bluuebunny/crossref_metadata_2025_split huggingface dataset:
Perceptual Expectations do not Modulate Image Repetition Effects as Measured by Event-Related Potentials
Authors: Feuerriegel Daniel , Churches Owen , Coussens Scott , Keage Hannah A. D. 
Published: May 2017

AbstractRepeated stimulus presentation leads to complex changes in cortical neuron response properties, commonly known as repetition suppression or stimulus-specific adaptation. Circuit-based models of repetition suppression provide a framework for investigating patterns of repetition effects that propagate through cortical hierarchies. To further develop such models it is critical to determine whether (and if so, when) repetition effects are modulated by top-down influences, such as those related to perceptual expectation. We investigated this by presenting pairs of repeated and alternating face images, and orthogonally manipulating expectations regarding the likelihood of stimulus repetition. Event-related potentials (ERPs) were recorded from n=39 healthy adults, to map the spatiotemporal progression of stimulus repetition and expectation effects, and interactions between these factors, using mass univariate analyses. We also tested whether the ability to predict unrepeated (compared to repeated) face identities could influence the magnitude of observed repetition effects, by presenting separate blocks with predictable and unpredictable alternating faces. Multiple repetition and expectation effects were identified between 99-800ms from stimulus onset, which did not statistically interact at any point. Repetition effects in blocks with predictable alternating faces were smaller than in unpredictable alternating face blocks between 117-179ms and 506-652ms, and larger between 246-428ms. ERP repetition effects appear not to be modulated by perceptual expectations, supporting separate mechanisms for repetition and expectation suppression. However, previous studies that aimed to test for repetition effects, in which the repeated (but not unrepeated) stimulus was predictable, are likely to have conflated repetition and stimulus predictability effects.Highlights- ERP face image repetition effects were apparent between 99-800ms from stimulus onset- Expectations of stimulus image properties did not modulate face repetition effects- The predictability of unrepeated stimuli influenced repetition effect magnitudes
An anisotropic attraction model for the diversity and robustness of cell arrangement in nematodes
Authors: Yamamoto Kazunori , Kimura Akatsuki 
Published: May 2017

AbstractIn early embryogenesis stages in animals, cells are arranged into a species-specific pattern in a robust manner. The cell arrangement patterns are diverse, even among close relatives. We evaluated how the diversity and robustness are achieved in developing embryos. We succeeded in reproducing different patterns of cell arrangements observed in various nematode species usingCaenorhabditis elegansembryos by changing the eggshell shapes. This implies that the diversity of cell arrangements can be explained by differences in a shape parameter. Additionally, we found that the cell arrangement was robust against eggshell deformation. Computational modeling revealed that, in addition to repulsion forces, attraction forces are sufficient for this robustness. Genetic perturbation experiments demonstrated that attraction forces derived from cell adhesion are necessary for the robustness. The proposed model accounts for both diversity and robustness of cell arrangements and contributes to our understanding of how diversity and robustness are achieved in developing embryos.
A high resolution atlas of gene expression in the domestic sheep (Ovis aries)
Authors: Clark EL , Bush SJ , McCulloch MEB , Farquhar IL , Young R , Lefevre L , Pridans C , Tsang HG , Wu C , Afrasiabi C , Watson M , Whitelaw CB , Freeman TC , Summers KM , Archibald AL , Hume DA 
Published: May 2017

AbstractSheep are a key source of meat, milk and fibre for the global livestock sector, and an important biomedical model. Global analysis of gene expression across multiple tissues has aided genome annotation and supported functional annotation of mammalian genes. We present a large-scale RNA-Seq dataset representing all the major organ systems from adult sheep and from several juvenile, neonatal and prenatal developmental time points. TheOvis ariesreference genome (Oar v3.1) includes 27,504 genes (20,921 protein coding), of which 25,350 (19,921 protein coding) had detectable expression in at least one tissue in the sheep gene expression atlas dataset. Network-based cluster analysis of this dataset grouped genes according to their expression pattern. The principle of ‘guilt by association’ was used to infer the function of uncharacterised genes from their co-expression with genes of known function. We describe the overall transcriptional signatures present in the sheep gene expression atlas and assign those signatures, where possible, to specific cell populations or pathways. The findings are related to innate immunity by focusing on clusters with an immune signature, and to the advantages of cross-breeding by examining the patterns of genes exhibiting the greatest expression differences between purebred and crossbred animals. This high-resolution gene expression atlas for sheep is, to our knowledge, the largest transcriptomic dataset from any livestock species to date. It provides a resource to improve the annotation of the current reference genome for sheep, presenting a model transcriptome for ruminants and insight into gene, cell and tissue function at multiple developmental stages.Author SummarySheep are ruminant mammals kept as livestock for the production of meat, milk and wool in agricultural industries across the globe. Genetic and genomic information can be used to improve production traits such as disease resiliance. The sheep genome is however missing important information relating to gene function and many genes, which may be important for productivity, have no informative gene name. This can be remedied using RNA-Sequencing to generate a global expression profile of all protein-coding genes, across multiple organ systems and developmental stages. Clustering genes based on their expression profile across tissues and cells allows us to assign function to those genes. If for example a gene with no informative gene name is expressed in macrophages and is found within a cluster of known macrophage related genes it is likely to be involved in macrophage function and play a role in innate immunity. This information improves the quality of the reference genome and provides insight into biological processes underlying the complex traits that influence the productivity of sheep and other livestock species.
In uterodiffusion tensor imaging of the fetal brain: a reproducibility study
Authors: Jakab András , Tuura Ruth O`Gorman , Kellenberger Christian , Scheer Ianina 
Published: May 2017

AbstractOur purpose was to evaluate the within-subject reproducibility of in uterodiffusion tensor imaging (DTI) metrics and the visibility of major white matter structures.Images for 30 fetuses (20-33. postmenstrual weeks, normal neurodevelopment: 6 cases, cerebral pathology: 24 cases) were acquired on 1.5T or 3.0T MRI. DTI with 15 diffusion-weighting directions was repeated three times for each case, TR/TE: 2200/63 ms, voxel size: 1*1 mm, slice thickness: 3-5 mm, b-factor: 700 s/mm2. Reproducibility was evaluated from structure detectability, variability of DTI measures using the coefficient of variation (CV), image correlation and structural similarity across repeated scans for six selected structures. The effect of age, scanner type, presence of pathology was determined using Wilcoxon rank sum test.White matter structures were detectable in the following percentage of fetuses in at least two of the three repeated scans: corpus callosum genu 76%, splenium 64%, internal capsule, posterior limb 60%, brainstem fibers 40% and temporooccipital association pathways 60%. The mean CV of DTI metrics ranged between 3% and 14.6% and we measured higher reproducibility in fetuses with normal brain development. Head motion was negatively correlated with reproducibility, this effect was partially ameliorated by motion-correction algorithm using image registration. Structures on 3.0 T had higher variability both with- and without motion correction.Fetal DTI is reproducible for projection and commissural bundles during mid-gestation, however, in 16-30% of the cases, data were corrupted by artifacts, resulting in impaired detection of white matter structures. To achieve robust results for the quantitative analysis of diffusivity and anisotropy values, fetal-specific image processing is recommended and repeated DTI is needed to ensure the detectability of fiber pathways.AbbreviationsADaxial diffusivity;CCAcorpus callosum agenesis;CVcoefficient of variation,DTIdiffusion tensor imaging;FAfractional anisotropy;GWgestational week;MDmean diffusivity;RDradial diffusivity;ROIregion of interest;SSIMstructural similarity index
Identifying differential isoform abundance with RATs: a universal tool and a warning
Authors: Froussios Kimon , Mourão Kira , Simpson Gordon G. , Barton Geoffrey J. , Schurch Nick J. 
Published: May 2017

AbstractMotivationThe biological importance of changes in gene and transcript expression is well recognised and is reflected by the wide variety of tools available to characterise these changes. Regulation via Differential Transcript Usage (DTU) is emerging as an important phenomenon. Several tools exist for the detection of DTU from read alignment or assembly data, but options for detection of DTU from alignment-free quantifications are limited.ResultsWe present an R package named RATs – (Relative Abundance of Transcripts) – that identifies DTU transcriptome-wide directly from transcript abundance estimations. RATs is agnostic to quantification methods and exploits bootstrapped quantifications, if available, to inform the significance of detected DTU events. RATs contextualises the DTU results and shows good False Discovery performance (median FDR ≤0.05) at all replication levels. We applied RATs to a human RNA-seq dataset associated with idiopathic pulmonary fibrosis with three DTU events validated by qRT-PCR. RATs found all three genes exhibited statistically significant changes in isoform proportions based on Ensembl v60 annotations, but the DTU for two were not reliably reproduced across bootstrapped quantifications. RATs also identified 500 novel DTU events that are enriched for eleven GO terms related to regulation of the response to stimulus, regulation of immune system processes, and symbiosis/parasitism. Repeating this analysis with the Ensembl v87 annotation showed the isoform abundance profiles of two of the three validated DTU genes changed radically. RATs identified 414 novel DTU events that are enriched for five GO terms, none of which are in common with those previously identified. Only 141 of the DTU evens are common between the two analyses, and only 8 are among the 248 reported by the original study. Furthermore, the original qRT-PCR probes no longer match uniquely to their original transcripts, calling into question the interpretation of these data. We suggest parallel full-length isoform sequencing, annotation pre-filtering and sequencing of the transcripts captured by qRT-PCR primers as possible ways to improve the validation of RNA-seq results in future experiments.AvailabilityThe package is available through Github at https://github.com/bartongroup/Rats.
Pharmacological inhibition of the DNA damage checkpoint prevents radiation-induced oocyte death
Authors: Rinaldi Vera D. , Hsieh Kristin , Munroe Robert , Bolcun-Filas Ewelina , Schimenti John C. 
Published: May 2017

ABSTRACTOvarian function is directly correlated with survival of the primordial follicle reserve. Women diagnosed with cancer have a primary imperative of treating the cancer, but since the resting oocytes are hypersensitive to the DNA-damaging modalities of certain chemo- and radiotherapeutic regimens, such patients face the collateral outcome of premature loss of fertility and ovarian endocrine function. Current options for fertility preservation primarily include collection and cryopreservation of oocytes orin vitrofertilized oocytes, but this necessitates a delay in cancer treatment and additional assisted reproductive technology (ART) procedures. Here, we evaluated the potential of pharmacological preservation of ovarian function by inhibiting a key element of the oocyte DNA damage checkpoint response, checkpoint kinase 2 (CHK2; CHEK2). Whereas non-lethal doses of ionizing radiation (IR) eradicate immature oocytes in wild type mice, irradiatedChk2-/-mice retain their oocytes and thus, fertility. Using an ovarian culture system, we show that transient administration of the CHK2 inhibitor 2-(4-(4-Chlorophenoxy)phenyl)-1H-benzimidazole-5-carboxamide-hydrate (“CHK2iII”) blocked activation of the CHK2 targets TRP53 and TRP63 in response to sterilizing doses of IR, and preserved oocyte viability. After transfer into sterilized host females, these ovaries proved functional and readily yielded normal offspring. These results provide experimental evidence that chemical inhibition of CHK2 is a potentially valid treatment for preserving fertility and ovarian endocrine function of women exposed to DNA-damaging cancer therapies such as IR.Summary sentence:Oocytes, which are highly sensitive to DNA damage caused by certain cancer treatments, can be protected from radiation-induced death by an inhibitor of the checkpoint protein CHK2.
FORKS: Finding Orderings Robustly using k-means and Steiner trees
Authors: Sharma Mayank , Li Huipeng , Sengupta Debarka , Prabhakar Shyam , Jayadeva  
Published: May 2017

AbstractRecent advances in single cell RNA-seq technologies have provided researchers with unprecedented details of transcriptomic variation across individual cells. However, it has not been straightforward to infer differentiation trajectories from such data, due to the parameter-sensitivity of existing methods. Here, we present Finding Orderings Robustly using k-means and Steiner trees (FORKS), an algorithm that pseudo-temporally orders cells and thereby infers bifurcating state trajectories. FORKS, which is a generic method, can be applied to both single-cell and bulk differentiation data. It is a semi-supervised approach, in that it requires the user to specify the starting point of the time course. We systematically benchmarked FORKS and eight other pseudo-time estimation algorithms on six benchmark datasets, and found it to be more accurate, more reproducible, and more memory-efficient than existing methods for pseudo-temporal ordering. Another major advantage of our approach is its robustness – FORKS can be used with default parameter settings on a wide range of datasets.
Deletion ofEP4inS100a4-lineage cells reduces scar tissue formation during early but not later stages of tendon healing
Authors: Ackerman Jessica E. , Best Katherine T. , O’Keefe Regis J. , Loiselle Alayna E. 
Published: May 2017

AbstractTendon injuries heal via scar tissue rather than regeneration. This healing response forms adhesions between the flexor tendons in the hand and surrounding tissues, resulting in impaired range of motion and hand function. Mechanistically, inflammation has been strongly linked to adhesion formation, and Prostaglandin E2 (PGE2) is associated with both adhesion formation and tendinopathy. In the present study we tested the hypothesis that deletion of the PGE2 receptorEP4inS100a4-lineage cells would decrease adhesion formation. S100a4-Cre;EP4flox/flox(EP4cKOS100a4) repairs healed with improved gliding function at day 14, followed by impaired gliding at day 28, relative to wild type. Interestingly, EP4cKOS100a4resulted in only transient deletion ofEP4,suggesting up-regulation ofEP4in an alternative cell population in these mice. Loss ofEP4inScleraxis-lineage cells did not alter gliding function, suggesting thatScx-lineage cells are not the predominantEP4expressing population. In contrast, a dramatic increase in α-SMA+, EP4+ double-positive cells were observed in EP4cKOS100a4suggesting that EP4cKOS100a4repairs heal with increased infiltration of EP4 expressing α-SMA myofibroblasts, identifying a potential mechanism of late up-regulation ofEP4and impaired gliding function in EP4cKOS100a4tendon repairs.
High-Risk Human Papillomavirus E7 Alters Host DNA Methylome and RepressesHLA-EExpression in Human Keratinocytes
Authors: Cicchini Louis , Blumhagen Rachel Z. , Westrich Joseph A. , Meyers Mallory E. , Warren Cody J. , Siska Charlotte , Raben David , Kechris Katerina J. , Pyeon Dohun 
Published: May 2017

ABSTRACTHuman papillomavirus (HPV) infection distinctly alters methylation patterns in HPV-associated cancer. We have recently reported that HPV E7-dependent promoter hypermethylation leads to downregulation of the chemokineCXCL14and suppression of antitumor immune responses. To investigate the extent of gene expression dysregulated by HPV E7-induced DNA methylation, we analyzed parallel global gene expression and DNA methylation using normal immortalized keratinocyte lines, NIKS, NIKS-16, NIKS-18, and NIKS-16ΔE7. We show that expression of the MHC class I genes is downregulated in HPV-positive keratinocytes in an E7-dependent manner. Methylome analysis revealed hypermethylation at a distal CpG island (CGI) near theHLA-Egene in NIKS-16 cells compared to either NIKS cells or NIKS-16ΔE7 cells, which lack E7 expression. TheHLA-ECGI functions as an active promoter element which is dramatically repressed by DNA methylation. HLA-E protein expression on cell surface is downregulated by high-risk HPV16 and HPV18 E7 expression, but not by low-risk HPV6 and HPV11 E7 expression. Conversely, demethylation at theHLA-ECGI restores HLA-E protein expression in HPV-positive keratinocytes. Because HLA-E plays an important role in antiviral immunity by regulating natural killer and CD8+T cells, epigenetic downregulation ofHLA-Eby high-risk HPV E7 may contribute to virus-induced immune evasion during HPV persistence.
piClusterBusteR: Software for Automated Classification and Characterization of piRNA Cluster Loci
Authors: Schreiner Patrick , Atkinson Peter W. 
Published: May 2017

AbstractBackgroundPiwi-interacting RNAs (piRNAs) are sRNAs that have a distinct biogenesis and molecular function from siRNAs and miRNAs. The piRNA pathway is well-conserved and shown to play an important role in the regulatory capacity of germline cells in Metazoans. Significant subsets of piRNAs are generated from discrete genomic loci referred to as piRNA clusters. Given that the contents of piRNA clusters dictate the target specificity of primary piRNAs, and therefore the generation of secondary piRNAs, they are of great significance when considering transcriptional and post-transcriptional regulation on a genomic scale. A quantitative comparison of top piRNA cluster composition can provide further insight into piRNA cluster biogenesis and function.ResultsWe have developed software for general use, piClusterBusteR, which performs nested annotation of piRNA cluster contents to ensure high-quality characterization, provides a quantitative representation of piRNA cluster composition by feature, and makes available annotated and unannotated piRNA cluster sequences that can be utilized for downstream analysis. The data necessary to run piClusterBusteR and the skills necessary to execute this software on any species of interest are not overly burdensome for biological researchers.piClusterBusteR has been utilized to compare the composition of top piRNA generating loci amongst 13 Metazoan species. Characterization and quantification of cluster composition allows for comparison within piRNA clusters of the same species and between piRNA clusters of different species.ConclusionsWe have developed a tool that accurately, automatically, and efficiently describes the contents of piRNA clusters in any biological system that utilizes the piRNA pathway. The results from piClusterBusteR have provided an in-depth description and comparison of the architecture of top piRNA clusters within and between 13 species, as well as a description of annotated and unannotated sequences from top piRNA cluster loci in these Metazoans.piClusterBusteR is available for download on GitHub:https://github.com/pschreiner/piClusterBuster
BasecRAWller: Streaming Nanopore Basecalling Directly from Raw Signal
Authors: Stoiber Marcus , Brown James 
Published: May 2017

AbstractAll current nanopore basecalling applications begin with the segmentation of raw signal into discrete events, which are ultimately processed into called bases. We propose the basecRAWller algorithm, a pair of unidirectional recurrent neural networks that enables the calling of DNA bases in real time directly from the rawest form of nanopore output. This shift in nanopore basecalling provides a number of advantages over current processing pipelines including: 1) streaming basecalling, 2) tunable ratio of insertions to deletions, and 3) potential for streaming detection of modified bases. Key to the streaming basecalling capability is sequence prediction at a delay of less than 1/100th of a second, allowing future signal to continuously modulate sequence prediction. BasecRAWller is computationally efficient enabling basecalling at speeds faster than current nanopore instrument measurement speeds on a single core. Further, basecalling can be paused and resumed without any change in the resulting predicted sequence, transforming the potential applications for dynamic read rejection capabilities. The basecRAWller algorithm provides an alternative approach to nanopore basecalling at comparable accuracy and provides the community with the capacity to train their own basecRAWller neural networks with minimal effort.
Phoenix tourism within dark tourism
Authors: Miller DeMond Shondell , Gonzalez Christopher , Hutter Mark 
Published: May 2017

PurposeThe purpose of this paper is to address the knowledge gap in the field of dark tourism by understanding the phenomena of phoenix tourism, which focuses on the transformation and rebirth of places following death and disasters.Design/methodology/approachThe paper builds on existing theoretical understanding of dark tourism and disaster recovery to explore destination image recovery within the tourism industry. It uses phoenix tourism as a lens to understand the social, cultural and economic context of post-disaster tourism destination recovery and rebranding in the aftermath of the Indian Ocean Tsunami and Hurricane Katrina.FindingsA presentation of post-disaster strategies and recommendations are given with attention to the re-branding of images once associated with death and darkness to enhance a destination’s resilience.Practical ImplicationsFor local policymakers, tourism leaders, researchers and community developers, this research describes strategies that facilitate rebranding dark tourism sites, such as areas of rebirth or “phoenix tourism”, to enhance destination recovery image and to promote a more disaster- and risk-resilient tourism industry.Originality/valueThis paper bridges the knowledge gap by defining and contributing to the theoretical understanding of phoenix tourism as it identifies the what, how and why elements of the phenomena of phoenix tourism. Furthermore, the authors propose how to overcome negative destination images to preserve, present or redefine an image of a tourist destination “overcoming”, and eventual “rebirth” serves to re-calibrate resilience of the tourism industry and regional redevelopment.