bluuebunny/crossref_metadata_2025_split huggingface dataset:
Is it impossible to acquire absolute pitch in adulthood?
Authors: Wong Yetta Kwailing , Lui Kelvin F. H. , Yip Ken H.M. , Wong Alan C.-N. 
Published: July 2018

AbstractAbsolute pitch (AP) refers to the rare ability to name the pitch of a tone without external reference. It is widely believed that AP is only for the selected few with rare genetic makeup and early musical training during the critical period. Accordingly, acquiring AP in adulthood is impossible. Previous studies have not offered a strong test of the effect of training because of issues like small sample size and insufficient training. In three experiments, adults learned to name pitches in a computerized and personalized protocol for 12 to 40 hours. They improved considerably, with a continuous distribution of learning progress among them. 14% of the participants (6 out of 43) were able to name twelve pitches at accuracy of 90% or above, comparable to that of ‘AP possessors’ as defined in the literature. In general, AP learning showed classic characteristics of perceptual learning, including generalization of learning dependent on the training stimuli, and sustained improvement for at least one to three months. Overall, the finding that AP continues to be learnable in adulthood calls for reconsidering the role of learning in the occurrence of AP. The finding also pushes the field to pinpoint and explain, if any, the differences between the aspects of AP more trainable in adulthood and the aspects of AP that are potentially exclusive for the few exceptional AP possessors.
Evaluation of habitat protection under the European Natura 2000 conservation network – the example for Germany
Authors: Friedrichs Martin , Hermoso Virgilio , Bremerich Vanessa , Langhans Simone D. 
Published: July 2018

AbstractThe world’s largest network of protected areas - Natura 2000 (N2000) - has been implemented to protect Europe’s biodiversity. N2000 is built upon two cornerstones, the Birds Directive, which lists 230 bird species and the Habitats Directive, which lists next to a variety of species 230 habitat types, to be protected. There is evidence of the positive impact of the Directives on the EU’s biodiversity, although the overall improvement reported for species in favourable condition in the last assessment was low. However, most of the assessments are species focused, while habitats have received very little attention. Here we developed a generic workflow, which we exemplified for Germany, to assess the status of habitat coverage within the N2000 network, combining information from publicly available data sources. Applying the workflow allows identifying gaps in habitat protection, followed by the prioritization of potential areas of high protection value, using the conservation planning software Marxan. We found that, in Germany, N2000 covers all target habitats. However common habitats were proportionally underrepresented relative to rare ones, which contrasts with comparable studies for species. Moreover, the German case study suggests that especially highly protected areas (i.e. covered by more than 90% with N2000 sites) build an excellent basis towards a cost-effective and efficient conservation network. Our workflow provides a generic approach to deal with the popular problem of missing habitat distribution data outside of N2000 sites, information which is however crucial for managers to plan conservation action appropriately across Europe. To avoid a biased representation of habitat types within N2000, our results underpin the importance of defining qualitative and quantitative conservation targets which will allow assessing the trajectory of habitat protection in Europe as well as adjusting the network accordingly - a future necessity in the light of climate change.
Physiological Dynamic Compression Regulates Central Energy Metabolism in Primary Human Chondrocytes
Authors: Salinas Daniel , Mumey Brendan M. , June Ronald K. 
Published: July 2018

AbstractChondrocytes use the pathways of central metabolism to synthesize molecular building blocks and energy for cartilage homeostasis. An interesting feature of thein vivochondrocyte environment is the cyclical loading generated in various activities (e.g. walking). However, it is unknown if central metabolism is altered by mechanical loading. We hypothesized that physiological dynamic compression alters central metabolism in chondrocytes to promote production of amino acid precursors for matrix synthesis. We measured the expression of central metabolites (e.g. glucose, its derivatives, and relevant co-factors) for primary human osteoarthritic chondrocytes in response to 0-30 minutes of compression. To analyze the data, we used principal components analysis and ANOVA simultaneous components analysis, as well as metabolic ﬂux analysis. Compression induced metabolic responses consistent with our hypothesis. Additionally, these data show that chondrocyte samples from different patient donors exhibit different sensitivity to compression. Most important, we ﬁnd that grade IV osteoarthritic chondrocytes are capable of synthesizing non-essential amino acids and precursors in response to mechanical loading. These results suggest that further advances in metabolic engineering of chondrocyte mechanotransduction may yield novel translational strategies for cartilage repair.
The return to water in ancestralXenopuswas accompanied by a novel mechanism for producing and shaping vocal signals
Authors: Kwong-Brown Ursula , Tobias Martha L. , Elias Damian O. , Hall Ian C. , Elemans Coen P.H. , Kelley Darcy B. 
Published: July 2018

AbstractSpecies-specific vocal signals allow listeners to locate potential mates. During the tetrapod transition from water to land, lungs replaced gills, allowing expiration to drive sound production. Several groups,e.g. cetaceans and some frogs, then returned to water. Here we explore how air-driven sound production changed upon re-entry and how essential acoustic information on species identity was preserved in the secondarily aquatic frogXenopus. We filmed movements of cartilage and muscles during evoked sound production in isolated larynges. Our results refute the current theory forXenopusvocalization, cavitation, and instead favor sound production by mechanical excitation of laryngeal resonance modes following rapid separation of laryngeal arytenoid discs. The resulting frequency resonance modes (dyads) are intrinsic to the larynx rather than due to neuromuscular control. We show that dyads are a distinctive acoustic signature across species. While dyad component frequencies overlap across species, their ratio is shared within eachXenopusclade and thus provide information on species identity, potentially facilitating both conspecific localization and ancient species divergence.
Triggering mechanisms for motor actions: A mini meta-analysis and experimental data
Authors: Leow Li-Ann , Uchida Aya , Egberts Jamie-Lee , Riek Stephan , Lipp Ottmar V. , Tresilian James , Marinovic Welber 
Published: July 2018

AbstractMotor actions can be released much sooner than normal when the go-signal is of very high intensity (> 100dBa). Although statistical evidence from individual studies has been mixed, it has been assumed that sternocleidomastoid (SCM) muscle activity could be used to distinguish between two neural circuits involved in movement triggering. We summarized meta-analytically the available evidence for this hypothesis, comparing the difference in premotor reaction time (RT) of actions where SCM activity was elicited (SCM+ trials) by loud acoustic stimuli against trials in which it was absent (SCM- trials). We found ten studies, all reporting comparisons between SCM+ and SCM- trials. Our mini meta-analysis showed that premotor RTs are faster in SCM+ than in SCM- trials. We also present experimental data showing the effects of foreperiod predictability can induce differences in RT that would be of similar size to those attributed to the activation of different neurophysiological pathways to trigger prepared actions. We discuss plausible physiological mechanisms that would explain differences in premotor RTs between SCM+ and SCM-trials.
IDEA: a web server for Interactive Differential Expression Analysis with R Packages
Authors: Zhao Qi , Xie Yubin , Nie Peng , Diao Rucheng , Sun Lichen , Zuo Zhixiang , Ren Jian 
Published: July 2018

AbstractDifferential expression (DE) analysis is a fundamental task in the downstream analysis of the next-generation sequencing (NGS) data. Up to now, a number of R packages have been developed for detecting differentially expressed genes. Although R language has an interaction-oriented programming design, for many biology researchers, a lack of basic programming skills has greatly hindered the application of these R packages. To address this issue, we developed the Interactive Differential Expression Analyzer (IDEA), a Shiny-based web application integrating the differential expression analysis related R packages into a graphical user interface (GUI), allowing users to run the analysis without writing any new code. A wide variety of charts and tables are generated to facilitate the interpretation of the results. In addition, IDEA also provides a combined analysis framework which helps to reconcile any discrepancy from different computational methods. As a public data analysis server, IDAE is implemented in HTML, CSS and JavaScript, and is freely available at http://idea.renlab.org.
Gut Microbial succession during conventionalization of germfree chicken
Authors: Thomas Milton , Wongkuna Supapit , Ghimire Sudeep , Doerner Kinchel C. , Singery Aaron , Nelson Eric , Woyengo Tofuko , Chankhamhaengdecha Surang , Janvilisri Tavan , Scaria Joy 
Published: July 2018

AbstractA gnotobiotic chicken model was developed to study the succession of intestinal microflora from hatching to 18 days of age. Intestinal samples were collected from a local population of feral chickens and administered orally to germ-free 3 day old chicks. Animals were enthanized on 0, 9 and 18 days of age and intestinal samples were collected and subjected to genomic analysis. The five most prevalent phyla were Bacteroidetes (45.73±3.35%), Firmicutes (36.47±2.60%), Proteobacteria (8.28±0.91%), Actinobacteria (5.09±0.52%), and Spriochetes (2.10±0.38%). Principle coordinate analysis indicated the 0, 9 day and 18 day variables clustered together and the microbial communities changed temporally. The Morista-Horn index values ranged from 0.72 to 1, indicating the communities at 0, 9 or 18 days were more similar than dissimilar. The predicted functional profiles of the microbiomes of 0, 9 and 18 days were also similar. These results indicate the gnotobiotic chicks stably maintain the phylogentic diversity and predicted metabolic functionality of the inoculum community.ImportanceThe domestic chicken is the cornerstone of animal agriculture worldwide with a flock population exceeding 40 billion birds/year. It serves as the economically valuable source of protein globally. Microbiome of poultry has important effects on chicken growth, feed conversion, immune status and pathogen resistance. The significance of our research is in developing a gnotobiotic chicken model to study chicken gut microbiota function. Our experimental model shows that young germfree chicks are able to colonize diverse set of gut bacteria. Therefore, besides using this model to study mechanisms of gut microbiota interactions in the chicken gut, our model could be also used for applied aspects such as determining the safety and efficacy of new probiotic strains derived from chicken gut microbiota.
A new computational method for membrane compressibility: Bilayer mechanical thickness revisited
Authors: Doktorova M. , LeVine M.V. , Khelashvili G. , Weinstein H. 
Published: July 2018

ABSTRACTBecause lipid bilayers can bend and stretch in ways similar to thin elastic sheets, physical models of bilayer deformation have utilized mechanical constants such as the moduli for bending rigidity (κC) and area compressibility (KA). However, the use of these models to quantify the energetics of membrane deformation associated with protein-membrane interactions and the membrane response to stress is often hampered by the shortage of experimental data suitable for the estimation of the mechanical constants of various lipid mixtures. While computational tools such as Molecular Dynamics (MD) simulations can provide alternative means to estimateKAvalues, current approaches suffer significant technical limitations. Here, we present a novel computational framework that allows for a direct estimation ofKAvalues for individual bilayer leaflets. The theory is based on the concept of elasticity and derivesKAfrom real-space analysis of local thickness fluctuations sampled in MD simulations. We explore and validate the model on a large set of single and multicomponent bilayers of different lipid composition and sizes, simulated at different temperatures. The calculated bilayer compressibility moduli agree with values estimated previously from experiments and those obtained from a standard computational method based on a series of constrained tension simulations. We further validate our framework in a comparison with an existing polymer brush model (PBM) and confirm the PBM’s predicted linear relationship with proportionality coefficient of 24 using elastic parameters calculated from the simulation trajectories. The robustness of the results that emerge from the new method allows us to revisit the origins of the bilayer mechanical (compressible) thickness and in particular, its dependence on acyl chain unsaturation and the presence of cholesterol.
Impact of Different Acoustic Components on EEG-based Auditory Attention Decoding in Noisy and Reverberant Conditions
Authors: Aroudi Ali , Mirkovic Bojana , De Vos Maarten , Doclo Simon 
Published: July 2018

AbstractRecently, a least-squares-based method has been proposed to decode auditory attention from single-trial EEG recordings for an acoustic scenario with two competing speakers. This method aims at reconstructing the attended speech envelope from the EEG recordings using a trained spatio-temporal filter. While the performance of this method has been mainly studied for noiseless and anechoic acoustic conditions, it is important to fully understand its performance in realistic noisy and reverberant acoustic conditions. In this paper, we investigate auditory attention decoding (AAD) using EEG recordings for different acoustic conditions (anechoic, reverberant, noisy, and reverberant-noisy). In particular, we investigate the impact of different acoustic conditions for AAD filter training and for decoding. In addition, we investigate the influence on the decoding performance of the different acoustic components (i.e. reverberation, background noise and interfering speaker) in the reference signals used for decoding and the training signals used for computing the filters. First, we found that for all considered acoustic conditions it is possible to decode auditory attention with a decoding performance larger than 90%, even when the acoustic conditions for AAD filter training and for decoding are different. Second, when using reference signals affected by reverberation and/or background noise, a comparable decoding performance as when using clean reference signals can be obtained. In contrast, when using reference signals affected by the interfering speaker, the decoding performance significantly decreases. Third, the experimental results indicate that it is even feasible to use training signals affected by reverberation, background noise and/or the interfering speaker for computing the filters.
Cancer cell exosomes can initiate malignant cell transformation
Authors: Stefanius Karoliina , Servage Kelly A. , de Souza Santos Marcela , Toombs Jason , Gray Hillery Fields , Chimalapati Suneeta , Kim Min S. , Brekken Rolf A. , Orth Kim 
Published: July 2018

AbstractCancer evolves through a multistep process that occurs by the temporal accumulation of genetic mutations mediated by intracellular and extracellular cues. We observe that exosomes isolated from pancreatic cancer cells, but not normal pancreatic cells, can initiate the first step of malignant cell transformation. Injection of exosome-initiated transformed cells into mice results in aggressive tumor growth. Using proteomic profiling and DNA sequencing of exosome-treated and transformed cells, we show that cancer cell exosomes act as a classic initiator by causing random genetic changes in recipient cells. Our studies provide new insight into a function of cancer cell exosomes and how they might specifically contribute to orchestrated local cell transformation.One Sentence SummaryExosomes function as aninitiatorof tumor formation.
Allatostatin C/AstC-R2 is a Novel Pathway to Modulate Circadian Activity Pattern in Drosophila
Authors: Díaz Madelen M. , Schlichting Matthias , Abruzzi Katharine C. , Rosbash Michael 
Published: July 2018

AbstractSix neuropeptides are expressed within the Drosophila brain circadian network. Our previous mRNA profiling suggested that AllatostatinC is a seventh neuropeptide and specifically expressed in dorsal clock neurons (DN1s). Our results here show that AstC is indeed expressed in DN1s, where it oscillates. AstC is also expressed in two less well-characterized circadian neuronal clusters, the DN3s and lateral posterior neurons (LPNs). Behavioral experiments indicate that clock neuron-derived AstC is required to mediate evening locomotor activity under short (winter-like) photoperiods. The AstC-Receptor 2 (AstC-R2) is expressed in LNds, the clock neurons that drive evening locomotor activity, and AstC-R2 is required in these neurons to modulate the same short photoperiod evening phenotype. Ex vivo calcium imaging indicates that AstC directly inhibits a single LNd neuron. The results suggest that a novel AstC/AstC-R2 signaling pathway, from dorsal circadian neurons to an LNd, regulates the behavioral response to changing photoperiod in Drosophila.
The hyperstability and composition ofGiardia’s ventral disc highlights the remarkable versatility of microtubule organelles
Authors: Nosala C. , Hagen K.D. , Chase T.M. , Jones K. , Loudermilk R. , Nguyen K. , Dawson S.C. 
Published: July 2018

AbstractGiardiais a common protistan parasite that causes diarrheal disease worldwide. Motile trophozoites colonize the small intestine, attaching to the villi with the ventral disc, a unique and complex microtubule (MT) organelle. Attachment to the host epithelium allowsGiardiato resist peristalsis during infection of the host gastrointestinal tract. Despite our emerging view of the complexity of ventral disc architecture, we are still in the very preliminary stages of understanding how specific structural elements contribute to disc stability or generate forces for attachment. The ventral disc is a large, dome-shaped, spiral MT array decorated with microribbon-crossbridge protein complexes (MR-CB) that extend upward into the cytoplasm. To find additional disc-associated proteins (DAPs), we used a modified method for disc biochemical fractionation in high salt followed by shotgun proteomic analyses and validation by GFP-tagging. Using this method in conjunction with an ongoing subcellular localization screen, we identified 54 new DAPs. Of the 87 DAPs confirmed to date, 54 localize only to the disc, and the remainder localize to additional structures including the flagella, basal bodies, or median body. Almost one third of the known DAPs lack any homology to proteins in other eukaryotes and another one third simply contain ankyrin repeat domains. Many DAPs localize to specific structural regions of the disc, including the ventral groove region and disc margin. Lastly, we show that spiral singlet MT array comprising the disc is hyperstable and lacks dynamic instability, and we attribute these unique properties to the presence of both novel DAPs as well conserved MAPs and MIPs that are known to stabilize ciliary doublet and triplet MTs.
Distinct profiles of temporal and frontoparietal cortex in representing actions across vision and language
Authors: Wurm Moritz F. , Caramazza Alfonso 
Published: July 2018

AbstractBoth temporal and frontoparietal brain areas are associated with the representation of knowledge about the world, in particular about actions. However, what these brain regions represent and precisely how they differ remains unknown. Here, we reveal fundamentally distinct functional profiles of lateral temporal and frontoparietal cortex: Using fMRI-based MVPA we found that frontoparietal areas encode representations of observed actions and corresponding written sentences in an overlapping way, but these representations did not generalize across stimulus type. By contrast, only left lateral posterior temporal cortex (LPTC) encoded action representations that generalize across observed action scenes and sentences. The representational organization of stimulus-general action information in LPTC could be predicted from models that describe basic agent-patient relations (object- and person-directedness) and the general semantic similarity between actions. The match between action videos and sentences in LPTC and its representational profile indicate that this region encodes general, conceptual aspects of actions whereas frontoparietal representations appear to be tied to specific stimulus types.
Differential expression of PKCα and -β in the zebrafish retina
Authors: Haug Marion F. , Berger Manuela , Gesemann Matthias , Neuhauss Stephan C. F. 
Published: July 2018

AbstractThe retina is a complex neural circuit in which visual information is transmitted and processed from light perceiving photoreceptors to projecting retinal ganglion cells. Much of the computational power of the retina rests on signal integrating interneurons, such as bipolar cells in the outer retina. While mammals possess about 10 different bipolar cell types, zebrafish (Danio rerio) has at least six ON-type, seven OFF-type, and four mixed-input bipolar cells. Commercially available antibodies against bovine and human conventional protein kinase C (PKC) α and -β are frequently used as markers for retinal ON-bipolar cells in different species, despite the fact that it is not known which bipolar cell subtype(s) they actually label.Moreover, the expression pattern of the five prkc genes (coding for PKC proteins) has not been systematically determined. While prkcg is not expressed in retinal tissue, the other four prkc (prkcaa, prkcab, prkcba, prkcbb) transcripts were found in different parts of the inner nuclear layer and some as well in the retinal ganglion cell layer.Immunohistochemical analysis in adult zebrafish retina using PKCα and PKCβ antibodies showed an overlapping immunolabeling of ON-bipolar cells that are most likely of the BON s6L or RRod type and of the BON s6 type. However, comparison of transcript expression with immunolabling, implies that these antibodies are not specific for one single zebrafish conventional PKC, but rather detect a combination of PKC -α and -β variants.