bluuebunny/crossref_metadata_2025_split huggingface dataset:
Native and engineered clifednamide biosynthesis in multipleStreptomycesspp
Authors: Qi YuncI , Ding Edward , Blodgett Joshua A.V. 
Published: October 2017

ABSTRACTPolycyclic tetramate macrolactam (PTM) natural products are produced by actinomycetes and other bacteria. PTMs are often bioactive, and the simplicity of their biosynthetic clusters make them attractive for bioengineering. Clifednamide-type PTMs fromStreptomycessp. JV178 contain a distinctive ketone group, suggesting the existence of a novel PTM oxidizing enzyme. Here, we report the new cytochrome P450 enzyme (CftA) is required for clifednamide production. Genome mining was used to identify several new clifednamide producers, some having improved clifednamide yields. Using a parallel synthetic biology approach, CftA isozymes were used to engineer the ikarugamycin pathway ofStreptomycessp. NRRL F-2890 to yield clifednamides. Further, we observed that strong CftA expression leads to the production of a new PTM, clifednamide C. We demonstrate the utility of both genome mining and synthetic biology to rapidly increase clifednamide production and identify a PTM tailoring enzyme for rational molecule design.
The experience of vivid autobiographical reminiscence is supported by personal semantic representations in the precuneus
Authors: Sreekumar Vishnu , Nielson Dylan M. , Smith Troy A. , Dennis Simon J. , Sederberg Per B. 
Published: October 2017

AbstractRecent studies have suggested that the human posteromedial cortex (PMC), which includes core regions of the default mode network (DMN), plays an important role in episodic memory. Whereas various roles relating to self-relevant processing and memory retrieval have been attributed to different subsystems within this broad network, the nature of representations and the functional roles they support in these brain regions remain unspecified. Here, we describe the whole-brain networks that representsubjective, self-relevant aspects of real-world events during autobiographical recollection. Nine participants wore a device to record images from their lives for a period of two to four weeks (lifelogging phase) and indicated the personally-salient attributes (i.e., personal semantics) of each episode by choosing multiple content tags. Two to four weeks after the lifelogging phase, participants relived their experiences in an fMRI scanner cued by images chosen from their own lives. Representational Similarity Analysis revealed a broad network, including parts of the DMN, that represented personal semantics during autobiographical reminiscence. Furthermore, within this network, the right precuneus represented personally relevant content during vivid recollection but not during non-vivid recollection. The precuneus is a hub within the DMN and has been implicated in metacognitive ability for memory retrieval. Our results suggest a more specific mechanism underlying the phenomenology of vivid reminiscence, supported by personal semantic representations in the precuneus.
Finding cell-specific expression patterns in the early Ciona embryo with single-cell RNA-seq
Authors: Ilsley Garth R. , Suyama Ritsuko , Noda Takeshi , Satoh Nori , Luscombe Nicholas M. 
Published: October 2017

AbstractSingle-cell RNA-seq has been established as a reliable and accessible technique enabling new types of analyses, such as identifying cell types and studying spatial and temporal gene expression variation and change at single-cell resolution. Recently, single-cell RNA-seq has been applied to developing embryos, which offers great potential for finding and characterising genes controlling the course of development along with their expression patterns. In this study, we applied single-cell RNA-seq to the 16-cell stage of the Ciona embryo, a marine chordate and performed a computational search for cell-specific gene expression patterns. We recovered many known expression patterns from our single-cell RNA-seq data and despite extensive previous screens, we succeeded in finding new cell-specific patterns, which we validated by in situ and single-cell qPCR.
NGSphy: phylogenomic simulation of next-generation sequencing data
Authors: Escalona Merly , Rocha Sara , Posada David 
Published: October 2017

AbstractMotivationAdvances in sequencing technologies have made it feasible to obtain massive datasets for phylogenomic inference, often consisting of large numbers of loci from multiple species and individuals. The phylogenomic analysis of next-generation sequencing (NGS) data implies a complex computational pipeline where multiple technical and methodological decisions are necessary that can influence the final tree obtained, like those related to coverage, assembly, mapping, variant calling and/or phasing.ResultsTo assess the influence of these variables we introduce NGSphy, an open-source tool for the simulation of Illumina reads/read counts obtained from haploid/diploid individual genomes with thousands of independent gene families evolving under a common species tree. In order to resemble real NGS experiments, NGSphy includes multiple options to model sequencing coverage (depth) heterogeneity across species, individuals and loci, including off-target or uncaptured loci. For comprehensive simulations covering multiple evolutionary scenarios, parameter values for the different replicates can be sampled from user-defined statistical distributions.AvailabilitySource code, full documentation and tutorials including a quick start guide are available athttp://github.com/merlyescalona/ngsphy.Contactmerlyescalona@uvigo.es.dposada@uvigo.es
Interactions of pathogenic and commensal strains of Mannheimia haemolytica with differentiated bovine airway epithelial cells grown at an air-liquid interface
Authors: Cozens Daniel , Sutherland Erin , Lauder Miquel , Taylor Geraldine , Berry Catherine C. , Davies Robert L. 
Published: October 2017

AbstractMannheimia haemolyticaserotype A2 is a common commensal species present in the nasopharynx of healthy cattle. However, prior to the onset of bovine pneumonic pasteurellosis, there is sudden increase inM. haemolyticaserotype A1 within the upper respiratory tract. The events during this selective proliferation of serotype A1 strains are poorly characterised. In this investigation, a differentiated bovine airway epithelial cell culture was used to study the interactions of A1 and A2 bovine isolates with the respiratory epithelium. This model reproduced the key defences of the airway epithelium, including tight junctions and mucociliary clearance. Although initial adherence of the serotype A1 strains was low, by 12 hours post-infection the bacteria was able to traverse the tight junctions to form foci of infection below the apical surface. The size, density and number of these foci increased with time, as did the cytopathic effects observed in the bovine bronchial epithelial cells. Penetration ofM. haemolyticaA1 into the sub-apical epithelium was shown to be through transcytosis but not paracytosis. Commensal A2 bovine isolates however were not capable of colonising the model to a high degree, and did not penetrate the epithelium following initial adherence at the apical surface. This difference in their ability to colonise the respiratory epithelium may account for the sudden proliferation of serotype A1 in the onset of pneumonia pasteurellosis. The pathogenesis observed was replicated by virulent A2 ovine isolates; however colonisation was 10-fold lower in comparison to bovine A1 strains. This investigation provides new insight into the interactions ofM. haemolyticawith bovine airway epithelial cells which are occurringin vivoduring pneumonia pasteurellosis.
Allele-specific CRISPR/Cas9 genome editing of the single-base P23H mutation for rhodopsin associated dominant retinitis pigmentosa
Authors: Li Pingjuan , Kleinstiver Benjamin P. , Leon Mihoko Y. , Prew Michelle S. , Navarro-Gomez Daniel , Greenwald Scott H. , Pierce Eric A. , Joung J. Keith , Liu Qin 
Published: October 2017

AbstractTreatment strategies for dominantly inherited disorders typically involve silencing or ablating the pathogenic allele. CRISPR/Cas nucleases have shown promise in allele-specific knockout approaches when the dominant allele creates unique protospacer adjacent motifs (PAMs) that can lead to allele restricted targeting. Here, we present a spacer-mediated allele-specific knockout approach that utilizes both SpCas9 variants and truncated single guide RNAs (trusgRNAs) to achieve efficient discrimination of a single-nucleotide mutation in rhodopsin (Rho)-P23H mice, a model of dominant retinitis pigmentosa (RP). We found that approximately 45% of the mutant P23H allele was edited at DNA level, and that the relative RNA expression of wild-type Rho was about 2.8 times more than that of mutant Rho in treated retinas. Furthermore, the progression of photoreceptor cell degeneration in outer nuclear layer was significantly delayed in treated regions of the Rho-P23H retinas at five weeks of age. Our proof-of-concept study therefore outlines a general strategy that could potentially be expanded to examine the therapeutic benefit of allele-specific gene editing approach to treat human P23H patient. Our study also extends allele-specific editing strategies beyond discrimination within the PAM sites, with potentially broad applicability to other dominant diseases.
Predicting cancer outcomes from histology and genomics using convolutional networks
Authors: Mobadersany Pooya , Yousefi Safoora , Amgad Mohamed , Gutman David A , Barnholtz-Sloan Jill S , Velazquez Vega Jose Enrique , Brat Daniel J , Cooper Lee AD 
Published: October 2017

ABSTRACTCancer histology reflects underlying molecular processes and disease progression, and contains rich phenotypic information that is predictive of patient outcomes. In this study, we demonstrate a computational approach for learning patient outcomes from digital pathology images using deep learning to combine the power of adaptive machine learning algorithms with traditional survival models. We illustrate how this approach can integrate information from both histology images and genomic biomarkers to predict time-to-event patient outcomes, and demonstrate performance surpassing the current clinical paradigm for predicting the survival of patients diagnosed with glioma. We also provide techniques to visualize the tissue patterns learned by these deep learning survival models, and establish a framework for addressing intratumoral heterogeneity and training data deficits.
A blueprint for human whole-cell modeling
Authors: Szigeti Balázs , Roth Yosef D. , Sekar John A. P. , Goldberg Arthur P. , Pochiraju Saahith C. , Karr Jonathan R. 
Published: October 2017

AbstractWhole-cell models of human cells are a central goal of systems biology. Such models could help researchers understand cell biology and help physicians treat disease. Despite significant challenges, we believe that human whole-cell models are rapidly becoming feasible. To develop a plan for achieving human whole-cell models, we analyzed the existing models of individual cellular pathways, surveyed the biomodeling community, and reflected on our experience developing whole-cell models of bacteria. Based on these analyses, we propose a plan for a project, termed theHuman Whole-Cell Modeling Project, to achieve human whole-cell models. The foundations of the plan include technology development, standards development, and interdisciplinary collaboration.
Harvesting straw in Poland and Finland
Authors: Joensuu Katri , Sinkko Taija 
Published: October 2017

Purpose
There is growing interest in using crop residues, particularly cereal straw, to replace fossil fuels in heat and electricity production. The purpose of the present study was to assess and compare the environmental impacts of straw production in two European Union countries, Poland and Finland.

Design/methodology/approach
The selected environmental impacts were greenhouse gas (GHG) emissions, biodiversity and soil physical quality. The latter was represented by the indicators of soil erosion and compaction. For biodiversity and erosion assessment, the authors used two methods that could be used with existing easily accessible data and thus did not require excessive fieldwork.

Findings
Compared to the fossil reference fuel, coal, straw production caused minimal GHG emissions in both of the subject countries. Biodiversity and erosion impacts were greater in Poland, while the potential risk of soil compaction caused by field traffic is greater in Finland.

Originality/value
The study provides insight into the impacts of bioenergy production on biodiversity and soil quality, of which there is currently limited knowledge.
Professional value and ethical self-regulation in the development of modern librarianship
Authors: Hansson Joacim 
Published: October 2017

Purpose
The purpose of this paper is twofold: first, to make a contribution to the theoretical understanding of documents and documentary agency in society through examples from a defined institutional and professional setting; and second, to create an understanding for the role of ethical codes in the process of defining and developing modern librarianship.

Design/methodology/approach
This study analyses the role of documentation carrying content of professional ethics in the formulation of modern librarianship. This is done through a series of example documents of various kinds, such as founding charters, peer handbooks and ethical codes systematically analysed through the use of document theory and theory on institutional change.

Findings
The findings of this study suggest that documents pronouncing ethical self-regulation within librarianship play a primarily legitimising role in situations where new types of libraries emerge or when libraries adapt to social change. The study proposes legitimacy as a key aspect of documentality, thus supplementing the established understanding of the concept.

Originality/value
This study is the first to analyse the role of ethical codes in libraries using document theory. It brings new knowledge to the role of ethical self-regulation in librarianship over time and in different institutional contexts. In suggesting a developed definition of documentality, it contributes to the theoretical understanding of the role of documents and documentation in institutions and in society at large.
“Google is not fun”: an investigation of how Swedish teenagers frame online searching
Authors: Andersson Cecilia 
Published: October 2017

PurposeThe purpose of this paper is to investigate the role of Google in everyday online searching activities of Swedish teenagers in different contexts.Design/methodology/approachThe study is qualitative and material has been produced through interviews and observations in two different schools with participants aged 15-16. Goffman’s frame analysis provides the analytical lens for studying how activities are assigned meaning.FindingsThree different framings in relation to using Google and googling are identified in the material: Google and fact-finding, Google as a neutral infrastructure, and Google as an authority. There is an interplay between activity, context, and interaction in defining the role of Google. In relation to school, the fact-finding framing is more pronounced whereas the infrastructure framing comes forth more in their free time activities. The authority framing cuts across both framings and underpins their trust in the search engine.Originality/valueThe study addresses the way that Google is embedded in online activities and how the search engine is viewed in various contexts, as well as how it is made invisible in some contexts. Previous research has not addressed Google’s role in specific in relation to various everyday uses.
Social relevance assessments for virtual worlds
Authors: Costello Kaitlin Light 
Published: October 2017

PurposeThe purpose of this paper is to introduce the concept of social relevance assessments, which are judgments made by individuals when they seek out information within virtual social worlds such as online support groups (OSGs).Design/methodology/approachConstructivist grounded theory was employed to examine the phenomenon of information exchange in OSGs for chronic kidney disease. In-depth interviews were conducted with 12 participants, and their posts in three OSGs were also harvested. Data were analyzed using inductive content analysis and the constant comparative method. Theoretical sampling was conducted until saturation was reached. Member checking, peer debriefing, and triangulation were used to verify results.FindingsThere are two levels of relevance assessment that occur when people seek out information in OSGs. First, participants evaluate the OSG to determine whether or not the group is an appropriate place for information exchange about kidney disease. Second, participants evaluate individual users on the OSG to see if they are appropriate people with whom to exchange information. This often takes the form of similarity assessment, whereby people try to determine whether or not they are similar to specific individuals on the forums. They use a variety of heuristics to assess similarity as part of this process.Originality/valueThis paper extends the author’s understanding of relevance in information science in two fundamental ways. Within the context of social information exchange, relevance is socially constructed and is based on social characteristics, such as age, shared beliefs, and experience. Moreover, relevance is assessed both when participants seek out information and when they disclose information, suggesting that the conception of relevance as a process that occurs primarily during information seeking is limited.
Three key affordances for serendipity
Authors: Björneborn Lennart 
Published: October 2017

PurposeSerendipity is an interesting phenomenon to study in information science as it plays a fundamental – but perhaps underestimated – role in how we discover, explore, and learn in all fields of life. The purpose of this paper is to operationalize the concept of serendipity by providing terminological “building blocks” for understanding connections between environmental and personal factors in serendipitous encounters. Understanding these connections is essential when designing affordances in physical and digital environments that can facilitate serendipity.Design/methodology/approachIn this paper, serendipity is defined as what happens when we, in unplanned ways, encounter resources (information, things, people, etc.) that we find interesting. In the outlined framework, serendipity is understood as an affordance, i.e., a usage potential when environmental and personal factors correspond with each other. The framework introduces three key affordances for facilitating serendipity: diversifiability, traversability, and sensoriability, covering capacities of physical and digital environments to be diversified, traversed, and sensed. The framework is structured around couplings between the three key affordances and three key personal serendipity factors: curiosity, mobility, and sensitivity. Ten sub-affordances for serendipity and ten coupled personal sub-factors are also briefly outlined. Related research is compared with and mapped into the framework aiming at a theoretical validation. The affordance approach to serendipity is discussed, including different degrees and types of serendipity.FindingsAll the terminological “building blocks” in the framework are seen to resonate with the included related research. Serendipity is found to be a commonplace phenomenon in everyday life. It is argued that we cannot “engineer” nor “design” serendipityper se, but can design affordances for serendipity. Serendipity may thus be intended by designers, but must always be unplanned by users. The outlined affordance approach to serendipity points to the importance of our sensory-motor abilities to discover and explore serendipitous affordances.Research limitations/implicationsImplications of the framework for designing physical and digital environments with affordances for serendipity are briefly considered. It is suggested that physical environments may have a primacy regarding affordances of sensoriability for facilitating serendipity, and digital environments a primacy regarding traversability, whereas physical and digital environments may afford similar degrees of diversifiability. In future research, the framework needs further empirical validation in physical and digital environments.Originality/valueNo other research has been found addressing affordances for serendipity and connections between environmental and personal factors in similarly detailed ways. The outlined framework and typology may function as a baseline for further serendipity studies.
Cultural heritage as digital noise: nineteenth century newspapers in the digital archive
Authors: Jarlbrink Johan , Snickars Pelle 
Published: October 2017

PurposeThe purpose of this paper is to explore and analyze the digitized newspaper collection at the National Library of Sweden, focusing on cultural heritage as digital noise. In what specific ways are newspapers transformed in the digitization process? If the digitized document is not the same as the source document – is it still a historical record, or is it transformed into something else?Design/methodology/approachThe authors have analyzed the XML files fromAftonbladet1830 to 1862. The most frequent newspaper words not matching a high-quality references corpus were selected to zoom in on the noisiest part of the paper. The variety of the interpretations generated by optical character recognition (OCR) was examined, as well as texts generated by auto-segmentation. The authors have made a limited ethnographic study of the digitization process.FindingsThe research shows that the digital collection ofAftonbladetcontains extreme amounts of noise: millions of misinterpreted words generated by OCR, and millions of texts re-edited by the auto-segmentation tool. How the tools work is mostly unknown to the staff involved in the digitization process? Sticking to any idea of a provenance chain is hence impossible, since many steps have been outsourced to unknown factors affecting the source document.Originality/valueThe detail examination of digitally transformed newspapers is valuable to scholars depending on newspaper databases in their research. The paper also highlights the fact that libraries outsourcing digitization processes run the risk of losing control over the quality of their collections.
Getting-to-know
Authors: Sköld Olle 
Published: October 2017

PurposeThe purpose of this paper is to investigate the sociocultural underpinnings of wiki-based knowledge production in the videogame domain, and to elucidate how these underpinnings relate to the formation of wikis as resources of videogame documentation.Design/methodology/approachThe paper is based on a three-month ethnographic investigation of knowledge practices on the Dark Souls Wiki (DSW). In focus of the analysis were the boundaries and knowledge aims of the DSW, together with how its contributors organized inquiries and used various sources, methods of investigation, and ways of warranting knowledge claims.FindingsThe principal result of the paper is an empirical account of how the DSW functions as a culture of knowledge production, and how the content and structure of the wiki connects to the knowledge practices of its contributors. Four major factors that influenced knowledge practices on the wiki were identified: the structures and practices established by the community’s earlier wiki efforts; principles and priorities that informed wiki knowledge practices; the characteristics of the videogame in focus of the site’s knowledge-building work; the extent and types of relevant documentation provided by videogame industry, the videogaming press included.Originality/valuePrevious research has shown interest in investigating the mechanisms by which community-created knowledge and online resources of documentation emerge, and how these are utilized in play. There is, however, little research seeking to elucidate the sociocultural structures and practices that determine and sustain collaborative online videogame knowledge production.