Comparison of ecosystem processes in a woodland and prairie pond with different hydroperiods

Shallow lakes and ponds constitute a significant number of water bodies worldwide. Many are heterotrophic, indicating that they are likely net contributors to global carbon cycling. Climate change is likely to have important impacts on these waterbodies. In this study, we examined two small Minnesota ponds; a permanent woodland pond and a temporary prairie pond. The woodland pond had lower levels of phosphorus and phytoplankton than the prairie pond. Using the open water oxygen method, we found the prairie pond typically had a higher level of gross primary production (GPP) and respiration (R) than the woodland pond, although the differences between the ponds varied with season. Despite the differences in GPP and R between the ponds the net ecosystem production was similar with both being heterotrophic. Since abundant small ponds may play an important role in carbon cycling and are likely to undergo changes in temperature and hydroperiod associated with climate change, understanding pond metabolism is critical in predicting impacts and designing management schemes to mitigate changes

Invisible Belfast:Flat ontologies and remediation of the post-conflict city

[in]visible Belfast was a research-driven indie alternate reality game (ARG) that ran for 6 weeks during the spring of 2011 in Belfast and was subsequently adapted, 5 years later into a fictional documentary for BBC Radio 4. The ARG is a participatory and dispersed narrative, which the audience play through. The text expands outward across both physical and digital platforms to create a mystery for the players using everyday platforms. The ARG is a product of media convergence and at its heart transmedial, defined by its complexity and modes of participation. The fictional radio documentary which remediated the ARG into a more simple linear structure, but possibly a more complex narrative form, retells parts of the story for new audiences. The premise of [in]visible belfast – the game and later the documentary – is itself an adaptation of writer Ciaran Carson’s novel The Star Factory (1997): a postmodern adventure through the complex psychogeography of Belfast. A trail through the labyrinthine text, which paints the history of Belfast in poetic prose. This article will map the concept’s journey from novel to game to radio, contextualising its development within its political and urban landscape and charting the remediation of the narratives as they fold out across multiple media and complex story arches. The article will draw together ideas from previous publications on ARG, transmediality and complex textualities from the authors and reflect on the textual trajectories that the remediation of the narrative has taken from the original book, through the ARG, into the radio documentary. Building upon recent approaches from environmental philosopher Tim Morton and games theorist Ian Bogost, the authors argue that Belfast’s history propels medial adaptations of a particular kind, characterised by a ‘flat’ ontology of space and time and a sort of diffuse and dark urban experience for designers/producers and players/listeners

Learning a Factor Model via Regularized PCA

We consider the problem of learning a linear factor model. We propose a regularized form of principal component analysis (PCA) and demonstrate through experiments with synthetic and real data the superiority of resulting estimates to those produced by pre-existing factor analysis approaches. We also establish theoretical results that explain how our algorithm corrects the biases induced by conventional approaches. An important feature of our algorithm is that its computational requirements are similar to those of PCA, which enjoys wide use in large part due to its efficiency

Recovering critique in an age of datafication

This article starts out from the need for critical work on processes of datafication and their consequences for the constitution of social knowledge and the social world. Current social science work on datafication has been greatly shaped by the theoretical approach of Bruno Latour, as reflected in the work of Actor Network Theory and Science and Technology Studies (ANT/STS). The article asks whether this approach, given its philosophical underpinnings, provides sufficient resources for the critical work that is required in relation to datafication. Drawing on Latour’s own reflections about the flatness of the social, it concludes that it does not, since key questions, in particular about the nature of social order cannot be asked or answered within ANT. In the article’s final section, three approaches from earlier social theory are considered as possible supplements to ANT/STS for a social science serious about addressing the challenges that datafication poses for society

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

Materializing digital collecting: an extended view of digital materiality

If digital objects are abundant and ubiquitous, why should consumers pay for, much less collect them? The qualities of digital code present numerous challenges for collecting, yet digital collecting can and does occur. We explore the role of companies in constructing digital consumption objects that encourage and support collecting behaviours, identifying material configuration techniques that materialise these objects as elusive and authentic. Such techniques, we argue, may facilitate those pleasures of collecting otherwise absent in the digital realm. We extend theories of collecting by highlighting the role of objects and the companies that construct them in materialising digital collecting. More broadly, we extend theories of digital materiality by highlighting processes of digital material configuration that occur in the pre-objectification phase of materialisation, acknowledging the role of marketing and design in shaping the qualities exhibited by digital consumption objects and consequently related consumption behaviours and experiences

Examining the generalizability of research findings from archival data

This initiative examined systematically the extent to which a large set of archival research findings generalizes across contexts. We repeated the key analyses for 29 original strategic management effects in the same context (direct reproduction) as well as in 52 novel time periods and geographies; 45% of the reproductions returned results matching the original reports together with 55% of tests in different spans of years and 40% of tests in novel geographies. Some original findings were associated with multiple new tests. Reproducibility was the best predictor of generalizability-for the findings that proved directly reproducible, 84% emerged in other available time periods and 57% emerged in other geographies. Overall, only limited empirical evidence emerged for context sensitivity. In a forecasting survey, independent scientists were able to anticipate which effects would find support in tests in new samples