bluuebunny/crossref_metadata_2025_split huggingface dataset:
De novodraft assembly of theBotrylloides leachiigenome provides further insight into tunicate evolution
Authors: Blanchoud Simon , Rutherford Kim , Zondag Lisa , Gemmell Neil J. , Wilson Megan J. 
Published: June 2017

AbstractTunicates are marine invertebrates that compose the closest phylogenetic group to the vertebrates. This chordate subphylum contains a particularly diverse range of reproductive methods, regenerative abilities and life-history strategies. Consequently, tunicates provide an extraordinary perspective into the emergence and diversity of chordate traits. To gain further insights into the evolution of the tunicate phylum, we have sequenced the genome of the colonial StolidobranchianBotrylloides leachii.We have produced a high-quality (90 % BUSCO genes) 159 Mb assembly, containing 82 % of the predicted total 194 Mb genomic content. TheB. leachiigenome is much smaller than that ofBotryllus schlosseri(725 Mb), but comparable to those ofCiona robustaandMolgula oculata(both 160 Mb). We performed an orthologous clustering between five tunicate genomes that highlights sets of genes specific to some species, including a large group unique to colonial ascidians with gene ontology terms including cell communication and immune response.By analysing the structure and composition of the conserved gene clusters, we identified many examples of multiple cluster breaks and gene dispersion, suggesting that several lineage-specific genome rearrangements occurred during tunicate evolution. In addition, we investigate lineage-specific gene gain and loss within the Wnt, Notch and retinoic acid pathways. Such examples of genetic change within these highly evolutionary conserved pathways commonly associated with regeneration and development may underlie some of the diverse regenerative abilities observed in the tunicate subphylum. These results supports the widely held view that tunicate genomes are evolving particularly rapidly.
A Bayesian approach to multivariate and multilevel modelling with non-random missingness for hierarchical clinical proteomics data
Authors: Zeng Irene SL , Lumley Thomas , Ruggierol Katya , Middleditch Martin 
Published: June 2017

AbstractHigh throughput mass-spectrometry-based proteomics data from clinical studies brings challenges to statistical analysis. The challenges originate from the hierarchical levels of protein abundance data and interactions between clinical study design and experimental design. The non-random missingness of the measurements from a vast amount of information also adds complexity in data analysis. We propose multivariate multilevel models to analyse protein abundances and to handle abundance-dependent missingness within a Bayesian framework. The proposed model enables the variance decomposition at different levels of the data hierarchy and provides shrinkage of protein-level estimates for a group of proteins. A logistic missingness and censored model with informative prior is used to handle incomplete data. Hamiltonian MC/No-U-Turn Sampling and Gibb MCMC algorithms are created to derive the posterior distribution of study parameters; Hamiltonian MC is demonstrated to gain more efficiency for these high-dimensional correlated data. Improvements of the proposed missing data model is compared to the univariate mixed effect model and the multivariate-multilevel model using complete data in a simulated study and a clinical proteomics study. The proposed model framework can be used in other types of data with similar structure and Non Random Missingness mechanism (MNAR).
Targeting neuronal activity-regulated neuroligin-3 dependency for high-grade glioma therapy
Authors: Venkatesh Humsa S. , Tam Lydia T. , Woo Pamelyn J. , Nagaraja Surya , Gillespe Shawn M. , Lennon James , Ni Jing , Duveau Damien Y. , Morris Patrick J. , Zhao Jean J. , Thomas Craig J. , Monje Michelle 
Published: June 2017

AbstractNeuronal activity promotes high-grade glioma (HGG) growth. An important mechanism mediating this neural regulation of brain cancer is activity-dependent cleavage and secretion of the synaptic molecule and glioma mitogen neuroligin-3 (Nlgn3), but the therapeutic potential of targeting Nlgn3 in glioma remains to be defined. We demonstrate a striking dependence of HGG growth on microenvironmental Nlgn3 and determine a targetable mechanism of secretion. Patient-derived orthotopic xenografts of pediatric glioblastoma, diffuse intrinsic pontine glioma and adult glioblastoma fail to grow in Nlgn3 knockout mice. Glioma exposure to Nlgn3 results in numerous signaling consequences, including early focal adhesion kinase activation upstream of PI3K-mTOR. Nlgn3 is cleaved from both neurons and oligodendrocyte precursor cells via the ADAM10 sheddase. Administration of ADAM10 inhibitors robustly blocks HGG xenograft growth. This work defines the therapeutic potential of and a promising strategy for targeting Nlgn3 secretion in the glioma microenvironment, which could prove transformative for treatment of HGG.
The Decision Decoding ToolBOX (DDTBOX) – A multivariate pattern analysis toolbox for event-related potentials
Authors: Bode Stefan , Feuerriegel Daniel , Bennett Daniel , Alday Phillip M. 
Published: June 2017

AbstractIn recent years, neuroimaging research in cognitive neuroscience has increasingly used multivariate pattern analysis (MVPA) to investigate higher cognitive functions. Here we present DDTBOX, an open-source MVPA toolbox for electroencephalography (EEG) data. DDTBOX runs under MATLAB and is well integrated with the EEGLAB/ERPLAB and Fieldtrip toolboxes (Delorme and Makeig, 2004; Lopez-Calderon and Luck, 2014; Oostenveld et al. 2011). It trains support vector machines (SVMs) on patterns of event-related potential (ERP) amplitude data, following or preceding an event of interest, for classification or regression of experimental variables. These amplitude patterns can be extracted across space/electrodes (spatial decoding), time (temporal decoding), or both (spatiotemporal decoding). DDTBOX can also extract SVM feature weights, generate empirical chance distributions based on shuffled-labels decoding for group-level statistical testing, provide estimates of the prevalence of decodable information in the population, and perform a variety of corrections for multiple comparisons. It also includes plotting functions for single subject and group results. DDTBOX complements conventional analyses of ERP components, as subtle multivariate patterns can be detected that would be overlooked in standard analyses. It further allows for a more explorative search for information when no ERP component is known to be specifically linked to a cognitive process of interest. In summary, DDTBOX is an easy-to-use and open-source toolbox that allows for characterising the time-course of information related to various perceptual and cognitive processes. It can be applied to data from a large number of experimental paradigms and could therefore be a valuable tool for the neuroimaging community.
Cyclic electron flow inChlamydomonas reinhardtii
Authors: Nawrocki W. J. , Bailleul B. , Cardol P. , Rappaport F. , Wollman F.-A. , Joliot P. 
Published: June 2017

AbstractCyclic electron flow (CEF), one of the major alternative electron transport pathways to the primary linear electron flow (LEF) in chloroplasts has been discovered in the middle of the last century. It is defined as a return of the reductants from the acceptor side of the Photosystem I (PSI) to the pool of its donors via the cytochromeb6f, and has proven essential for photosynthesis. However, despite many efforts aimed at its characterisation, the pathway and regulation of CEF remain equivocal, and its physiological significance remains to be properly defined. Here we use novel spectroscopic approaches to measure CEF in transitory conditions in the green algaChlamydomonas reinhardtii.We show that CEF operates at the same maximal rate regardless of the oxygen concentration, and that the latter influences LEF, rather than CEF in vivo, which questions the recent hypotheses about the CEF supercomplex formation. We further reveal that the pathways proposed for CEF in the literature are inconsistent with the kinetic information provided by our measurements. We finally provide cues on the regulation of CEF by light.
Natural variation in stochastic photoreceptor specification and color preference inDrosophila
Authors: Anderson Caitlin , Reiss India , Zhou Cyrus , Cho Annie , Siddiqi Haziq , Mormann Ben , Avelis Cameron M. , Bergland Alan , Roberts Elijah , Taylor James , Vasiliauskas Daniel , Johnston Robert J. 
Published: June 2017

AbstractEach individual perceives the world in a unique way, but little is known about the genetic basis of variation in sensory perception. Here we investigated natural variation in the development and function of the color vision system ofDrosophila. In the fly eye, the random mosaic of color-detecting R7 photoreceptor subtypes is determined by stochastic expression of the transcription factor Spineless (Ss). Individual R7s randomly choose between SsONor SsOFFfates at a ratio of 65:35, resulting in unique patterns but consistent proportions of cell types across genetically identical retinas. In a genome wide association study, we identified a naturally occurring insertion in a regulatory DNA element in thessgene that lowers the ratio of SsONto SsOFFcells. This change in photoreceptor fates shifts the innate color preference of flies from green to blue. The genetic variant increases the binding affinity for Klumpfuss (Klu), a zinc finger transcriptional repressor that regulatesssexpression. Klu is expressed at intermediate levels to determine the normal ratio of SsONto SsOFFcells. Thus, binding site affinity and transcription factor levels are finely tuned to regulate stochastic on/off gene expression, setting the ratio of alternative cell fates and ultimately determining color preference.
Mappingin vivogenetic interactomics through Cpf1 crRNA array screening
Authors: Chow Ryan D. , Wang Guangchuan , Codina Adan , Ye Lupeng , Chen Sidi 
Published: June 2017

AbstractGenetic interactions lay the foundation of biological networks in virtually all organisms. Due to the complexity of mammalian genomes and cellular architectures, unbiased mapping of genetic interactionsin vivois challenging. Cpf1 is a single effector RNA-guided nuclease that enables multiplexed genome editing using crRNA arrays. Here we designed a Cpf1 crRNA array library targeting all pairwise permutations of the most significantly mutated nononcogenes, and performed double knockout screens in mice using a model of malignant transformation as well as a model of metastasis. CrRNA array sequencing revealed a quantitative landscape of all single and double knockouts. Enrichment, synergy and clonal analyses identified many unpredicted drivers and co-drivers of transformation and metastasis, with epigenetic factors as hubs of these highly connected networks. Our study demonstrates a powerful yet simple approach forin vivomapping of unbiased genetic interactomes in mammalian species at a phenotypic level.
Faster than the brain’s speed of light: Retinocortical interactions differ in high frequency activity when processing darks and lights
Authors: Westner Britta U. , Dalal Sarang S. 
Published: June 2017

AbstractVisual processing of dark visual stimuli has been hypothesized to occur faster relative to bright stimuli. We investigated the timing, processing, and propagation of neural activity in response to darks and lights, operationalized as light offset and onset, in the human visual system by recording electroretinography (ERG) simultaneously with magnetoencephalography (MEG) in humans. We discovered that dark onset resulted in 75–95 Hz retinal activity that we call thedark retinal oscillatory potential, occurring with the same latency as the analogous but more broadband (55–195 Hz) oscillatory potential at light onset. Both retinal oscillations coupled with subsequent cortical activity of corresponding bandwidths, but cortical responses for darks indeed occurred earlier than for lights. Darks therefore propagate from retina to cortex more quickly than lights, potentially resulting from a thalamic advantage. Furthermore, we found that this propagation is effectuated by high frequency retinocortical coupling of narrow bandwidth for darks but wide bandwidth for lights.
FUCCI tracking shows that Neurog3 levels vary with cell-cycle phase in endocrine-biased pancreatic progenitors
Authors: Bechard Matthew E. , Bankaitis Eric D. , Ustione Alessandro , Piston David W. , Magnuson Mark A. , Wright Christopher V.E. 
Published: June 2017

AbstractNeurog3HIendocrine-committing cells are generated from a population of Sox9+mitotic progenitors with only a low level ofNeurog3transcriptional activity (Neurog3TA.LO). Low-level Neurog3 protein, inNeurog3TA.LOcells, is required to maintain their mitotic endocrine-lineage-primed status. Herein, we describe aNeurog3-driven FUCCI cell-cycle reporter (Neurog3P2A.FUCCI) derived from aNeurog3BAC transgenic reporter that functions as a loxed cassette acceptor (LCA). In cycling Sox9+Neurog3TA.LOprogenitors, the majority of cells in S-G2-M phases have undetectable levels of Neurog3 with increased expression of endocrine progenitor markers, while those in G1have low Neurog3 levels with increased expression of endocrine differentiation markers. These findings support a model in which variations in Neurog3 protein levels are coordinated with cell-cycle phase progression inNeurog3TA.LOprogenitors with entrance into G1triggering a concerted effort, beyond increasing Neurog3 levels, to maintain an endocrine-lineage-primed state by initiating expression of the downstream endocrine differentiation program prior to endocrine-commitment.
Working against “pedagogic work”
Authors: Fane Jennifer , Schulz Samantha 
Published: June 2017

PurposeEquipping pre-service teachers with the skills and knowledge needed to teach health in socially critical ways requires pre-service teachers to examine and critique individualistic understandings of health. The purpose of this paper is to use Bourdieu’s concepts of the bodily hexis (the body as both separate from society (autonomous individuals) and the body as socially mediated (the influence of social forces upon individuals)) and pedagogic work to investigate the challenges of redressing the reproduction of individualistic conceptualizations of health in teacher education.Design/methodology/approachThe paper focusses on an analysis of 31 pre-service teachers’ reflective writing in a foundational health education course, which sought to engage students in thinking about health in socially critical ways. A systematic and procedural form of document analysis was employed to examine and interpret data to investigate the ways in which students were engaging with the socially critical health discourses and course content.FindingsThe findings evidence that while students attempted to engage with and demonstrate their knowledge of a socially critical view of health, contradictions, or places where students unknowingly slipped into individualistic ways of thinking appeared frequently across the data. Findings are presented to elucidate challenges facing pre-service teachers in teaching the AC:HPE curriculum.Practical implicationsFindings suggest the need for teacher educators to employ pedagogic practices that can disrupt previous pedagogic work, serving to challenge and interrogate current constructions of health, and delve deeply into critical discourses through interchange and reflection.Originality/valueThis paper extends the current scholarship of Bourdieusian theoretical concepts in relation to critical health discourses and pedagogies.
Democratic school health education in a post-communist country
Authors: Boberova Zuzana , Paakkari Leena , Ropovik Ivan , Liba Jozef 
Published: June 2017

Purpose
The purpose of this paper is to discuss the findings of an intervention program built on the concept of children’s health literacy, particularly on its citizenship component. This intervention program employed the Investigation-Vision-Action-Change model for action-oriented teaching, where children were supported to investigate different health issues that affect them, create visions about desirable changes, and act toward desirable change. The intervention was implemented in the conditions of a post-communist country (Slovakia) where the majority of health education programs are behaviorally oriented, without giving space to children’s own perceptions and decisions. The study seeks to explore whether fostering children’s participation in forming the school environment improves the three selected factors of school well-being, namely, children’s perception of school, their subjective well-being, and violent behavior in school.

Design/methodology/approach
A cluster-randomized controlled trial design was used where ten classes of children aged nine to ten years were randomly assigned to either experimental (n=89) or control group (n=96). The dependent variables were pre- and post-tested using measures drawn from the Health Behavior in School-aged Children study for Slovakia.

Findings
The intervention program was shown to yield empirically robust effects, given the significant improvement in children’s perceptions about school, violent behavior, and their well-being, with medium-to-large effect sizes (Hedges’s g ranging from 0.74 to 0.96).

Originality/value
The present study offers an effective approach to enhance the respect for the children’s views on issues that affect them, particularly within post-communist conditions.
LGBTQ youth activism and school: challenging sexuality and gender norms
Authors: McGlashan Hayley , Fitzpatrick Katie 
Published: June 2017

PurposePrevious research examining the experiences of lesbian, gay, bisexual, trans and queer (LGBTQ) youth in schools suggests that schools are not inclusive places for non-heterosexual students. Some scholars, however, suggest that a continued focus on how these young people are marginalised is itself a problem, and that research should also focus on strengths and what is working. The purpose of this paper is to examine the activities of a group of LGBTQ students in one school in Auckland, New Zealand.Design/methodology/approachThe study employed a critical ethnographic approach in a diverse co-educational, public high school in Auckland, New Zealand. The researcher spent 3-5 days per week at the school throughout three terms (32 weeks) of the 2016 school year and participated, observed and interviewed students and teachers. Post-structural theory was used to analyse the ethnographic materials.FindingsThe study found that LGBTQ students actively challenged the heteronorms of their school. They met regularly to discuss issues, support each other and to plan activist initiatives. These initiatives, in turn, impacted the environment of the school and made LGBTQ students more visible. This visibility, however, also created tensions as students grappled with their identities and the public space of school.Originality/valueDespite a wealth of research in education on the exclusion of young people at the intersection of gender, sexuality and other identity positions, there is very little research that reports on school-wide health promotion initiatives that both engage young people as leaders and participants in their schools, and work towards creating safe and empowering spaces for LGBTQ youth.
Faculty use of Twitter in higher education teaching
Authors: Hull Kevin , Dodd Julie E. 
Published: June 2017

Purpose
The purpose of this paper is to determine how higher education teachers are using Twitter in their classroom to engage, educate, and inform students. The results were measured against Chickering and Gamson (1987) “Seven principles for good practice in undergraduate education.”

Design/methodology/approach
A survey was sent to college and university educators throughout the country who were identified as teachers who use Twitter in their classroom. These educators were asked about their Twitter use, their opinions of Twitter, the impact the social network has had on student learning, the students’ reactions to using Twitter, and how Twitter supported pedagogical best practices, including the “Seven principles for good practice in undergraduate education”.

Findings
The educators reported that student response to using Twitter in the classroom was overwhelmingly positive and that Twitter has positively impacted student learning. The results also indicate that college educators consider that Twitter use in classes does support the seven principles.

Research limitations/implications
While college instructors from a wide range of institutions, locations, subject types, and experience levels were surveyed, a limitation is that only their opinions are being examined. Future research may wish to examine the Twitter accounts of these professors to determine if they are using Twitter in the manner that they think they are. Results from the survey could then be compared with the tweet content.

Originality/value
While previous research has examined how students use and appreciate Twitter in the classroom, this is one of the first studies to examine how the social network is implemented from an instructor viewpoint. The results demonstrate value to instructors. For instructors, the value lies in the knowledge that Twitter has had a positive impact on classroom success for students and that using the social network promotes best practices in pedagogy, supporting constructivism, experiential learning, and the “Seven principles for good practice in undergraduate education”. For administrators, the value lies in the fact that many instructors have had success using Twitter and that more should be encouraged to do the same in their classrooms.