bluuebunny/crossref_metadata_2025_split huggingface dataset:
Two social brains: neural mechanisms of intersubjectivity
Authors: Vogeley Kai 
Published: July 2017

It is the aim of this article to present an empirically justified hypothesis about the functional roles of the two social neural systems, namely the so-called ‘mirror neuron system’ (MNS) and the ‘mentalizing system’ (MENT, also ‘theory of mind network’ or ‘social neural network’). Both systems are recruited during cognitive processes that are either related to interaction or communication with other conspecifics, thereby constituting intersubjectivity. The hypothesis is developed in the following steps: first, the fundamental distinction that we make between persons and things is introduced; second, communication is presented as the key process that allows us to interact with others; third, the capacity to ‘mentalize’ or to understand the inner experience of others is emphasized as the fundamental cognitive capacity required to establish successful communication. On this background, it is proposed that MNS serves comparably early stages of social information processing related to the ‘detection’ of spatial or bodily signals, whereas MENT is recruited during comparably late stages of social information processing related to the ‘evaluation’ of emotional and psychological states of others. This hypothesis of MNS as a social detection system and MENT as a social evaluation system is illustrated by findings in the field of psychopathology. Finally, new research questions that can be derived from this hypothesis are discussed.
This article is part of the themed issue ‘Physiological determinants of social behaviour in animals’.
MassBlast: A workflow to accelerate RNA-seq and DNA database analysis
Authors: Veríssimo André , Bassard Jean-Etienne , Julien-Laferrière Alice , Sagot Marie-France , Vinga Susana 
Published: July 2017

AbstractSummaryCurrent workflows for sequence analysis heavily depend on user input and manual curation. New specialized tools and methods are appearing all the time, but the actions required for a full analysis are disconnected and very time-consuming. The software we propose, MassBlast, combines BLAST+ and an automated workflow analysis to filter the results and significantly improve the annotation of multiple sequencing databases for exploring new biosynthetic pathways and new protein families, among other applications. MassBlast is fully configurable and reproducible.Availability and ImplementationThe MassBlast package is written in Ruby. Source code and releases are freely available from Github (https://github.com/averissimo/mass-blast) for all major platforms (Linux, MS Windows and OS X) under the GPLv3 license.Contactandre.verissimo@tecnico.ulisboa.pt
Changes in extracellular matrix cause RPE cells to make basal deposits and activate the alternative complement pathway
Authors: Fernandez-Godino Rosario , Bujakowska Kinga M. , Pierce Eric A. 
Published: July 2017

ABSTRACTThe design of efficient therapies for age-related macular degeneration (AMD) is limited by our understanding of the pathogenesis of basal deposits, which form between retinal pigment epithelium (RPE) and Bruch’s membrane (BrM) early in disease, and involve activation of the complement system. To investigate the roles of BrM, RPE and complement in AMD, we generated ARPE-19 cells with the p.R345W mutation inEFEMP1, which causes early-onset macular degeneration. The ARPE-19-EFEMP1R345W/R345Wcells make abnormal extracellular matrix (ECM) that binds active complement C3 and causes the formation of basal deposits by normal human fetal (hf)RPE cells. hfRPE cells grown on abnormal ECM or BrM explants from AMD donors show chronic activation of the alternative complement pathway by excessive deposition of C3b. This process is exacerbated by impaired ECM turnover via increased matrix metalloproteinase-2 (MMP-2) activity. Therapies that target ECM synthesis and turnover and activation of C3 could be effective for early AMD.
Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0
Authors: Koch Mathilde , Duigou Thomas , Carbonell Pablo , Faulon Jean-Loup 
Published: July 2017

AbstractBackgroundNetwork generation tools coupled with chemical reaction rules have been mainly developed for synthesis planning and more recently for metabolic engineering. Using the same core algorithm, these tools apply a set of rules to a source set of compounds, stopping when a sink set of compounds has been produced. When using the appropriate sink, source and rules, this core algorithm can be used for a variety of applications beyond those it has been developed for.ResultsHere, we showcase the use of the open source workflow RetroPath2.0. First, we mathematically prove that we can generate all structural isomers of a molecule using a reduced set of reaction rules. We then use this enumeration strategy to screen the chemical space around a set of monomers and predict their glass transition temperatures, as well as around aminoglycosides to search structures maximizing antibacterial activity. We also perform a screening around aminoglycosides with enzymatic reaction rules to ensure biosynthetic accessibility. We finally use our workflow on anE. colimodel to completeE. colimetabolome, with novel molecules generated using promiscuous enzymatic reaction rules. These novel molecules are searched on the MS spectra of anE. colicell lysate interfacing our workflow with OpenMS through the KNIME analytics platform.ConclusionWe provide an easy to use and modify, modular, and open-source workflow. We demonstrate its versatility through a variety of use cases including, molecular structure enumeration, virtual screening in the chemical space, and metabolome completion. Because it is open source and freely available on MyExperiment.org, workflow community contributions should likely expand further the features of the tool, even beyond the use cases presented in the paper.
Motor expertise facilitates the precision of state extrapolation in perception
Authors: Ludolph Nicolas , Plöger Jannis , Giese Martin A. , Ilg Winfried 
Published: July 2017

AbstractPredicting the behavior of objects in the environment is an important requirement to overcome latencies in the sensorimotor system and realize precise actions in rapid situations. Internal forward models that were acquired during motor training might not only be used for efficiently controlling fast motor behavior but also to facilitate extrapolation performance in purely perceptual tasks. In this study, we investigated whether preceding virtual cart-pole balancing training facilitates the ability to extrapolate the pole motion. We compared a group of 10 subjects, proficient in performing the cart-pole balancing task, to 10 naïve subjects. Our results demonstrate that preceding motor training increases the precision of pole movement extrapolation, although extrapolation is not trained explicitly. Additionally, we modelled subjects’ behaviors and show that the difference in extrapolation performance can be explained by individual differences in the accuracy of internal forward models. When subjects are provided with feedback about the true pole movement in a second phase, both groups improve rapidly. The results indicate that the perceptual capability to extrapolate the state of the cart-pole system accurately is implicitly trained during motor learning. We discuss these results in the context of shared representations and action-perception transfer.
Facultative adjustment of paternal care in the face of female infidelity in dunnocks
Authors: Santos Eduardo S. A. , Nakagawa Shinichi 
Published: July 2017

AbstractA much-debated issue is whether or not males should reduce parental care when they lose paternity (i.e. the certainty of paternity hypothesis). While there is general support for this relationship across species, within-population evidence is still contentious. Among the main reasons behind such problem is the confusion discerning between-from within-individual patterns. Here, we tested this hypothesis empirically by investigating the parental care of male dunnocks(Prunella modularis)in relation to paternity. We used a thorough dataset of observations in a wild population, genetic parentage, and a within-subject centring statistical approach to disentangle paternal care adjustment within-male and between males. We found support for the certainty of paternity hypothesis, as there was evidence for within-male adjustment in paternal care when socially monogamous males lost paternity to extra-pair sires. There was little evidence of a between-male effect overall. Our findings show that monogamous males adjust paternal care when paired to the same female partner. We also show that – in monogamous broods – the proportion of provisioning visits made by males yields fitness benefits in terms of fledging success. Our results suggest that socially monogamous females that engage in extra-pair behaviour may suffer fitness costs, as their partners’ reduction in paternal care can negatively affect fledging success.
Cortical circuit-based lossless neural integrator for perceptual decision-making
Authors: Lee Jung H. , Tsunada Joji , Vijayan Sujith , Cohen Yale E. 
Published: July 2017

AbstractThe intrinsic uncertainty of sensory information (i.e., evidence) does not necessarily deter an observer from making a reliable decision. Indeed, uncertainty can be reduced by integrating (accumulating) incoming sensory evidence. It is widely thought that this accumulation is instantiated via recurrent rate-code neural networks. Yet, these networks do not fully explain important aspects of perceptual decision-making, such as a subject’s ability to retain accumulated evidence during temporal gaps in the sensory evidence. Here, we utilized computational models to show that cortical circuits can switch flexibly between ‘retention’ and ‘integration’ modes during perceptual decision-making. Further, we found that, depending on how the sensory evidence was readout, we could simulate ‘stepping’ and ‘ramping’ activity patterns, which may be analogous to those seen in different studies of decision-making in the primate parietal cortex. This finding may reconcile these previous empirical studies because it suggests these two activity patterns emerge from the same mechanism.
Mechanisms of surface antigenic variation in the human pathogenic fungusPneumocystis jirovecii
Authors: Schmid-Siegert Emanuel , Richard Sophie , Luraschi Amanda , Mühlethaler Konrad , Pagni Marco , Hauser Philippe M. 
Published: July 2017

AbstractMicrobial pathogens commonly escape the human immune system by varying surface proteins. We investigated the mechanisms used for that purpose byPneumocystis jirovecii.This uncultivable fungus is an obligate pulmonary pathogen which causes pneumonia in immuno-compromised individuals, a major life-threatening infection. Long-read PacBio sequencing was used to assemble a core of subtelomeres of a singleP. jiroveciistrain from a bronchoalveolar lavage fluid specimen of a single patient. A total of 113 genes encoding surface proteins were identified, including 28 pseudogenes. These genes formed a subtelomeric gene superfamily which included five families encoding adhesive GPI-anchored glycoproteins, and one family encoding excreted glycoproteins. Numerical analyses suggested that diversification of the glycoproteins relies on mosaic genes created by ectopic recombination, and occurs only within each family. DNA motifs suggested that all genes are expressed independently, except those of the family encoding the most abundant surface glycoproteins which are subject to mutually exclusive expression. PCR analyses showed that exchange of the expressed gene of the latter family occurs frequently, possibly favoured by the location of the genes proximal to the telomere because this allows concomitant telomere exchange. Our observations suggest that (i)P. jiroveciicell surface is made of a complex mixture of different surface proteins, with a majority of a single isoform of the most abundant glycoprotein, (ii) genetic mosaicism within each family ensures variation of the glycoproteins, and (iii) the strategy of the fungus consists in the continuous production of new subpopulations composed of cells which are antigenically different.
Optical inhibition of zebrafish behavior with anion channelrhodopsins
Authors: Mohamed Gadisti Aisha , Cheng Ruey-Kuang , Ho Joses , Krishnan Seetha , Mohammad Farhan , Claridge-Chang Adam , Jesuthasan Suresh 
Published: July 2017

AbstractIn behavioral analysis, optical electrical silencing provides a way to test neuronal necessity. Two light-gated anion channels, GtACR1 and GtACR2, have recently been shown—in neuronal culture and inDrosophila—to inhibit neurons potently. Here, we test the usefulness of these channels in zebrafish. When the GtACRs were expressed in motor neurons and actuated with blue or green light, fish spontaneous movement was inhibited. In GtACR1-expressing fish, only 3 µW/mm2of light was sufficient to have an effect; GtACR2, which is poorly trafficked, required stronger illumination. After light offset, GtACR-expressing fish movement increased; this suggested that termination of light-induced neural inhibition may lead to depolarization. Consistent with this, two-photon imaging of spinal neurons showed that intracellular calcium also increased following light offset. The activity elicited at light offset needs to be taken into consideration in experimental design, although this property may help provide insight into the effects of stimulating a circuit transiently. These results show that GtACR1 and GtACR2 can be used to optically inhibit neurons in zebrafish, and thus to test neural circuit necessity.
Comparison of fine-scale recombination maps in fungal plant pathogens reveals dynamic recombination landscapes and intragenic hotspots
Authors: Stukenbrock Eva H. , Dutheil Julien Y. 
Published: July 2017

AbstractMeiotic recombination is an important driver of evolution. Variability in the intensity of recombination across chromosomes can affect sequence composition, nucleotide variation and rates of adaptation. In many organisms recombination events are concentrated within short segments termed recombination hotspots. The variation in recombination rate and positions of recombination hotspot can be studied using population genomics data and statistical methods. In this study, we conducted population genomics analyses to address the evolution of recombination in two closely related fungal plant pathogens: the prominent wheat pathogenZymoseptoria triticiand a sister species infecting wild grassesZymoseptoria ardabiliae. We specifically addressed whether recombination landscapes, including hotspot positions, are conserved in the two recently diverged species and if recombination contributes to rapid evolution of pathogenicity traits. We conducted a detailed simulation analysis to assess the performance of methods of recombination rate estimation based on patterns of linkage disequilibrium, in particular in the context of high nucleotide diversity. Our analyses reveal overall high recombination rates, a lack of suppressed recombination in centromeres and significantly lower recombination rates on chromosomes that are known to be accessory. The comparison of the recombination landscapes of the two species reveals a strong correlation of recombination rate at the megabase scale, but little correlation at smaller scales. The recombination landscapes in both pathogen species are dominated by frequent recombination hotspots across the genome including coding regions, suggesting a strong impact of recombination on gene evolution. A significant but small fraction of these hotspots co-localize between the two species, suggesting that hotspots dynamics contribute to the overall pattern of fast evolving recombination in these species.
A mouse model of necrotic biliary pancreatitis induced by combining gallstone formation and ligation of the biliary-pancreatic duct
Authors: Yuan Zuobiao , Zheng Junyuan , Mei Zhu , Hu Guoyong , Zeng Yue 
Published: July 2017

AbstractObjectiveThe aim of the present investigation is to develop a mouse model of biliary pancreatitis with characteristics of both gallstone formation and pancreatitis, mimicking the human etiology and pathphysiological character.DesignMale C57BL/6 mice were fed with chow, high fat/cholesterol and lithogenic diet for 12 weeks respectively. Laparotomy was done followed by ligation of pancreatic duct (PD), bile duct and pancreatic duct (BPD), or sham operation.ResultsLittle or no evidence of pancreatitis was observed in PD group of mice fed with chow or high fat/cholesterol diet, or in the tail of pancreata removed from animals fed with lithogenic diet. In the head of pancreas, pancreas damage was dramatically more severe in the lithogenic group. When bile reflux was blocked by BPD, pancreas damage markedly reduced to level of chow diet group. The lithogenic diet group also developed significantly more severe multi organ dysfunction syndrome (MODS) in the lung, kidney and liver. The severity of pancreatitis is associated with persistent high bile level of cholesterol and bile acid after obstruction of the biliary-pancreatic duct. Cholesterol crystal aggravated injury of pancreatic acinar cells caused by taurocholate. After obstruction of the biliary-pancreatic duct, in the lithogenic diet group, liver Abcg8 and Cyp7a1 was up-regulated, compared to the control group.ConclusionWe developed a mouse model of severe biliary pancreatitis in both local pancreas damage and MODS. This model provides a sound explanation for the Opie theory dilemma and a potential therapeutical direction in clinical practice as well.Summary statementA biliary pancreatitis has characters of both gallstone and pancreatitis, mimicking human etiology and pathophysiology, which gave a clear answer to the long time Opie theory dilemma.
Biochemical characterization and essentiality ofPlasmodiumfumarate hydratase
Authors: Jayaraman Vijay , Suryavanshi Arpitha , Kalale Pavithra , Kunala Jyothirmai , Balaram Hemalatha 
Published: July 2017

ABSTRACTPlasmodium falciparum(Pf), the causative agent of malaria has an iron-sulfur cluster-containing class I fumarate hydratase (FH) that catalyzes the interconversion of fumarate to malate, a well-known reaction in the tricarboxylic acid cycle. In humans, the same reaction is catalyzed by class II FH that has no sequence or structural homology with the class I enzyme. Fumarate, generated in large quantities in the parasite as a byproduct of AMP synthesis is converted to malate by the action of FH, and subsequently used in the generation of the key metabolites oxaloacetate, aspartate and pyruvate. Here we report on the kinetic characterization of purified recombinant PfFH, functional complementation offhdeficiency inEscherichia coliand mitochondrial localization in the parasite. The substrate analog, mercaptosuccinic acid was found to be a potent inhibitor of PfFH with a Kivalue in the nanomolar range. Knockout of thefhgene was not possible inP. bergheiwhen drug-selection of the transfectants was performed in BALB/c mice while the gene was amenable to knockout when C57BL/6 mice were used as host, thereby indicating mouse-strain dependent essentiality of thefhgene to the parasite.
A Fluorogenic Array Tag for Temporally Unlimited Single Molecule Tracking
Authors: Ghosh Rajarshi P , Franklin J Matthew , Draper Will E. , Shi Quanming , Liphardt Jan T. 
Published: July 2017

AbstractCellular processes take place over many timescales, prompting the development of precision measurement technologies that cover milliseconds to hours. Here we describe ArrayG, a bipartite fluorogenic system composed of a GFP-nanobody array and monomeric wtGFP binders. The free binders are initially dim but brighten 15 fold upon binding the array, suppressing background fluorescence. By balancing rates of intracellular binder production, photo-bleaching, and stochastic binder exchange on the array, we achieved temporally unlimited tracking of single molecules. Fast (20-180Hz) tracking of ArrayG tagged kinesins and integrins, for thousands of frames, revealed repeated state-switching and molecular heterogeneity. Slow (0.5 Hz) tracking of single histones for as long as 1 hour showed fractal dynamics of chromatin. We also report ArrayD, a DHFR-nanobody-array tag for dual color imaging. The arrays are aggregation resistant and combine high brightness, background suppression, fluorescence replenishment, and extended choice of fluorophores, opening new avenues for seeing and tracking single molecules in living cells.
Do Sigmoidal Acquisition Curves Indicate Conformity?
Authors: Smaldino Paul E. , Aplin Lucy M. , Farine Damien R. 
Published: July 2017

ABSTRACTThe potential for behaviours to spread via cultural transmission has profound implications for our understanding of social dynamics and evolution. Several studies have provided empirical evidence that local traditions can be maintained in animal populations via conformist learning (i.e. copying the majority). A conformist bias can be characterized by a sigmoidal relationship between a behavior’s prevalence in the population and an individual’s propensity to adopt that behavior. For this reason, the presence of conformist learning in a population is often inferred from a sigmoidal acquisition curve in which the overall rate of adoption for the behavior is taken as the dependent variable. However, the validity of sigmoidal acquisition curves as evidence for conformist learning has recently been challenged by models suggesting that such curves can arise via alternative learning rules that do not involve conformity. We review these models, and find that the proposed alternative learning mechanisms either rely on faulty or unrealistic assumptions, or apply only in very specific cases. We therefore recommend that sigmoidal acquisition curves continue to be taken as evidence for conformist learning. Our paper also highlights the importance of understanding the generative processes of a model, rather than only focusing solely on the patterns produced. By studying these processes, our analysis suggests that current practices by empiricists have provided robust evidence for conformist transmission in both humans and non-human animals.
KinFin: Software for taxon-aware analysis of clustered protein sequences
Authors: Laetsch Dominik R. , Blaxter Mark L. 
Published: July 2017

AbstractThe field of comparative genomics is concerned with the study of similarities and differences between the information encoded in the genomes of organisms. A common approach is to define gene families by clustering protein sequences based on sequence similarity, and analyse protein cluster presence and absence in different species groups as a guide to biology. Due to the high dimensionality of these data, downstream analysis of protein clusters inferred from large numbers of species, or species with many genes, is non-trivial, and few solutions exist for transparent, reproducible and customisable analyses. We present KinFin, a streamlined software solution capable of integrating data from common file formats and delivering aggregative annotation of protein clusters. KinFin delivers analyses based on systematic taxonomy of the species analysed, or on user-defined groupings of taxa, for example sets based on attributes such as life history traits, organismal phenotypes, or competing phylogenetic hypotheses. Results are reported through graphical and detailed text output files. We illustrate the utility of the KinFin pipeline by addressing questions regarding the biology of filarial nematodes, which include parasites of veterinary and medical importance. We resolve the phylogenetic relationships between the species and explore functional annotation of proteins in clusters in key lineages and between custom taxon sets, identifying gene families of interest. KinFin can easily be integrated into existing comparative genomic workflows and promotes transparent and reproducible analysis of clustered protein data.