bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metabolic cost calculations of gait using musculoskeletal energy models, a comparison study
Authors: Koelewijn Anne D. , Heinrich Dieter , van den Bogert Antonie J. 
Published: March 2019

AbstractThis paper compares predictions of metabolic energy expenditure in gait using seven metabolic energy expenditure models to assess their correlation with experimental data. Ground reaction forces, marker data, and pulmonary gas exchange data were recorded for six walking trials at combinations of two speeds, 0.8 m/s and 1.3 m/s, and three inclines, −8% (downhill), level, and 8% (uphill). The metabolic cost, calculated with the metabolic energy models was compared to the metabolic cost from the pulmonary gas exchange rates. A repeated measures correlation showed that all models correlated well with experimental data, with correlations of at least 0.9. The model by Bhargava et al. [7] and the model by Lichtwark and Wilson [21] had the highest correlation, 0.96. The model by Margaria [23] predicted the increase in metabolic cost following a change in dynamics best in absolute terms.
Correlating Synaptic Ultrastructure and Function at the Nanoscale
Authors: Maus Lydia , Altas Bekir , Rhee JeongSeop , Brose Nils , Imig Cordelia , Cooper Benjamin H. 
Published: March 2019

SUMMARYDespite similarities in the composition of the molecular release machinery, synapses can exhibit strikingly different functional transmitter release properties and short- and long-term plasticity characteristics. To address the question whether ultrastructural differences could contribute to this functional synaptic heterogeneity, we employed a combination of hippocampal organotypic slice cultures, high-pressure freezing, freeze substitution, and 3D-electron tomography to resolve the spatial organization of vesicle pools at individual active zones (AZ) in two functionally distinct synapses, namely Schaffer collateral (SC) and mossy fiber (MF) synapses. We found that mature MF and SC synapses harbor equal numbers of docked vesicles at their AZs, MF synapses at rest exhibit a second pool of possibly ‘tethered’ vesicles in the AZ vicinity, and MF synapses contain at least three morphological types of docked vesicles, indicating that differences in the ultrastructural organization of MF and SC synapses may contribute to their respective functional properties and corresponding plasticity characteristics.
A test of the evolution of increased competitive ability in two invaded regions
Authors: Rotter Michael C. , Vallejo-Marin Mario , Holeski Liza M. 
Published: March 2019

AbstractFinding patterns that predict and explain the success of non-native species has been an important focus in invasion ecology. The evolution of increased competitive ability (EICA) hypothesis has been a frequently used framework to understand invasion success. Evolution of increased competitive ability predicts that 1. Non-native populations will escape from coevolved specialist herbivores and this release from specialist herbivores should result in relaxed selection pressure on specialist-related defense traits, 2. There will be a trade-off between allocation of resources for resistance against specialist herbivores and allocation to traits related to competitive ability and 3. This shift will allow more allocation to competitive ability traits.We tested the predictions of EICA in the model plant Mimulus guttatus, a native of western North America (WNA). We compared how well the predictions of EICA fit patterns in two non-native regions, the United Kingdom (UK) and eastern North America (ENA). Coupled with extensive herbivore surveys we quantified genetic variation for herbivore resistance traits and fitness/ competitive ability traits to test adherence to the predictions of EICA in a common greenhouse environment.Herbivore communities differed significantly between WNA, UK, and ENA populations with evidence of specialist herbivore escape in the UK, but not necessarily the ENA plants. Compared to native plants, resistance traits were lower in non-native UK plants with the exception of trichome density, while the non-native ENA plants had equivalent or higher levels of herbivore resistance traits. The UK plants had increased competitive traits than native plants while the ENA plants had equivalent competitive traits to native plants. The UK plants, but not the ENA plants, showed some signs of tradeoffs between resistance traits and fitness/ competitive ability.Synthesis. Plants from the UK conformed to predictions of EICA more closely than those from ENA. The UK invasion is an older, more successful invasion, suggesting that support for EICA may be highest in more successful invasions. The lack of comprehensive conformity of either non-native region to the predictions of EICA also leaves room for other hypotheses that may add to our mechanistic understanding of the success of non-native plant invasions.
Comparative genomic analysis of three salmonid species identifies functional candidate genes involved in resistance to the intracellular bacteriaPiscirickettsia salmonis
Authors: Yáñez José M. , Yoshida Grazyella M. , Parra Ángel , Correa Katharina , Barría Agustín , Bassini Liane N. , Christensen Kris A. , López Maria E. , Carvalheiro Roberto , Lhorente Jean P. , Pulgar Rodrigo 
Published: March 2019

AbstractPiscirickettsia salmonisis the etiological agent of Salmon Rickettsial Syndrome (SRS), and is responsible for considerable economic losses in salmon aquaculture. The bacteria affect coho salmon (CS) (Oncorhynchus kisutch), Atlantic salmon (AS) (Salmo salar) and rainbow trout (RT) (Oncorhynchus mykiss) in several countries, including: Norway, Canada, Scotland, Ireland and Chile. We used Bayesian genome-wide association (GWAS) analyses to investigate the genetic architecture of resistance toP. salmonisin farmed populations of these species. Resistance to SRS was defined as the number of days to death (DD) and as binary survival (BS). A total of 828 CS, 2,130 RT and 2,601 AS individuals were phenotyped and then genotyped using ddRAD sequencing, 57K SNP Affymetrix® Axiom® and 50K Affymetrix® Axiom® SNP panels, respectively. Both trait of SRS resistance in CS and RT, appeared to be under oligogenic control. In AS there was evidence of polygenic control of SRS resistance. To identify candidate genes associated with resistance, we applied a comparative genomics approach in which we systematically explored the complete set of genes adjacent to SNPs which explained more than 1% of the genetic variance of resistance in each salmonid species (533 genes in total). Thus, genes were classified based on the following criteria: i) shared function of their protein domains among species, ii) shared orthology among species, iii) proximity to the SNP explaining the highest proportion of the genetic variance and, iv) presence in more than one genomic region explaining more than 1% of the genetic variance within species. Our results allowed us to identify 120 candidate genes belonging to at least one of the four criteria described above. Of these, 21 of them were part of at least two of the criteria defined above and are suggested to be strong functional candidates influencingP. salmonisresistance. These genes are related to diverse biological processes, such as: kinase activity, GTP hydrolysis, helicase activity, lipid metabolism, cytoskeletal dynamics, inflammation and innate immune response, which seem essential in the host response againstP. salmonisinfection. These results provide fundamental knowledge on the potential functional genes underpinning resistance againstP. salmonisin three salmonid species.
Consequences of consumer origin and omnivory on stability in experimental food web modules
Authors: Granados Monica , Pagnucco Katie S. , Ricciardi Anthony 
Published: March 2019

AbstractFood web stability, a fundamental characteristic of ecosystems, is influenced by the nature and strength of species interactions. Theory posits that food webs are stabilized by omnivory and disrupted by novel consumers.To test the effects of secondary consumer origin and trophic level on basal resource stability, we constructed crayfish-snail-algae modules using four congeneric species of crayfish (Faxonius spp.), two from native populations (F. propinquus and F. virilis) and two from non-native populations (F. limosus and F. rusticus). We performed surgical manipulations of crayfish feeding structures to create omnivore food web and predator food chain modules. We compared the temporal stability of these modules using measures of the coefficient of variation of the basal resource (benthic algae).Consistent with theoretical and empirical predictions, food web modules with omnivory had the lowest coefficient of variation. However, contrary to prediction, we did not find consistently higher coefficients of variation in modules with non-native species. Rather, across species, we found the lowest coefficient of variation in modules with one of the non-native species (F. rusticus) and one native species (F. virilis), owing to stronger interactions between these crayfish species and their snail and algal food resources.The results suggest that omnivory is indeed stabilizing and that very weak interactions or very low attack rates of the consumer on the basal resource can be unstable. Thus, we demonstrate that omnivores may have different impacts than predators when introduced into a novel ecosystem, differences that can supersede the effect of species identity.
Genetic evaluation modeling of the Tunisian dairy cattle: assessment of the test-day model (TDM) and lactation model (L305) in accordance to the flock size
Authors: Ressaissi Yosra , Ben Hmouda Mohamed 
Published: March 2019

SUMMARYGenetic evaluation in dairy cattle has been commonly carried following the lactation model (L305) and the test-day model (TDM), the purpose of this study was to test the adjustment and the accuracy of these main models in relation to the size of the Tunisian dairy flocks while assessing the effect of genealogical data availability on both approaches. Data were obtained from the Tunisian official milk recording system and cows were classified in accordance to the flock sizes into eight groups. Genetic parameters and breeding values were estimated per size group for 305-days (L305) and daily milk yields (TDM) through two animal models and by using 3 pedigrees of different quality. Contemporary groups were defined as herd*calving year for L305 and as herd*control year for TDM. Genetic evaluation approaches were compared by connecting the different obtained results. Fixed factors were observed to be differently significant per group of flock size explaining a specific variance of the average milk yield and that small flocks are mostly affected by environmental factors. Using TDM and an equilibrated pedigree file, genetic parameters were higher, breeding values were fairly compared leading to a more objective ranking of the cows and a better illustration of genetic variabilities between the flock groups. Low genetic variability and significant contribution of unfavorable environmental conditions were observed within the Tunisian dairy flocks.
Single-cell transcriptomics reveals multiple neuronal cell types in human midbrain-specific organoids
Authors: Smits Lisa M. , Magni Stefano , Grzyb Kamil , Antony Paul MA. , Krüger Rejko , Skupin Alexander , Bolognin Silvia , Schwamborn Jens C. 
Published: March 2019

AbstractHuman stem cell-derived organoids have great potential for modelling physiological and pathological processes. They recapitulatein vitrothe organisation and function of a respective organ or part of an organ. Human midbrain organoids (hMOs) have been described to contain midbrain-specific dopaminergic neurons that release the neurotransmitter dopamine. However, the human midbrain contains also additional neuronal cell types, which are functionally interacting with each other. Here, we analysed hMOs at high-resolution by means of single-cell RNA-sequencing (scRNA-seq), imaging and electrophysiology to unravel cell heterogeneity. Our findings demonstrate that hMOs show essential neuronal functional properties as spontaneous electrophysiological activity of different neuronal subtypes, including dopaminergic, GABAergic, and glutamatergic neurons. Recapitulating thesein vivofeatures makes hMOs an excellent tool forin vitrodisease phenotyping and drug discovery.
Shared genetic background between children and adults with attention deficit/hyperactivity disorder
Authors: Rovira Paula , Demontis Ditte , Sánchez-Mora Cristina , Zayats Tetyana , Klein Marieke , Mota Nina Roth , Weber Heike , Garcia-Martínez Iris , Pagerols Mireia , Vilar Laura , Arribas Lorena , Richarte Vanesa , Corrales Montserrat , Fadeuilhe Christian , Bosch Rosa , Español Martin Gemma , Almos Peter , Doyle Alysa E. , Grevet Eugenio Horacio , Grimm Oliver , Halmøy Anne , Hoogman Martine , Hutz Mara , Jacob Christian P. , Kittel-Schneider Sarah , Knappskog Per M. , Lundervold Astri J. , Rivero Olga , Rovaris Diego Luiz , Salatino-Oliveira Angelica , da Silva Bruna Santos , Svirin Evgenij , Sprooten Emma , Strekalova Tatyana ,   ADHD Working Group of the Psychiatric Genomics Consortium,   23andMe Research team, Arias-Vasquez Alejandro , Sonuga-Barke Edmund J.S. , Asherson Philip , Dotto Bau Claiton Henrique , Buitelaar Jan K. , Cormand Bru , Faraone Stephen V. , Haavik Jan , Johansson Stefan E. , Kuntsi Jonna , Larsson Henrik , Lesch Klaus-Peter , Reif Andreas , Rohde Luis Augusto , Casas Miquel , Børglum Anders D. , Franke Barbara , Ramos-Quiroga Josep Antoni , Artigas María Soler , Ribasés Marta 
Published: March 2019

AbstractAttention deficit/hyperactivity disorder (ADHD) is a common neurodevelopmental disorder characterized by age-inappropriate symptoms of inattention, impulsivity and hyperactivity that persist into adulthood in the majority of the diagnosed children. Despite several risk factors during childhood predicting the persistence of ADHD symptoms into adulthood, the genetic architecture underlying the trajectory of ADHD over time is still unclear. We set out to study the contribution of common genetic variants to the risk for ADHD across the lifespan by conducting meta-analyses of genome-wide association studies on persistent ADHD in adults and ADHD in childhood separately and comparing the genetic background between them in a total sample of 17,149 cases and 32,411 controls. Our results show nine new independent loci and support a shared contribution of common genetic variants to ADHD in children and adults. No subgroup heterogeneity was observed among children, while this group consists of future remitting and persistent individuals. We report similar patterns of genetic correlation of ADHD with other ADHD-related datasets and different traits and disorders among adults, children and when combining both groups. These findings confirm that persistent ADHD in adults is a neurodevelopmental disorder and extend the existing hypothesis of a shared genetic architecture underlying ADHD and different traits to a lifespan perspective.
Cell Specific Reactivation of Epicardium at the Origin of Fibro-Fatty Remodeling of the Atrial Myocardium
Authors: Suffee Nadine , Moore-Morris Thomas , Mougenot Nathalie , Dilanian Gilles , Berthet Myriam , Jagla Bernd , Proukhnitzky Julie , Prince Pascal Le , Tregouet David A , Pucéat Michel , Hatem Stéphane N 
Published: March 2019

AbstractEpicardium, the mesothelium covering the heart, is composed of multipotent cells and is reactivated following myocardial injury in adults. Herein, we provide evidence for activation of atrial epicardium in aged patients with diseased atria and in murine models of atrial remodeling. Epicardial activation contributed to fibro-fatty infiltration of sub-epicardium that contained a number of cells co-expressing markers of epicardial progenitors and fibroblasts. Indeed, using genetic lineage tracing of adult epicardium, we demonstrate the epicardial origin of fibroblasts within fibro-fatty infiltrates. A subpopulation of adult epicardial-derived cells (aEPDCs) expressing PDGFRα, niched in the sub-epicardium, were isolated and differentiated into myofibroblast in the presence of angiotensin-II. Furthermore, single cell RNA-seq analysis identified several clusters of aEPDCs and revealed transition from adipogenic to fibrogenic cells. In conclusion, a subset of aEPDCs, pre-programmed towards a specific cell fate, contributes to fibro-fatty infiltration of sub-epicardium of diseased atria.
VIVA (VIsualization of VAriants): A VCF file visualization tool
Authors: Tollefson George A. , Schuster Jessica , Gelin Fernando , Ragavendran Ashok , Restrepo Isabel , Stey Paul , Padbury James , Uzun Alper 
Published: March 2019

ABSTRACTThe volume and pace of data accumulation from high-throughput sequencing studies have been amplified by recent rapid technological advances in biological sciences. Visualization of genomic data is essential for quality control, exploration, and interpretation. Here, we describe a user-friendly visualization tool for variant call format (VCF) files with which the users can interactively evaluate and share genomic data, as well as create publication quality graphics.
Heterogeneous profiles of coupled sleep oscillations in human hippocampus
Authors: Cox Roy , Rüber Theodor , Staresina Bernhard P , Fell Juergen 
Published: March 2019

AbstractCross-frequency coupling of sleep oscillations is thought to mediate memory consolidation. While the hippocampus is deemed central to this process, detailed knowledge of which oscillatory rhythms interact in the sleeping human hippocampus is lacking. Combining intracranial hippocampal and non-invasive electroencephalography from twelve neurosurgical patients, we characterized spectral power and coupling during non-rapid eye movement (NREM) and rapid eye movement (REM) sleep. Hippocampal coupling was extensive, with the majority of channels expressing spectral interactions. NREM consistently showed delta–ripple coupling, but ripples were also modulated by slow oscillations (SOs) and sleep spindles. SO–delta and SO–theta coupling, as well as interactions between delta/theta and spindle/beta frequencies also occurred. During REM, limited interactions between delta/theta and beta frequencies emerged. Moreover, oscillatory organization differed substantially between i) hippocampus and scalp, ii) sites along the anterior-posterior hippocampal axis, and iii) individuals. Overall, these results extend and refine our understanding of hippocampal sleep oscillations.
Properties of individual hippocampal synapses influencing NMDA-receptor activation by spontaneous neurotransmission
Authors: Metzbower Sarah R. , Joo Yuyoung , Benavides David R. , Blanpied Thomas A. 
Published: March 2019

AbstractNMDA receptor (NMDAR) activation is critical for maintenance and modification of synapse strength. Specifically, NMDAR activation by spontaneous glutamate release has been shown to mediate forms of synaptic plasticity as well as synaptic development. Interestingly, there is evidence that within individual synapses each release mode may be segregated such that postsynaptically there are distinct pools of responsive receptors. In order to examine potential regulators of NMDAR activation due to spontaneous glutamate release in cultured rat hippocampal neurons, we utilized GCaMP6f imaging at single synapses in concert with confocal and super-resolution imaging. Using these single spine approaches, we found that Ca2+entry activated by spontaneous release tends to be carried by GluN2B-NMDARs. Additionally, the amount of NMDAR activation varies greatly both between synapses and within synapses, and is unrelated to spine and synapse size, but does correlate loosely with synapse distance from the soma. Despite the critical role of spontaneous activation of NMDARs in maintaining synaptic function, their activation seems to be controlled factors other than synapse size or synapse distance from the soma. It is most likely that NMDAR activation by spontaneous release influenced variability in subsynaptic receptor position, release site position, vesicle content, and channel properties. Therefore, spontaneous activation of NMDARs appears to be regulated distinctly from other receptor types, notably AMPARs, within individual synapses.Significance StatementUnderstanding the underlying synaptic mechanisms for learning and memory is critically important to the field of neuroscience and for human health. A key neurotransmitter receptor type involved in learning is the NMDA receptor, and exploration of its regulation is vital. In this study, we optimized optical tools to allow detailed characterization of NMDA receptor activity at single synapses, along with analysis of structural features of the imaged synapses. The amount of receptor activation is independent of the size of the synapse, but weakly dependent on synapse position within the dendritic tree. Notably, we found that NMDA receptors activated following spontaneous neurotransmitter release tend be GluN2B-containing receptors. Thus, the unique mechanisms that regulate the number and positioning of these receptors within synapses will have important consequences for control of synaptic development and signaling.
Contribution of self- and other-regarding motives to (dis)honesty
Authors: Shuster Anastasia , Levy Dino J 
Published: March 2019

AbstractWhy would people tell the truth when there is an obvious gain in lying and no risk of being caught? Previous work suggests the involvement of two motives, self-interest and regard for others. However, it remains unknown if these motives are related or independently contribute to (dis)honesty, and what are the neural instantiations of these motives. Using a modified Message Game task, in which a Sender sends a dishonest (yet profitable) or honest (less profitable) message to a Receiver, we found that these two motives contributed to dishonesty independently. Furthermore, the two motives involve distinct brain networks: the LPFC tracked potential value to self, whereas the rTPJ tracked potential losses to other, and individual differences in motives modulated these neural responses. Finally, activity in the vmPFC represented a balance of the two motives unique to each participant. Taken together, our results suggest that (dis)honest decisions incorporate at least two separate cognitive and neural processes – valuation of potential profits to self and valuation of potential harm to others.
Decorating Microbially Produced Protein Nanowires with Peptide Ligands
Authors: Ueki Toshiyuki , Walker David J.F. , Tremblay Pier-Luc , Nevin Kelly P. , Ward Joy E. , Woodard Trevor L. , Nonnenmann Stephen S. , Lovley Derek R. 
Published: March 2019

AbstractThe potential applications of electrically conductive protein nanowires (e-PNs) harvested fromGeobacter sulfurreducensmight be greatly expanded if the outer surface of the wires could be modified to confer novel sensing capabilities or to enhance binding to other materials. We developed a simple strategy for functionalizing e-PNs with surface-exposed peptide ligands. TheG. sulfurreducensgene for the monomer that assembles into e-PNs was modified to add known peptide ligands at the carboxyl terminus of the monomer. Strains ofG. sulfurreducenswere constructed that fabricated synthetic e-PNs with a six-histidine ‘His-tag’ or both the His-tag and a nine-peptide ‘HA-tag’ exposed on the outer surface. Addition of the peptide ligands did not diminish e-PN conductivity. The abundance of HA-tag in e-PNs was controlled by placing expression of the gene for the synthetic monomer with the HA-tag under transcriptional regulation. These studies suggest broad possibilities for tailoring e-PN properties for diverse applications.