| 1. |
- Corander, Jukka, et al.
(författare)
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Bayesian Unsupervised Learning of DNA Regulatory Binding Regions
- 2009
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Ingår i: Advances in Artificial Intelligence. - : Hindawi Publishing Corporation. - 1687-7470 .- 1687-7489. ; , s. 219743-
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Tidskriftsartikel (refereegranskat)abstract
- Identification of regulatory binding motifs, that is, short specific words, within DNA sequences is a commonly occurring problem in computational bioinformatics. A wide variety of probabilistic approaches have been proposed in the literature to either scan for previously known motif types or to attempt de novo identification of a fixed number (typically one) of putative motifs. Mostapproaches assume the existence of reliable biodatabase information to build probabilistic a priori description of the motif classes. Examples of attempts to do probabilistic unsupervised learning about the number of putative de novo motif types and theirpositions within a set of DNA sequences are very rare in the literature. Here we show how such a learning problem can be formulated using a Bayesian model that targets to simultaneously maximize the marginal likelihood of sequence data arising under multiple motif types as well as under the background DNA model, which equals a variable length Markov chain. It is demonstrated how the adopted Bayesian modelling strategy combined with recently introduced nonstandard stochastic computation tools yields a more tractable learning procedure than is possible with the standard Monte Carlo approaches. Improvements and extensions of the proposed approach are also discussed.
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| 2. |
- Gnad, Daniel, 1987-, et al.
(författare)
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Beyond Stars – Generalized Topologies for Decoupled Search
- 2022
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Ingår i: Proceedings of the Thirty-Second International Conference on Automated Planning and Scheduling, ICAPS 2022. - : AAAI Press. - 9781577358749 ; , s. 110-118
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Konferensbidrag (refereegranskat)abstract
- Decoupled search decomposes a classical planning task by partitioning its variables such that the dependencies between the resulting factors form a star topology. In this topology, a single center factor can interact arbitrarily with a set of leaf factors. The leaves, however, can interact with each other only indirectly via the center. In this work, we generalize this structural requirement and allow arbitrary topologies. The components must not overlap, i.e., each state variable is assigned to exactly one factor, but the interaction between factors is not restricted. We show how this generalization is connected to star topologies, which implies the correctness of decoupled search with this novel type of decomposition. We introduce factoring methods that automatically identify these topologies on a given planning task. Empirically, the generalized factorings lead to increased applicability of decoupled search on standard IPC benchmarks, as well as to superior performance compared to known factoring methods.
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| 3. |
- Han, Mei, et al.
(författare)
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Promoted Self-construction of β-NiOOH in Amorphous High Entropy Electrocatalysts for the Oxygen Evolution Reaction
- 2022
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Ingår i: Applied Catalysis B. - : Elsevier. - 0926-3373 .- 1873-3883. ; 301
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Tidskriftsartikel (refereegranskat)abstract
- The exploration of an efficient electrocatalyst for the oxygen evolution reaction (OER) is urgently required for sustainable renewable-energy conversion and storage. Due to the increased chemical complexity, multimetallic catalysts provide flexibility to alter their electronic and crystal structure to attain a superior intrinsic catalytic activity via synergistic effects, which is seldom accomplished using single metal catalysts. However, the high chemical complexity increases the difficulty to prepare elemental homogenous catalysts and reveal their synergistic effect during OER process, which further hinder the design of multimetallic catalysts. Here, high entropy concept is utilized to design an NiFeCoMnAl oxide with amorphous structure as OER catalyst. The direct evidence of active Ni sites is provided by the operando Raman measurements and Fe can modify oxygen intermediates binding energy on Ni sites. The X-ray photoelectron spectroscopy (XPS) and X-ray absorption spectroscopy (XAS) reveal that the incorporation of Mn can construct the electron-rich environment of active Ni center, and the relatively lower oxidation state of Ni facilitates the self-construction of β-NiOOH intermediates, which shows promoted OER activity as confirmed by density functional theory calculations. Doping Co can enhance the conductivity and doping Al leads to the formation of nanoporous structure through dealloying process, thus each component is essential for improving OER performance. The optimized NiFeCoMnAl catalyst exhibits an overpotential of 190 mV at 10 mA cm-2 in 1 M KOH solution, much superior to the ternary and quaternary counterparts. This work sheds light on understanding the origin of high entropy catalysts’ OER activity and thereby enables the rational design of multinary transition metallic catalysts.
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| 4. |
- Whitehouse, Daniel P., et al.
(författare)
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Relationship of admission blood proteomic biomarkers levels to lesion type and lesion burden in traumatic brain injury : A CENTER-TBI study
- 2022
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Ingår i: EBioMedicine. - : Elsevier. - 2352-3964. ; 75
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Tidskriftsartikel (refereegranskat)abstract
- Background: We aimed to understand the relationship between serum biomarker concentration and lesion type and volume found on computed tomography (CT) following all severities of TBI.Methods: Concentrations of six serum biomarkers (GFAP, NFL, NSE, S100B, t-tau and UCH-L1) were measured in samples obtained <24 hours post-injury from 2869 patients with all severities of TBI, enrolled in the CENTER-TBI prospective cohort study (NCT02210221). Imaging phenotypes were defined as intraparenchymal haemorrhage (IPH), oedema, subdural haematoma (SDH), extradural haematoma (EDH), traumatic subarachnoid haemorrhage (tSAH), diffuse axonal injury (DAI), and intraventricular haemorrhage (IVH). Multivariable polynomial regression was performed to examine the association between biomarker levels and both distinct lesion types and lesion volumes. Hierarchical clustering was used to explore imaging phenotypes; and principal component analysis and k-means clustering of acute biomarker concentrations to explore patterns of biomarker clustering.Findings: 2869 patient were included, 68% (n=1946) male with a median age of 49 years (range 2-96). All severities of TBI (mild, moderate and severe) were included for analysis with majority (n=1946, 68%) having a mild injury (GCS 13-15). Patients with severe diffuse injury (Marshall III/IV) showed significantly higher levels of all measured biomarkers, with the exception of NFL, than patients with focal mass lesions (Marshall grades V/VI). Patients with either DAI+IVH or SDH+IPH+tSAH, had significantly higher biomarker concentrations than patients with EDH. Higher biomarker concentrations were associated with greater volume of IPH (GFAP, S100B, t-tau;adj r2 range:0·48-0·49; p<0·05), oedema (GFAP, NFL, NSE, t-tau, UCH-L1;adj r2 range:0·44-0·44; p<0·01), IVH (S100B;adj r2 range:0.48-0.49; p<0.05), Unsupervised k-means biomarker clustering revealed two clusters explaining 83·9% of variance, with phenotyping characteristics related to clinical injury severity.Interpretation: Interpretation: Biomarker concentration within 24 hours of TBI is primarily related to severity of injury and intracranial disease burden, rather than pathoanatomical type of injury.
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| 5. |
- Kish, Laszlo B., et al.
(författare)
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Does Information Have Mass?
- 2013
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Ingår i: Proceedings of the IEEE. - 0018-9219 .- 1558-2256. ; 101:9, s. 1895-1899
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- This article addresses the fundamental question of minimum mass related to a bit of information from the angles of quantum physics and special relativity. The results indicate that there are different answers depending on the physical situation, and sometimes the mass can even be negative. It tends to be skeptical about the earlier mass estimations, mentioned above, because the results indicate that the electron's mass does not play a role in any one of them. Finally, in a seemingly related but actually different and independent context of measured inaccuracies of the gravitation constant, it refers to experiments on the weight transient of memory devices after information writing and erasure.
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| 6. |
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| 7. |
- Narula, Neeraj, et al.
(författare)
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Associations of Antibiotics, Hormonal Therapies, Oral Contraceptives, and Long-Term NSAIDS With Inflammatory Bowel Disease: Results From the Prospective Urban Rural Epidemiology (PURE) Study.
- 2023
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Ingår i: Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association. - : Elsevier BV. - 1542-7714. ; 21:10
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Tidskriftsartikel (refereegranskat)abstract
- Several medications have been suspected to contribute to the etiology of inflammatory bowel disease (IBD). This study assessed the association between medication use and the risk of developing IBD using the Prospective Urban Rural Epidemiology cohort.This was a prospective cohort study of 133,137 individuals between the ages of 20 and 80 from 24 countries. Country-specific validated questionnaires documented baseline and follow-up medication use. Participants were followed up prospectively at least every 3 years. The main outcome was the development of IBD, including Crohn's disease (CD) and ulcerative colitis (UC). Short-term (baseline but not follow-up use) and long-term use (baseline and subsequent follow-up use) were evaluated. Results are presented as adjusted odds ratios (aORs) with 95% CIs.During a median follow-up period of 11.0 years (interquartile range, 9.2-12.2 y), there were 571 incident IBD cases (143 CD and 428 UC). Incident IBD was associated significantly with baseline antibiotic (aOR, 2.81; 95% CI, 1.67-4.73; P= .0001) and hormonal medication use (aOR, 4.43; 95% CI, 1.78-11.01; P= .001). Among females, previous or current oral contraceptive use also was associated with IBD development (aOR, 2.17; 95% CI, 1.70-2.77; P < .001). Nonsteroidal anti-inflammatory drug users also were observed to have increased odds of IBD (aOR, 1.80; 95% CI, 1.23-2.64; P= .002), which was driven by long-term use (aOR, 5.58; 95% CI, 2.26-13.80; P < .001). All significant results were consistent in direction for CD and UC with low heterogeneity.Antibiotics, hormonal medications, oral contraceptives, and long-term nonsteroidal anti-inflammatory drug use were associated with increased odds of incident IBD after adjustment for covariates.
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| 8. |
- Nightingale, Andrea
(författare)
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Commons and Alternative Rationalities: Subjectivity, Emotion and the (Non)rational Commons
- 2015
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Ingår i: Patterns of Commoning. - 9781937146832 ; , s. 298-308
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Bokkapitel (refereegranskat)abstract
- When I tell people that I work on inshore fisheries management the response is inevitably disparaging. Most people continue to assume that the commons is an ecological disaster waiting to happen and that all fishermen are greedy individuals. Yet my experience on the west coast of Scotland suggests that the fishing ground is governed by a variety of rationalities and subjectivities that often override the desire to maximize individual benefit. The question is how to understand these rationalities and subjectivities and what they mean for governance of the commons. When I first began thinking about ideas of subjectivity and emotion in relation to fisheries most people thought I was crazy. Talk to fishermen about their feelings? But it quickly became clear that I was on the right track. As one fishermen’s advocate said to me, laughing, “People are definitely not rational, especially fishermen. They make decisions based on other factors.” I became fascinated by what some of these “other” factors might be. My project begins with the excellent work done by Ostrom (1992) and others on design principles for the commons . Design principles focus on the institutional rules and norms required for effective management of collective resources. This work has been done within a rational choice framework, however, which leaves little space for understanding alternative rationalities or “non-rational” behaviors. If we simply add in perspectives on gender, kinship relations, emotional attachments to resources and land- and seascapes to our understanding of design principles, it prevents us from exploring how design principles emerge in the first place. Rather, I suggest we need to explore how institutions, resources and societies are co-emergent. This starting point shows how the “design” of a commons is a product of interactions, histories and relationships that need to be continually renewed . Taking co-emergence as a starting point has major implications for how we understand the dynamics of the commons. It is not a question of explaining how resource use affects the commons, but rather a question of exploring how the commons, as an institution, a place and an ecosystem, is embedded within and productive of the societies that use the commons. The two cannot be neatly separated, spatially, temporally or analytically. In terms of management, we need to understand how social processes both emerge from the commons ecosystem and are reflected in it.
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| 9. |
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