| 1. |
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| 2. |
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| 3. |
- Abolfathi, Bela, et al.
(författare)
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The Fourteenth Data Release of the Sloan Digital Sky Survey : First Spectroscopic Data from the Extended Baryon Oscillation Spectroscopic Survey and from the Second Phase of the Apache Point Observatory Galactic Evolution Experiment
- 2018
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Ingår i: Astrophysical Journal Supplement Series. - : IOP Publishing Ltd. - 0067-0049 .- 1538-4365. ; 235:2
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Tidskriftsartikel (refereegranskat)abstract
- The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) has been in operation since 2014 July. This paper describes the second data release from this phase, and the 14th from SDSS overall (making this Data Release Fourteen or DR14). This release makes the data taken by SDSS-IV in its first two years of operation (2014-2016 July) public. Like all previous SDSS releases, DR14 is cumulative, including the most recent reductions and calibrations of all data taken by SDSS since the first phase began operations in 2000. New in DR14 is the first public release of data from the extended Baryon Oscillation Spectroscopic Survey; the first data from the second phase of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE-2), including stellar parameter estimates from an innovative data-driven machine-learning algorithm known as "The Cannon"; and almost twice as many data cubes from the Mapping Nearby Galaxies at APO (MaNGA) survey as were in the previous release (N = 2812 in total). This paper describes the location and format of the publicly available data from the SDSS-IV surveys. We provide references to the important technical papers describing how these data have been taken (both targeting and observation details) and processed for scientific use. The SDSS web site (www.sdss.org) has been updated for this release and provides links to data downloads, as well as tutorials and examples of data use. SDSS-IV is planning to continue to collect astronomical data until 2020 and will be followed by SDSS-V.
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| 4. |
- Ballesteros, Miguel, et al.
(författare)
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Going to the Roots of Dependency Parsing
- 2013
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Ingår i: Computational linguistics - Association for Computational Linguistics (Print). - : MIT Press. - 0891-2017 .- 1530-9312. ; 39:1, s. 5-13
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Tidskriftsartikel (refereegranskat)abstract
- Dependency trees used in syntactic parsing often include a root node representing a dummy word prefixed or suffixed to the sentence, a device that is generally considered a mere technical convenience and is tacitly assumed to have no impact on empirical results. We demonstrate that this assumption is false and that the accuracy of data-driven dependency parsers can in fact be sensitive to the existence and placement of the dummy root node. In particular, we show that a greedy, left-to-right, arc-eager transition-based parser consistently performs worse when the dummy root node is placed at the beginning of the sentence (following the current convention in data-driven dependency parsing) than when it is placed at the end or omitted completely. Control experiments with an arc-standard transition-based parser and an arc-factored graph-based parser reveal no consistent preferences but nevertheless exhibit considerable variation in results depending on root placement. We conclude that the treatment of dummy root nodes in data-driven dependency parsing is an underestimated source of variation in experiments and may also be a parameter worth tuning for some parsers.
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| 5. |
- Ballesteros, Miguel, et al.
(författare)
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MaltOptimizer : Fast and Effective Parser Optimization
- 2016
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Ingår i: Natural Language Engineering. - 1351-3249 .- 1469-8110. ; 22:2, s. 187-213
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Tidskriftsartikel (refereegranskat)abstract
- Statistical parsers often require careful parameter tuning and feature selection. This is a nontrivial task for application developers who are not interested in parsing for its own sake, and it can be time-consuming even for experienced researchers. In this paper we present MaltOptimizer, a tool developed to automatically explore parameters and features for MaltParser, a transition-based dependency parsing system that can be used to train parser's given treebank data. MaltParser provides a wide range of parameters for optimization, including nine different parsing algorithms, an expressive feature specification language that can be used to define arbitrarily rich feature models, and two machine learning libraries, each with their own parameters. MaltOptimizer is an interactive system that performs parser optimization in three stages. First, it performs an analysis of the training set in order to select a suitable starting point for optimization. Second, it selects the best parsing algorithm and tunes the parameters of this algorithm. Finally, it performs feature selection and tunes machine learning parameters. Experiments on a wide range of data sets show that MaltOptimizer quickly produces models that consistently outperform default settings and often approach the accuracy achieved through careful manual optimization.
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| 6. |
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| 7. |
- Blanton, Michael R., et al.
(författare)
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Sloan Digital Sky Survey IV : Mapping the Milky Way, Nearby Galaxies, and the Distant Universe
- 2017
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Ingår i: Astronomical Journal. - : IOP Publishing Ltd. - 0004-6256 .- 1538-3881. ; 154:1
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Tidskriftsartikel (refereegranskat)abstract
- We describe the Sloan Digital Sky Survey IV (SDSS-IV), a project encompassing three major spectroscopic programs. The Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2) is observing hundreds of thousands of Milky Way stars at high resolution and. high signal-to-noise ratios in the near-infrared. The Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey is obtaining spatially resolved spectroscopy for thousands of nearby galaxies (median z similar to 0.03). The extended Baryon Oscillation Spectroscopic Survey (eBOSS) is mapping the galaxy, quasar, and neutral gas distributions between z similar to 0.6 and 3.5 to constrain cosmology using baryon acoustic oscillations, redshift space distortions, and the shape of the power spectrum. Within eBOSS, we are conducting two major subprograms: the SPectroscopic IDentification of eROSITA Sources (SPIDERS), investigating X-ray AGNs. and galaxies in X-ray clusters, and the Time Domain Spectroscopic Survey (TDSS), obtaining spectra of variable sources. All programs use the 2.5 m Sloan Foundation Telescope at the. Apache Point Observatory; observations there began in Summer 2014. APOGEE-2 also operates a second near-infrared spectrograph at the 2.5 m du Pont Telescope at Las Campanas Observatory, with observations beginning in early 2017. Observations at both facilities are scheduled to continue through 2020. In keeping with previous SDSS policy, SDSS-IV provides regularly scheduled public data releases; the first one, Data Release 13, was made available in 2016 July.
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| 8. |
- de Lhoneux, Miryam, 1990-, et al.
(författare)
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Recursive Subtree Composition in LSTM-Based Dependency Parsing
- 2019
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Ingår i: Proceedings of the 2019 Conference of the North American Chapter of the Association for Computational Linguistics. - Stroudsburg : Association for Computational Linguistics. - 9781950737130 ; , s. 1566-1576
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Konferensbidrag (refereegranskat)abstract
- The need for tree structure modelling on top of sequence modelling is an open issue in neural dependency parsing. We investigate the impact of adding a tree layer on top of a sequential model by recursively composing subtree representations (composition) in a transition-based parser that uses features extracted by a BiLSTM. Composition seems superfluous with such a model, suggesting that BiLSTMs capture information about subtrees. We perform model ablations to tease out the conditions under which composition helps. When ablating the backward LSTM, performance drops and composition does not recover much of the gap. When ablating the forward LSTM, performance drops less dramatically and composition recovers a substantial part of the gap, indicating that a forward LSTM and composition capture similar information. We take the backward LSTM to be related to lookahead features and the forward LSTM to the rich history-based features both crucial for transition-based parsers. To capture history-based information, composition is better than a forward LSTM on its own, but it is even better to have a forward LSTM as part of a BiLSTM. We correlate results with language properties, showing that the improved lookahead of a backward LSTM is especially important for head-final languages.
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| 9. |
- Diéguez-Uribeondo, Javier, et al.
(författare)
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Phylogenetic relationships among plant and animal parasites, and saprotrophs in Aphanomyces (Oomycetes)
- 2009
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Ingår i: Fungal Genetics and Biology. - : Elsevier BV. - 1087-1845 .- 1096-0937. ; 46:5, s. 365-376
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Tidskriftsartikel (refereegranskat)abstract
- Molecular phylogenetic relationships among 12 species of Aphanomyces de Bary (Oomycetes) were analyzed based on 108 ITS sequences of nuclear rDNA. Sequences used in the analyses belonged to the major species currently available in pure culture and GenBank. Bayesian, maximum likelihood, and maximum parsimony analyses support that Aphanomyces constitutes a monophyletic group. Three independent lineages were found: (i) plant parasitic, (ii) animal parasitic, and (iii) saprotrophic or opportunistic parasitic. Sexual reproduction appeared to be critical in plant parasites for survival in soil environments while asexual reproduction seemed to be advantageous for exploiting specialization in animal parasitism. Repeated zoospore emergence seems to be an advantageous property for both plant and animal parasitic modes of life. Growth in unspecific media was generally faster in saprotrophs compared with parasitic species. A number of strains and GenBank sequences were found to be misidentified. It was confirmed molecularly that Aphanomyces piscicida and Aphanomyces invadans appear to be conspecific, and found that Aphanomyces iridis and Aphanomyces euteiches are closely related, if not the same, species. This study has shown a clear evolutionary separation between Aphanomyces species that are plant parasites and those that parasitize animals. Saprotrophic or opportunistic species formed a separate evolutionary lineage except Aphanomyces stellatus whose evolutionary position has not yet been resolved.
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| 10. |
- Leon, Miguel, et al.
(författare)
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Feature Selection of EEG Oscillatory Activity Related to Motor Imagery Using a Hierarchical Genetic Algorithm
- 2019
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Ingår i: 2019 IEEE Congress on Evolutionary Computation, CEC 2019 - Proceedings. - : Institute of Electrical and Electronics Engineers Inc.. - 9781728121536 ; , s. 87-94
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Konferensbidrag (refereegranskat)abstract
- Motor Imagery (MI) classification from neural activity is thought to represent valuable information that can be provided as real-time feedback during rehabilitation after for example a stroke. Previous studies have suggested that MI induces partly subject-specific EEG activation patterns, suggesting that individualized classification models should be created. However, due to fatigue of the user, only a limited number of samples can be recorded and, for EEG recordings, each sample is often composed of a large number of features. This combination leads to an undesirable input data set for classification. In order to overcome this constraint, we propose a new methodology to create and select features from the EEG signal in two steps. First, the input data is divided into different windows to reduce the cardinality of the input. Secondly, a Hierarchical Genetic Algorithm is used to select relevant features using a novel fitness function which combines the data reduction with a correlation feature selection measure. The methodology has been tested on EEG oscillatory activity recorded from 6 healthy volunteers while they performed an MI task. Results have successfully proven that a classification above 75% can be obtained in a restrictive amount of time (0.02 s), reducing the number of features by almost 90%.
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| 11. |
- Madrigal-Gonzalez, Jaime, et al.
(författare)
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Climate reverses directionality in the richness-abundance relationship across the World's main forest biomes
- 2020
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Ingår i: Nature Communications. - : Nature Publishing Group. - 2041-1723. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- More tree species can increase the carbon storage capacity of forests (here referred to as the more species hypothesis) through increased tree productivity and tree abundance resulting from complementarity, but they can also be the consequence of increased tree abundance through increased available energy (more individuals hypothesis). To test these two contrasting hypotheses, we analyse the most plausible pathways in the richness-abundance relationship and its stability along global climatic gradients. We show that positive effect of species richness on tree abundance only prevails in eight of the twenty-three forest regions considered in this study. In the other forest regions, any benefit from having more species is just as likely (9 regions) or even less likely (6 regions) than the effects of having more individuals. We demonstrate that diversity effects prevail in the most productive environments, and abundance effects become dominant towards the most limiting conditions. These findings can contribute to refining cost-effective mitigation strategies based on fostering carbon storage through increased tree diversity. Specifically, in less productive environments, mitigation measures should promote abundance of locally adapted and stress tolerant tree species instead of increasing species richness. Correlations between tree species diversity and tree abundance are well established, but the direction of the relationship is unresolved. Here the authors use path models to estimate plausible causal pathways in the diversity-abundance relationship across 23 global forests regions, finding a lack of general support for a positive diversity-abundance relationship, which is prevalent in the most productive lands on Earth only
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| 12. |
- Madrigal-Gonzalez, Jaime, et al.
(författare)
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Disentangling the relative role of climate change on tree growth in an extreme Mediterranean environment
- 2018
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Ingår i: Science of the Total Environment. - : Elsevier. - 0048-9697 .- 1879-1026. ; 642, s. 619-628
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Tidskriftsartikel (refereegranskat)abstract
- Climate change can impair ecosystem functions and services in extensive dry forests worldwide. However, attribution of climate change impacts on tree growth and forest productivity is challenging due to multiple interannual patterns of climatic variability associated with atmospheric and oceanic circulations. Moreover, growth responses to rising atmospheric CO2, namely carbon fertilization, as well as size ontogenetic changes can obscure the climate change signature as well. Here we apply Structural Equation Models (SEM) to investigate the relative role of climate change on tree growth in an extreme Mediterranean environment (i.e., extreme in terms of the combination of sandy-unconsolidated soils and climatic aridity). Specifically, we analyzed potential direct and indirect pathways by which different sources of climatic variability (i.e. warming and precipitation trends, the North Atlantic Oscillation, [NAO]; the Mediterranean Oscillation, MOO: the Atlantic Mediterranean Oscillation, [AMO]) affect aridity through their control on local climate (in terms of mean annual temperature and total annual precipitation), and subsequently tree productivity, in terms of basal area increments (BAI). Our results support the predominant role of Diameter at Breast Height (DHB) as the main growth driver. In terms of climate, NAO and AMO are the most important drivers of tree growth through their control of aridity (via effects of precipitation and temperature, respectively). Furthermore and contrary to current expectations, our findings also support a net positive role of climate warming on growth over the last 50 years and suggest that impacts of climate warming should be evaluated considering multi-annual and multi-decadal periods of local climate defined by atmospheric and oceanic circulation in the North Atlantic.
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| 13. |
- Mate, Diana, et al.
(författare)
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Switching from blue to yellow : altering the spectral properties of a high redox potential laccase by directed evolution
- 2013
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Ingår i: Biocatalysis and Biotransformation. - : Informa Healthcare. - 1024-2422 .- 1029-2446. ; 31:1, s. 8-21
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Tidskriftsartikel (refereegranskat)abstract
- During directed evolution to functionally express the high redox potential laccase from the PM1 basidiomycete in Saccharomyces cerevisiae, the characteristic max. absorption at the T1 copper site (Abs610T1Cu) was quenched, switching the typical blue color of the enzyme to yellow. To det. the mol. basis of this color change, we characterized the original wild-type laccase and its evolved mutant. Peptide printing and MALDI-TOF anal. confirmed the absence of contaminating protein traces that could mask the Abs610T1Cu, while conservation of the redox potential at the T1 site was demonstrated by spectroelectrochem. redox titrns. Both wild-type and evolved laccases were capable of oxidizing a broad range of substrates (ABTS, guaiacol, DMP, synapic acid) and they displayed similar catalytic efficiencies. The laccase mutant could only oxidize high redox potential dyes (Poly R-478, Reactive Black 5, Azure B) in the presence of exogenous mediators, indicating that the yellow enzyme behaves like a blue laccase. The main consequence of over-expressing the mutant laccase was the generation of a six-residue N-terminal acidic extension, which was assocd. with the failure of the STE13 protease in the Golgi compartment giving rise to alternative processing. Removal of the N-terminal tail had a neg. effect on laccase stability, secretion and its kinetics, although the truncated mutant remained yellow. The results of CD spectra anal. suggested that polyproline helixes were formed during the directed evolution altering spectral properties. Moreover, introducing the A461T and S426N mutations in the T1 environment during the first cycles of lab. evolution appeared to mediate the alterations to Abs610T1Cu by affecting its coordinating sphere. This laccase mutant is a valuable departure point for further protein engineering towards different fates.
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| 14. |
- Molina, Antonio, et al.
(författare)
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Coogoon Valles, western Arabia Terra : Hydrological evolution of a complex Martian channel system
- 2017
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Ingår i: Icarus. - : Elsevier. - 0019-1035 .- 1090-2643. ; 293, s. 27-44
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Tidskriftsartikel (refereegranskat)abstract
- Coogoon Valles is an intricate fluvial system, and its main channel was formed during the Noachian period through the erosion of the clay-bearing basement of the Western Arabia Terra. This region is characterized by a thinner crust compared to the rest of the highlands and by the occurrence of massive phyllosilicate-bearing materials. The origin of this region is still under discussion. Its surface has been exposed to a large-scale volcanism, and several episodes of extensive denudation were primarily controlled by fluvial activity. In this regard, the study of the oldest channels in Arabia Terra is crucial for understanding the global geological evolution of early Mars. The reactivation of the hydrological system by sapping followed by aeolian erosion had reshaped the channel, as well as exposed ancient materials and landforms. The examination of the bed deposits suggests an old episode of detrital sedimentation covering the Noachian basement followed by an erosive event that formed the current Coogoon Valles configuration. A complex system of deltas and alluvial fans is situated at the termination of this channel, which has been proposed as a landing site for the upcoming ExoMars and Mars 2020 missions.
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| 15. |
- Nivre, Joakim, 1962-, et al.
(författare)
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MaltOptimizer: A System for MaltParser Optimization.
- 2012
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Ingår i: Proceedings of the Eighth International Conference on Language Resources and Evaluation (LREC). - : European Language Resources Association. - 9782951740877
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Konferensbidrag (refereegranskat)
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| 16. |
- Nivre, Joakim, 1962-, et al.
(författare)
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MaltOptimizer: An Optimization Tool for MaltParser
- 2012
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Ingår i: Proceedings of the Demonstrations at the 13th Conference of the European Chapter of the Association for Computational Linguistics (EACL). - : Association for Computational Linguistics. - 9781937284190 ; , s. 58-62
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Konferensbidrag (refereegranskat)
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| 17. |
- Stanaway, Jeffrey D., et al.
(författare)
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Global, regional, and national comparative risk assessment of 84 behavioural, environmental and occupational, and metabolic risks or clusters of risks for 195 countries and territories, 1990-2017: A systematic analysis for the Global Burden of Disease Study 2017
- 2018
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Ingår i: The Lancet. - 1474-547X .- 0140-6736. ; 392:10159, s. 1923-1994
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Tidskriftsartikel (refereegranskat)abstract
- Background The Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2017 comparative risk assessment (CRA) is a comprehensive approach to risk factor quantification that offers a useful tool for synthesising evidence on risks and risk-outcome associations. With each annual GBD study, we update the GBD CRA to incorporate improved methods, new risks and risk-outcome pairs, and new data on risk exposure levels and risk- outcome associations. Methods We used the CRA framework developed for previous iterations of GBD to estimate levels and trends in exposure, attributable deaths, and attributable disability-adjusted life-years (DALYs), by age group, sex, year, and location for 84 behavioural, environmental and occupational, and metabolic risks or groups of risks from 1990 to 2017. This study included 476 risk-outcome pairs that met the GBD study criteria for convincing or probable evidence of causation. We extracted relative risk and exposure estimates from 46 749 randomised controlled trials, cohort studies, household surveys, census data, satellite data, and other sources. We used statistical models to pool data, adjust for bias, and incorporate covariates. Using the counterfactual scenario of theoretical minimum risk exposure level (TMREL), we estimated the portion of deaths and DALYs that could be attributed to a given risk. We explored the relationship between development and risk exposure by modelling the relationship between the Socio-demographic Index (SDI) and risk-weighted exposure prevalence and estimated expected levels of exposure and risk-attributable burden by SDI. Finally, we explored temporal changes in risk-attributable DALYs by decomposing those changes into six main component drivers of change as follows: (1) population growth; (2) changes in population age structures; (3) changes in exposure to environmental and occupational risks; (4) changes in exposure to behavioural risks; (5) changes in exposure to metabolic risks; and (6) changes due to all other factors, approximated as the risk-deleted death and DALY rates, where the risk-deleted rate is the rate that would be observed had we reduced the exposure levels to the TMREL for all risk factors included in GBD 2017.
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| 18. |
- Zumarraga, Miren, et al.
(författare)
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Altering the laccase functionality by in vivo assembly of mutant libraries with different mutational spectra
- 2008
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Ingår i: Proteins. - : Wiley. - 0887-3585. ; 71:1, s. 250-260
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Tidskriftsartikel (refereegranskat)abstract
- The generation of diversity for directed protein evolution experiments shows an important bottleneck in the in vitro random mutagenesis protocols. Most Of them are biased towards specific changes that eventually confer a predicted and conservative mutational spectrum, limiting the exploration of the vast protein space. The current work describes a simple methodology to in vivo recombine mutant libraries with different nucleotide bias created by in vitro methods. This in vivo assembly was based on the accurate physiology of Saccharomyces cerevisiae, which as host, provided its high homologous recombination frequency to shuffle the libraries in a nonmutagenic way. The fungal thermophilic laccase from Myceliophthora thermophila expressed in S. cerevisiae was submitted to this protocol under the selective pressure of high concentrations of organic solvents. Mutant 2E9 with similar to 3-fold better kinetics than parent type showed two consecutive amino acid changes (G614D -GGC/GAC- and E615K -GAG/AAG-) because of the in vivo shuffling of the mutant libraries. Both mutations are located in the C-terminal tail that is specifically processed at the Golgi during the maturation of the protein by the Kex2 protease. Notoriously, the oxygen consumption at the T2/T3 trinuclear copper cluster was altered and the catalytic copper at the T1 site was perturbed showing differences in its redox potential and geometry. The change in the isoelectric point of C-terminal extension upon mutations seems to affect the folding of the protein at the posttranslational processing steps providing new insights in the significance of the C-terminal tail for the functionality of the ascomycete laccases.
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| 19. |
- Zumarraga, Miren, et al.
(författare)
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Combinatorial saturation mutagenesis of the Myceliophthora thermophila laccase T2 mutant : the connection between the C-terminal plug and the conserved 509VSG511 tripeptide
- 2008
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Ingår i: Combinatorial chemistry & high throughput screening. - : Bentham Science Publishers Ltd.. - 1386-2073 .- 1875-5402. ; 11:10, s. 807-816
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Tidskriftsartikel (refereegranskat)abstract
- A mutant laccase from the Ascomycete Myceliophthora thermophila has been submitted to iterative cycles of combinatorial satn. mutagenesis through in vivo overlap extension in Saccharomyces cerevisiae. Over 180,000 clones were explored, among which the S510G mutant revealed a direct interaction between the conserved 509VSG511 tripeptide, located in the neighborhood of the T1 site, and the C-terminal plug. The KmO2 value of the mutant increased 1.5-fold, and the electron transfer pathway between the reducing substrate and the T1 copper ion was altered, improving the catalytic efficiency towards non-phenolic and phenolic substrates by about 3- and 8-fold. Although the geometry at the T1 site was perturbed by the mutation, paradoxically the laccase redox potential was not significantly altered. Together, the results obtained in this study suggest that the 509VSG511 tripeptide may play a hitherto unrecognized role in regulating the traffic of oxygen through the C-terminal plug, the latter blocking access to the T2/T3 copper cluster in the native enzyme.
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| 20. |
- Zumarraga, Miren, et al.
(författare)
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In vitro evolution of a fungal laccase in high concentrations of organic cosolvents
- 2007
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Ingår i: Chemistry and Biology. - : Elsevier BV. - 1879-1301 .- 1074-5521. ; 14:9, s. 1052-1064
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Tidskriftsartikel (refereegranskat)abstract
- Fungal laccases are remarkable green catalysts that have a broad substrate specificity and many potential applications in bioremediation, lignocellulose processing, organic synthesis, and more. However, most of these transformations must be carried out at high concentrations of organic cosolvents in which laccases undergo unfolding, thereby losing their activity. We have tailored a thermostable laccase that tolerates high concentrations of cosolvents, the genetic product of five rounds of directed evolution expressed in Saccharomyces cerevisiae. This evolved laccase-R2 variant-was capable of resisting a wide array of cosolvents at concentrations as high as 50% (v/v). Intrinsic laccase features such as the redox potential and the geometry of catalytic coppers varied slightly during the course of the molecular evolution. Some mutations at the protein surface stabilized the laccase by allowing additional electrostatic and hydrogen bonding to occur.
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