bluuebunny/crossref_metadata_2025_split huggingface dataset:
8Visual Culture
Authors: Lewis India 
Published: May 2019

Abstract
This chapter addresses books published in the field of visual culture in 2018 and is divided into three sections: 1. Art and the Internet; 2. Art and Society, and 3. Artists and Their Environment. The books under review cover a broad range of subjects within their specialities, but reflect general trends in contemporary writing and study in the field of visual culture. The first section explores how art critics and those in the field are continuing to deal with visual culture’s relationship with the Internet and digital media (Daniel Birnbaum, Michelle Kuo, eds. More Than Real: Art in the Digital Age; Eva Respini, ed., Art in the Age of the Internet: 1989 to Today). The second section looks at books about art in the social sphere (Kim Snepvangers and Donna Mathewson Mitchell, eds., Beyond Community Engagement: Transforming Dialogues in Art, Education, and the Cultural Sphere; Ole Marius Hylland and Erling Bjurström, eds., Aesthetics and Politics: A Nordic Perspective on How Cultural Policy Negotiates the Agency of Music and Arts; Gary Alan Fine, Talking Art: The Culture of Practice and the Practice of Culture in MFA Education). The third and final section looks at how artists negotiate their environment, responding to and altering their surroundings (Sarah Lowndes, Contemporary Artists Working Outside the City: Creative Retreat; Gabriel N. Gee and Alison Vogelaar, eds., Changing Representations of Nature and the City: The 1960s–1970s and Their Legacies).
A Multi-Breed Reference Panel and Additional Rare Variation Maximizes Imputation Accuracy in Cattle
Authors: Rowan Troy N. , Hoff Jesse L. , Crum Tamar E. , Taylor Jeremy F. , Schnabel Robert D. , Decker Jared E. 
Published: May 2019

AbstractBackgroundThe use of array-based SNP genotyping in the beef and dairy industries has produced an astounding amount of medium-to-low density genomic data in the last decade. While low-density assays work exceptionally well in the context of genomic prediction, they are less useful in mapping and causal variant discovery. This project focuses on maximizing imputation accuracies to the marker set of two high-density research assays, the Illumina Bovine HD, and the GGP-F250 which contains a large proportion of rare and potentially functional variants (~850,000 total SNPs). This 850K SNP set is well-suited for both imputation to sequence-level genotypes and direct downstream analysis.ResultsWe find that a large multi-breed composite imputation reference comprised of 36,131 samples with either HD and/or F250 genotypes significantly increases imputation accuracy compared to a standard within-breed reference panel, particularly at low minor allele frequencies. Imputation accuracies were maximized when an individual’s ancestry was adequately represented in the composite reference, particularly with complete 850K genotypes. The addition of rare content from the F250 to our composite reference panel significantly increased the imputation accuracy of rare variants found exclusively on the HD. Additionally, we identify 50,000 variants as an ideal starting density for 850K imputation.ConclusionUsing high-density genotypes on all available individuals in a multi-breed reference panel maximizes imputation accuracy for all cattle populations. Admixed breeds or those sparsely represented in the composite reference are still imputed at high accuracy which will increase further as the reference panel grows. We expect that the addition of rare variation from the F250 will increase the accuracy of imputation at the sequence level.
A Population Genomics Analysis of the Native Irish Galway Sheep Breed
Authors: McHugo Gillian P. , Browett Sam , Randhawa Imtiaz A. S. , Howard Dawn J. , Mullen Michael P. , Richardson Ian W. , Park Stephen D. E. , Magee David A. , Scraggs Erik , Dover Michael , Correia Carolina N. , Hanrahan James P. , MacHugh David E. 
Published: May 2019

SUMMARYThe Galway sheep population is the only native Irish sheep breed and represents an important livestock genetic resource, which is currently categorised as “at-risk”. In the present study, comparative population genomics analyses of Galway sheep and other sheep populations of European origin were used to investigate the microevolution and recent genetic history of the breed. These analyses support the hypothesis that British Leicester sheep were used in the formation of the Galway breed and suggest more recent gene flow from the Suffolk sheep breed. When compared to conventional and endangered breeds, the Galway breed was intermediate in effective population size, genomic inbreeding and runs of homozygosity. This indicates that, although the Galway breed is declining, it is still relatively genetically diverse and that conservation and management plans informed by genomic information may aid its recovery. The Galway breed also exhibited distinct genomic signatures of artificial or natural selection when compared to other breeds, which highlighted candidate genes that may be involved in meat and wool production.
Comparison of miRNA profiling methods using synthetic miRNA pools and standardized exRNA samples reveals substantial performance differences
Authors: Godoy Paula M. , Barczak Andrea J. , DeHoff Peter , Srinivasan Srimeenakshi , Das Saumya , Erle David J. , Laurent Louise C. 
Published: May 2019

SUMMARYMicroRNAs (miRNAs) found in biofluids play functional roles in health and in disease pathogenesis, underpinning their potential as clinical biomarkers. Several platforms for measurement of extracellular RNAs have recently become available. We evaluated the reproducibility, accuracy, sensitivity, and specificity of four miRNA quantification platforms, including one widely used discovery approach (small RNA-seq) and three targeted platforms (FirePlex, EdgeSeq, and nCounter). Using pools of synthetic miRNAs, we observed that reproducibility was highest for RNA-seq and EdgeSeq, that all three targeted platforms had lower bias than RNA-seq, and that RNA-seq had the best ability to distinguish between present and absent sequences. Overall reproducibility was lower for plasma samples than synthetic miRNA pools. We compared expression of placental miRNAs in plasma from pregnant and non-pregnant women and observed expected differences with RNA-seq and EdgeSeq, but not FirePlex or nCounter. We conclude that differences in performance among miRNA profiling platforms impact their relative utility as potential assay systems for clinical biomarkers.
A Freely Available, Self-Calibrating Software for Automatic Measurement of Freezing Behavior
Authors: Amorim Felippe E. , Moulin Thiago C. , Amaral Olavo B. 
Published: May 2019

ABSTRACTFreezing behavior is commonly used as a measure of associative fear memory. It can be measured by a trained observer, but this task is time-consuming and subject to variation. Commercially available software packages can also be used to quantify freezing; however, they can be expensive and usually require various parameters to be adjusted by the researcher, leading to additional work and variability in results. With this in mind, we developed Phobos, a freely available, self-calibrating software that measures freezing in a set of videos using a brief manual quantification performed by the user to automatically adjust parameters. To optimize the software, we used four different video sets with different features in order to determine the most relevant parameters, the amount of videos needed for calibration and the minimum criteria to consider it reliable. The results of four different users were compared in order to test intra- and interobserver variability in manual and automated freezing scores. Our results suggest that Phobos can be an inexpensive, simple and reliable tool for measurement of fear-related behavior, with intra- and interuser variability similar to that obtained with manual scoring.
Second Harmonic Generation Spectroscopy of Membrane Probe Dynamics in Gram-Positive Bacteria
Authors: Miller L. N. , Brewer W. T. , Williams J. D. , Fozo E. M. , Calhoun T. R. 
Published: May 2019

ABSTRACTBacterial membranes are complex mixtures with dispersity that is dynamic over scales of both space and time. In order to capture adsorption onto and transport within these mixtures, we conduct simultaneous second harmonic generation (SHG) and two photon fluorescence measurements on two different gram-positive bacterial species as the cells uptake membrane-specific probe molecules. Our results show that SHG can not only monitor the movement of small molecules across membrane leaflets, but is also sensitive to higher-level ordering of the molecules within the membrane. Further, we show that the membranes of Staphylococcus aureus remain more dynamic after longer times at room temperature in comparison to Enterococcus faecalis. Our findings provide insight into the variability of activities seen between structurally similar molecules in gram-positive bacteria while also demonstrating the power of SHG to examine these dynamics.STATEMENT OF SIGNIFICANCEBacterial membranes are highly adept at discerning and modifying their interactions with different small molecules in their environment. Here we show how second harmonic generation (SHG) spectroscopy can track the dynamics of structurally similar membrane probes in two gram-positive bacterial species. Our results reveal behavior that is dependent on both the probe molecule and the membrane composition. Specifically, we observe flip-flop between leaflets for one molecule, while the other molecule produces a signal indicative of larger scale ordering in the membrane. These phenomena can all be explained by considering potential differences in the membrane fluidity and surface charge between the two bacterial species. Overall, our work highlights the dynamic differences between bacterial membranes and SHG’s sensitivity to probing these systems.
SAME-clustering: Single-cell Aggregated Clustering via Mixture Model Ensemble
Authors: Huh Ruth , Yang Yuchen , Jiang Yuchao , Shen Yin , Li Yun 
Published: May 2019

ABSTRACTClustering is an essential step in the analysis of single cell RNA-seq (scRNA-seq) data to shed light on tissue complexity including the number of cell types and transcriptomic signatures of each cell type. Due to its importance, novel methods have been developed recently for this purpose. However, different approaches generate varying estimates regarding the number of clusters and the single-cell level cluster assignments. This type of unsupervised clustering is challenging and it is often times hard to gauge which method to use because none of the existing methods outperform others across all scenarios. We present SAME-clustering, a mixture model-based approach that takes clustering solutions from multiple methods and selects a maximally diverse subset to produce an improved ensemble solution. We tested SAME-clustering across 15 scRNA-seq datasets generated by different platforms, with number of clusters varying from 3 to 15, and number of single cells from 49 to 32,695. Results show that our SAME-clustering ensemble method yields enhanced clustering, in terms of both cluster assignments and number of clusters. The mixture model ensemble clustering is not limited to clustering scRNA-seq data and may be useful to a wide range of clustering applications.
PD-1 expression during acute infection is repressed through a LSD1- Blimp-1 axis
Authors: Bally Alexander P. R. , Neeld Dennis K. , Lu Peiyuan , Majumder Parimal , Tang Yan , Barwick Benjamin G. , Wang Qing , Boss Jeremy M. 
Published: May 2019

AbstractDuring prolonged exposure to antigens, such as chronic viral infections, sustained T cell receptor (TCR) signaling can result in T cell exhaustion mediated in part by expression of Programmed cell death-1 (PD-1) encoded by thePdcd1gene. Here, dynamic changes in histone H3K4 modifications at thePdcd1locus during ex vivo and in vivo activation of CD8 T cells, suggested a potential role for the histone H3 lysine 4 demethylase LSD1 in regulating PD-1 expression. CD8 T cells lacking LSD1 expressed higher levels ofPdcd1mRNA following ex vivo stimulation, as well as increased surface levels of PD-1 during acute but not chronic infection with lymphocytic choriomeningitis virus (LCMV). Blimp-1, a known repressor of PD-1, recruited LSD1 to thePdcd1gene during acute but not chronic LCMV infection. Loss of DNA methylation atPdcd1’s promoter proximal regulatory regions is highly correlated with its expression. However, following acute LCMV infection where PD-1 expression levels return to near base line, LSD1-deficient CD8 T cells failed to remethylate thePdcd1locus to the levels of wild-type cells. Finally, in a murine melanoma model, the frequency of PD-1 expressing tumor infiltrating LSD1-deficient CD8 T cells was greater than wild-type. Thus, LSD1 is recruited to thePdcd1locus by Blimp-1, downregulates PD-1 expression by facilitating the removal of activating histone marks, and is important for remethylation of the locus. Together, these data provide insight into the complex regulatory mechanisms governing T cell immunity and the regulation of a critical T cell checkpoint gene.Key PointsLSD1 suppress PD-1 expression following acute infection or transient induction.Blimp-1 binding to the Pdcd1 locus is required to recruit LSD1.LSD1 is required to fully remethylate the PD-1 proximal promoter region.
Scalable and cost-effective ribonuclease-based rRNA depletion for transcriptomics
Authors: Huang Yiming , Sheth Ravi U , Kaufman Andrew , Wang Harris H 
Published: May 2019

AbstractBacterial RNA sequencing (RNA-seq) is a powerful approach for quantitatively delineating the global transcriptional profiles of microbes in order to gain deeper understanding of their physiology and function. Cost-effective bacterial RNA-seq requires efficient physical removal of ribosomal RNA (rRNA), which otherwise dominates transcriptomic reads. However, current methods to effectively deplete rRNA of diverse non-model bacterial species are lacking. Here, we describe a probe and ribonuclease based strategy for bacterial rRNA removal. We implemented the method using either chemically synthesized oligonucleotides or amplicon-based single-stranded DNA probes and validated the technique on three novel gut microbiota isolates from three distinct phyla. We further showed that different probe sets can be used on closely related species. We provide a detailed methods protocol, probe sets for >5,000 common microbes from RefSeq, and an online tool to generate custom probe libraries. This approach lays the groundwork for large-scale and cost-effective bacterial transcriptomics studies.
Transferrin plays a central role to maintain coagulation balance by interacting with clotting factors
Authors: Tang Xiaopeng , Zhang Zhiye , Fang Mingqian , Han Yajun , Wang Sheng , Xue Min , Li Yaxiong , Zhang Li , Wu Jian , Yang Biqing , Lu Qiumin , Du Xiaoping , Lai Ren 
Published: May 2019

SummaryCoagulation balance is maintained through fine-tuning interactions among clotting factors. Physiological concentrations of clotting factors are huge difference. Especially, coagulation proteases’ concentration (pM to nM) is much lower than their natural inactivator antithrombin III (AT-III, ∼3 μM). Here we show that transferrin (normal plasma concentration ∼40 μM) interacts with fibrinogen, thrombin, FXIIa and AT-III with different affinity to maintain coagulation balance. Normally, transferrin is sequestered by binding with fibrinogen (normal plasma concentration ∼10 μM) with a molar ratio of 4:1. In atherosclerosis, abnormally up-regulated transferrin interacts with and potentiates thrombin/FXIIa and blocks AT-III’s inactivation on coagulation proteases by binding to AT-III, and thus induces hypercoagulability. In mouse models, transferrin-overexpression aggravated atherosclerosis while transferrin-knockdown, anti-transferrin antibody or designed peptides interfering transferrin-thrombin/FXIIa interactions alleviated it. Collectively, these findings identify transferrin as a clotting factor and an adjuster for maintaining coagulation balance and modify the coagulation cascade.
Learning to select actions shapes recurrent dynamics in the corticostriatal system
Authors: Márton Christian D. , Schultz Simon R. , Averbeck Bruno B. 
Published: May 2019

AbstractLearning to select appropriate actions based on their values is fundamental to adaptive behavior. This form of learning is supported by fronto-striatal systems. The dorsal-lateral prefrontal cortex (dlPFC) and the dorsal striatum (dSTR), which are strongly interconnected, are key nodes in this circuitry. Substantial experimental evidence, including neurophysiological recordings, have shown that neurons in these structures represent key aspects of learning. The computational mechanisms that shape the neurophysiological responses, however, are not clear. To examine this, we developed a recurrent neural network (RNN) model of the dlPFC-dSTR circuit and trained it on an oculomotor sequence learning task. We compared the activity generated by the model to activity recorded from monkey dlPFC and dSTR in the same task. This network consisted of a striatal component which encoded action values, and a prefrontal component which selected appropriate actions. After training, this system was able to autonomously represent and update action values and select actions, thus being able to closely approximate the representational structure in corticostriatal recordings. We found that learning to select the correct actions drove action-sequence representations further apart in activity space, both in the model and in the neural data. The model revealed that learning proceeds by increasing the distance between sequence-specific representations. This makes it more likely that the model will select the appropriate action sequence as learning develops. Our model thus supports the hypothesis that learning in networks drives the neural representations of actions further apart, increasing the probability that the network generates correct actions as learning proceeds. Altogether, this study advances our understanding of how neural circuit dynamics are involved in neural computation, showing how dynamics in the corticostriatal system support task learning.
Measuring mRNA translation in neuronal processes and somata by tRNA-FRET
Authors: Koltun Bella , Ironi Sivan , Gershoni-Emek Noga , Barrera Iliana , Hleihil Mohammad , Nanguneri Siddharth , Sasmal Ranjan , Agasti Sarit S. , Nair Deepak , Rosenblum Kobi 
Published: May 2019

AbstractIn neurons, the specific spatial and temporal localization of protein synthesis is of great importance for function and survival. In this work, we visualized tRNA and protein synthesis events in fixed and live mouse primary cortical culture using fluorescently-labeled tRNAs. We were able to characterize the distribution and movement of tRNAs in different neuronal sub-compartments and to study their association with the ribosome. We found that tRNA motion in neural processes is lower than in somata and corresponds to patterns of slow transport mechanisms, and that larger tRNA puncta co-localize with translational machinery components and are likely the functional fraction. Furthermore, chemical induction of LTP in culture revealed GluR-dependent biphasic up-regulation of mRNA translation with a similar effect in dendrites and somata. Importantly, measurement of protein synthesis in neurons with high resolutions offers new insights into neuronal function in health and disease states.
Loss of the Alzheimer’s-linked bridging integrator 1 (BIN1) protein affects synaptic structure and disrupts tau localisation and release
Authors: Glennon Elizabeth B. , Lau Dawn H-W , Gabriele Rebecca M.C. , Taylor Matthew F. , Troakes Claire , Elliott Christina , Killick Richard , Hanger Diane P. , Perez-Nievas Beatriz G. , Noble Wendy 
Published: May 2019

AbstractBackgroundPost-translational modifications of tau modify its interaction with binding partners and cause tau mislocalisation and altered tau function in Alzheimer’s disease (AD). The AD risk gene BIN1, is a binding partner for tau, however the mechanism by which BIN1 influences tau function is not fully understood. We hypothesised that BIN1 modulates AD risk by causing damaging tau mis-sorting to the synapse.MethodsTau and BIN1 levels, distribution and interactions were assessed in post-mortem control and AD brain and in primary neurons. In primary neurons, tau was further examined using structured illumination microscopy and immunoblotting following BIN1 knockdown, BIN1-tau interactions were examined using proximity ligation assays and tau release from neurons was measured by sensitive sandwich ELISA.ResultsProline 216 in tau was identified as critical for tau interaction with the BIN1-SH3 domain, and tau phosphorylation at serine/threonine residues disrupted this interaction. Subcellular fractionation showed that BIN1 is lost from the cytoplasm of AD brain and this correlated with the mislocalisation of phosphorylated tau to synapses. Mimicking BIN1 loss in AD by knockdown of the protein in primary neurons altered the structure of dendritic spines, caused phosphorylated tau to mis-sort to synapses and reduced the physiological release of predominantly dephosphorylated tau.ConclusionsThese data suggest that BIN1 loss in AD allows phosphorylated tau to be mis-sorted to synapses which likely alters the integrity of the post-synapse, alongside reducing the functionally important release of physiological forms of tau.
The zinc finger proteins ZC3H20 and ZC3H21 stabilise mRNAs encoding membrane proteins and mitochondrial proteins in insect-formTrypanosoma brucei
Authors: Liu Bin , Marucha Kevin Kamanyi , Clayton Christine 
Published: May 2019

SummaryZC3H20 and ZC3H21 are related trypanosome proteins with two C(x)8C(x)5C(x)3H zinc finger motifs. ZC3H20 is unstable in mammalian-infective bloodstream forms, but becomes more abundant as they transform to growth-arrested stumpy form, while ZC3H21 appears only in the procyclic form of the parasite, which infects Tsetse flies. Each protein binds to several hundred mRNAs, with overlapping but not identical specificities. Both increase expression of bound mRNAs, probably through recruitment of the MKT1-PBP1 complex. At least seventy of the bound mRNAs decrease after RNAi targeting ZC3H20 or ZC3H20 and ZC3H21; their products include procyclic-specific proteins of the plasma membrane and energy metabolism. Simultaneous depletion of ZC3H20 and ZC3H21 causes procyclic forms to shrink and stop growing; in addition to decreases in target mRNAs, there are other changes suggestive of loss of developmental regulation. The bloodstream-form specific protein RBP10 controls ZC3H20 and ZC3H21 expression. Interestingly, some ZC3H20/21 target mRNAs also bind to and are repressed by RBP10, allowing for dynamic regulation as RBP10 decreases and ZC3H20 and ZC3H21 increase during differentiation.