| 1. |
- Wang, Xiaofeng, et al.
(author)
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Evidence for type ia supernova diversity from ultraviolet observations with the hubble space telescope
- 2012
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In: Astrophysical Journal. - 0004-637X .- 1538-4357. ; 749:2, s. 126-
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Journal article (peer-reviewed)abstract
- We present ultraviolet (UV) spectroscopy and photometry of four Type Ia supernovae (SNe 2004dt, 2004ef, 2005M, and 2005cf) obtained with the UV prism of the Advanced Camera for Surveys on the Hubble Space Telescope. This data set provides unique spectral time series down to 2000 angstrom. Significant diversity is seen in the near-maximum-light spectra (similar to 2000-3500 angstrom) for this small sample. The corresponding photometric data, together with archival data from Swift Ultraviolet/Optical Telescope observations, provide further evidence of increased dispersion in the UV emission with respect to the optical. The peak luminositiesmeasured in the uvw1/F250W filter are found to correlate with the B-band light-curve shape parameter Delta m(15)(B), but with much larger scatter relative to the correlation in the broadband B band (e.g., similar to 0.4 mag versus similar to 0.2 mag for those with 0.8 mag < Delta m(15)(B) < 1.7 mag). SN 2004dt is found as an outlier of this correlation (at > 3 sigma), being brighter than normal SNe Ia such as SN 2005cf by similar to 0.9 mag and similar to 2.0 mag in the uvw1/F250W and uvm2/F220W filters, respectively. We show that different progenitor metallicity or line-expansion velocities alone cannot explain such a large discrepancy. Viewing-angle effects, such as due to an asymmetric explosion, may have a significant influence on the flux emitted in the UV region. Detailed modeling is needed to disentangle and quantify the above effects.
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| 2. |
- Bretman, Amanda, et al.
(author)
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Systematic approaches to assessing high-temperature limits to fertility in animals
- 2024
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In: Journal of Evolutionary Biology. - 1010-061X .- 1420-9101.
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Journal article (peer-reviewed)abstract
- Critical thermal limits (CTLs) gauge the physiological impact of temperature on survival or critical biological function, aiding predictions of species range shifts and climatic resilience. Two recent Drosophila species studies, using similar approaches to determine temperatures that induce sterility (thermal fertility limits [TFLs]), reveal that TFLs are often lower than CTLs and that TFLs better predict both current species distributions and extinction probability. Moreover, many studies show fertility is more sensitive at less extreme temperatures than survival (thermal sensitivity of fertility [TSF]). These results present a more pessimistic outlook on the consequences of climate change. However, unlike CTLs, TFL data are limited to Drosophila, and variability in TSF methods poses challenges in predicting species responses to increasing temperature. To address these data and methodological gaps, we propose 3 standardized approaches for assessing thermal impacts on fertility. We focus on adult obligate sexual terrestrial invertebrates but also provide modifications for other animal groups and life-history stages. We first outline a gold-standard protocol for determining TFLs, focussing on the effects of short-term heat shocks and simulating more frequent extreme heat events predicted by climate models. As this approach may be difficult to apply to some organisms, we then provide a standardized TSF protocol. Finally, we provide a framework to quantify fertility loss in response to extreme heat events in nature, given the limitations in laboratory approaches. Applying these standardized approaches across many taxa, similar to CTLs, will allow robust tests of the impact of fertility loss on species responses to increasing temperatures. Graphical AbstractOverview of the systematic methods (A, C, and D) to simultaneously assay lethal limits and thermal fertility limits or (B and E) thermal sensitivity of fertility. These are most easily applied to laboratory settings but can be used for assessing the fertility of wild-caught animals that have been exposed to natural temperatures.
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| 3. |
- Canal, Cristina, et al.
(author)
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Relevance of microstructure for the early antibiotic release of fresh and pre-set calcium phosphate cements
- 2013
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In: Acta Biomaterialia. - : Elsevier BV. - 1742-7061 .- 1878-7568. ; 9:9, s. 8403-8412
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Journal article (peer-reviewed)abstract
- Calcium phosphate cements (CPCs) have great potential as carriers for controlled release and vectoring of drugs in the skeletal system. However, a lot of work still has to be done in order to obtain reproducible and predictable release kinetics. A particular aspect that adds complexity to these materials is that they cannot be considered as stable matrices, since their microstructure evolves during the setting reaction.The aims of the present work were to analyze the effect of the microstructural evolution of the CPC during the setting reaction on the release kinetics of the antibiotic doxycycline hyclate and to assess the effect of the antibiotic on the microstructural development of the CPC. The incorporation of the drug in the CPC modified the textural and microstructural properties of the cements by acting as a nucleating agent for the heterogeneous precipitation of hydroxyapatite crystals, but did not affect its antibacterial activity. In vitro release experiments were carried out on readily prepared cements (fresh CPCs), and compared to those of pre-set CPCs. No burst release was found in any formulation. A marked difference in release kinetics was found at the initial stages; the evolving microstructure of fresh CPCs led to a two-step release. Initially, when the carrier was merely a suspension of a-TCP particles in water, a faster release was recorded, which rapidly evolved to a zero-order release. In contrast, pre-set CPCs released doxycycline following non-Fickian diffusion. The final release percentage was related to the total porosity and entrance pore size of each biomaterial.
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| 4. |
- Canal, David, et al.
(author)
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Socio-ecological factors shape the opportunity for polygyny in a migratory songbird
- 2020
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In: Behavioral Ecology. - 1045-2249. ; 31:2, s. 598-609
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Journal article (peer-reviewed)abstract
- Why females pair with already mated males and the mechanisms behind variation in such polygynous events within and across populations and years remain open questions. Here, we used a 19-year data set from a pied flycatcher (Ficedula hypoleuca) population to investigate, through local networks of breeding pairs, the socio-ecological factors related to the probability of being involved in a polygynous event in both sexes. Then, we examined how the breeding contexts experienced by individuals shaped the spatial and temporal separation between broods of polygamous males. The probability of polygyny decreased with the distance between nests. Indeed, secondary females were often close neighbors of primary females, although the distance between both nests increased slightly with increasing synchrony between them. The probability of polygyny was also related to the breeding time of individuals because early breeding males were more likely to become polygynous with late-breeding females. Throughout the season, there was substantial variation in the temporal separation between primary and secondary broods, and this separation was, in turn, related to the breeding asynchrony of the polygamous males (in the primary nest) relative to the neighbors. Polygynous males that bred late relative to their neighbors had a short time window to attract a second female and, thus, the breeding interval between their primary and secondary broods was reduced. Overall, the spatial proximity between polygynous males’ broods and, if the opportunity existed, their temporal staggering are compatible with a male strategy to maximize paternity and reduce the costs of caring for two broods, though the effect of female’s interest, either primary or secondary, cannot be fully ruled out. We highlight that a comprehensive assessment of the breeding contexts faced by individuals is essential to understand mating decisions and reconcile the discrepancies raised by previous work on social polygyny. Lay Summary: Local social-ecological contexts determine mating decisions in a songbird. Using a novel approach that allows consideration of the local breeding contexts faced by each individual in the population, we show that breeding time in relation to the neighbors is key to become both polygynous (males) and secondary (females). Further, the spatial and temporal separations between polygynous males’ broods, which vary substantially throughout the season, arise mainly from the males’ own interests to maximize paternity.
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| 5. |
- Culina, Antica, et al.
(author)
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Connecting the data landscape of long-term ecological studies : The SPI-Birds data hub
- 2021
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In: Journal of Animal Ecology. - : John Wiley & Sons. - 0021-8790 .- 1365-2656. ; 90:9, s. 2147-2160
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Journal article (peer-reviewed)abstract
- The integration and synthesis of the data in different areas of science is drastically slowed and hindered by a lack of standards and networking programmes. Long-term studies of individually marked animals are not an exception. These studies are especially important as instrumental for understanding evolutionary and ecological processes in the wild. Furthermore, their number and global distribution provides a unique opportunity to assess the generality of patterns and to address broad-scale global issues (e.g. climate change). To solve data integration issues and enable a new scale of ecological and evolutionary research based on long-term studies of birds, we have created the SPI-Birds Network and Database ()-a large-scale initiative that connects data from, and researchers working on, studies of wild populations of individually recognizable (usually ringed) birds. Within year and a half since the establishment, SPI-Birds has recruited over 120 members, and currently hosts data on almost 1.5 million individual birds collected in 80 populations over 2,000 cumulative years, and counting. SPI-Birds acts as a data hub and a catalogue of studied populations. It prevents data loss, secures easy data finding, use and integration and thus facilitates collaboration and synthesis. We provide community-derived data and meta-data standards and improve data integrity guided by the principles of Findable, Accessible, Interoperable and Reusable (FAIR), and aligned with the existing metadata languages (e.g. ecological meta-data language). The encouraging community involvement stems from SPI-Bird's decentralized approach: research groups retain full control over data use and their way of data management, while SPI-Birds creates tailored pipelines to convert each unique data format into a standard format. We outline the lessons learned, so that other communities (e.g. those working on other taxa) can adapt our successful model. Creating community-specific hubs (such as ours, COMADRE for animal demography, etc.) will aid much-needed large-scale ecological data integration.
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| 6. |
- Deb, Sontosh K, et al.
(author)
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The fifth international hackathon for developing computational cloud-based tools and resources for pan-structural variation and genomics
- 2024
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In: F1000Research. - 2046-1402. ; 13, s. 1-33
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Journal article (peer-reviewed)abstract
- BackgroundThe goal of the Fifth Annual Baylor College of Medicine & DNAnexus Structural Variation Hackathon was to push forward the research on structural variants (SVs) by rapidly developing and deploying open-source software. The event took place in-person and virtually in August 2023, when 49 scientists from 14 countries and 8 U.S. states collaboratively worked on projects to address critical gaps in the field of genomics. The hackathon projects concentrated on developing bioinformatic workflows for the following challenges: RNA transcriptome comparison, simulation of mosaic variations, metagenomics, Mendelian variation, SVs in plant genomics, and assembly vs. mapping SV calling comparisons.MethodsAs a starting point we used publicly available data from state-of-the-art long- and short-read sequencing technologies. The workflows developed during the hackathon incorporated open-source software, as well as scripts written using Bash and Python. Moreover, we leveraged the advantages of Docker and Snakemake for workflow automation.ResultsThe results of the hackathon consists of six prototype bioinformatic workflows that use open-source software for SV research. We made the workflows scalable and modular for usability and reproducibility. Furthermore, we tested the workflows on example public data to show that the workflows can work. The code and the data produced during the event have been made publicly available on GitHub (https://github.com/collaborativebioinformatics) to reproduce and built upon in the future.ConclusionsThe following sections describe the motivation, lessons learned, and software produced by teams during the hackathon. Here, we describe in detail the objectives, value propositions, implementation, and use cases for our workflows. In summary, the article reports the advancements in the development of software for SV detection made during the hackathon.
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| 7. |
- Dougherty, Liam R., et al.
(author)
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A systematic map of studies testing the relationship between temperature and animal reproduction
- 2024
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In: Ecological Solutions and Evidence. - : John Wiley & Sons. - 2688-8319. ; 5:1
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Journal article (peer-reviewed)abstract
- Exposure to extreme temperatures can negatively affect animal reproduction, by disrupting the ability of individuals to produce any offspring (fertility), or the number of offspring produced by fertile individuals (fecundity). This has important ecological consequences, because reproduction is the ultimate measure of population fitness: a reduction in reproductive output lowers the population growth rate and increases the extinction risk. Despite this importance, there have been no large-scale summaries of the evidence for effect of temperature on reproduction.We provide a systematic map of studies testing the relationship between temperature and animal reproduction. We systematically searched for published studies that statistically test for a direct link between temperature and animal reproduction, in terms of fertility, fecundity or indirect measures of reproductive potential (gamete and gonad traits).Overall, we collated a large and rich evidence base, with 1654 papers that met our inclusion criteria, encompassing 1191 species.The map revealed several important research gaps. Insects made up almost half of the dataset, but reptiles and amphibians were uncommon, as were non-arthropod invertebrates. Fecundity was the most common reproductive trait examined, and relatively few studies measured fertility. It was uncommon for experimental studies to test exposure of different life stages, exposure to short-term heat or cold shock, exposure to temperature fluctuations, or to independently assess male and female effects. Studies were most often published in journals focusing on entomology and pest control, ecology and evolution, aquaculture and fisheries science, and marine biology. Finally, while individuals were sampled from every continent, there was a strong sampling bias towards mid-latitudes in the Northern Hemisphere, such that the tropics and polar regions are less well sampled.This map reveals a rich literature of studies testing the relationship between temperature and animal reproduction, but also uncovers substantial missing treatment of taxa, traits, and thermal regimes. This database will provide a valuable resource for future quantitative meta-analyses, and direct future studies aiming to fill identified gaps.
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| 9. |
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| 10. |
- Klawonn, Anna, et al.
(author)
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Microglial activation elicits a negative affective state through prostaglandin-mediated modulation of striatal neurons
- 2021
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In: Immunity. - : CELL PRESS. - 1074-7613 .- 1097-4180. ; 54:2, s. 225-234.e6
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Journal article (peer-reviewed)abstract
- Microglia are activated in many neurological diseases and have been suggested to play an important role in the development of affective disorders including major depression. To investigate how microglial signaling regulates mood, we used bidirectional chemogenetic manipulations of microglial activity in mice. Activation of microglia in the dorsal striatum induced local cytokine expression and a negative affective state characterized by anhedonia and aversion, whereas inactivation of microglia blocked aversion induced by systemic inflammation. Interleukin-6 signaling and cyclooxygenase-1 mediated prostaglandin synthesis in the microglia were critical for the inflammation-induced aversion. Correspondingly, microglial activation led to a prostaglandin-dependent reduction of the excitability of striatal neurons. These findings demonstrate a mechanism by which microglial activation causes negative affect through prostaglandin-dependent modulation of striatal neurons and indicate that interference with this mechanism could milden the depressive symptoms in somatic and psychiatric diseases involving microglial activation.
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| 11. |
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| 12. |
- Mestres, Gemma, 1984-, et al.
(author)
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In vivo efficiency of antimicrobial inorganic bone grafts in osteomyelitis Treatments
- 2019
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In: Materials science & engineering. C, biomimetic materials, sensors and systems. - : Elsevier BV. - 0928-4931 .- 1873-0191. ; 97, s. 84-95
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Journal article (peer-reviewed)abstract
- The purpose of the present work was to evaluate in vivo different antimicrobial therapies to eradicate osteomyelitis created in the femoral head of New Zealand rabbits. Five phosphate-based cements were evaluated: calcium phosphate cements (CPC) and calcium phosphate foams (CPF), both in their pristine form and loaded with doxycycline hyclate, and an intrinsic antimicrobial magnesium phosphate cement (MPC; not loaded with an antibiotic). The cements were implanted in a bone previously infected with Staphylococcus aureus to discern the effects of the type of antibiotic administration (systemic vs. local), porosity (microporosity, i.e. <5 μm vs. macroporosity, i.e. >5 μm) and type of antimicrobial mechanism (release of antibiotic vs. intrinsic antimicrobial activity) on the improvement of the health state of the infected animals. A new method was developed, with a more comprehensive composite score that integrates 5 parameters of bone infection, 4 parameters of bone structural integrity and 4 parameters of bone regeneration. This method was used to evaluate the health state of the infected animals, both before and after osteomyelitis treatment. The results showed that the composite score allows to discern statistically significant differences between treatments that individual evaluations were not able to identify. Despite none of the therapies completely eradicated the infection, it was observed that macroporous materials (CPF and CPFd, the latter loaded with doxycycline hyclate) and intrinsic antimicrobial MPC allowed a better containment of the osteomyelitis. This study provides novel insights to understand the effect of different antimicrobial therapies in vivo, and a promising comprehensive methodology to evaluate the health state of the animals was developed. We expect that the implementation of such methodology could improve the criteria to select a proper antimicrobial therapy.
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| 13. |
- Murari, A., et al.
(author)
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A control oriented strategy of disruption prediction to avoid the configuration collapse of tokamak reactors
- 2024
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In: Nature Communications. - 2041-1723 .- 2041-1723. ; 15:1
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Journal article (peer-reviewed)abstract
- The objective of thermonuclear fusion consists of producing electricity from the coalescence of light nuclei in high temperature plasmas. The most promising route to fusion envisages the confinement of such plasmas with magnetic fields, whose most studied configuration is the tokamak. Disruptions are catastrophic collapses affecting all tokamak devices and one of the main potential showstoppers on the route to a commercial reactor. In this work we report how, deploying innovative analysis methods on thousands of JET experiments covering the isotopic compositions from hydrogen to full tritium and including the major D-T campaign, the nature of the various forms of collapse is investigated in all phases of the discharges. An original approach to proximity detection has been developed, which allows determining both the probability of and the time interval remaining before an incoming disruption, with adaptive, from scratch, real time compatible techniques. The results indicate that physics based prediction and control tools can be developed, to deploy realistic strategies of disruption avoidance and prevention, meeting the requirements of the next generation of devices.
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| 16. |
- Potti, Jaime, et al.
(author)
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Tres décadas de crímenes y usurpaciones de nidos en la vida en los nidales del papamoscas cerrojillo ficedula hypoleuca
- 2021
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In: Ardeola. - : Ardeola. - 0570-7358. ; 68:2, s. 315-333
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Journal article (peer-reviewed)abstract
- Summary . Pied Flycatchers Ficedula hypoleuca are known to be victims of nest killings in contexts of competition for nest boxes. However, there is only anecdotal information on their opposite role as perpetrators of nest takeovers and occasional killings of other songbirds. Over 31 years we examined whether competition with Great Tits Parus major over nest box ownership is a significant source of mortality for Pied Flycatchers and whether the increase in Pied Flycatcher populations affected the use of nest boxes by the smallest tit species, the Blue Tit Cyanistes caeruleus and Coal Tit Periparus ater, in two forests in the central Iberian Mountain Range. We found 31 Pied Flycatchers killed inside nest boxes. The Great Tit was the most frequent species to which the killings were attributed. Followed by Pied Flycatchers themselves and Nuthatches Sitta europaea. We confirmed the killing by Pied Flycatchers of at least two conspecific males and one incubating female Coal Tit, with one killer male identified. Large increases in population densities of flycatchers after nest box deployment in the two study areas seem to have triggered an intensification of agonistic interactions among their potential occupants, resulting in an increase of takeovers by Pied Flycatchers of nest boxes initially owned by the smallest tit species. Great Tits are not a serious threat for Pied Flycatchers breeding in the study area, most likely due to their preference for natural holes over the nest box types most frequently installed. The interactions of Pied Flycatchers with Blue and Coal Tits for the ownership of nest boxes do not seem to cause significant mortality in the species involved. However, aggressive usurpations of nest boxes by Pied Flycatchers surely have negative impacts on the reproductive success of the victims through their eviction from suitable nesting sites. - Potti, J., Camacho, C., Canal, D. & Martínez-Padilla, J. (2021). Three decades of crimes and misdemeanours in the nest box life of European Pied Flycatchers Ficedula hypoleuca. Ardeola, 68: 315-333.
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