bluuebunny/crossref_metadata_2025_split huggingface dataset:
Network-enabled efficient image restoration for 3D microscopy of turbid biological specimens
Authors: Xiao Le , Fang Chunyu , Wang Yarong , Yu Tingting , Zhao Yuxuan , Zhu Dan , Fei Peng 
Published: May 2020

AbstractThough three-dimensional (3D) fluorescence microscopy has been an essential tool for modern life science research, the light scattering by biological specimens fundamentally prevents its more widespread applications in live imaging. We hereby report a deep-learning approach, termed ScatNet, that enables reversion of 3D fluorescence microscopy from high-resolution targets to low-quality, light-scattered measurements, thereby allowing restoration for a single blurred and light-scattered 3D image of deep tissue, with achieving improved resolution and signal-to-noise ratio. Our approach can computationally extend the imaging depth for current 3D fluorescence microscopes, without the addition of complicated optics. Combining ScatNet approach with cutting-edge light-sheet fluorescence microscopy, we demonstrate that the image restoration of cell nuclei in the deep layer of live Drosophila melanogaster embryos at single-cell resolution. Applying our approach to two-photon excitation microscopy, we could improve the signal and resolution of neurons in mouse brain beyond the photon ballistic region.
Genetic architecture and lifetime dynamics of inbreeding depression in a wild mammal
Authors: Stoffel M.A. , Johnston S.E. , Pilkington J.G. , Pemberton J.M 
Published: May 2020

AbstractInbreeding depression is ubiquitous, but we still know little about its genetic architecture and precise effects in wild populations. Here, we combine long-term life-history data with 417K imputed SNP genotypes for 5,952 wild Soay sheep to explore inbreeding depression on a key fitness component, annual survival. Inbreeding manifests in long runs of homozygosity (ROH), which make up nearly half of the genome in the most inbred individuals. The ROH landscape varies widely across the genome, with islands where up to 87% and deserts where only 4% of individuals have ROH. The fitness consequences of inbreeding are severe; a 10% increase in individual inbreeding FROHis associated with a 60% reduction in the odds of survival in lambs, though inbreeding depression decreases with age. Finally, a genome-wide association scan on ROH shows that many loci with small effects and five loci with larger effects contribute to inbreeding depression in survival.
bbsBayes: An R Package for Hierarchical Bayesian Analysis of North American Breeding Bird Survey Data
Authors: Edwards Brandon P.M. , Smith Adam C. 
Published: May 2020

AbstractThe North American Breeding Bird Survey (BBS) is the primary ecological monitoring program used to assess the population, status, and trend of North American birds. As such, accessible analysis of BBS data is crucial to wildlife conservation/management and ecological science in North America. The R packagebbsBayeswas developed as a wrapper for the analysis of BBS data using hierarchical Bayesian models, including the models currently used by the Canadian Wildlife Service and the United States Geological Survey. The goal ofbbsBayesis to provide an accessible package for anyone in the conservation community to estimate population trajectories (time-series) and trends (rates of change) for any of the 400+ bird species monitored by the BBS, and to allow more advance users to easily access the data and model-templates necessary to customize an analysis for their research.
De novo transcriptome assembly, functional annotation and characterization of the Atlantic bluefin tuna (Thunnus thynnus) larval stage
Authors: Luca Marisaldi , Danilo Basili , Giorgia Gioacchini , Oliana Carnevali 
Published: May 2020

AbstractOver the last two decades, many efforts have been invested in attempting to close the life cycle of the iconic Atlantic bluefin tuna (Thunnus thynnus) and develop a true aquaculture-based market. However, the limited molecular resources nowadays available represent a clear limitation towards the domestication of this species. To fill such a gap of knowledge, we assembled and characterized a de novo larval transcriptome by taking advantage of publicly available databases with the final goal of better understanding the larval development. The assembled transcriptome comprised 37,117 protein-coding transcripts, of which 13,633 full-length (>80% coverage), with an Ex90N50 of 3,061 bp and 76% of complete and single-copy core vertebrate genes orthologues. Of these transcripts, 34,980 had a hit against the EggNOG database and 14,983 with the KAAS annotation server. By comparing our data with a set of representative fish species proteomes, it was found that 78.4% of the tuna transcripts were successfully included in orthologous groups. Codon usage bias was identified for processes such as translation, peptide biosynthesis, muscle development and ion transport, supporting the idea of mechanisms at play in regulating stability and translation efficiency of transcripts belonging to key biological processes during the larval growth. The information generated by this study on the Atlantic bluefin tuna represent a relevant improvement of the transcriptomic resources available to the scientific community and lays the foundation for future works aimed at exploring in greater detail physiological responses at molecular level in different larval stages.
A Specific Neuroligin3-αNeurexin1 Code Regulates GABAergic Synaptic Function in Mouse Hippocampus
Authors: Uchigashima Motokazu , Konno Kohtarou , Demchak Emily , Cheung Amy , Watanabe Takuya , Keener David , Abe Manabu , Le Timmy , Sakimura Kenji , Sasaoka Toshikuni , Uemura Takeshi , Kawasawa Yuka Imamura , Watanabe Masahiko , Futai Kensuke 
Published: May 2020

AbstractSynapse formation and regulation require interactions between pre- and postsynaptic proteins, notably cell adhesion molecules (CAMs). It has been proposed that the functions of neuroligins (Nlgns), postsynaptic CAMs, rely on the formation of trans-synaptic complexes with neurexins (Nrxns), presynaptic CAMs. Nlgn3 is a unique Nlgn isoform that localizes at both excitatory and inhibitory synapses. However, Nlgn3 function mediated via Nrxn interactions is unknown. Here, we demonstrate that Nlgn3 localizes at postsynaptic sites apposing vesicular glutamate transporter 3-expressing (VGT3+) inhibitory terminals and regulates VGT3+ inhibitory interneuron-mediated synaptic transmission in mouse organotypic slice cultures. Gene expression analysis of interneurons revealed that the αNrxn1+AS4 splice isoform is highly expressed in VGT3+ interneurons as compared with other interneurons. Most importantly, postsynaptic Nlgn3 requires presynaptic αNrxn1+AS4 expressed in VGT3+ interneurons to regulate inhibitory synaptic transmission. Our results indicate that specific Nlgn-Nrxn interactions generate distinct functional properties at synapses.
ColTapp, an automated image analysis application for efficient microbial colony growth dynamics quantification
Authors: Bär Julian , Boumasmoud Mathilde , Kouyos Roger , Zinkernagel Annelies S. , Vulin Clément 
Published: May 2020

AbstractPhenotypic heterogeneity occurs in a population of genetically identical bacteria due to stochastic molecular fluctuations and environmental variations. In extreme cases of phenotypic heterogeneity, a fraction of the bacterial population enters dormancy, and these metabolically inactive or non-dividing bacteria persist through most antibiotic challenges. These subpopulations of persister cells are difficult to study in patient samples. However, the proportion of persisters in a sample can be accessed by physically separating bacteria on a plate measuring the time until colonies become visible as dormant bacteria resume growth later than their active counterparts and form smaller colonies.Here, we present ColTapp (Colony Time-lapse app), an application dedicated to bacterial colony growth quantification, freely available for download together with its MATLAB source code or as a MacOS/Windows executable. ColTapp’s intuitive graphical user interface allows users without prior coding knowledge to analyze endpoint or time-lapse images of colonies on agar plates. Colonies are detected automatically, and their radius can be tracked over time. Downstream analyses to derive colony lag time and growth rate are implemented.We demonstrate here the applicability of ColTapp on a dataset ofStaphyloccocus aureuscolony time-lapse images. Colonies on dense plates reached saturation early, biasing lag time estimation from endpoint images. This bias can be reduced by considering the area available to each colony on a plate.By facilitating the analysis of colony growth dynamics in clinical settings, this application will enable a new type of diagnostics, oriented towards personalized antibiotic therapies.
Seasonal variation in sexual readiness in a facultatively sexual freshwater cnidarian with diapausing eggs
Authors: Tökölyi Jácint , Gergely Réka , Miklós Máté 
Published: May 2020

AbstractFacultative sexuality combines clonal propagation with sexual reproduction within a single life cycle. Clonal propagation enables quick population growth and the occupancy of favorable habitats. Sex, on the other hand, results in the production of offspring that are more likely to survive adverse conditions (such as the resting eggs of many freshwater invertebrates). In seasonal environments, the timing of sex is often triggered by environmental cues signaling the onset of winter (e.g. temperature drop or changes in photoperiod). Organisms switching to sex to produce resting eggs under these conditions face a trade-off: responding too early to an environmental cue increases the chances of missing out in clonal propagation, while having a delayed response to deteriorating conditions entails the risk of parental mortality before sexual reproduction could be completed. To mitigate these risks, increased sensitivity towards environmental cues with the onset of the winter might be an adaptive strategy. To test this hypothesis, we investigated sexual propensity and time to gonadogenesis in clonal strains derived from spring- and autumn-collected polyps ofHydra oligactis, a facultatively sexual freshwater cnidarian where sex only occurs prior to the onset of winter. We show that autumn-collected individuals and their asexual offspring have a higher propensity for sex and require less time for gonad development compared to strains established from spring-collected individuals that were kept under similar conditions in the laboratory. To see if the above results can be explained by phenotypic plasticity in sexual readiness, we exposed cold-adapted lab strains to different lengths of warm periods. We found that sexual propensity increases with warm exposure. Our results suggest that reciprocal cold and warm periods are required for sex induction inH. oligactis, which would ensure proper timing of sex in this species. Increased sensitivity to environmental deterioration might help maximize fitness in environments that have both a predictable (seasonal) and an unpredictable component.
A Personalized Switched Systems Approach for the Optimal Control of Ventricular Assist Devices based on Atrioventricular Plane Displacement
Authors: Zeile Clemens , Rauwolf Thomas , Schmeisser Alexander , Mizerski Jeremi Kaj , Braun-Dullaeus Rüdiger C. , Sager Sebastian 
Published: May 2020

AbstractObjectiveA promising treatment for congestive heart failure is the implementation of a left ventricular assist device (LVAD) that works as a mechanical pump. Modern LVADs work with adjustable constant rotor speed and provide therefore continuous blood flow; however, recently undertaken efforts try to mimic pulsatile blood flow by oscillating the pump speed. This work proposes an algorithmic framework to construct and evaluate optimal pump speed policies.MethodsWe use a model that captures the atrioventricular plane displacement, which is a physiological indicator for heart failure. We employ mathematical optimization to adapt this model to patient specific data and to find optimal pump speed policies with respect to ventricular unloading and aortic valve opening. To this end, we reformulate the cardiovascular dynamics into a switched system and thereby reduce nonlinearities. We consider system switches that stem from varying the constant pump speed and that are state dependent such as valve opening or closing.ResultsAs a proof of concept study, we personalize the model to a selected patient with respect to ventricular pressure. The model fitting results in a root-mean-square deviation of about 6 mmHg. Optimized constant and piecewise constant rotor speed profiles improve the default initialized solution by 31% and 68% respectively.ConclusionThese in silico findings demon-strate the potential of personalized hemodynamical optimization for the LVAD therapy.SignificanceLVADs and their optimal configuration are active research fields. Mathematical optimization enhances our understanding of how LVADs should provide pulsatility.
Phenotype-dependent habitat choice is too weak to cause assortative mating between Drosophila melanogaster strains differing in light sensitivity
Authors: Peralta-Rincón Juan Ramón , Aoulad Fatima Zohra , Prado Antonio , Edelaar Pim 
Published: May 2020

AbstractOver the last few years, matching habitat choice has gained attention as a mechanism for maintaining biodiversity and driving speciation. It revolves around the idea that individuals select the habitat in which they perceive to obtain greater fitness after a prior evaluation of their local performance across heterogeneous environments. This results in individuals with similar ecological traits converging to the same patches, and hence could indirectly cause assortative mating when mating occurs in those patches.White-eyed mutants ofDrosophilafruit flies have a series of disadvantages compared to wild type flies, including a poorer performance under bright light. It has been previously reported that, when given a choice, wild typeDrosophila simulanspreferred a brightly lit habitat while white-eyed mutants occupied a dimly lit one. This spatial segregation allowed the eye color polymorphism to be maintained for several generations, whereas normally it is quickly replaced by the wild type.Here we compare the habitat choice decisions of white-eyed and wild type flies in another species,D. melanogaster. We released groups of flies in a light gradient and recorded their departure and settlement behavior. Departure depended on sex and phenotype, but not on the light conditions of the release point. Settlement depended on sex, and on the interaction between phenotype and light conditions of the point of settlement. Nonetheless, simulations showed that this differential habitat use by the phenotypes would only cause a minimal degree of assortative mating in this species.
Gap junction mediated feed-forward inhibition ensures ultra precise temporal patterning in vocal behavior
Authors: Chagnaud Boris P. , Perelmuter Jonathan , Forlano Paul , Bass Andrew H. 
Published: May 2020

AbstractPrecise neuronal firing is especially important for behaviors highly dependent on the correct sequencing and timing of muscle activity patterns, such as acoustic signalling. We show that extreme temporal precision in motoneuronal firing within a hindbrain network that directly determines call duration, pulse repetition rate and fundamental frequency in a teleost fish, the Gulf toadfish, depends on gap junction-mediated, feed-forward glycinergic inhibition that generates a period of reduced probability of motoneuron activation. Super-resolution microscopy confirms glycinergic release sites contacting motoneuron somata and dendrites. Synchronous motoneuron activity can also induce action potential firing in pre-motoneurons, a feature that could figure prominently into motor timing. Gap junction-mediated, feed-forward glycinergic inhibition provides a novel means for achieving temporal precision in the millisecond range for rapid modulation of an acoustic signal and perhaps other motor behaviors.
Rationalizing PROTAC-mediated ternary complex formation using Rosetta
Authors: Bai Nan , Kirubakaran Palani , Karanicolas John 
Published: May 2020

AbstractPROTACs are molecules that combine a target-binding warhead with an E3 ligase-recruiting moiety; by drawing the target protein into a ternary complex with the E3 ligase, PROTACs induce target protein degradation. While PROTACs hold exciting potential as chemical probes and as therapeutic agents, development of a PROTAC typically requires synthesis of numerous analogs to thoroughly explore variations on the chemical linker; without extensive trial and error, it is unclear how to link the two protein-recruiting moieties to promote formation of a productive ternary complex. Here, we describe a structure-based computational method for evaluating suitability of a given linker for ternary complex formation. Our method uses Rosetta to dock the protein components, then builds the PROTAC from its component fragments into each binding mode; complete models of the ternary complex are then refined. We apply this approach to retrospectively evaluate multiple PROTACs from the literature, spanning diverse target proteins. We find that modeling ternary complex formation is sufficient to explain both activity and selectivity reported for these PROTACs, implying that other cellular factors are not key determinants of activity in these cases. We further find that interpreting PROTAC activity is best approached using an ensemble of structures of the ternary complex rather than a single static conformation, and that members of a structurally-conserved protein family can be recruited by the same PROTAC through vastly different binding modes. To encourage adoption of these methods and promote further analyses, we disseminate both the computational methods and the models of ternary complexes.Significance StatementRecent years have brought a flood of interest in developing compounds that selectively degrade protein targets in cells, as exemplified by PROTACs. Fully realizing the promise of PROTACs to transform chemical biology by delivering degraders of diverse and undruggable protein targets has been impeded, however, by the fact that designing a suitable chemical linker between the functional moieties requires extensive trial and error. Here, we describe a structure-based computational method to predict PROTAC activity. We envision that this approach will allow design and optimization of PROTACs for efficient target degradation, selection of E3 ligases best suited for pairing with a given target protein, and understanding the basis by which PROTACs can exhibit different target selectivity than their component warheads.
Welcome to the jungle: Algal turf negatively affects recruitment of a Caribbean octocoral
Authors: Wells Christopher D. , Martínez-Quintana Ángela , Tonra Kaitlyn J. , Lasker Howard R. 
Published: May 2020

ABSTRACTAlgal cover has increased and scleractinian coral cover has steadily declined over the past 40 years on Caribbean coral reefs. In contrast, octocoral abundance has increased at those sites where octocoral abundances have been monitored. The effects of algal cover on recruitment may be a key component in these patterns, as upright octocoral recruits have the potential to escape competition with algae by growing above the ubiquitous algal turfs. However, the impacts of algal turf on octocorals have not been tested.We used laboratory and field recruitment experiments to examine impacts of algal turf on settlement and then survival of newly-settled octocorals. Tiles were preconditioned on a Caribbean reef, allowing algae to settle and grow. Tiles were then partitioned into three treatments: lightly scrubbed (0% turf cover), left alone (19% turf cover), or kept for 15 days in a sea table without fish or large invertebrate herbivores (50% turf cover). Planulae of the common Caribbean octocoralPlexaura homomallawere allowed to settle and metamorphose on the tiles for six days. Tiles were then deployed onto a reef and survival of those recruits was monitored for seven weeks. Settlers that recruited to the tiles after deployment to the reef were also monitored.Laboratory recruitment rate was significantly higher in lower turf cover treatments. Field survival was significantly reduced by increased turf cover; for every 1% increase in turf cover, polyps died 1.3% faster. In a model parameterized by the observed field survival, polyps exposed to 100% turf cover had a 2% survival rate over 51 days, while polyps exposed to no turf cover had a 32% survival rate over the same time.Synthesis. We found that high densities of turf algae can significantly inhibit recruitment of octocorals. Octocoral survival rates were similar to those published for scleractinians, but field settlement rates were much higher, which likely contributes to the higher resilience of octocorals to disturbances. The factors that influence recruitment are critical in understanding the dynamics of octocorals on Caribbean reefs as continuing declines in scleractinian cover may lead to more octocoral-dominated communities in the Caribbean.
Neuronal activity remodels the F-actin based submembrane lattice in dendrites but not axons of hippocampal neurons
Authors: Lavoie-Cardinal Flavie , Bilodeau Anthony , Lemieux Mado , Gardner Marc-André , Wiesner Theresa , Laramée Gabrielle , Gagné Christian , De Koninck Paul 
Published: May 2020

AbstractThe nanoscale organization of the F-actin cytoskeleton in neurons comprises membrane-associated periodical rings, bundles, and longitudinal fibers. The F-actin rings have been observed predominantly in axons but only sporadically in dendrites, where fluorescence nanoscopy reveals various patterns of F-actin arranged in mixed patches. These complex dendritic F-actin patterns pose a challenge for investigating quantitatively their regulatory mechanisms. We developed here a weakly supervised deep learning segmentation approach of fluorescence nanoscopy images of F-actin in cultured hippocampal neurons. This approach enabled the quantitative assessment of F-actin remodeling, revealing the disappearance of the rings during neuronal activity in dendrites, but not in axons. The dendritic F-actin cytoskeleton of activated neurons remodeled into longitudinal fibers. We show that this activity-dependent remodeling involves Ca2+and NMDA-dependent mechanisms. This highly dynamic restructuring of dendritic F-actin based submembrane lattice into longitudinal fibers may serve to support activity-dependent membrane remodeling, protein trafficking and neuronal plasticity.
Remnants of the Balbiani body are required for formation of RNA transport granules inXenopusoocytes
Authors: Yang Chao , Wilson Gena M. , Champion Matthew M. , Huber Paul W. 
Published: May 2020

AbstractFragmentation of the Balbiani body inXenopusoocytes engenders a region extending from the germinal vesicle (GV) towards the vegetal pole that is enriched in mitochondria. This area is later transversed by RNA that is being localized to the vegetal cortex. Inhibition of mitochondrial ATP synthesis prevents the perinuclear formation of these RNA transport granules that can be reversed by the nonhydrolyzable ATP analog, adenosine 5’-(βγ-imido) triphosphate. The protein composition and sensitivity of the transport granules to hexanediol indicate that they are liquid phase condensates. Mitochondria in the remnants of the Balbiani body produce a region of elevated ATP that appears to act as a hydrotrope to support the perinuclear phase transition leading to granule formation.SummaryMitochondria in the remnants of the Balbiani body produce elevated levels of ATP required for the formation of liquid phase condensates containing RNA transport granules.