approaches, making systematic comparisons between studies challenging. Here, we show that a single epithelial monolayer of Madin Darby Canine Kidney (MDCK) cells can exhibit two types of local tissue kinematics, pulsations and long range coherent flows. We analyzed these distinct motions by using quantitative live imaging. We also report that these motions can be controlled with internal and external cues such as specific inhibitors, and friction modulation of the substrate by microcontact printing method. We further demonstrate with a unified vertex model that both behaviors depend on the competition between velocity alignment and random diffusion of cell polarization. When alignment and diffusion are comparable, a pulsatile flow emerges, whereas the tissue undergoes long-range flows when velocity alignment dominates. We propose that environmental friction, acto-myosin distributions, and cell polarization kinetics are important in regulating the dynamics of tissue morphogenesis.
On the presence of elusive sea slugs and snails in the western Mediterranean (Mollusca: Gastropoda): new records
Authors: Salvador Xavier , Fernández-Vilert Robert , Moles Juan 
Published: July 2020

AbstractCitizen science provides us with much information about charismatic taxa such as the opisthobranchs, thus contributing enormously to enlarging the geographic distribution of species. This study collects new records of elusive sea slugs and snails in the Western Mediterranean coast (especially in the Catalan coast and the French Mediterranean coast) and contributes to new ecological information regarding phenology, diet, and behaviour. Out of the 36 species reported here, 20 correspond to new records in the Catalan coast (NE Spain), three are new records of pelagic pteropods for the Spanish coast, and 10 other species are new records for the French Mediterranean coast. All records have been registered at the online database of the NGO named Catalan Opisthobranch Research Group (GROC). This study highlights the importance of sampling at night and, especially, in shallow, often-understudied waters, which usually gather high species diversity. We believe the high-quality pictures and related species’ information will serve future researchers and divers find and recognize these species in the Mediterranean basin.
Decoding the covert shift of spatial attention from electroencephalographic signals permits reliable control of a brain-computer interface
Authors: Reichert Christoph , Dürschmid Stefan , Bartsch Mandy V. , Hopf Jens-Max , Heinze Hans-Jochen , Hinrichs Hermann 
Published: July 2020

AbstractObjectiveOne of the main goals of brain-computer interfaces (BCI) is to restore communication abilities in patients. BCIs often use event-related potentials (ERPs) like the P300 which signals the presence of a target in a stream of stimuli. The P300 and related approaches, however, are inherently limited, as they require many stimulus presentations to obtain a usable control signal. Many approaches depend on gaze-direction to focus the target, which is also not a viable approach in many cases, because eye movements might be impaired in potential users. Here we report on a BCI that avoids both shortcomings by decoding spatial target information, independent of gaze shifts.ApproachWe present a new method to decode from the electroencephalogram (EEG) covert shifts of attention to one out of four targets simultaneously presented in the left and right visual field. The task is designed to evoke the N2pc component – a hemisphere lateralized response, elicited over the occipital scalp contralateral to the attended target. The decoding approach involves decoding of the N2pc based on data-driven estimation of spatial filters and a correlation measure.Main resultsDespite variability of decoding performance across subjects, 22 out of 24 subjects performed well above chance level. Six subjects even exceeded 80% (cross-validated: 89%) correct predictions in a four-class discrimination task. Hence, the single-trial N2pc proves to be a component that allows for reliable BCI control. An offline analysis of the EEG data with respect to their dependence on stimulation time and number of classes demonstrates that the present method is also a workable approach for two-class tasks.SignificanceOur method extends the range of strategies for gaze-independent BCI control. The proposed decoding approach has the potential to be efficient in similar applications intended to decode ERPs.
The influence of autotoxicity on the dynamics of vegetation spots
Authors: Iuorio Annalisa , Veerman Frits 
Published: July 2020

AbstractPlant autotoxicity has proved to play an essential role in the behaviour of local vegetation. We analyse a reaction-diffusion-ODE model describing the interactions between vegetation, water, and autotoxicity. The presence of autotoxicity is seen to induce movement and deformation of spot patterns in some parameter regimes, a phe-nomenon which does not occur in classical biomass-water models. We aim to analytically quantify this novel feature, by studying travelling wave solutions in one spatial dimension. We use geometric singular perturbation theory to prove the existence of symmetric, stationary and non-symmetric, travelling pulse solutions, by constructing appropriate homoclinic orbits in the associated 5-dimensional dynamical system. In the singularly perturbed context, we perform an extensive scaling analysis of the dynamical system, identifying multiple asymptotic scaling regimes where (travelling) pulses may or may not be constructed. We show that, while the analytically constructed stationary pulse corresponds to its numerical counterpart, there is a discrepancy between the numerically observed travelling pulse and its analytical counterpart. Our findings indicate how the inclusion of an additional ODE may significantly influence the properties of classical biomass-water models of Klausmeier/Gray–Scott type.