bluuebunny/crossref_metadata_2025_split huggingface dataset:
Disruptions in White Matter Maturation and Mediation of Cognitive Development in Youth on the Psychosis Spectrum
Authors: Hegarty Catherine E. , Jolles Dietsje D. , Mennigen Eva , Jalbrzikowski Maria , Bearden Carrie E. , Karlsgodt Katherine H. 
Published: September 2018

AbstractBackground:Psychosis onset typically occurs in adolescence, and subclinical psychotic experiences peak in adolescence as well. Adolescence is also a time of critical neural and cognitive maturation. Using cross-sectional data from the Philadelphia Neurodevelopmental Cohort, we examine whether regional white matter (WM) development is disrupted in psychosis spectrum (PS) youth whether WM maturation mediates the relationship between age and cognition in typically developing (TD) and PS youth. A third group with intermediate symptom severity (limited PS [LPS]) was included in follow-up analyses to determine whether age-related disruptions in WM scaled with symptom severity.Methods:We examined WM microstructure, as assessed via diffusion tensor imaging, in 707 individuals (aged 10–22 years; 499 TD, 171 PS, 37 LPS) by using Tract-Based Spatial Statistics. Multiple regressions were used to evaluate age x group interactions on regional WM indices. Mediation analyses were conducted using a bootstrapping approach.Results:There were age x group interactions on fractional anisotropy (FA) in the superior longitudinal fasciculus (SLF) and retrolenticular internal capsule (RLIC). SLF FA mediated the relationship between age and Complex Cognition in TD, but not PS. Further, inclusion of LPS youth showed that the relationship between age and SLF FA decreased with increasing symptom severityConclusions:Our results show aberrant age-related changes in SLF and RLIC FA in PS youth. SLF development supports emergence of specific higher-order cognitive functions in TD youth, but not in PS. Future mechanistic explanations for these relationships could facilitate development of earlier and refined targets for therapeutic interventions.
Calculating the Mutual Information Between Two Spike Trains
Authors: Houghton Conor 
Published: September 2018

AbstractIt is difficulty to estimate the mutual information between spike trains because established methods require more data than is usually available. Kozachenko-Leonenko estimators promise to solve this problem, but include a smoothing parameter which must be set. It is proposed here that the smoothing parameter can be selected by maximizing the estimated unbiased mutual information. This is tested on fictive data and shown to work very well.
Cell and tissue type independent age-associated DNA methylation changes are not rare but common
Authors: Zhu Tianyu , Zheng Shijie C , Paul Dirk S. , Horvath S. , Teschendorff Andrew E. 
Published: September 2018

AbstractAge-associated DNA methylation changes have been widely reported across many different tissue and cell types. Epigenetic ‘clocks’ that can predict chronological age with a surprisingly high degree of accuracy appear to do so independently of tissue and cell-type, suggesting that a component of epigenetic drift is cell-type independent. However, the relative amount of age-associated DNAm changes that are specific to a cell or tissue type versus the amount that occurs independently of cell or tissue type is unclear and a matter of debate, with a recent study concluding that most epigenetic drift is tissue-specific. Here, we perform a novel comprehensive statistical analysis, including matched multi cell-type and multi-tissue DNA methylation profiles from the same individuals and adjusting for cell-type heterogeneity, demonstrating that a substantial amount of epigenetic drift, possibly over 70%, is shared between significant numbers of different tissue/cell types. We further show that ELOVL2 is not unique and that many other CpG sites, some mapping to genes in the Wnt and glutamate receptor signaling pathways, are altered with age across at least 10 different cell/tissue types. We propose that while most age-associated DNAm changes are shared between cell-types that the putative functional effect is likely to be tissue-specific.
Complex interactions between local adaptation, plasticity, and sex affect vulnerability to warming in a widespread marine copepod
Authors: Sasaki Matthew , Hedberg Sydney , Richardson Kailin , Dam Hans G. 
Published: September 2018

AbstractPredicting the response of populations to climate change requires knowledge of thermal performance. Genetic differentiation and phenotypic plasticity affect thermal performance, but the effects of sex and developmental temperatures often go uncharacterized. We used common garden experiments to test for effects of local adaptation, developmental phenotypic plasticity, and individual sex on thermal performance of the ubiquitous copepod,Acartia tonsa. Females had higher thermal tolerance than males in both populations, while the Florida population had higher thermal tolerance compared to the Connecticut population. An effect of developmental phenotypic plasticity on thermal tolerance was observed only in the Connecticut population. Ignoring sex-specific differences may result in a severe underestimation of population-level impacts of warming (i.e. - population decline due to sperm limitation). Further, despite having a higher thermal tolerance, southern populations may be more vulnerable to warming as they lack the ability to respond to increases in temperature through phenotypic plasticity.
Revealing multi-scale population structure in large cohorts
Authors: Diaz-Papkovich Alex , Anderson-Trocmé Luke , Gravel Simon 
Published: September 2018

AbstractGenetic structure in large cohorts results from technical, sampling and demographic variation. Visualisation is therefore a first step in most genomic analyses. However, existing data exploration methods struggle with unbalanced sampling and the many scales of population structure. We investigate an approach to dimension reduction of genomic data that combines principal components analysis (PCA) with uniform manifold approximation and projection (UMAP) to succinctly illustrate population structure in large cohorts and capture their relationships on local and global scales. Using data from large-scale genomic datasets, we demonstrate that PCA-UMAP effectively clusters closely related individuals while placing them in a global continuum of genetic variation. This approach reveals previously overlooked subpopulations within the American Hispanic population and fine-scale relationships between geography, genotypes, and phenotypes in the UK population. This opens new lines of investigation for demographic research and statistical genetics. Given its small computational cost, PCA-UMAP also provides a general-purpose approach to exploratory analysis in population-scale datasets.Author summaryBecause of geographic isolation, individuals tend to be more genetically related to people living nearby than to people living far. This is an example of population structure, a situation where a large population contains subgroups that share more than the average amount of DNA. This structure can tell us about human history, and it can also have a large effect on medical studies. We use a newly developed method (UMAP) to visualize population structure from three genomic datasets. Using genotype data alone, we reveal numerous subgroups related to ancestry and correlated with traits such as white blood cell count, height, and FEV1, a measure used to detect airway obstruction. We demonstrate that UMAP reveals previously unobserved patterns and fine-scale structure. We show that visualizations work especially well in large datasets containing populations with diverse backgrounds, which are rapidly becoming more common, and that unlike other visualization methods, we can preserve intuitive connections between populations that reflect their shared ancestries. The combination of these results and the effectiveness of the strategy on large and diverse datasets make this an important approach for exploratory analysis for geneticists studying ancestral events and phenotype distributions.
A comprehensive reference transcriptome resource for the Iberian ribbed newtPleurodeles waltl, an emerging model for developmental and regeneration biology
Authors: Matsunami Masatoshi , Suzuki Miyuki , Haramoto Yoshikazu , Fukui Akimasa , Inoue Takeshi , Yamaguchi Katsushi , Uchiyama Ikuo , Mori Kazuki , Tashiro Kosuke , Ito Yuzuru , Takeuchi Takashi , Suzuki Ken-ichi T , Agata Kiyokazu , Shigenobu Shuji , Hayashi Toshinori 
Published: September 2018

AbstractUrodele amphibian newts have unique biological properties, notably including prominent regeneration ability. Iberian ribbed newt,Pleurodeles waltl, is a promising model newt along with the successful development of the easy breeding system and efficient transgenic and genome editing methods. However, genetic information ofP. waltlwas limited. In the present study, we conducted an intensive transcriptome analysis ofP. waltlusing RNA-sequencing to build gene models and annotate them. We generated 1.2 billion Illumina reads from a wide variety of samples across 11 different tissues and 9 time points during embryogenesis. They were assembled into 202,788 non-redundant contigs that appear to cover nearly complete (~98%)P. waltlprotein-coding genes. Using the gene set as a reference, our gene network analysis identified regeneration-, developmental-stage-, and tissue-specific co-expressed gene modules. Ortholog analyses with other vertebrates revealed the gene repertoire evolution of amphibians which includes urodele-specific loss ofbmp4and duplications ofwnt11b. Our transcriptome resource will enhance future research employing this emerging model animal for regeneration research as well as other areas such as developmental biology, stem cell biology, cancer research, ethology and toxico-genomics. These data are available via our portal website, iNewt (http://www.nibb.ac.jp/imori/main/).
A divergent hepatitis D-like agent in birds
Authors: Wille Michelle , Netter Hans J. , Littlejohn Margaret , Yuen Lilly , Shi Mang , Eden John-Sebastian , Klaassen Marcel , Holmes Edward C. , Hurt Aeron C. 
Published: September 2018

AbstractHepatitis delta virus (HDV) is currently only found in humans, and is a satellite virus that depends on hepatitis B virus (HBV) envelope proteins for assembly, release and entry. Using meta-transcriptomics, we identified the genome of a novel HDV-like agent in ducks. Sequence analysis revealed secondary structures that were shared with HDV, including self-complementarity and ribozyme features. The predicted viral protein shares 32% amino acid similarity to the small delta antigen of HDV and comprises a divergent phylogenetic lineage. The discovery of an avian HDV-like agent has important implications for the understanding of the origins of HDV and subviral agents.ImportanceHepatitis delta virus (HDV) is currently only found in humans, and coinfections of HDV and Hepatitis B virus (HBV) in humans result in severe liver disease. There are a number of hypotheses for the origin of HDV, although a key component of all is that HDV only exists in humans. Here, we describe a novel deltavirus-like agent identified in wild birds. Although this agent is genetically divergent, it exhibits important similarities to HDV, such as the presence of ribosymes and self-complementarity. The discovery of an avian HDV-like agent challenges our understanding of both the origin and the co-evolutionary relationships of subviral agents with helper viruses.
Coculturing bacteria leads to reduced phenotypic heterogeneities
Authors: Heyse Jasmine , Buysschaert Benjamin , Props Ruben , Rubbens Peter , Skirtach Andre G. , Waegeman Willem , Boon Nico 
Published: September 2018

AbstractIsogenic bacterial populations are known to exhibit phenotypic heterogeneity at the single cell level. Because of difficulties in assessing the phenotypic heterogeneity of a single taxon in a mixed community, the importance of this deeper level of organisation remains relatively unknown for natural communities. In this study, we have used membrane-based microcosms that allow the probing of the phenotypic heterogeneity of a single taxon while interacting with a synthetic or natural community. Individual taxa were studied under axenic conditions, as members of a coculture with physical separation, and as a mixed culture. Phenotypic heterogeneity was assessed through both flow cytometry and Raman spectroscopy. Using this setup, we investigated the effect of microbial interactions on the individual phenotypic heterogeneities of two interacting drinking water isolates. We have demonstrated that interactions between these bacteria lead to an adjustment of their individual phenotypic diversities, and that this adjustment is conditional on the bacterial taxon.ImportanceLaboratory studies have shown the impact of phenotypic heterogeneity on the survival and functionality of isogenic populations. As phenotypic heterogeneity is known to play an important role in pathogenicity and virulence, antibiotics resistance, biotechnological applications and ecosystem properties, it is crucial to understand its influencing factors. An unanswered question is whether bacteria in mixed communities influence the phenotypic heterogeneity of their community partners. We found that coculturing bacteria leads to a reduction in their individual phenotypic heterogeneities, which led us to the hypothesis that the individual phenotypic diversity of a taxon is dependent on the community composition.
Synergistic antifungal effect of amphotericin B-loaded PLGA nanoparticles based ultrasound against C. albicans biofilms
Authors: Yang Min , Du Kaiyue , Hou Yuru , Xie Shuang , Dong Yu , Li Dairong , Du Yonghong 
Published: September 2018

AbstractC. albicans is human opportunistic pathogens that cause superficial and life-threatening infections. An important reason for the failure of current antifungal drugs is related to biofilm formation mostly associated with implanted medical device. The present study aims to investigate the synergistic antifungal efficacy of low-frequency and low-intensity ultrasound combined with amphotericin B-loaded PLGA nanoparticles (AmB-NPs) on C.albicans biofilms. AmB-NPs were prepared by a double emulsion method and demonstrated the lower toxicity than free AmB, after which biofilms were established and treated with ultrasound and AmB-NPs separately or jointly in vitro and in vivo. The results demonstrated the activity, biomass, and proteinase and phospholipase activities of biofilms were decreased significantly after the combination treatment of AmB-NPs with 42 KHz ultrasound irradiation at an intensity of 0.30 W/cm2 for 15 min compared to the control, the AmB alone or the ultrasound alone treatment (P < 0.01), and the morphology of biofilms was altered remarkably after jointly treatment under CLSM observation and detection, especially thickness thinning and structure loosing. Furthermore, the same synergistic effects were proved in a subcutaneous catheter biofilm rat model. The result of colony forming units of catheter fungus loading exhibited a significant reduction after AmB-NPs and ultrasound jointly treatment for 7 days continuous therapy, and the CLSM images revealed that the biofilm on the catheter surface was substantially eliminated. Our study may provide a new noninvasive, safe and effective application to C.albicans biofilm infection therapy.
Bioprospecting the solar panel microbiome: high-throughput screening for antioxidant bacteria in aCaenorhabditis elegansmodel
Authors: Tanner Kristie , Martorell Patricia , Genovés Salvador , Ramón Daniel , Zacarías Lorenzo , Rodrigo María Jesús , Peretó Juli , Porcar Manuel 
Published: September 2018

AbstractMicrobial communities that are exposed to sunlight typically share a series of adaptations to deal with the radiation they are exposed to, including efficient DNA repair systems, pigment production and protection against oxidative stress, which makes these environments good candidates for the search of novel antioxidant microorganisms. In this research project, we isolated potential antioxidant pigmented bacteria from a dry and highly-irradiated extreme environment: solar panels. High-throughputin vivoassays usingCaenorhabiditis elegansas an experimental model demonstrated the high antioxidant and ultraviolet-protection properties of these bacterial isolates that proved to be rich in carotenoids. Our results suggest that solar panels harbor a microbial community that includes strains with potential applications as antioxidants.
Effects of individuation and grouping on face representations in the visual cortex
Authors: Kim Hyehyeon , Kim Gayoung , Lee Sue-Hyun 
Published: September 2018

AbstractTop-down signals can influence our visual perception by providing guidance on information processing. Especially, top-down control between two basic frameworks, “Individuation” and “grouping”, is critical for information processing during face perception. Individuation of faces supports identity recognition while grouping subserves higher category level face perception such as race or gender. However, it still remains elusive how top-down dependent control between individuation and grouping affects cortical representations during face perception. Here we performed an fMRI experiment to investigate whether representations across early and high-level visual areas can be altered by top-down control between individuation and grouping process during face perception. Focusing on neural response patterns across the early visual cortex (EVC) and the face-selective area (the fusiform face area (FFA)), we found that the discriminability of individual faces from the response patterns was strong in the FFA but weak in the EVC during the individuation task whereas the EVC but not the FFA showed significant face discrimination during the grouping tasks. Thus, these findings suggest that the representation of face information across the early and high-level visual cortex is flexible depending on the top-down control of the perceptual framework between individuation and grouping.
The Evolution of Early-Life Effects on Social Behaviour – Why Should Social Adversity Carry Over to the Future?
Authors: Kuijper Bram , Johnstone Rufus A. 
Published: September 2018

AbstractNumerous studies have shown that social adversity in early life can have long-lasting negative consequences for social behaviour in adulthood, consequences that may in turn be propagated to future generations. Given these intergenerational effects, it is puzzling why natural selection might favour such sensitivity to an individual’s early social environment. To address this question, we model the evolution of social sensitivity in the development of in helping behaviours, showing that natural selection indeed favours individuals whose tendency to help others is dependent on early-life social experience. We find that natural selection typically favours positive social feedbacks, in which individuals who received more help in early life are also more likely to help others in adulthood, while individuals who received no early-life help develop low tendencies to helping others later in life. This positive social sensitivity is favoured because of an intergenerational relatedness feedback: patches with many helpers tend to be more productive, leading to higher relatedness within the local group, which in turn favours higher levels of help in the next generation.
Effects of zooplankton carcasses degradation on freshwater bacterial community composition and implications for carbon cycling
Authors: Kolmakova Olesya V. , Gladyshev Michail I. , Fonvielle Jérémy André , Ganzert Lars , Hornick Thomas , Grossart Hans-Peter 
Published: September 2018

AbstractNon-predatory mortality of zooplankton provides an abundant, yet, little studied source of high quality labile organic matter (LOM) in aquatic ecosystems. Using laboratory microcosms, we followed the decomposition of organic carbon of fresh 13C-labelled Daphnia carcasses by natural bacterioplankton. The experimental setup comprised blank microcosms i.e. artificial lake water without any organic matter additions (B), and microcosms either amended with natural humic matter (H), fresh Daphnia carcasses (D) or both, i.e. humic matter and Daphnia carcasses (HD). Most of the carcass carbon was consumed and respired by the bacterial community within 15 days of incubation. A shift in the bacterial community composition shaped by labile carcass carbon and by humic matter was observed. Nevertheless, we did not observe a quantitative change in humic matter degradation by heterotrophic bacteria in the presence of LOM derived from carcasses. However, carcasses were the main factor driving the bacterial community composition suggesting that the presence of large quantities of dead zooplankton might affect the carbon cycling in aquatic ecosystems. Our results imply that organic matter derived from zooplankton carcasses is efficiently remineralized by a highly specific bacterial community, but doesn’t interfere with the bacterial turnover of more refractory humic matter.
The R package divDyn for quantifying diversity dynamics using fossil sampling data
Authors: Á. T. Kocsis , C. J. Reddin , J. Alroy , W. Kiessling 
Published: September 2018

SummaryUnbiased time series of diversity dynamics are vital for quantifying the grand history of life. Applications include identifying ancient mass extinctions and inferring both biotic and abiotic controls on diversification rates.We introduce divDyn, a new R package that facilitates the calculation of taxonomic richness, extinction and origination rates from time-binned fossil sampling data. State-of-the-art sampling completeness metrics, counting protocols, and sampling standardisation functions permit the reconstruction of biologically meaningful time series. Additional functions permit the partitioning of turnover rates by trait and environmental affinity.We display Phanerozoic-scale diversity dynamics of marine invertebrates using the divDyn package. Using the core function and standard subsampling options, we revisit earlier assessments of declining extinction and origination rates over time and of equilibrial diversity dynamics to assess their methodological dependency.The modular and fast implementation of published methods ensures traceability, reproducibility, and comparability of future studies.
Single-cell RNA-seq analysis maps the development of human fetal retina
Authors: Lu Yufeng , Yi Wenyang , Wu Qian , Zhong Suijuan , Zuo Zhentao , Zhao Fangqi , Zhang Mei , Tsai Nicole , Zhuo Yan , He Sheng , Zhang Jun , Duan Xin , Wang Xiaoqun , Xue Tian 
Published: September 2018

AbstractVision starts with image formation at the retina, which contains diverse neuronal cell types that extract, process, and relay visual information to higher order processing centers in the brain. Though there has been steady progress in defining retinal cell types, very little is known about retinal development in humans, which starts well before birth. In this study, we performed transcriptomic profiling of developing human fetal retina from gestational weeks 12 to 27 using single-cell RNA-seq (scRNA-seq) and used pseudotime analysis to reconstruct the developmental trajectories of retinogenesis. Our analysis reveals transcriptional programs driving differentiation down four different cell types and suggests that Müller glia (MG) can serve as embryonic progenitors in early retinal development. In addition, we also show that transcriptional differences separate retinal progenitor cells (RPCs) into distinct subtypes and use this information to reconstruct RPC developmental trajectories and cell fate. Our results support a hierarchical program of differentiation governing cell-type diversity in the developing human retina. In summary, our work details comprehensive molecular classification of retinal cells, reconstructs their relationships, and paves the way for future mechanistic studies on the impact of gene regulation upon human retinogenesis.