bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of FlowVR: a virtual reality game for improvement of depressive mood
Authors: Bittner Lukas , Mostajeran Fariba , Steinicke Frank , Gallinat Jürgen , Kühn Simone 
Published: October 2018

AbstractObjectiveThis study evaluated the efficacy of FlowVR, a virtual reality (VR) game designed to improve mood and reduce feelings of depression. The aim is to contribute to the question of whether and how VR could be used for depression therapy, as research in this area is quite rare.Method18 healthy participants (9 female; Mage = 25.9) underwent three conditions, playing FlowVR in VR with a head-mounted display, playing FlowVR on a tablet or reading a text on a tablet. For each condition, they were tested on a separate day at the same time of day within a two-week period. Before and after every condition participants completed the Becks Depression Inventory II (BDI-II), the state part of the State-Trait-Anxiety-Depression-Inventory (STADI(S)) and the Positive Affect Negative Affect Schedule-Expanded Form (PANAS-X).ResultsWhile the participants showed only a reduction in acute anxiety in the control and the tablet conditions, they showed improved affectivity in all variables measured in the VR condition. In addition, VR had significantly better results than the control condition in improving positive affectivity, negative affectivity and acute feelings of depression. Using a less conservative statistical approach, these significant differences could also be found between the tablet and the VR condition. There were no significant differences between the tablet and the control condition.ConclusionThe results indicate that due to its immersive nature, VR can be used effectively to improve mood and temporarily reduce feelings of depression. Long-term effects of FlowVR on participants with depression must be investigated in consecutive research.
SpliceVisuL: Visualization of Bidirectional Long Short-term Memory Networks for Splice Junction Prediction
Authors: Dutta Aparajita , Dalmia Aman , Athul R , Singh Kusum Kumari , Anand Ashish 
Published: October 2018

AbstractNeural models have been able to obtain state-of-the-art performances on several genome sequence-based prediction tasks. Such models take only nucleotide sequences as input and learn relevant features on its own. However, extracting the interpretable motifs from the model remains a challenge. This work explores various existing visualization techniques in their ability to infer relevant sequence information learned by a recurrent neural network (RNN) on the task of splice junction identification. The visualization techniques have been modulated to suit the genome sequences as input. The visualizations inspect genomic regions at the level of a single nucleotide as well as a span of consecutive nucleotides. This inspection is performed based on modification of input sequences (perturbation-based) or the embedding space (back-propagation based). We infer features pertaining to both canonical and non-canonical splicing from a single neural model. Results indicate that the visualization techniques produce comparable performance for branchpoint detection. However, in case of canonical donor and acceptor junction motifs, perturbation based visualizations perform better than back-propagation based visualizations and vice-versa for non-canonical motifs.
Pinnularia baeticasp. nov. (Bacillarophyceae): a new diatom species found in an alkaline mountain lagoon in the south of Europe (Granada, Spain)
Authors: Fernádez-Moreno David , Luís Ana T. , Sánchezcastillo Pedro M. 
Published: October 2018

AbstractA new benthic freshwater diatom species belonging to the genusPinnulariawas found in Laguna Seca of Sierra Seca in the north of the province of Granada, Spain.Pinnularia baeticasp.nov. is proposed as a new species based on observations under light (LM) and scanning electron microscopy (SEM) and its special ecology typical of a calcareous lagoon. The most similar taxa toP. baeticaisP. atlasiiand with more differencesP. infirmaand the last two were studied through material obtained in lagoons of northern Morocco. Although there are similarities in the morphological characters of the frustule, it was possible to verify through LM and SEM micrographs, evident differences between P. baetica and the other two taxa; on the one end,P. baeticahas a panduriform shape more pronounced thanP. infirmaand bigger size. On the other hand, the absence of spines inP. baeticaand the more convergent striation at the poles are the main differences with P. atlasi.Phylum Ochrophyta Caval.-Sm. (Cavalier-Smith 1995)Class Bacillariophyceae Haeckel emend. Medlin & Kaczmarska (Medlin & Kaczmarska 2004)SubclassBacillariophycidaeRound (Round et al. 1990)OrderNaviculales(Bessey 1907 sensu emend)Family Pinnulariaceae D.G. Mann, 1990, GenusPinnulariaC.G. Ehrenberg, 1843Pinnularia baeticaFernández Moreno & Sánchez Castillo sp. nov
Bayesian inference of neuronal ensembles
Authors: Diana Giovanni , Sainsbury Thomas T. J. , Meyer Martin P. 
Published: October 2018

AbstractIn many areas of the brain, both spontaneous and stimulus-evoked activity can manifest as synchronous activation of neuronal ensembles. The characterization of ensemble structure and dynamics provides important insights into how brain computations are distributed across neural networks. The proliferation of experimental techniques for recording the activity of neuronal ensembles calls for a comprehensive statistical method to describe, analyze and characterize these high dimensional datasets. Here we introduce a generative model of synchronous activity to describe spontaneously active neural ensembles. Unlike existing methods, our analysis provides a simultaneous estimation of ensemble composition, dynamics and statistical features of these neural populations, including ensemble noise and activity rate. We also introduce ensemble “coherence” as a measure of within-ensemble synchrony. We have used our method to characterize population activity throughout the tectum of larval zebrafish, allowing us to make statistical inference on the spatiotemporal organization of tectal ensembles, their composition and the logic of their interactions. We have also applied our method to functional imaging and neuropixels recordings from the mouse, allowing us to relate the activity of identified ensembles to specific behaviours such as running or changes in pupil diameter.
Altered protein quality control contributes to noise-induced hearing loss
Authors: Jongkamonwiwat Nopporn , Wong Ann C. Y. , Ramirez Miguel A , Pak Kwang , Wang Yi-Zhi , Ryan Allen F. , Savas Jeffrey N. 
Published: October 2018

AbstractExposure to damaging levels of noise is the most common cause of hearing loss and impairs high frequency hearing in more than 15 % of adult Americans. Using mice exposed to increasing levels of noise in combination with quantitative proteomics, we tested how noise insults remodel the cochlear proteome both acutely and after a two-week recovery period. We used ABR & DPOAE recordings to define the intensity of noise exposure necessary to produce temporary or permanent threshold shifts (TTS, PTS) in young adult mice and found noise at 94 and 105 dB SPL levels for 30 minutes elicits TTS and PTS, respectively. We quantified thousands of proteins and found that noise insults cause a rapid increase rather than a decrease in the levels of many proteins involved with protein homeostasis, myelin, cytoskeletal structures, and cell junctions such as the synapse. The vast majority of proteins with increased levels immediately after noise exposure showed normal levels after two weeks of recovery. However, several proteins involved in oxidative stress and neuroprotection had significantly increased levels only after the recovery period suggesting they play in important role in regeneration. Interestingly, a small panel of mitochondrial proteins were significantly altered only in PTS conditions suggesting potential discrete protein mechanisms. Our discovery-based proteomic analysis extends the recent description of noise-induced cochlear synaptopathy and shows that noise insults drive a robust proteostasis response. These data provide a new understanding of noise sensitive proteins and may inform the development of effective preventiative strategies or therapies for NIHL.
PROCYCLIC Trypanosoma brucei CELL CYCLE is IMPAIRED at the G1 STAGE by the PRESENCE of POLY (ADP-RIBOSE) in the NUCLEUS
Authors: Schlesinger Mariana , Vilchez Larrea Salomé C. , Fernández Villamil Silvia H. 
Published: October 2018

AbstractPreviously we demonstrated that an excess of poly (ADP-ribose) in the nucleus makes procyclic parasites more sensitive to hydrogen peroxide. However, the effect of an altered-PAR metabolism under standard conditions has not been addressed yet. Here we have analyzed the behavior of the growth curve of transgenic parasites that present this phenotype and studied cell cycle progression in synchronized cultures by flow cytometry and immunofluorescence. We have demonstrated that an excess of nuclear poly (ADP-ribose) produces a delay in the G1 phase of the cell cycle. Moreover, for the first time we have shown that poly (ADP-ribose) occurs at specific points very close to the mature basal body, suggesting there could be a link between the kinetoplast and poly (ADP-ribose) metabolism.
Robust estimation of sulcal morphology
Authors: Madan Christopher R. 
Published: October 2018

AbstractWhile it is well established that cortical morphology differs in relation to a variety of inter-individual factors, it is often characterized using estimates of volume, thickness, surface area, or gyrification. Here we developed a computational approach for estimating sulcal width and depth that relies on cortical surface reconstructions output by FreeSurfer. While other approaches for estimating sulcal morphology exist, studies often require the use of multiple brain morphology programs that have been shown to differ in their approaches to localize sulcal landmarks, yielding morphological estimates based on inconsistent boundaries. To demonstrate the approach, sulcal morphology was estimated in three large sample of adults across the lifespan, in relation to aging. A fourth sample is additionally used to estimate test-retest reliability of the approach. This toolbox is now made freely available as supplemental to this paper: https://cmadan.github.io/calcSulc/.
Genetic distance and social compatibility in the aggregation behavior of Japanese toad tadpoles
Authors: Hase Kazuko , Abe Masato S. , Shimada Masakazu 
Published: October 2018

AbstractFrom microorganism to vertebrates, living things often exhibit social aggregation. One of anuran larvae, dark-bodied toad tadpoles (genus Bufo) are known to aggregate against predators. When individuals share genes from a common ancestor for whom social aggregation was a functional trait, they are also likely to share common recognition cues regarding association preferences, while greater genetic distances make cohesive aggregation difficult. In this study, we conducted quantitative analyses to examine aggregation behavior among three lineages of toad tadpoles: Bufo japonicus japonicus, B. japonicus formosus, and B. gargarizans miyakonis. To determine whether there is a correlation between cohesiveness and genetic similarity among group members, we conducted an aggregation test using 42 cohorts consisting of combinations drawn from a laboratory-reared set belonging to distinct clutches. As genetic indices, we used mitochondrial DNA (mtDNA) and major histocompatibility complex (MHC) class II alleles. The results clearly indicated that aggregation behavior in toad tadpoles is directly influenced by genetic distances based on mtDNA sequences and not on MHC haplotypes. Cohesiveness among heterogeneous tadpoles is negatively correlated with the geographic dispersal of groups. Our findings suggest that social incompatibility among toad tadpoles reflects phylogenetic relationships.
Integrity and stability of virulence plasmids fromPseudomonas syringaeare modulated by mobile genetic elements and multiple toxin-antitoxin systems
Authors: Bardaji Leire , Añorga Maite , Echeverría Myriam , Ramos Cayo , Murillo Jesús 
Published: October 2018

AbstractBackgroundVirulence plasmids are critically exposed to genetic decay and loss, particularly inPseudomonas syringaestrains because of their high content of mobile genetic elements and their exploitation of environmental niches outside of the plant host. The demonstrated high plasticity and adaptability of P. syringae plasmids, involving the acquisition and loss of large DNA regions, contrasts with their usual high stability and the maintenance of key virulence genes in free living conditions. The identification of plasmid stability determinants and mechanisms will help to understand their evolution and adaptability to agroecosystems as well as to develop more efficient control measures.ResultsWe show that the three virulence plasmids ofP. syringaepv. savastanoi NCPPB 3335 contain diverse functional stability determinants, including three toxin-antitoxin systems (TA) in both pPsv48A and pPsv48C, whereas one of the two replicons of pPsv48C can confer stable inheritance by itself. Loss of pPsv48A increased by two orders of magnitude upon functional inactivation of its TA systems. However, inactivation of the TA systems from pPsv48C did not result in its curing but led to the recovery of diverse deletion derivatives. One type consisted in the deletion of an 8.3 kb fragment, with a frequency of 3.8 ± 0.3 × 10−3, by recombination between two copies of MITEPsy2. Likewise, IS801promoted the occurrence of deletions of variable size by one-ended transposition with a frequency of 5.5 ± 2.1 × 10−4, 80 % of which resulted in the loss of virulence geneidi. These deletion derivatives were stably maintained in the population by replication mediated byrepJ, which is adjacent to IS801. IS801also promoted deletions in plasmid pPsv48A, either by recombination or one-ended transposition. In all cases, functional TA systems contributed significantly to reduce the occurrence of plasmid deletionsin vivo.ConclusionsVirulence plasmids fromP. syringaeharbour a diverse array of stability determinants with a variable contribution to plasmid persistence. Additionally, multiple TA systems favour the long-term survival and integrity of virulence plasmids, as well as the maintenance of pathogenicity genes in free-living conditions. This strategy is likely widespread amongst native plasmids ofP. syringaeand other bacteria.
Unravelling intra- and intersegmental neuronal connectivity between central pattern generating networks in a multi-legged locomotor system
Authors: Daun Silvia , Mantziaris Charalampos , Tóth Tibor I. , Büschges Ansgar , Rosjat Nils 
Published: October 2018

AbstractAnimal walking results from a complex interplay of central pattern generating networks (CPGs), local sensory signals expressing position, velocity and forces generated in the legs, and coordinating signals between neighboring ones. In the stick insect, in particular, intra- and intersegmental coordination is conveyed by these sensory signals. The rhythmic activity of the CPGs, hence of the legs, can be modified by the aforementioned sensory signals. However, the precise nature of the interaction between the CPGs and these sensory signals has remained largely unknown. Experimental methods aiming at finding out details of these interactions, often apply the muscarinic acetylcholine receptor agonist, pilocarpine in order to induce rhythmic activity in the CPGs, hence in the motoneurons of the segmental ganglia. Using this general approach, we removed the influence of sensory signals and investigated the putative connections between CPGs associated with the coxa-trochanter (CTr)-joint in the different segments (legs) in more detail. The experimental data underwent phase-difference analysis and Dynamic Causal Modelling (DCM). These methods can uncover the underlying coupling structure and strength between pairs of segmental ganglia (CPGs). We set up different coupling schemes (models) for DCM and compared them using Bayesian Model Selection (BMS). Models with contralateral connections in each segment and ipsilateral connections on both sides, as well as the coupling from the meta- to the ipsilateral prothoracic ganglion were preferred by BMS to all other types of models tested. Moreover, the intrasegmental coupling strength in the mesothoracic ganglion was the strongest and most stable in all three ganglia.
Testosterone modulates status-specific patterns of cooperation in a social network
Authors: Ryder T. Brandt , Dakin Roslyn , Vernasco Ben J. , Evans Brian S. , Horton Brent M. , Moore Ignacio T. 
Published: October 2018

SummaryStable cooperation requires plasticity whereby individuals are able to express competitive or cooperative behaviors depending on social context. To date, however, the physiological mechanisms that underlie behavioral variation in cooperative systems are poorly understood. We studied hormone-mediated behavior in the wire-tailed manakin (Pipra filicauda), a gregarious songbird whose cooperative partnerships are crucial for fitness. We used automated telemetry to monitor > 36,000 cooperative interactions among male manakins over three field seasons, and we examined how circulating testosterone affects cooperation using > 500 hormone samples. Observational data show that in non-territorial floater males, high testosterone is associated with increased cooperative behaviors and subsequent ascension to territorial status. In territory-holding males, however, both observational and experimental evidence demonstrate that high testosterone antagonizes cooperation. Moreover, circulating testosterone explains significant variation (2-8%) in social behavior within each status class. Collectively, our findings show that the hormonal control of cooperation depends on a male’s social status. We propose that the status-dependent reorganization of hormone-regulatory pathways can facilitate stable cooperative partnerships, and thus provide direct fitness benefits for males.
N-terminal β-strand underpins biochemical specialization of an ATG8 isoform
Authors: Zess Erin K. , Jensen Cassandra , Cruz-Mireles Neftaly , De la Concepcion Juan Carlos , Sklenar Jan , Imre Richard , Roitinger Elisabeth , Hughes Richard , Belhaj Khaoula , Mechtler Karl , Menke Frank L.H. , Bozkurt Tolga , Banfield Mark J. , Kamoun Sophien , Maqbool Abbas , Dagdas Yasin F. 
Published: October 2018

AbstractATG8 is a highly-conserved ubiquitin-like protein that modulates autophagy pathways by binding autophagic membranes and numerous proteins, including cargo receptors and core autophagy components. Throughout plant evolution, ATG8 has expanded from a single protein in algae to multiple isoforms in higher plants. However, the degree to which ATG8 isoforms have functionally specialized to bind distinct proteins remains unclear. Here, we describe a comprehensive protein-protein interaction resource, obtained using in planta immunoprecipitation followed by mass spectrometry, to define the potato ATG8 interactome. We discovered that ATG8 isoforms bind distinct sets of plant proteins with varying degrees of overlap. This prompted us to define the biochemical basis of ATG8 specialization by comparing two potato ATG8 isoforms using both in vivo protein interaction assays and in vitro quantitative binding affinity analyses. These experiments revealed that the N-terminal β-strand—and, in particular, a single amino acid polymorphism—underpins binding specificity to the substrate PexRD54 by shaping the hydrophobic pocket that accommodates this protein’s ATG8 interacting motif. Additional proteomics experiments indicated that the N-terminal β-strand shapes the ATG8 interactor profiles, defining interaction specificity with about 80 plant proteins. Our findings are consistent with the view that ATG8 isoforms comprise a layer of specificity in the regulation of selective autophagy pathways in plants.
The RED scheme: Rate-constant estimation from pre-steady state weighted ensemble simulations
Authors: DeGrave Alex J. , Bogetti Anthony T. , Chong Lillian T. 
Published: October 2018

AbstractWe present the Rate from Event Durations (RED) scheme, a new scheme that more efficiently calculates rate constants using the weighted ensemble path sampling strategy. This scheme enables rate-constant estimation from shorter trajectories by incorporating the probability distribution of event durations, or barrier crossing times, from a simulation. We have applied the RED scheme to weighted ensemble simulations of a variety of rare-event processes that range in complexity: residue-level simulations of protein conformational switching, atomistic simulations of Na+/Cl− association in explicit solvent, and atomistic simulations of protein-protein association in explicit solvent. Rate constants were estimated with up to 50% greater efficiency than the original weighted ensemble scheme. Importantly, our method accounts for systematic error when using data from the entire simulation. The RED scheme is relevant to any simulation strategy that involves unbiased trajectories of similar length to the most probable event duration, including weighted ensemble, milestoning, and standard simulations as well as the construction of Markov state models.
eIF3b and eIF3i relocate together to the ribosomal subunit interface during translation initiation and modulate start codon selection
Authors: Llácer Jose L. , Hussain Tanweer , Dong Jinsheng , Gordiyenko Yuliya , Hinnebusch Alan G. 
Published: October 2018

ABSTRACTDuring eukaryotic translational initiation, the 48S ribosomal pre-initiation complex (PIC) scans the 5’ untranslated region of mRNA until it encounters a start codon. We present a single particle electron cryomicroscopy (cryo-EM) reconstruction of a yeast 48S PIC in an open scanning-competent state in which eIF3b is observed bound on the 40S subunit interface. eIF3b is re-located with eIF3i from their solvent-interface locations observed in other PIC structures; however, eIF3i is not in contact with the 40S. Re-processing of micrographs of our previous 48S PIC in a closed state using currently available tools reveal a similar re-location of eIF3b and eIF3i from the solvent to subunit interface. Genetic analysis indicates that high fidelity initiation in vivo depends strongly on eIF3b interactions at the subunit interface that either promote the closed conformation of the PIC on start codon selection or facilitate subsequent relocation back to the solvent side of the 40S subunit.
Patterned expression of Pannexin 1 channels in the adult cerebellar Purkinje cells
Authors: Ady Visou , Dubayle David , Blanc Pascale Le , Shestopalov Valery , Meunier Claude , Levenes Carole 
Published: October 2018

AbstractPannexin1 (PanX1) are recently discovered proteins that can form large pore channels at the cell surface. They have been implicated in ATP-dependent cell-to-cell communication and in several pathophysiological processes such as inflammation, cell death and epilepsy. Using immunohistochemistry in the adult mouse, we describe the presence of PanX1 in the deep cerebellar nuclei, in large cells of the granular layer, presumably Golgi interneurones, in some Bergmann glia radial processes as well as in the soma and dendrites of Purkinje cells. In the latter, PanX1, like many other proteins, distribute heterogeneously. Only Zebrin II-positive Purkinje cells express PanX1, in accordance with the so-called “zebra-striped” modular architecture of the cerebellum. This distribution in zebra-stripes suggest that PanX1 may contribute to the control of ensemble activity within cerebellar microdomains or to the response of Purkinje cell to excitotoxicity and cell-death messages.