bluuebunny/crossref_metadata_2025_split huggingface dataset:
Body height in young adult men and risk of dementia later in adult life
Authors: Jørgensen Terese Sara Høj , Christensen Gunhild Tidemann , Christensen Kaare , Sørensen Thorkild IA , Osler Merete 
Published: August 2019

ABSTRACTThis study examined the relationship between body height and dementia and explored the impact of intelligence level, educational attainment, early life environment and familial factors. A total of 666,333 men, 70,608 brothers, and 7,388 twin brothers born 1939-1959 and examined at the conscript board were followed in Danish nationwide registers (1969-2016). Cox regression models were applied to analyze the association between body height and dementia. Within-brothers and within-twin pair analyses were conducted to explore the role of shared familial factors including partly shared genetics. In total, 10,599 men were diagnosed with dementia. The association between one z-score difference in body height and dementia (HR: 0.90, 95%CI: 0.89;0.90) was inverse and weakened slightly after adjustment for intelligence test scores and educational level. The within-brother analyses revealed a smaller estimate for dementia diagnosis the cohort analyses of brothers. The twin analysis showed similar, though less clear associations, which were not statistically significant.
Model-driven generation of artificial yeast promoters
Authors: Kotopka Benjamin J. , Smolke Christina D. 
Published: August 2019

AbstractPromoters play a central role in controlling gene regulation; however, a small set of promoters is used for most genetic construct design in the yeast Saccharomyces cerevisiae. Generating and utilizing models that accurately predict protein expression from promoter sequences would enable rapid generation of novel useful promoters and facilitate synthetic biology efforts in this model organism. We measured the gene expression activity of over 675,000 unique sequences in a constitutive promoter library, and over 327,000 sequences in an inducible promoter library. Training an ensemble of convolutional neural networks jointly on the two datasets enabled very high (R2 > 0.79) predictive accuracies on multiple sequence-activity prediction tasks. We developed model-guided design strategies which yielded large, sequence-diverse sets of novel promoters exhibiting activities similar to current best-in-class sequences. In addition to providing large sets of new promoters, our results show the value of model-guided design as an approach for generating useful DNA parts.
Place cell map genesis via competitive learning and conjunctive coding in the dentate gyrus
Authors: Kim Soyoun , Jung Dajung , Royer Sébastien 
Published: August 2019

AbstractPlace cells exhibit spatially selective firing fields and collectively map the continuum of positions in environments; how such network pattern develops with experience remains unclear. Here, we recorded putative granule (GC) and mossy (MC) cells from the dentate gyrus (DG) over 27 days as mice repetitively ran through a sequence of objects fixed onto a treadmill belt. We observed a progressive transformation of GC spatial representations, from a sparse encoding of object locations and periodic spatial intervals to increasingly more single, evenly dispersed place fields, while MCs showed little transformation and preferentially encoded object locations. A competitive learning model of the DG reproduced GC transformations via the progressive integration of landmark-vector cells and grid cell inputs and required MC-mediated feedforward inhibition to evenly distribute GC representations, suggesting that GCs progressively encode conjunctions of objects and spatial information via competitive learning, while MCs help homogenize GC spatial representations.
Computational approaches for parametric imaging of dynamic PET data
Authors: Crisci S , Piana M , Ruggiero V , Scussolini M 
Published: August 2019

AbstractParametric imaging of nuclear medicine data exploits dynamic functional images in order to reconstruct maps of kinetic parameters related to the metabolism of a specific tracer injected in the biological tissue. From a computational viewpoint, the realization of parametric images requires the pixel-wise numerical solution of compartmental inverse problems that are typically ill-posed and nonlinear. In the present paper we introduce a fast numerical optimization scheme for parametric imaging relying on a regularized version of the standard affine-scaling Trust Region method. The validation of this approach is realized in a simulation framework for brain imaging and comparison of performances is made with respect to a regularized Gauss-Newton scheme and a standard nonlinear least-squares algorithm.
Prompt rewetting of drained peatlands reduces climate warming despite methane emissions
Authors: Günther Anke , Barthelmes Alexandra , Huth Vytas , Joosten Hans , Jurasinski Gerald , Koebsch Franziska , Couwenberg John 
Published: August 2019

AbstractPeatlands are strategic areas for climate change mitigation because of their matchless carbon stocks. Drained peatlands release this carbon to the atmosphere as carbon dioxide (CO2). Peatland rewetting effectively stops these CO2 emissions, but also re-establishes the emission of methane (CH4).Essentially, management must choose between CO2 emissions from drained or CH4 emissions from rewetted peatland. This choice must consider radiative effects and atmospheric lifetimes of both gases, with CO2 being a weak but persistent and CH4 a strong but short-lived greenhouse gas. The resulting climatic effects are, thus, strongly time-dependent. We used a radiative forcing model to compare forcing dynamics of global scenarios for future peatland management using areal data from the Global Peatland Database. Our results show that CH4 radiative forcing does not undermine the climate change mitigation potential of peatland rewetting. Instead, postponing rewetting increases the long-term warming effect of continued CO2 emissions. Warnings against CH4 emissions from rewetted peatlands are therefore unjustified and counterproductive.
Parallel channels for motion feature extraction in the pretectum and tectum of larval zebrafish
Authors: Wang Kun , Hinz Julian , Zhang Yue , Thiele Tod R. , Arrenberg Aristides B 
Published: August 2019

AbstractNon-cortical visual areas in vertebrate brains extract different stimulus features, such as motion, object size and location, to support behavioural tasks. The optic tectum and pretectum, two primary visual areas, are thought to fulfil complementary biological functions in zebrafish to support prey capture and optomotor stabilisation behaviour. However, the adaptations of these brain areas to behaviourally relevant stimulus statistics are unknown. Here, we used calcium imaging to characterize the receptive fields of 1,926 motion-sensitive neurons in diencephalon and midbrain. We show that many caudal pretectal neurons have large receptive fields (RFs), whereas RFs of tectal neurons are smaller and mostly size-selective. RF centres of large-size RF neurons in the pretectum are predominantly located in the lower visual field, while tectal neurons sample the upper-nasal visual field more densely. This tectal visual field sampling matches the expected prey item locations, suggesting that the tectal magnification of the upper-nasal visual field might be an adaptation to hunting behaviour. Finally, we probed optomotor responsiveness and found that even relatively small stimuli drive optomotor swimming, if presented in the lower-temporal visual field, suggesting that the pretectum preferably samples information from this region on the ground to inform optomotor behaviour. Our characterization of the parallel processing channels for non-cortical motion feature extraction provides a basis for further investigation into the sensorimotor transformations of the zebrafish brain and its adaptations to habitat and lifestyle.
Are Sources of EEG and MEG rhythmic activity the same? An analysis based on BC-VARETA
Authors: Riaz Usama , Razzaq Fuleah A. , Paz-Linares Deirel , Areces-Gonzalez Ariosky , Huang Sunpei , Gonzalez-Moreira Eduardo , Bringas Vega Maria L. , Montes Eduardo Martinez , Iglesias José Enrique Alvarez , Valdés-Sosa Pedro A. 
Published: August 2019

AbstractIn the resting state (closed or open eyes) the electroencephalogram (EEG) and the magnetoencephalogram (MEG) exhibit rhythmic brain activity is typically the 10 Hz alpha rhythm. It has a topographic frequency spectral distribution that is, quite similar for both modalities--something not surprising since both EEG and MEG are generated by the same basic oscillations in thalamocortical circuitry. However, different physical aspects underpin the two types of signals. Does this difference lead to a different distribution of reconstructed sources for EEG and MEG rhythms? This question is important for the transferal of results from one modality to the other but has surprisingly received scant attention till now. We address this issue by comparing eyes open EEG source spectra recorded from 70 subjects from the Cuban Human Brain Mapping project with the MEG of 70 subjects from the Human Connectome Project. Source spectra for each voxel and frequencies between 0-50Hz with 100 frequency points were obtained via a novel sparse-covariance inverse method (BC-VARETA) based on individualized BEM head models with subject-specific regularization parameters (noise to signal ratio). We performed a univariate permutation-based rank test among sources of both modalities and found out no differences. To carry out an unbiased comparison we computed sources from eLORETA and LCMV, performed the same permutation-based comparison, and found the same results we got with BC-VARETA.
Associations of adverse lifetime experiences with brain structure in 7003 UK Biobank participants
Authors: Gheorghe Delia A. , Li Chenlu , Gallacher John , Bauermeister Sarah 
Published: August 2019

AbstractBackgroundExperiences of chronic stress and trauma are major risk factors for psychiatric illness. Evidence suggests that adversity-related changes in brain structure and function accelerate this vulnerability. It is yet to be determined whether neuroendocrine effects on the brain are a result of the interference with neural development during sensitive periods or a consequence of cumulative lifetime adversity. To address this question, the present study investigated the associations between brain structure and self-reported data of childhood and adult adversity using machine learning techniques and structural equation models (SEM).MethodsThe UK Biobank resource was used to access Imaging Derived Phenotypes (IDPs) of grey matter and white matter tract integrity of 7003 participants, together with selected childhood and adult adversity data. Latent measures of adversity and imaging phenotypes were estimated to evaluate their associations using SEM.ResultsWe demonstrated that increased incidence of childhood adversity events may be associated with smaller grey matter in frontal, insular, subcallosal and cerebellar regions of the brain. There were no significant associations between brain phenotypes and negative experiences during adulthood.ConclusionsUsing a large population cohort dataset, this study contributes to the suggestion that childhood adversity may determine grey matter reductions in brain regions, which are putatively sensitive to the neurotoxic effects of chronic stress. Furthermore, it provides novel evidence to support the “sensitive periods” model though which adversity affects the brain.
A multilayer perspective for inferring spatial and social functioning in animal movement networks
Authors: Mourier Johann , Lédée Elodie J. I. , Jacoby David M. P. 
Published: August 2019

ABSTRACTAnimal movement patterns are increasingly analysed as spatial networks. Currently, structures of complex movements are typically represented as a single-layer (or monoplex) network. However, aggregating individual movements, to generate population-level inferences, considerably reduces information on how individual or species variability influences spatial connectivity and thus identifying the mechanisms driving network structure remains difficult.Here, we propose incorporating the recent conceptual advances in multilayer network analyses with the existing movement network approach to improve our understanding of the complex interaction between spatial and/or social drivers of animal movement patterns.Specifically, we explore the application and interpretation of this framework using an empirical example of shark movement data gathered using passive remote sensors in a coral reef ecosystem. We first show how aggregating individual movement networks can lead to the loss of information, potentially misleading our interpretation of movement patterns. We then apply multilayer network analyses linking individual movement networks (i.e. layers) to the probabilities of social contact between individuals (i.e. interlayer edges) in order to explore the functional significance of different locations to an animal’s ecology.This approach provides a novel and holistic framework incorporating individual variability in behaviour and inter-individual interactions. We discuss how this approach can be used in applied ecology and conservation to better assess the ecological significance of variable space use by mobile animals within a population. Further, we argue that the uptake of multilayer networks will significantly broaden our understanding of long-term ecological and evolutionary processes, particularly in the context of information or disease transfer between individuals.
ZapA tetramerization is required for midcell localization and ZapB interaction in Escherichia coli
Authors: Meiresonne Nils Y. , den Blaauwen Tanneke 
Published: August 2019

AbstractBacterial cell division is guided by FtsZ treadmilling precisely at midcell. FtsZ itself is regulated by FtsZ associated proteins (Zaps) that couple it to different cellular processes. ZapA is known to enhance FtsZ bundling but also forms the synchronizing link with chromosome segregation through ZapB and matS bound MatP. ZapA exists as dimers and tetramers in the cell. Using the ZapAI83E mutant that only forms dimers, this paper investigates the effects of ZapA multimerization state on its interaction partners and cell division. By employing (fluorescence) microscopy and Förster Resonance Energy Transfer in vivo it is shown that; dimeric ZapA is unable to complement a zapA deletion strain and localizes diffusely through the cell but still interacts with FtsZ that is not part of the cell division machinery. Dimeric ZapA is unable to recruit ZapB, which localizes in its presence unipolarly in the cell. Interestingly, the localization profiles of the chromosome and unipolar ZapB anticorrelate. The work presented here confirms previously reported in vitro effects of ZapA multimerization in vivo and further places it in a broader context by revealing the strong implications for ZapB localization and ter linkage.
Accelerating Inflammation Resolution to Counteract Chemical Cutaneous Injury
Authors: Achanta Satyanarayana , Chintagari Narendranath Reddy , Balakrishna Shrilatha , Liu Boyi , Jordt Sven-Eric 
Published: August 2019

AbstractChemical exposure to vesicants such as sulfur mustard (SM), and electrophilic riot control agents such as 2-chlorobenzalmalononitrile (CS) tear gas agent, cause strong cutaneous inflammation. Classical anti-inflammatory treatments have focused on interference with target initiation and maintenance of inflammation, with mixed outcomes. Inflammation is broadly classified into three temporal phases, initiation, amplification and maintenance, and resolution. Resolution of inflammation was thought to be a passive process but the recent body of literature shows that resolution is an active process and is mediated by fatty acid-derived mediators (specialized pro-resolving mediators, SPMs). We hypothesized that accelerating resolution phase of inflammation may attenuate the exaggerated inflammatory response following chemical threat exposure, leading to decreased morbidity and improved recovery. In this study, SPMs, such as Resolvin D1 (RvD1) and Resolvin D2 (RvD2), were administered to mice at nanogram doses post-exposure to an SM analog, 2-chloroethyl-ethyl-sulfide (CEES) or CS tear gas agent. SPMs decreased edema (ear thickness and punch biopsy weights), pro-inflammatory cytokines (IL-1β, CXCL1/KC, MIP2) and protease marker (MMP-9), and vascular leakage (determined by IRDye 800 CW PEG) while improving histopathology in cutaneous chemical injury mouse models. These results support our hypothesis and pave the way for SPMs for further development as potential medical countermeasures for chemical threat agents-induced skin injuries.
Tertiary lymphoid tissue develops during normal aging in mice and humans
Authors: Ligon Marianne M. , Wang Caihong , Jennings Zoe , Schulz Christian , DeJong Erica N. , Lowder Jerry L. , Bowdish Dawn M. E. , Mysorekar Indira U. 
Published: August 2019

ABSTRACTAging has multifaceted effects on the immune system in the context of systemic responses to specific vaccines and pathogens, but how aging affects tissue-specific immunity is not well-defined. Chronic bladder inflammation is highly prevalent in older women, but mechanisms by which aging promotes these pathologies remain unknown. Here we report distinct, age-associated changes to the immune compartment in the otherwise normal female (but not in male) mouse urinary bladder and parallel changes in older women with chronic bladder inflammation. In aged mice, the bladder epithelium became more permeable, and the homeostatic immune landscape shifted from a limited, innate immune-predominant surveillance to an inflammatory, adaptive immune-predominant environment. Strikingly, lymphoid cells were organized into tertiary lymphoid tissues, hereafter named bladder tertiary lymphoid tissue (bTLT). Analogous bTLTs were found in older women, many of whom had a history of recurrent urinary tract infection (UTI). Aged mice responded poorly to experimental UTI, experiencing spontaneous recurrences at higher rates than young mice. However, bTLT formation was dependent on aging and independent of infection. Furthermore, bTLTs in aged mice played a role inde novoantibody responses and urinary IgA production by recruitment of naive B cells that form germinal centers and mature into IgA-secreting plasma cells. Finally, TNFα was a key driver of bTLT formation, as aged TNFα-/-mice lacked bTLTs. Both aged TNFα-/-and wild type mice exhibited increased bladder permeability, suggesting that epithelial dysfunction may be an upstream mediator of chronic, age-associated bladder inflammation. Thus, bTLTs arise as a function of age and may underlie chronic, age-associated bladder inflammation. Our model establishes a platform for further investigation of age-association tissue inflammation and translation to new treatment strategies.One Sentence SummaryMice develop bladder tertiary lymphoid tissue (bTLT) during aging that is dependent on TNFα and independent of urinary tract infection.
The periphery and the core properties explain the omnigenic model in the human interactome
Authors: Wang Bingbo , Glass Kimberly , Röhl Annika , Santolini Marc , Croteau-Chonka Damien C. , Weiss Scott T. , Raby Benjamin A. , Sharma Amitabh 
Published: August 2019

AbstractUnderstanding the connectivity patterns of genes in a localized disease neighborhood or disease module in a molecular interaction network (interactome) is a key step toward advancing the knowledge about molecular mechanisms underlying a complex disease. In this work, we introduce a framework that detects peripheral and core regions of a disease in the human interactome. We leverage gene expression data on 104 diseases and analyze the connectivity of differentially expressed genes (quantified by a p-value < 0.05) and their topological membership in the network to distinguish between peripheral and core genes. Per definition, peripheral and core genes are topologically different and we show that they also differ biologically. Core genes are more enriched for Genome-wide association study (GWAS) and Online Mendelian Inheritance in Man (OMIM) data, whereas peripheral genes are more shared across different disease states and their overlap helps predict disease proximity in the human interactome. Based on this observation, we propose a flower model to explain the organization of genes in the human interactome, with core genes of different diseases as the petals and the peripheral genes as the (shared) stem. We show that this network model is an important step towards finding novel drug targets and improving disease classification. Overall, we were able to demonstrate how perturbations percolate through the human interactome and contribute to peripheral and core regions, an important novel feature of the omnigenic model.
Defining variation in pre-human ecosystems can guide conservation: An example from a Caribbean coral reef
Authors: O’Dea Aaron , Lepore Mauro , Altieri Andrew H. , Chan Melisa , Morales-Saldaña Jorge Manuel , Muñoz Nicte-Ha , Pandolfi John M. , Toscano Marguerite A. , Zhao Jian-xin , Dillon Erin M. 
Published: August 2019

AbstractThere is a consensus that Caribbean coral reefs are a pale shadow of what they once were, yet a reef’s pre-human state is typically assumed or estimated using space-for-time substitution approaches. These approaches may fail to account for past variation before human impact which could mislead conservation priorities and actions. In this study we use a suite of fossilised mid-Holocene (7.2-5.6 ka) fringing reefs in Caribbean Panama to define the Historical Range of Variation (HRV) in coral community structure before human-impact to provide context for the states of modern reefs in the same area. Using the abundances of coral taxa to quantify communities, we found that most of the modern coral communities exist in novel ecosystem states with no fossil precedence. We do however identify one modern reef that is indistinguishable in coral community structure from the mid-Holocene reefs. Reef-matrix cores show that the community on this reef has remained in a stable state for over 760 years, suggesting long-term resistance to the region-wide shift to novel states. Without historical context this robust and stable reef would be overlooked since it does not fulfil expectations of what a “pristine” coral reef should look like. This example illustrates how defining past variation using the fossil record can place modern degradation in historical context and improve conservation recommendations.