375 research outputs found

    Impacts of climate change, land-use change and phosphorus reduction on phytoplankton in the River Thames (UK)

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    Potential increases of phytoplankton concentrations in river systems due to global warming and changing climate could pose a serious threat to the anthropogenic use of surface waters. Nevertheless, the extent of the effect of climatic alterations on phytoplankton concentrations in river systems has not yet been analysed in detail. In this study, we assess the impact of a change in precipitation and temperature on river phytoplankton concentration by means of a physically-based model. A scenario-neutral methodology has been employed to evaluate the effects of climate alterations on flow, phosphorus concentration and phytoplankton concentration of the River Thames (southern England). In particular, five groups of phytoplankton are considered, representing a range of size classes and pigment phenotypes, under three different land-use/land-management scenarios to assess their impact on phytoplankton population levels. The model results are evaluated within the framework of future climate projections, using the UK Climate Projections 09 (UKCP09) for the 2030s. The results of the model demonstrate that an increase in average phytoplankton concentration due to climate change is highly likely to occur, with the magnitude varying depending on the location along the River Thames. Cyanobacteria show significant increases under future climate change and land use change. An expansion of intensive agriculture accentuates the growth in phytoplankton, especially in the upper reaches of the River Thames. However, an optimal phosphorus removal mitigation strategy, which combines reduction of fertiliser application and phosphorus removal from wastewater, can help to reduce this increas

    Lumpability Abstractions of Rule-based Systems

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    The induction of a signaling pathway is characterized by transient complex formation and mutual posttranslational modification of proteins. To faithfully capture this combinatorial process in a mathematical model is an important challenge in systems biology. Exploiting the limited context on which most binding and modification events are conditioned, attempts have been made to reduce the combinatorial complexity by quotienting the reachable set of molecular species, into species aggregates while preserving the deterministic semantics of the thermodynamic limit. Recently we proposed a quotienting that also preserves the stochastic semantics and that is complete in the sense that the semantics of individual species can be recovered from the aggregate semantics. In this paper we prove that this quotienting yields a sufficient condition for weak lumpability and that it gives rise to a backward Markov bisimulation between the original and aggregated transition system. We illustrate the framework on a case study of the EGF/insulin receptor crosstalk.Comment: In Proceedings MeCBIC 2010, arXiv:1011.005

    Differentiating BPD in adolescents with NSSI disorder: the role of adverse childhood experiences and current social relationships

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    Background: As borderline personality disorder (BPD) is increasingly considered a lifespan developmental disorder, we need to focus on risk factors and precursors in the developmental pathways to BPD, in order to enable early detection and intervention. Within this developmental pathway, adolescence is a crucial phase in the light of the manifestation of the disorder. Relational factors such as adverse childhood experiences and current relational problems can be considered important in adolescents who are at-risk for BPD. Nonsuicidal self-injury (NSSI) is a key precursor for adolescent BPD and one of the most promising targets for early detection and intervention of BPD. Methods: In a clinical sample of 152 adolescents engaging in nonsuicidal self-injury (NSSI) disorder referred to mental healthcare in Germany, this study investigated whether we can differentiate who has BPD from 1) adverse childhood experiences; and 2) the quality of current relationships, both with parents and peers. BPD was assessed both categorically as a dichotomized score and dimensionally as a continuous score. Results: More adverse childhood experiences, but not low quality of current social relationships, were related to more BPD symptoms and an increased risk for meeting full criteria for BPD. In the dimensional model, current social relationship quality with parents and peers did not show a moderating (protecting or aggravating) effect on the association between adverse childhood experiences and BPD. Using a categorical approach, however, the association between childhood adversity and meeting full criteria for BPD was higher in individuals reporting higher quality of current parent-child relationship. Conclusions: These results highlight adverse childhood experiences as risk factors of BPD, while the role of current social relationships seems more complex

    Impacts of climate change, land-use change and phosphorus reduction on phytoplankton in the River Thames (UK)

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    Potential increases of phytoplankton concentrations in river systems due to global warming and changing climate could pose a serious threat to the anthropogenic use of surface waters. Nevertheless, the extent of the effect of climatic alterations on phytoplankton concentrations in river systems has not yet been analysed in detail. In this study, we assess the impact of a change in precipitation and temperature on river phytoplankton concentration by means of a physically-based model. A scenario-neutral methodology has been employed to evaluate the effects of climate alterations on flow, phosphorus concentration and phytoplankton concentration of the River Thames (southern England). In particular, five groups of phytoplankton are considered, representing a range of size classes and pigment phenotypes, under three different land-use/land-management scenarios to assess their impact on phytoplankton population levels. The model results are evaluated within the framework of future climate projections, using the UK Climate Projections 09 (UKCP09) for the 2030s. The results of the model demonstrate that an increase in average phytoplankton concentration due to climate change is highly likely to occur, with the magnitude varying depending on the location along the River Thames. Cyanobacteria show significant increases under future climate change and land use change. An expansion of intensive agriculture accentuates the growth in phytoplankton, especially in the upper reaches of the River Thames. However, an optimal phosphorus removal mitigation strategy, which combines reduction of fertiliser application and phosphorus removal from wastewater, can help to reduce this increase in phytoplankton concentration, and in some cases, compensate for the effect of rising temperature

    Computing Distances between Probabilistic Automata

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    We present relaxed notions of simulation and bisimulation on Probabilistic Automata (PA), that allow some error epsilon. When epsilon is zero we retrieve the usual notions of bisimulation and simulation on PAs. We give logical characterisations of these notions by choosing suitable logics which differ from the elementary ones, L with negation and L without negation, by the modal operator. Using flow networks, we show how to compute the relations in PTIME. This allows the definition of an efficiently computable non-discounted distance between the states of a PA. A natural modification of this distance is introduced, to obtain a discounted distance, which weakens the influence of long term transitions. We compare our notions of distance to others previously defined and illustrate our approach on various examples. We also show that our distance is not expansive with respect to process algebra operators. Although L without negation is a suitable logic to characterise epsilon-(bi)simulation on deterministic PAs, it is not for general PAs; interestingly, we prove that it does characterise weaker notions, called a priori epsilon-(bi)simulation, which we prove to be NP-difficult to decide.Comment: In Proceedings QAPL 2011, arXiv:1107.074

    ScreenTrack: Using a Visual History of a Computer Screen to Retrieve Documents and Web Pages

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    Computers are used for various purposes, so frequent context switching is inevitable. In this setting, retrieving the documents, files, and web pages that have been used for a task can be a challenge. While modern applications provide a history of recent documents for users to resume work, this is not sufficient to retrieve all the digital resources relevant to a given primary document. The histories currently available do not take into account the complex dependencies among resources across applications. To address this problem, we tested the idea of using a visual history of a computer screen to retrieve digital resources within a few days of their use through the development of ScreenTrack. ScreenTrack is software that captures screenshots of a computer at regular intervals. It then generates a time-lapse video from the captured screenshots and lets users retrieve a recently opened document or web page from a screenshot after recognizing the resource by its appearance. A controlled user study found that participants were able to retrieve requested information more quickly with ScreenTrack than under the baseline condition with existing tools. A follow-up study showed that the participants used ScreenTrack to retrieve previously used resources and to recover the context for task resumption.Comment: CHI 2020, 10 pages, 7 figure

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

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    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

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

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    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

    Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

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