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  1. AU="Thomas P. Quinn"
  2. AU="Grant, April"
  3. AU="Naddaf, Elie"
  4. AU="Park, Do-Hyun"
  5. AU="Posti, Jussi P"
  6. AU="Singh, Gargi"
  7. AU="Fuhrman, Dana Y"
  8. AU="Cholak, Spencer"
  9. AU="Tanowitz, Herbert B."
  10. AU="Gao, Jia-Pei"
  11. AU="Alvarez-Lerma, Francisco"
  12. AU="Junno, Juho-Antti"
  13. AU="Livermore, Polly"
  14. AU="Pervin, Irin"
  15. AU=Upadhyay Avnish K AU=Upadhyay Avnish K
  16. AU="Yabu, Hiroshi"
  17. AU="Soares, Mario J."
  18. AU="Haeusler, Gabrielle M"
  19. AU="Wang, Weiqing"
  20. AU="Fehr, Fabio"
  21. AU="Sasirekha, R" AU="Sasirekha, R"
  22. AU="Rajendraprasad, Girish"
  23. AU="Golbek, Thaddeus W"
  24. AU="Pranav Keshan"

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  1. Artikel ; Online: Human effects on brown bear diel activity may facilitate subadults foraging on Pacific salmon

    James P. Kilfoil / Thomas P. Quinn / Aaron J. Wirsing

    Global Ecology and Conservation, Vol 42, Iss , Pp e02407- (2023)

    2023  

    Abstract: Humans can markedly alter the temporal activity of wildlife. The ecological consequences of such temporal shifts are poorly understood but can lead to reduced fitness, increased competition, and trophic cascades under certain conditions. Furthermore, if ... ...

    Abstract Humans can markedly alter the temporal activity of wildlife. The ecological consequences of such temporal shifts are poorly understood but can lead to reduced fitness, increased competition, and trophic cascades under certain conditions. Furthermore, if individuals or species vary in their tolerance of human disturbance, then more resiliant individuals/species may be able to exploit resources eschewed by their more human-tolerant counterparts. Here, we explored the potential of a “temporal-shield” offered by human disturbance, using brown bears (Ursus arctos) foraging on sockeye salmon (O. nerka) in southwestern Alaska as a model system. We deployed motion-activated cameras on six salmon spawning streams over five summers (2013–2018), capturing footage of 1935 independent bear encounters including single adult bears (n = 1612), females with cubs (n = 197) and subadults (n = 126). Using a von Mises circular kernel density estimation procedure, we estimated the overlap of activity for each bear group type relative to humans observed on our cameras (n = 932 encounters; all researchers). All bears avoided peak times of human activity, but socially-subordinate subadults exhibited significantly higher overlap with humans (23 %) as compared to females with cubs and single adults (11 % and 12 %, respectively). Furthermore, subadult bears increased their overlap with human activity over the course of each sampling year, while females with cubs and single adults generally decreased their overlap. These results highlight that the effects of human-disturbance on large carnivores can be complex and may allow for increased foraging opportunities for socially subordinate, but more human-tolerant, individuals.
    Schlagwörter Behavior ; Carnivore ; Human disturbance ; Intraspecific competition ; Predator ; Ursus arctos ; Ecology ; QH540-549.5
    Thema/Rubrik (Code) 590
    Sprache Englisch
    Erscheinungsdatum 2023-04-01T00:00:00Z
    Verlag Elsevier
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  2. Artikel ; Online: Visualizing balances of compositional data

    Thomas P. Quinn

    F1000Research, Vol

    A new alternative to balance dendrograms [version 1; referees: 2 approved]

    2018  Band 7

    Abstract: Balances have become a cornerstone of compositional data analysis. However, conceptualizing balances is difficult, especially for high-dimensional data. Most often, investigators visualize balances with the balance dendrogram, but this technique is not ... ...

    Abstract Balances have become a cornerstone of compositional data analysis. However, conceptualizing balances is difficult, especially for high-dimensional data. Most often, investigators visualize balances with the balance dendrogram, but this technique is not necessarily intuitive and does not scale well for large data. This manuscript introduces the 'balance' package for the R programming language. This package visualizes balances of compositional data using an alternative to the balance dendrogram. This alternative contains the same information coded by the balance dendrogram, but projects data on a common scale that facilitates direct comparisons and accommodates high-dimensional data. By stripping the branches from the tree, 'balance' can cleanly visualize any subset of balances without disrupting the interpretation of the remaining balances. As an example, this package is applied to a publicly available meta-genomics data set measuring the relative abundance of 500 microbe taxa.
    Schlagwörter Medicine ; R ; Science ; Q
    Sprache Englisch
    Erscheinungsdatum 2018-08-01T00:00:00Z
    Verlag F1000 Research Ltd
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  3. Artikel ; Online: Two decades of change in sea star abundance at a subtidal site in Puget Sound, Washington.

    Helen R Casendino / Katherine N McElroy / Mark H Sorel / Thomas P Quinn / Chelsea L Wood

    PLoS ONE, Vol 18, Iss 6, p e

    2023  Band 0286384

    Abstract: Long-term datasets can reveal otherwise undetectable ecological trends, illuminating the historical context of contemporary ecosystem states. We used two decades (1997-2019) of scientific trawling data from a subtidal, benthic site in Puget Sound, ... ...

    Abstract Long-term datasets can reveal otherwise undetectable ecological trends, illuminating the historical context of contemporary ecosystem states. We used two decades (1997-2019) of scientific trawling data from a subtidal, benthic site in Puget Sound, Washington, USA to test for gradual trends and sudden shifts in total sea star abundance across 11 species. We specifically assessed whether this community responded to the sea star wasting disease (SSWD) epizootic, which began in 2013. We sampled at depths of 10, 25, 50 and 70 m near Port Madison, WA, and obtained long-term water temperature data. To account for species-level differences in SSWD susceptibility, we divided our sea star abundance data into two categories, depending on the extent to which the species is susceptible to SSWD, then conducted parallel analyses for high-susceptibility and moderate-susceptibility species. The abundance of high-susceptibility sea stars declined in 2014 across depths. In contrast, the abundance of moderate-susceptibility species trended downward throughout the years at the deepest depths- 50 and 70 m-and suddenly declined in 2006 across depths. Water temperature was positively correlated with the abundance of moderate-susceptibility species, and uncorrelated with high-susceptibility sea star abundance. The reported emergence of SSWD in Washington State in the summer of 2014 provides a plausible explanation for the subsequent decline in abundance of high-susceptibility species. However, no long-term stressors or mortality events affecting sea stars were reported in Washington State prior to these years, leaving the declines we observed in moderate-susceptibility species preceding the 2013-2015 SSWD epizootic unexplained. These results suggest that the subtidal sea star community in Port Madison is dynamic, and emphasizes the value of long-term datasets for evaluating patterns of change.
    Schlagwörter Medicine ; R ; Science ; Q
    Thema/Rubrik (Code) 333
    Sprache Englisch
    Erscheinungsdatum 2023-01-01T00:00:00Z
    Verlag Public Library of Science (PLoS)
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  4. Artikel ; Online: Personalized single-cell networks

    Haripriya Harikumar / Thomas P. Quinn / Santu Rana / Sunil Gupta / Svetha Venkatesh

    BioData Mining, Vol 14, Iss 1, Pp 1-

    a framework to predict the response of any gene to any drug for any patient

    2021  Band 15

    Abstract: Abstract Background The last decade has seen a major increase in the availability of genomic data. This includes expert-curated databases that describe the biological activity of genes, as well as high-throughput assays that measure gene expression in ... ...

    Abstract Abstract Background The last decade has seen a major increase in the availability of genomic data. This includes expert-curated databases that describe the biological activity of genes, as well as high-throughput assays that measure gene expression in bulk tissue and single cells. Integrating these heterogeneous data sources can generate new hypotheses about biological systems. Our primary objective is to combine population-level drug-response data with patient-level single-cell expression data to predict how any gene will respond to any drug for any patient. Methods We take 2 approaches to benchmarking a “dual-channel” random walk with restart (RWR) for data integration. First, we evaluate how well RWR can predict known gene functions from single-cell gene co-expression networks. Second, we evaluate how well RWR can predict known drug responses from individual cell networks. We then present two exploratory applications. In the first application, we combine the Gene Ontology database with glioblastoma single cells from 5 individual patients to identify genes whose functions differ between cancers. In the second application, we combine the LINCS drug-response database with the same glioblastoma data to identify genes that may exhibit patient-specific drug responses. Conclusions Our manuscript introduces two innovations to the integration of heterogeneous biological data. First, we use a “dual-channel” method to predict up-regulation and down-regulation separately. Second, we use individualized single-cell gene co-expression networks to make personalized predictions. These innovations let us predict gene function and drug response for individual patients. Taken together, our work shows promise that single-cell co-expression data could be combined in heterogeneous information networks to facilitate precision medicine.
    Schlagwörter Computer applications to medicine. Medical informatics ; R858-859.7 ; Analysis ; QA299.6-433
    Thema/Rubrik (Code) 004
    Sprache Englisch
    Erscheinungsdatum 2021-08-01T00:00:00Z
    Verlag BMC
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  5. Artikel ; Online: HIV Capsid Inhibitors Beyond PF74

    Carole McArthur / Fabio Gallazzi / Thomas P. Quinn / Kamal Singh

    Diseases, Vol 7, Iss 4, p

    2019  Band 56

    Abstract: Human immunodeficiency virus (HIV) capsid plays important roles at multiple stages of viral replication. At the initial stages, controlled uncoating (disassembly) of the capsid ensures efficient reverse transcription of the single-stranded RNA genome, ... ...

    Abstract Human immunodeficiency virus (HIV) capsid plays important roles at multiple stages of viral replication. At the initial stages, controlled uncoating (disassembly) of the capsid ensures efficient reverse transcription of the single-stranded RNA genome, into the double-stranded DNA. Whereas at later stages, a proper assembly of capsid ensures the formation of a mature infectious virus particle. Hence, the inhibition of capsid assembly and/or disassembly has been recognized as a potential therapeutic strategy, and several capsid inhibitors have been reported. Of these, PF-3450074 (PF74) has been extensively studied. Recently reported GS-CA inhibitors (GS-CA1 and GS-6207), have shown a strong potential and appear to contain a PF74 scaffold. The location of resistance mutations and the results of structural studies further suggest that GS-CA compounds and PF74 share the same binding pocket, which is located between capsid monomers. Additionally, phenylalanine derivatives containing the PF74 scaffold show slightly enhanced capsid inhibiting activity. A comparison of capsid structures in complex with host factors and PF74, reveals the presence of common chemical entities at topologically equivalent positions. Here we present the status of capsid inhibitors that contain PF74 scaffolds and propose that the PF74 scaffold may be used to develop strong and safe capsid inhibitors.
    Schlagwörter human immunodeficiency virus ; capsid ; assembly ; small molecule inhibitors ; pf74 ; gs-ca1 ; gs-6207 ; disassembly ; uncoating ; Medicine ; R
    Thema/Rubrik (Code) 540
    Sprache Englisch
    Erscheinungsdatum 2019-10-01T00:00:00Z
    Verlag MDPI AG
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  6. Artikel ; Online: DeepTRIAGE

    Adham Beykikhoshk / Thomas P. Quinn / Samuel C. Lee / Truyen Tran / Svetha Venkatesh

    BMC Medical Genomics, Vol 13, Iss S3, Pp 1-

    interpretable and individualised biomarker scores using attention mechanism for the classification of breast cancer sub-types

    2020  Band 10

    Abstract: Abstract Background Breast cancer is a collection of multiple tissue pathologies, each with a distinct molecular signature that correlates with patient prognosis and response to therapy. Accurately differentiating between breast cancer sub-types is an ... ...

    Abstract Abstract Background Breast cancer is a collection of multiple tissue pathologies, each with a distinct molecular signature that correlates with patient prognosis and response to therapy. Accurately differentiating between breast cancer sub-types is an important part of clinical decision-making. Although this problem has been addressed using machine learning methods in the past, there remains unexplained heterogeneity within the established sub-types that cannot be resolved by the commonly used classification algorithms. Methods In this paper, we propose a novel deep learning architecture, called DeepTRIAGE (Deep learning for the TRactable Individualised Analysis of Gene Expression), which uses an attention mechanism to obtain personalised biomarker scores that describe how important each gene is in predicting the cancer sub-type for each sample. We then perform a principal component analysis of these biomarker scores to visualise the sample heterogeneity, and use a linear model to test whether the major principal axes associate with known clinical phenotypes. Results Our model not only classifies cancer sub-types with good accuracy, but simultaneously assigns each patient their own set of interpretable and individualised biomarker scores. These personalised scores describe how important each feature is in the classification of any patient, and can be analysed post-hoc to generate new hypotheses about latent heterogeneity. Conclusions We apply the DeepTRIAGE framework to classify the gene expression signatures of luminal A and luminal B breast cancer sub-types, and illustrate its use for genes as well as the GO and KEGG gene sets. Using DeepTRIAGE, we calculate personalised biomarker scores that describe the most important features for classifying an individual patient as luminal A or luminal B. In doing so, DeepTRIAGE simultaneously reveals heterogeneity within the luminal A biomarker scores that significantly associate with tumour stage, placing all luminal samples along a continuum of severity.
    Schlagwörter Breast cancer ; Precision medicine ; TCGA ; Deep learning ; Internal medicine ; RC31-1245 ; Genetics ; QH426-470
    Thema/Rubrik (Code) 004
    Sprache Englisch
    Erscheinungsdatum 2020-02-01T00:00:00Z
    Verlag BMC
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  7. Artikel: Selection on the timing of migration and breeding: A neglected aspect of fishing‐induced evolution and trait change

    Tillotson, Michael D / Thomas P Quinn

    Fish and fisheries. 2018 Jan., v. 19, no. 1

    2018  

    Abstract: Fishing can drive changes in important phenotypic traits through plastic and evolutionary pathways. Size‐selective harvest is a primary driver of such trait change, has received much attention in the literature and is now commonly considered in ... ...

    Abstract Fishing can drive changes in important phenotypic traits through plastic and evolutionary pathways. Size‐selective harvest is a primary driver of such trait change, has received much attention in the literature and is now commonly considered in fisheries management. The potential for selection on behavioural traits has received less study, but mounting evidence suggests that aggression, foraging behaviour and linked traits can also be affected by fishing. An important phenomenon that has received much less attention is selection on reproductive phenology (i.e., the timing of breeding). The potential for this type of “temporal selection” is widespread because there is often substantial variability in reproductive phenology within fish populations, and fisheries management strategies or fishermen's behaviours can cause fishing effort to vary greatly over time. For example, seasonal closures may expose only early or late breeding individuals to harvest as observed in a range of marine and freshwater fisheries. Such selection may induce evolutionary responses in phenological traits, but can also have demographic impacts such as shortened breeding seasons and reduced phenotypic diversity. These changes can in turn influence productivity, reduce the efficacy of management, exacerbate ongoing climate‐driven changes in phenology and reduce resilience to environmental change. In this essay, we describe how fisheries management can cause temporal variability in harvest, and describe the types of selection on temporal traits that can result. We then summarize the likely biological consequences of temporally selective fishing on populations and population complexes and conclude by identifying areas for future research.
    Schlagwörter aggression ; breeding ; breeding season ; evolution ; fish communities ; fisheries management ; fishermen ; foraging ; freshwater fisheries ; harvesting ; phenology ; phenotype ; phenotypic variation ; temporal variation
    Sprache Englisch
    Erscheinungsverlauf 2018-01
    Umfang p. 170-181.
    Erscheinungsort John Wiley & Sons, Ltd
    Dokumenttyp Artikel
    Anmerkung JOURNAL ARTICLE
    ZDB-ID 2024569-5
    ISSN 1467-2979 ; 1467-2960
    ISSN (online) 1467-2979
    ISSN 1467-2960
    DOI 10.1111/faf.12248
    Datenquelle NAL Katalog (AGRICOLA)

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  8. Artikel ; Online: Beyond Correlation in the Detection of Climate Change Impacts

    Michael D Tillotson / Thomas P Quinn

    PLoS ONE, Vol 11, Iss 4, p e

    Testing a Mechanistic Hypothesis for Climatic Influence on Sockeye Salmon (Oncorhynchus nerka) Productivity.

    2016  Band 0154356

    Abstract: Detecting the biological impacts of climate change is a current focus of ecological research and has important applications in conservation and resource management. Owing to a lack of suitable control systems, measuring correlations between time series ... ...

    Abstract Detecting the biological impacts of climate change is a current focus of ecological research and has important applications in conservation and resource management. Owing to a lack of suitable control systems, measuring correlations between time series of biological attributes and hypothesized environmental covariates is a common method for detecting such impacts. These correlative approaches are particularly common in studies of exploited fish species because rich biological time-series data are often available. However, the utility of species-environment relationships for identifying or predicting biological responses to climate change has been questioned because strong correlations often deteriorate as new data are collected. Specifically stating and critically evaluating the mechanistic relationship(s) linking an environmental driver to a biological response may help to address this problem. Using nearly 60 years of data on sockeye salmon from the Kvichak River, Alaska we tested a mechanistic hypothesis linking water temperatures experienced during freshwater rearing to population productivity by modeling a series of intermediate, deterministic relationships and evaluating temporal trends in biological and environmental time-series. We found that warming waters during freshwater rearing have profoundly altered patterns of growth and life history in this population complex yet there has been no significant correlation between water temperature and metrics of productivity commonly used in fisheries management. These findings demonstrate that pairing correlative approaches with careful consideration of the mechanistic links between populations and their environments can help to both avoid spurious correlations and identify biologically important, but not statistically significant relationships, and ultimately producing more robust conclusions about the biological impacts of climate change.
    Schlagwörter Medicine ; R ; Science ; Q
    Thema/Rubrik (Code) 333
    Sprache Englisch
    Erscheinungsdatum 2016-01-01T00:00:00Z
    Verlag Public Library of Science (PLoS)
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  9. Artikel ; Online: GraphDTA: Predicting drug–target binding affinity with graph neural networks

    Thin Nguyen / Hang Le / Thomas P. Quinn / Thuc Le / Svetha Venkatesh

    Abstract: AbstractThe development of new drugs is costly, time consuming, and often accompanied with safety issues. Drug repurposing can avoid the expensive and lengthy process of drug development by finding new uses for already approved drugs. In order to ... ...

    Abstract AbstractThe development of new drugs is costly, time consuming, and often accompanied with safety issues. Drug repurposing can avoid the expensive and lengthy process of drug development by finding new uses for already approved drugs. In order to repurpose drugs effectively, it is useful to know which proteins are targeted by which drugs. Computational models that estimate the interaction strength of new drug–target pairs have the potential to expedite drug repurposing. Several models have been proposed for this task. However, these models represent the drugs as strings, which is not a natural way to represent molecules. We propose a new model called GraphDTA that represents drugs as graphs and uses graph neural networks to predict drug–target affinity. We show that graph neural networks not only predict drug–target affinity better than non-deep learning models, but also outperform competing deep learning methods. Our results confirm that deep learning models are appropriate for drug–target binding affinity prediction, and that representing drugs as graphs can lead to further improvements.Availability of data and materialsThe proposed models are implemented in Python. Related data, pre-trained models, and source code are publicly available at https://github.com/thinng/GraphDTA.All scripts and data needed to reproduce the post-hoc statistical analysis are available from https://doi.org/10.5281/zenodo.3603523.
    Schlagwörter covid19
    Verlag biorxiv
    Dokumenttyp Artikel ; Online
    DOI 10.1101/684662
    Datenquelle COVID19

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  10. Artikel: Climate and conspecific density trigger pre-spawning mortality in sockeye salmon (Oncorhynchus nerka)

    Tillotson, Michael D / Thomas P. Quinn

    Fisheries research. 2017 Apr., v. 188

    2017  

    Abstract: Pre-spawning mortality (PSM) has been occasionally observed in association with high densities of adult Pacific salmon (Oncorhynchus spp.), but because large escapements are rare, the phenomenon remains poorly understood. A large spawning escapement (∼12 ...

    Abstract Pre-spawning mortality (PSM) has been occasionally observed in association with high densities of adult Pacific salmon (Oncorhynchus spp.), but because large escapements are rare, the phenomenon remains poorly understood. A large spawning escapement (∼12 times the 54year median, and 3X the previous maximum) to a small stream in Alaska provided a unique opportunity to explore the factors that contribute to density-driven spawning ground mortality. After comparing patterns of mortality in 2014 with over 20 years of prior abundance and environmental data, we identified low dissolved oxygen (DO) as likely contributing to PSM. We then utilized a fish habitat-DO model to explore the roles of density-dependent and -independent factors in reducing DO. Stream flow and spawning density were identified as primary drivers of oxygen availability. Despite suboptimal oxygen levels the salmon did not die abruptly. Rather, on average they lived as long as in previous years (mean=9.99 d), but many (55%) failed to complete spawning prior to death. Our results suggest that this mortality was ultimately a density-dependent process, exacerbated by low-flow conditions. Given projected effects of climate change on river flows and temperatures, similar events may occur more frequently in parts of the range of salmon where abundances remain high.
    Schlagwörter adults ; climate ; climate change ; death ; dissolved oxygen ; models ; mortality ; Oncorhynchus nerka ; oxygen ; rivers ; salmon ; spawning ; stream flow ; streams ; temperature ; Alaska
    Sprache Englisch
    Erscheinungsverlauf 2017-04
    Umfang p. 138-148.
    Erscheinungsort Elsevier B.V.
    Dokumenttyp Artikel
    ZDB-ID 406532-3
    ISSN 0165-7836
    ISSN 0165-7836
    DOI 10.1016/j.fishres.2016.12.013
    Datenquelle NAL Katalog (AGRICOLA)

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