bluuebunny/crossref_metadata_2025_split huggingface dataset:
Different bees, different needs: how nest-site requirements have shaped the decision-making processes in homeless honeybees (Apisspp.)
Authors: Beekman Madeleine , Oldroyd Benjamin P. 
Published: March 2018

During reproductive swarming, a honeybee swarm needs to decide on a new nest site and then move to the chosen site collectively. Most studies of swarming and nest-site selection are based on one species,Apis mellifera. Natural colonies ofA. melliferalive in tree cavities. The quality of the cavity is critical to the survival of a swarm. Other honeybee species nest in the open, and have less strict nest-site requirements, such as the open-nesting dwarf honeybeeApis florea.Apis floreabuilds a nest comprised of a single comb suspended from a twig. For a cavity-nesting species, there is only a limited number of potential nest sites that can be located by a swarm, because suitable sites are scarce. By contrast, for an open-nesting species, there is an abundance of equally suitable twigs. While the decision-making process of cavity-nesting bees is geared towards selecting the best site possible, open-nesting species need to coordinate collective movement towards areas with potential nest sites. Here, we argue that the nest-site selection processes ofA. floreaandA. melliferahave been shaped by each species' specific nest-site requirements. Both species use the same behavioural algorithm, tuned to allow each species to solve their species-specific problem.This article is part of the theme issue ‘Collective movement ecology’.
Fitness trade-offs of group formation and movement by Thomson's gazelles in the Serengeti ecosystem
Authors: Fryxell John M. , Berdahl Andrew M. 
Published: March 2018

Collective behaviours contributing to patterns of group formation and coordinated movement are common across many ecosystems and taxa. Their ubiquity is presumably due to altering interactions between individuals and their predators, resources and physical environment in ways that enhance individual fitness. On the other hand, fitness costs are also often associated with group formation. Modifications to these interactions have the potential to dramatically impact population-level processes, such as trophic interactions or patterns of space use in relation to abiotic environmental variation. In a wide variety of empirical systems and models, collective behaviour has been shown to enhance access to ephemeral patches of resources, reduce the risk of predation and reduce vulnerability to environmental fluctuation. Evolution of collective behaviour should accordingly depend on the advantages of collective behaviour weighed against the costs experienced at the individual level. As an illustrative case study, we consider the potential trade-offs on Malthusian fitness associated with patterns of group formation and movement by migratory Thomson's gazelles in the Serengeti ecosystem.This article is part of the theme issue ‘Collective movement ecology’.
Deep Learning Based BCI Control of a Robotic Service Assistant Using Intelligent Goal Formulation
Authors: Kuhner D. , Fiederer L.D.J. , Aldinger J. , Burget F. , Völker M. , Schirrmeister R.T. , Do C. , Bödecker J. , Nebel B. , Ball T. , Burgard W. 
Published: March 2018

AbstractAs autonomous service robots become more affordable and thus available for the general public, there is a growing need for user-friendly interfaces to control these systems. Control interfaces typically get more complicated with increasing complexity of the robotic tasks and the environment. Traditional control modalities as touch, speech or gesture commands are not necessarily suited for all users. While non-expert users can make the effort to familiarize themselves with a robotic system, paralyzed users may not be capable of controlling such systems even though they need robotic assistance most. In this paper, we present a novel framework, that allows these users to interact with a robotic service assistant in a closed-loop fashion, using only thoughts. The system is composed of several interacting components: non-invasive neuronal signal recording and co-adaptive deep learning which form the brain-computer interface (BCI), high-level task planning based on referring expressions, navigation and manipulation planning as well as environmental perception. We extensively evaluate the BCI in various tasks, determine the performance of the goal formulation user interface and investigate its intuitiveness in a user study. Furthermore, we demonstrate the applicability and robustness of the system in real world scenarios, considering fetch-and-carry tasks and tasks involving human-robot interaction. As our results show, the system is capable of adapting to frequent changes in the environment and reliably accomplishes given tasks within a reasonable amount of time. Combined with high-level planning using referring expressions and autonomous robotic systems, interesting new perspectives open up for non-invasive BCI-based human-robot interactions.
RaftProt V2: understanding membrane microdomain function through lipid raft proteomes
Authors: Mohamed Ahmed , Shah Anup , Chen David , Hill Michelle M. 
Published: March 2018

ABSTRACTCellular membranes feature dynamic submicrometer-scale lateral membrane domainsvariously referred to as lipid rafts, membrane rafts or glycosphingolipid-enriched microdomains (GEM). In order to understand the molecular functions of lipid rafts, numerous studies have utilized various biochemical methods to isolate and examine the protein composition of membrane rafts. However, interpretation of individual raft proteomics studies are confounded by the limitations of isolation methods and the dynamic nature of rafts. Knowledge-based approaches can facilitate biological data interpretation by integrating experimental evidence from existing studies. To this end, we previously developed RaftProt (http://lipid-raft-database.di.uq.edu.au/), a searchable database of mammalian lipid raft-associated proteins. Despite being a valuable and highly used resource, improvements in search capabilities and visualisation were still needed. Here, we present RaftProt V2 (http://raftprot.org), an improved update of RaftProt, enabling interrogation and integration of datasets at the cell/tissue type and UniRef/Gene level. Besides the addition of new datasets and re-mapping of all entries to both UniProt and UniRef IDs, we have annotated the level of experimental evidence for each protein entry. The search engine now allows for multiple protein or experiment searches where correlations, interactions or overlaps can be investigated. The web-interface has been completely re-designed and offers new interactive tools for data and subset selection, correlation analysis and network visualization. Overall, RaftProt aims to advance our understanding of lipid raft function by revealing the proteomes and pathways that are associated with membrane microdomains in diverse tissue and conditions.Database URL: http://raftprot.org
Pseudomonas syringaeevades phagocytosis in animal cells through type III effector-mediated inhibition of the LIM kinase-cofilin system
Authors: Yoon Sung-Jin , Lee Soohyun , Kim Jun-Seob , Lee Sang-Hyun , Choi Song , Min Jeong-Ki , Choi Inpyo , Park Young-Jun , Ryu Choong-Min 
Published: March 2018

ABSTRACTCertain animal and plant pathogenic bacteria have developed virulence factors (including effector proteins) that enable them to overcome host immunity. A plant pathogen,Pseudomonas syringaepv. tomato (Pto), secretes a large repertoire of effectors into plant cells via a type III secretory apparatus, thereby suppressing plant immunity. Here, we show that exposure toPtocaused sepsis in mice. Surprisingly, the effector HopQ1 disrupted phagocytosis by inhibiting actin rearrangement via a direct interaction with the LIM domain of the animal target protein LIM kinase, a key regulator of actin polymerization. The results provide new insights into cross-kingdom pathogenicity of bacteria. The current studies demonstrate that certain plant pathogenic bacteria such asPtocan be fatal in animals due to cross-kingdom host immune suppression.
Estimating the Contribution of Proteasomal Spliced Peptides to the HLA-I Ligandome
Authors: Mylonas Roman , Beer Ilan , Iseli Christian , Chong Chloe , Pak HuiSong , Gfeller David , Coukos George , Xenarios Ioannis , Müller Markus , Bassani-Sternberg Michal 
Published: March 2018

AbstractSpliced peptides are short protein fragments spliced together in the proteasome by peptide bond formation. True estimation of the contribution of proteasome-spliced peptides (PSPs) to the global Human Leukocyte Antigen (HLA) ligandome is critical. A recent study suggested that PSPs contribute up to 30% of the HLA ligandome. We performed a thorough reanalysis of the reported results using multiple computational tools and various validation steps and concluded that only a fraction of the proposed PSPs passes the quality filters. To better estimate the actual number of PSPs, we present an alternative workflow. We performed de-novo sequencing of the HLA-peptide spectra and discarded all de-novo sequences found in the UniProt database. We checked whether the remaining de-novo sequences could match spliced peptides from human proteins. The spliced sequences were appended to the UniProt fasta file, which was searched by two search tools at a FDR of 1%. We find that maximally 2-4% of the HLA ligandome could be explained as spliced protein fragments. The majority of these potential PSPs have good peptide-spectrum match properties and are predicted to bind the respective HLA molecules. However, it remains to be shown how many of these potential PSPs actually originate from proteasomal splicing events.
Large-scale neuroimaging and genetic study reveals genetic architecture of brain white matter microstructure
Authors: Zhao Bingxin , Zhang Jingwen , Ibrahim Joseph G. , Santelli Rebecca C. , Li Yun , Li Tengfei , Shan Yue , Zhu Ziliang , Zhou Fan , Liao Huiling , Nichols Thomas E. , Zhu Hongtu 
Published: March 2018

AbstractMicrostructural changes of white matter (WM) tracts are known to be associated with various neuropsychiatric disorders/diseases. Heritability of structural changes of WM tracts has been examined using diffusion tensor imaging (DTI) in family-based studies for different age groups. The availability of genetic and DTI data from recent large population-based studies offers opportunity to further improve our understanding of genetic contributions. Here, we analyzed the genetic architecture of WM tracts using DTI and single-nucleotide polymorphism (SNP) data of unrelated individuals in the UK Biobank (n ∼ 8000). The DTI parameters were generated using the ENIGMA-DTI pipeline. We found that DTI parameters are substantially heritable on most WM tracts. We observed a highly polygenic or omnigenic architecture of genetic influence across the genome as well as the enrichment of SNPs in active chromatin regions. Our bivariate analyses showed strong genetic correlations for several pairs of WM tracts as well as pairs of DTI parameters. We performed voxel-based analysis to illustrate the pattern of genetic effects on selected parts of the tract-based spatial statistics skeleton. Comparing the estimates from the UK Biobank to those from small population-based studies, we illustrated that sufficiently large sample size is essential for genetic architecture discovery in imaging genetics. We confirmed this finding with a simulation study.
Taxonomy annotation errors in 16S rRNA and fungal ITS sequence databases
Authors: Edgar Robert C. 
Published: March 2018

AbstractSequencing of the 16S ribosomal RNA (rRNA) gene and the fungal Internal Transcribed Spacer (ITS) region is widely used to survey microbial communities. Specialized ribosomal sequence databases have been developed to support this approach including Greengenes, SILVA and RDP. Most taxonomy annotations in these databases are predictions from sequence rather than authoritative assignments based on studies of type strains or isolates. Here, I investigate the error rates of taxonomy annotations in these databases. I found 253,485 sequences with conflicting annotations in SILVA v128 and Greengenes v13.5 at ranks up to phylum (9,644 conflicts), indicating that the annotation error rate in these databases is ~15%. I found that 34% of non-singleton genera have overlapping subtrees in the Greengenes tree from 2001 according to the RDP taxonomy, most of which are probably due to branching order errors in the Greengenes tree, which is therefore an unreliable guide to phylogeny. Using a blinded test, I estimated that the annotation error rate of the RDP database is ~10%.
Estimating the proportion of bystander selection for antibiotic resistance in the US
Authors: Tedijanto Christine , Olesen Scott , Grad Yonatan , Lipsitch Marc 
Published: March 2018

AbstractBystander selection -- the selective pressures exerted by antibiotics on microbial flora that are not the target pathogen of treatment -- is critical to understanding the total impact of broad-spectrum antibiotic use; however, to our knowledge, this effect has never been quantified. Using the 2010-2011 National Ambulatory Medical Care Survey and National Hospital Ambulatory Medical Care Survey (NAMCS/NHAMCS), the Human Microbiome Project, and additional carriage and etiological data from existing literature, we estimate the magnitude of bystander selection for a range of clinically relevant antibiotic-species pairs as the proportion of all exposures of an antibiotic experienced by a species for conditions in which that species was not the causative pathogen (“proportion of bystander exposures”). For outpatient prescribing in the United States, we find that this proportion over all included antibiotics is over 80% for 8 out of 9 organisms of interest. Low proportions of bystander exposure are often associated with infrequent bacterial carriage or a high proportion of antibiotic prescribing focused on conditions caused by the species of interest. Using the proportion of bystander exposures, we roughly estimate that S. aureus and E. coli may benefit from 90.7% and 99.7%, respectively, of the estimated reduction in antibiotic use due to pneumococcal conjugate vaccination, despite not being the pathogen targeted by the vaccine. These results underscore the importance of considering antibiotic exposures to bystanders, in addition to the targeted pathogen, in measuring the impact of antibiotic resistance interventions.Significance StatementThe forces that contribute to changing population prevalence of antibiotic resistance are not well understood. Bystander selection -- the inadvertent pressures imposed by antibiotics on the microbial flora other than the pathogen targeted by treatment -- is hypothesized to be a major factor in the propagation of antibiotic resistance, but its extent has not been characterized. We estimate the proportion of bystander exposures across a range of antibiotics and organisms and describe factors driving variability of these proportions. Impact estimates for antibiotic resistance interventions, including vaccination, are often limited to effects on a target pathogen. However, the reduction of antibiotic treatment for illnesses caused by the target pathogen may have the broader potential to decrease bystander selection pressures for resistance on many other organisms.
Transcriptional deconvolution reveals consistent functional subtypes of pancreatic cancer epithelium and stroma
Authors: He Jing , Maurer H. Carlo , Holmstrom Sam R. , Su Tao , Ahmed Aqeel , Hibshoosh Hanina , Chabot John A. , Oberstein Paul E. , Sepulveda Antonia R. , Genkinger Jeanine M. , Zhang Jiapeng , Iuga Alina C. , Califano Andrea , Bansal Mukesh , Olive Kenneth P. 
Published: March 2018

SummaryBulk tumor tissues comprise intermixed populations of neoplastic cells and multiple lineages of stromal cells. We used laser capture microdissection and RNA sequencing to disentangle the transcriptional programs active in the malignant epithelium and stroma of pancreatic ductal adenocarcinoma (PDA). This led to the development of a new algorithm (ADVOCATE) that accurately predicts the compartment fractions of bulk tumor samples and can computationally purify bulk gene expression data from PDA. We also present novel stromal subtypes, derived from 110 microdissected PDA stroma samples, that were enriched in extracellular matrix– and immune–associated processes. Finally, we applied ADVOCATE to systematically evaluate cross–compartment subtypes spanning four patient cohorts, revealing consistent functional classes and survival associations despite substantial compositional differences.
A mutation-led search for novel functional domains in MeCP2
Authors: Guy Jacky , Alexander-Howden Beatrice , FitzPatrick Laura , DeSousa Dina , Koerner Martha V. , Selfridge Jim , Bird Adrian 
Published: March 2018

AbstractMost missense mutations causing Rett syndrome affect domains of MeCP2 that have been shown to either bind methylated DNA or interact with a transcriptional co-repressor complex. Several mutations, however, including the C-terminal truncations that account for ~10% of cases, fall outside these characterised domains. We studied the molecular consequences of four of these “non-canonical” mutations in cultured neurons and mice to see if they reveal additional essential domains without affecting known properties of MeCP2. The results show that the mutations partially or strongly deplete the protein and also in some cases interfere with co-repressor recruitment. These mutations therefore impact the activity of known functional domains and do not invoke new molecular causes of Rett syndrome. The finding that a stable C-terminal truncation does not compromise MeCP2 function raises the possibility that small molecules which stabilise these mutant proteins may be of therapeutic value.
Cell-lineage specificity of primary cilia during epididymis post-natal development
Authors: Bernet Agathe , Bastien Alexandre , Soulet Denis , Jerczynski Olivia , Roy Christian , Alves Maira Bianchi Rodrigues , Lecours Cynthia , Tremblay Marie-Ève , Bailey Janice , Robert Claude , Belleannée Clémence 
Published: March 2018

AbstractPrimary cilia are sensory organelles that orchestrate major signaling pathways during organ development and homeostasis. By using a double Arl13b/mCherry-Cetn2/GFP transgenic mouse model, we characterized the spatio-temporal localization of primary cilia in the epididymis, from birth to adulthood. We report here a constitutive localisation of primary cilia in peritubular myoid cells and a dynamic profiling in differentiated epithelial cells throughout post-natal development. While primary cilia are present at the apical pole of the undifferentiated epithelial cells from birth to puberty, they are absent from the apical pole of the epithelium in adults, where they appear exclusively associated with cytokeratin 5-positive basal cells. Exogenous labeling of primary cilia marker Arl13b and IFT88 confirmed the cell lineage specific localization of primary cilia in basal cells and myoid cells in human epididymides. From whole epididymis tissues and serum-free cultures of DC2 murine epididymal principal cell lines we determined that primary cilia from the epididymis are associated with the polycystic kidney disease-related proteins polycystin 1 (PC1) and polycystin 2 (PC2), and Gli3 Hedgehog signaling transcription factor. Thus, our findings unveil the existence of primary cilia sensory organelles, which have the potential to mediate mechano/ chemo-signaling events in the epididymis.
Large-Scale Structure and Individual Fingerprints of Locally Coupled Sleep Oscillations
Authors: Cox Roy , Mylonas Dimitris S , Manoach Dara S , Stickgold Robert 
Published: March 2018

AbstractThe temporal coordination of slow oscillations and sleep spindles is believed to underlie processes of sleep-dependent memory consolidation and reorganization. Accumulating evidence of the predominantly local expression of these individual oscillatory rhythms suggests that their interaction may have a similar local component. However, it is unclear whether local coupling holds uniformly across the cortex, and whether and how these dynamics differ between fast and slow spindles, and sleep stages. Moreover, substantial individual variability in the expression of both spindles and slow oscillations raise the possibility that their cross-frequency interactions show similar individual differences. Using two nights of multi-channel electroencephalography recordings from 24 healthy individuals, we characterized the topography of slow oscillation-spindle coupling. We found that locally coupled oscillations occur over widespread cortical areas, but that their dynamics vary with spindle class, sleep stage, and location. Moreover, the phase of the slow oscillation cycle at which spindles were expressed differed markedly across individuals but was stable across nights. However, individual variability of coupling phase was not correlated with overnight memory change. These findings both add an important spatial aspect to our understanding of the temporal coupling of sleep oscillations and demonstrate the heterogeneity of coupling dynamics, which must be taken into account when formulating mechanistic accounts of sleep-related memory processing.
Semiology, clustering, periodicity and natural history of seizures in an experimental visual cortical epilepsy model
Authors: Chang Bao-Luen , Marco Leite , Snowball Albert , Chabrol Elodie , Lieb Andreas , Walker Matthew C. , Kullmann Dimitri M. , Schorge Stephanie , Wykes Robert C. 
Published: March 2018

SummaryObjectiveTo characterize a rat model of focal neocortical epilepsy for use in developing novel therapeutic strategies in a type of epilepsy that represents a significant unmet need.MethodsIntracortical tetanus toxin (TeNT) injection was used to induce epilepsy in rats. Seizures and their behavioural manifestations were evaluated with continuous video-electrocorticography telemetry.ResultsTeNT injection into rat primary visual cortex induced focal neocortical epilepsy without preceding status epilepticus. The latency to first seizure ranged from 3 to 7 days. Seizure duration was bimodal, with both short (approximately 30s) and long-lasting (>100s) seizures occurring in the same animals. Seizures were accompanied by non-motor features such as behavioural arrest, or motor seizures with or without evolution to generalized tonic-clonic seizures. Seizures were commoner during the sleep phase of a light-dark cycle. Seizure occurrence was not random, and tended to cluster with significantly higher probability of recurrence within 24 hours of a previous seizure. Across animals, the number of seizures in the first week could be used to predict the number of seizures in the following 22 days.SignificanceThe TeNT model of visual cortical epilepsy is a robust model of acquired focal neocortical epilepsy, and is well suited for preclinical evaluation of novel anti-epileptic strategies. We provide here a detailed analysis of the epilepsy phenotype, seizure activity, electrographic features, and the semiology. In addition we provide a predictive framework that can be used to reduce variation and consequently animal use in pre-clinical studies of potential treatments.Key PointsTetanus toxin injection into rat visual cortex induces focal cortical epilepsy.Electrographic seizures were associated with non-motor and motor features with or without evolution to generalized tonic-clonic seizures.Seizures could not be provoked by intermittent photic stimulation.Seizures were clustered in time and exhibited a circadian variation in frequency.The number of seizures in first week after seizure onset could be used to predict the total number of seizures in the following 3 weeks.