bluuebunny/crossref_metadata_2025_split huggingface dataset:
Segmenting accelerometer data from daily life with unsupervised machine learning
Authors: van Kuppevelt Dafne , Heywood Joe , Hamer Mark , Sabia Séverine , Fitzsimons Emla , van Hees Vincent 
Published: February 2018

AbstractPurpose:Accelerometers are increasingly used to obtain valuable descriptors of physical activity for health research. The cut-points approach to segment accelerometer data is widely used in physical activity research but requires resource expensive calibration studies and does not make it easy to explore the information that can be gained for a variety of raw data metrics. To address these limitations, we present a data-driven approach for segmenting and clustering the accelerometer data using unsupervised machine learning.Methods:The data used came from five hundred fourteen-year-old participants from the Millennium cohort study who wore an accelerometer (GENEActiv) on their wrist on one weekday and one weekend day. A Hidden Semi-Markov Model (HSMM), configured to identify a maximum of ten behavioral states from five second averaged acceleration with and without addition of x, y, and z-angles, was used for segmenting and clustering of the data. A cut-points approach was used as comparison.Results:Time spent in behavioral states with or without angle metrics constituted eight and five principal components to reach 95% explained variance, respectively; in comparison four components were identified with the cut-points approach. In the HSMM with acceleration and angle as input, the distributions for acceleration in the states showed similar groupings as the cut-points categories, while more variety was seen in the distribution of angles.Conclusion:Our unsupervised classification approach learns a construct of human behavior based on the data it observes, without the need for resource expensive calibration studies, has the ability to combine multiple data metrics, and offers a higher dimensional description of physical behavior. States are interpretable from the distributions of observations and by their duration.
MasterPATH: network analysis of functional genomics screening data
Authors: Rubanova Natalia , Polesskaya Anna , Campalans Anna , Pinna Guillaume , Kropp Jeremie , Harel-Bellan Annick , Morozova Nadya 
Published: February 2018

AbstractFunctional genomics employs several experimental techniques to investigate gene functions. These techniques such as loss-of-function screening and transcriptome profiling performed in a high-throughput manner give as result a list of genes involved in the biological process of interest. There exist several computational methods for analysis and interpretation of the list. The most widespread methods aim at investigation of biological processes significantly represented in the list or at extracting significantly represented subnetworks. Here we present a new exploratory network analysis method that employs the shortest path approach and centrality measure to uncover members of active molecular pathways leading to the studied phenotype based on the results of functional genomics screening data. We present the method and we demonstrate what data can be retrieved by its application to the terminal muscle differentiation miRNA loss-of-function screening and transcriptomic profiling data and to the ‘druggable’ loss-of-function RNAi screening data of the DNA repair process.
Two novel strains of Torulaspora delbrueckii isolated from the honey bee microbiome and their use in honey fermentation
Authors: Barry Joseph P. , Metz Mindy S. , Hughey Justin , Quirk Adam , Bochman Matthew L. 
Published: February 2018

AbstractYeasts are ubiquitous microbes found in virtually all environments. Many yeast species can ferment sugar into ethanol and CO2, and humans have taken advantage of these characteristics to produce fermented beverages for thousands of years. As a naturally abundant source of fermentable sugar, honey has had a central role in such fermentations since Neolithic times. However, as beverage fermentation has become industrialized, the processes have been streamlined, including the narrow and almost exclusive usage of yeasts in the genus Saccharomyces for fermentation. We set out to identify wild honey- or honey bee-related yeasts that can be used in honey fermentation. Here, we isolated two strains of Torulaspora delbrueckii from the gut of a locally collected honey bee. Both strains were able to ferment honey sugar into mead but failed to metabolize more than a modest amount of wort sugar in trial beer fermentations. Further, the meads fermented by the T. delbrueckii strains displayed better sensory characteristics than mead fermented by a champagne yeast. The combination of T. delbrueckii and champagne yeast strains was also able to rapidly ferment honey at an industrial scale. Thus, wild yeasts represent a largely untapped reservoir for the introduction of desirable sensory characteristics in fermented beverages such as mead.
A Hierarchical Anti-Hebbian Network Model for the Formation of Spatial Cells in Three-Dimensional Space
Authors: Soman Karthik , Chakravarthy Srinivasa , Yartsev Michael M. 
Published: February 2018

AbstractThree dimensional (3D) spatial cells in the mammalian hippocampalformationare believed to support the existence of 3D cognitive maps. Modeling studies are crucial to comprehend the neural principles governing the formation of these maps, yet to date very few have addressed this topic in 3D space. Here, we present a hierarchical network model for the formation of 3D spatial cells using anti-hebbian network. Built on empirical data, the model accounts for the natural emergence of 3D place, border and grid-cells as well as a new type of previously undescribed spatial cell type which we call plane cells. It further explains the plausible reason behind the place and grid-cell anisotropic coding that has been observed in rodents and the potential discrepancy with the predicted periodic coding during 3D volumetric navigation. Lastly, it provides evidence for the importance of unsupervised learning rules in guiding the formation of higher dimensional cognitive maps.
Pre-pregnant obesity of mothers in a multi-ethnic cohort is associated with cord blood metabolomic changes in offspring
Authors: Schlueter Ryan J. , Al-Akwaa Fadhl M. , Benny Paula A. , Gurary Alexandra , Xie Guoxiang , Jia Wei , Chun Shaw J. , Chern Ingrid , Garmire Lana X. 
Published: February 2018

AbstractMaternal obesity has become a growing global health concern that may predispose the offspring to medical conditions later in life. However, the metabolic link between maternal pre-pregnant obesity and healthy offspring has not yet been fully elucidated. In this study, we conducted a case-control study using coupled untargeted and targeted metabolomics approach, from the newborn cord blood metabolomes associated with a matched maternal pre-pregnant obesity cohort of 28 cases and 29 controls. The subjects were recruited from multi-ethnic populations in Hawaii, including rarely reported Native Hawaiian and other Pacific Islanders (NHPI). We found that maternal obesity was the most important factor contributing to differences in cord blood metabolomics. Using elastic net regularization based logistic regression model, we identified 29 metabolites as potential early-life biomarkers manifesting intrauterine effect of maternal obesity, with accuracy as high as 0.947 after adjusting for clinical confounding (maternal and paternal age and ethnicity, parity and gravidity). We validated the model results in a subsequent set of samples (N=30) with an accuracy of 0.822. Among the metabolites, six metabolites (galactonic acid, butenylcarnitine, 2-hydroxy-3-methylbutyric acid, phosphatidylcholine diacyl C40:3, 1,5-anhydrosorbitol, and phosphatidylcholine acyl-alkyl 40:3) were individually and significantly different between the maternal obese vs. norm-weight groups. Interestingly, Hydroxy-3-methylbutyric acid showed significnatly higher levels in cord blood from the NHPI group, compared to asian and caucasian groups. In summary, significant associations were observed between maternal pre-pregnant obesity and offspring metabolomics alternation at birth, revealing the inter-generational impact of maternal obesity.
Multisensory perception reflects individual differences in processing temporal correlations
Authors: Nidiffer Aaron R. , Diederich Adele , Ramachandran Ramnarayan , Wallace Mark T. 
Published: February 2018

AbstractSensory signals originating from a single event, such as audiovisual speech, are temporally correlated. Correlated signals are known to facilitate multisensory integration and binding. We sought to further elucidate the nature of this relationship, hypothesizing that multisensory perception will vary with the strength of audiovisual correlation. Human participants detected near-threshold amplitude modulations in auditory and/or visual stimuli. During audiovisual trials, the frequency and phase of auditory modulations were varied, producing signals with a range of correlations. After accounting for individual differences which likely reflect relative temporal processing abilities of participants’ auditory and visual systems, we found that multisensory perception varied linearly with strength of correlation. Diffusion modelling confirmed this and revealed that correlation is supplied to the decisional system as sensory evidence. These data implicate correlation as an important cue in audiovisual feature integration and binding and suggest correlational strength as an important factor for flexibility in these processes.
Characterizing the 3D structure and dynamics of chromosomes and proteins in a common contact matrix framework
Authors: Lindsay Richard J. , Pham Bill , Shen Tongye , McCord Rachel Patton 
Published: February 2018

AbstractAny conformational ensemble of biopolymers, whether they are proteins or chromosomes, can be described using contact matrices derived from experimental or computational studies. One powerful approach to extract meaningful information from these contact matrices is to perform principal component analysis (PCA) on the covariance matrix of the contact data. Indeed, PCA on Hi-C chromosome contact matrices has revealed the spatial segregation of active and inactive chromatin. Separately, PCA on contact matrices from snapshots of protein conformations has characterized correlated fluctuations of protein domains. However, despite the similarities of these data and analyses, there has been little synergy between the PCA approaches and the comparison of resulting biological insights obtained for protein and chromosome structures. We note that, to date, different styles of analyses were applied exclusively to each biomolecule type: explicit contact correlation analysis (E-PCA) for proteins and implicit contact correlation (I-PCA) for chromosomes. In this work, we compare the results of applying both methods to both classes of biopolymers. While I-PCA reveals only average features of 3D chromosome structure, we find that applying E-PCA to an ensemble of chromosome structures from microscopy data reveals the dominant motion (concerted fluctuation) of the chromosome. Applying E-PCA to Hi-C data across the human blood cell lineage isolates the aspects of chromosome structure that most strongly differentiate cell types. Conversely, when we apply I-PCA to simulation snapshots of two protein complexes, the major component reports the consensus features of the structure, while the previously applied E-PCA characterizes correlated deviations from the mean structure.
Continuous flash suppression and monocular pattern masking impact subjective awareness similarly
Authors: Knotts J.D. , Lau Hakwan , Peters Megan A. K. 
Published: February 2018

AbstractPeters & Lau (2015) found that when criterion bias is controlled for, there is no evidence for unconscious visual perception in normal observers, in the sense that they cannot directly discriminate a target above chance without knowing it. One criticism of that study is that the visual suppression method used, forward and backward masking (FBM), may be too blunt in the way it interferes with visual processing to allow for unconscious forced-choice discrimination. To investigate this question we compared FBM directly to continuous flash suppression (CFS) in a two-interval forced choice task. Although CFS is popular, and may be thought of as a more powerful visual suppression technique, we found no difference in the degree of perceptual impairment between the two suppression types. To the extent that CFS impairs perception, both objective discrimination and subjective awareness are impaired to similar degrees under FBM. This pattern was consistently observed across 3 experiments in which various experimental parameters were varied. These findings provide evidence for an ongoing debate about unconscious perception: normal observers cannot perform forced-choice discrimination tasks unconsciously.
Modeling Uncertainty in Grapevine Powdery Mildew Epidemiology Using Fuzzy Logic
Authors: Choudhury R. A. , Mahaffee W. F. , McRoberts N. , Gubler W. D. 
Published: February 2018

ABSTRACTPowdery mildew is the most important disease of grapevines worldwide. Despite the potential for rapid spread by the causal pathogen, grape powdery mildew has been effectively managed using fungicide applications applied based on a calendar schedule or modeled disease risk index. Various epidemiological models for predicting disease development or risk have helped to improve disease management. The Gubler-Thomas (GT) risk index is a popular disease risk model used by many growers in the western U.S. We modified the GT risk index using fuzzy logic to address both biological and mechanical uncertainty in the pathosystem. The spraying schedule suggested by the fuzzy-modified GT risk index was tested in eight site-years. Overall, the fuzzy-modified risk index maintained comparable levels of disease control as both the original model and a calendar based treatment, and had significantly less disease than the untreated control. The fungicide use efficiency of the fuzzy-modified GT risk index suggests that the updated risk index was significantly more efficient with fungicide applications than both the calendar and original GT risk index.
Hawkmoth flight in the unsteady wakes of flowers
Authors: Matthews Megan , Sponberg Simon 
Published: February 2018

AbstractFlying animals maneuver and hover through environments where wind gusts and flower wakes produce unsteady flow. Although both flight maneuvers and aerodynamic mechanisms have been studied independently, little is known about how these interact in an environment where flow is already unsteady. Moths forage from flowers by hovering in the flower’s wake. We investigate hawkmoths tracking a 3D-printed robotic flower in a wind tunnel. We visualize the flow in the wake and around the wings and compare tracking performance to previous experiments in a still air flight chamber. Like in still air, moths flying in the flower wake exhibit near perfect tracking at low frequencies where natural flowers move. However, tracking in the flower wake results in a larger overshoot between 2-5 Hz. System identification of flower tracking reveals that moths also display reduced-order dynamics in wind, compared to still air. Smoke visualization of the flower wake shows that the dominant vortex shedding corresponds to the same frequency band as the increased overshoot. Despite these large effects on tracking dynamics in wind, the leading edge vortex (LEV) remains bound to the wing throughout the wingstroke and does not burst. The LEV also maintains the same qualitative structure seen in steady air. Persistence of a stable LEV during decreased flower tracking demonstrates the interplay between hovering and maneuvering.Summary statementWe examined how moths maneuver in the wake of flowers and discover that flower tracking dynamics are simplified compared to still air, while the leading edge vortex does not burst and extends continuously across the wings and thorax.
An integrated approach to comprehensively map the molecular context of proteins
Authors: Liu Xiaonan , Salokas Kari , Tamene Fitsum , Varjosalo Markku 
Published: February 2018

AbstractProtein-protein interactions underlie almost all cellular functions. The comprehensive mapping of these complex cellular networks of stable and transient associations has been made available by affinity purification mass spectrometry (AP-MS) and more recently by proximity based labelling methods such as BioID. Due the advancements in both methods and MS instrumentation, an in-depth analysis of the whole human proteome is at grasps. In order to facilitate this, we designed and optimized an integrated approach utilizing MAC-tag combining both AP-MS and BioID in a single construct. We systematically applied this approach to 18 subcellular localization markers and generated a molecular context database, which can be used to define molecular locations for any protein of interest. In addition, we show that by combining the AP-MS and BioID results we can also obtain interaction distances within a complex. Taken together, our combined strategy offers comprehensive approach for mapping physical and functional protein interactions.
Transgenerational inheritance of shuffled symbiont communities in the coral Montipora digitata
Authors: Quigley Kate M. , Willis Bette L. , Kenkel Carly D. 
Published: February 2018

AbstractAdult organisms may “prime” their offspring for environmental change through a number of genetic and non-genetic mechanisms, termed parental effects. Some coral species can alter their thermal tolerance by shuffling the proportions of Symbiodinium types within their endosymbiotic communities, but it is unclear if this plasticity can be transferred to offspring in corals that have maternal symbiont transmission. We evaluated symbiont community composition in tagged colonies of Montipora digitata from Orpheus Island, Australia, over two successive annual spawning seasons, the second of which overlapped with the 2016 mass coral bleaching event on the Great Barrier Reef. We applied amplicon sequencing of the ITS2 locus to samples of four families (parent colonies and 10-12 eggs per family) to characterize their potential for symbiont shuffling and to determine if shuffled abundances were preserved in gametes. Symbiont cell densities and photochemical efficiencies of the symbionts’ photosystem II differed significantly among adults in 2016, suggesting differential responses to increased temperatures. Although abundances of the dominant symbiont haplotype, a representative of clade C15, did not differ among families or over time, low-abundance (“background”) ITS2 types differed more among years (2015 vs. 2016) than between life stages (parent vs. offspring). Results indicate that background symbiont shuffling can occur in a canonically ‘stable’ symbiosis, and that such plastic changes to the symbiont community are heritable. To our knowledge, this is the first evidence that shuffled Symbiodinium communities can be inherited by early life-history stages and supports the hypothesis that plastic changes in microbial communities may serve as a mechanism of rapid coral acclimation to changing environmental conditions.
Morphometric analysis of spread platelets identifies integrin αIIbβ3-specific contractile phenotype
Authors: Lickert Sebastian , Sorrentino Simona , Studt Jan-Dirk , Medalia Ohad , Vogel Viola , Schoen Ingmar 
Published: February 2018

AbstractHaemostatic platelet function is intimately linked to cellular mechanics and cytoskeletal morphology. How cytoskeletal reorganizations give rise to a highly contractile phenotype that is necessary for clot contraction remains poorly understood. To elucidate this processin vitro, we developed a morphometric screen to quantify the spatial organization of actin fibres and vinculin adhesion sites in single spread platelets. Platelets from healthy donors predominantly adopted a bipolar morphology on fibrinogen and fibronectin, whereas distinguishable, more isotropic phenotypes on collagen type I or laminin. Specific integrin αIIbβ3inhibitors induced an isotropic cytoskeletal organization in a dose-dependent manner. The same trend was observed with decreasing matrix stiffness. Circular F-actin arrangements in platelets from a patient with type II Glanzmann thrombasthenia (GT) were consistent with the residual activity of a small number of αIIbβ3integrins. Cytoskeletal morphologiesin vitrocan thus inform about platelet adhesion receptor identity and functionality, and integrin αIIbβ3mechanotransduction fundamentally determines the adoption of a highly contractile bipolar phenotype. Super-resolution microscopy and electron microscopies further confirmed the stress fibre-like contractile actin architecture. For the first time, our assay allows the unbiased and quantitative assessment of platelet morphologies and could help to identify defective platelet contractility contributing to elusive bleeding phenotypes.
A long-chain fatty acid elongase Elovl6 regulates mechanical damage–induced keratinocyte death and skin inflammation
Authors: Nakamura Yoshiyuki , Matsuzaka Takashi , Tahara-Hanaoka Satoko , Shibuya Kazuko , Shimano Hitoshi , Nakahashi-Oda Chigusa , Shibuya Akira 
Published: February 2018

AbstractMechanical damage on the skin not only affect the barrier function but also induce various immune responses, which trigger or exacerbate the inflammation in healthy individuals and patients with inflammatory skin diseases. However, how mechanical damage-induced skin inflammation is regulated remains largely unknown. Here, we show that mechanical damage due to tape stripping triggered keratinocyte death and release of danger-associated molecular patterns (DAMPs) such as high-mobility group box 1 protein (HMGB-1) and IL-1α, which induced production of proinflammatory cytokines and chemokines IL-1β and CXCL-1 by keratinocytes in mice. We also show that a long-chain fatty acid elongase Elovl6 is expressed in keratinocytes. Mice deficient in Elovl6 had increased epidermal levels of cis-vaccenic acid (CVA); this accelerated keratinocyte death triggered by tape stripping and release of DAMPs and exacerbated skin inflammation. Our results demonstrate that Elovl6 regulates mechanical damage–triggered keratinocyte death and skin inflammation.