| 1. |
- Björling, T., et al.
(författare)
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SrAlSiH : A polyanionic semiconductor hydride
- 2005
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Ingår i: Angewandte Chemie International Edition. - : Wiley. - 1433-7851 .- 1521-3773. ; 44:44, s. 7269-7273
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Tidskriftsartikel (refereegranskat)abstract
- (Chemical Equation Presented) Stable and semiconducting: Polyanionic hydrides represent a new class of main-group-metal hydrides with unforeseen hydrogen-coordination environments. The hydrogen atom in SrAlSiH is attached exclusively to Al and forms part of a layered [AlHSi]2- polyanion (see figure). This material is the first narrow bandgap semiconductor hydride and combines the high thermal stability of saline hydrides with the air and moisture stability of interstitial transition-metal hydrides.
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| 2. |
- Capo, Eric, et al.
(författare)
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Deltaproteobacteria andSpirochaetes-Like Bacteria AreAbundant Putative MercuryMethylators in Oxygen-DeficientWater and Marine Particles in theBaltic Sea
- 2020
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Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; , s. 1-11
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Tidskriftsartikel (refereegranskat)abstract
- Methylmercury (MeHg), a neurotoxic compound biomagnifying in aquatic food webs, can be a threat to human health via fish consumption. However, the compositionand distribution of the microbial communities mediating the methylation of mercury (Hg) to MeHg in marine systems remain largely unknown. In order to fill this knowledge gap, we used the Baltic Sea Reference Metagenome (BARM) dataset to study the abundance and distribution of the genes involved in Hg methylation (the hgcAB gene cluster). We determined the relative abundance of the hgcAB genes and their taxonomic identity in 81 brackish metagenomes that cover spatial,seasonal and redox variability in the Baltic Sea water column. The hgcAB genes were predominantly detected in anoxic water, but some hgcAB genes were alsodetected in hypoxic and normoxic waters. Phylogenetic analysis identified putative Hg methylators within Deltaproteobacteria, in oxygen-deficient water layers, but also Spirochaetes-like and Kiritimatiellaeota-like bacteria. Higher relative quantities of hgcAB genes were found in metagenomes from marine particles compared to free-living communities in anoxic water, suggesting that such particles are hotspot habitats for Hg methylators in oxygen-depleted seawater. Altogether, our work unveils the diversityof the microorganisms with the potential to mediate MeHg production in the BalticSea and pinpoint the important ecological niches for these microorganisms within themarine water column.
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| 3. |
- Cavalcante, Larissa Lopes, et al.
(författare)
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Analysis of fossil plant cuticles using vibrational spectroscopy: A new preparation protocol
- 2023
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Ingår i: Review of Palaeobotany and Palynology. - : Elsevier. - 0034-6667 .- 1879-0615. ; 316
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Tidskriftsartikel (refereegranskat)abstract
- Analyses for organic “fingerprints” on fossilized plant cuticles and pollen hold valuable chemotaxonomic and palaeoclimatic information, and are thus becoming more utilized by palaeobotanists. Plant cuticle and pollen composition are generally analyzed after standard treatments with several chemical reagents for mineral and mesophyll removal. However, the potential alterations on the fossil composition caused by the different cleaning reagents used are still poorly understood. We tested the effects of commonly used palaeobotanical processing methods on the spectra of fossilized cuticles from successions of Late Triassic to Early Jurassic age, including the gymnosperms Lepidopteris, Ginkgoites, Podozamites, Ptilozamites and Pterophyllum astartense. Our study shows that standard chemical processing caused chemical alterations that might lead to erroneous interpretation of the infrared (IR) spectra. The difference in pH caused by HCl induces changes in the proportion between the two bands at ~1720 and 1600 cm 1 (carboxylate and C-C stretch of aromatic compounds) indicating that the band at ~1610 cm 1 at least partially corresponds to carboxylate instead of C-C stretch of aromatic compounds. Interestingly, despite being used in high concentration, HF did not cause changes in the chemical composition of the cuticles. The most alarming changes were caused by the use of Schulze ’s solution, which resulted in the addition of both NO2 and (O)NO2 compounds in the cuticle. Consequently, a new protocol using H2CO3, HF, and H2O2 for preparing fossil plant cuticles aimed for chemical analyses is proposed, which provides an effective substitute to the conventional methods. In particular, a less aggressive and more sustainable alternative to Schulze’s solution is shown to be hydrogen peroxide, which causes only minor alteration of the fossil cuticle ’s chemical composition. Future work should carefully follow protocols, having in mind the impacts of different solutions used to treat leaves and other palaeobotanical material such as palynomorphs with aims to enable the direct comparison of spectra obtained in different studies.
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| 4. |
- De Colle, Mattia, et al.
(författare)
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Study of the Dissolution of Stainless-Steel Slag Minerals in Different Acid Environments to Promote Their Use for the Treatment of Acidic Wastewaters
- 2021
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Ingår i: Applied Sciences. - : MDPI AG. - 2076-3417. ; 11:24
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Tidskriftsartikel (refereegranskat)abstract
- Several stainless-steel slags have been successfully employed in previous studies as substitutes for lime in the treatment of industrial acidic wastewaters. This study deepens the knowledge of such application, by analyzing the neutralizing capacity of different slags related to their mineral compositions. To do so, firstly the chemical and mineral compositions of all the slag samples are assessed. Then, 0.5 g, 1 g, 2 g of each slag and 0.25 g and 0.5 g of lime are used to neutralize 100 g of 0.1 M HCl or HNO3 solutions. After the has neutralization occurred, the solid residues are extracted and analyzed using XRD spectroscopy. Then, the solubility of the minerals is assessed and ranked, by comparing the XRD spectra of the residues with the obtained pH values. The results show that minerals such as dicalcium silicate and bredigite are highly soluble in the selected experimental conditions, while minerals such as merwinite and akermanite, only partially. Moreover, Al-rich slags seem to perform poorly due to the formation of hydroxides, which generate extra protons. However, when the weight of slag is adequately adjusted, Al-rich slags can increase the pH values to higher levels compared to the other studied slags.
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| 5. |
- Dupont, Chris L., et al.
(författare)
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Functional Tradeoffs Underpin Salinity-Driven Divergence in Microbial Community Composition
- 2014
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:2, s. e89549-
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Tidskriftsartikel (refereegranskat)abstract
- Bacterial community composition and functional potential change subtly across gradients in the surface ocean. In contrast, while there are significant phylogenetic divergences between communities from freshwater and marine habitats, the underlying mechanisms to this phylogenetic structuring yet remain unknown. We hypothesized that the functional potential of natural bacterial communities is linked to this striking divide between microbiomes. To test this hypothesis, metagenomic sequencing of microbial communities along a 1,800 km transect in the Baltic Sea area, encompassing a continuous natural salinity gradient from limnic to fully marine conditions, was explored. Multivariate statistical analyses showed that salinity is the main determinant of dramatic changes in microbial community composition, but also of large scale changes in core metabolic functions of bacteria. Strikingly, genetically and metabolically different pathways for key metabolic processes, such as respiration, biosynthesis of quinones and isoprenoids, glycolysis and osmolyte transport, were differentially abundant at high and low salinities. These shifts in functional capacities were observed at multiple taxonomic levels and within dominant bacterial phyla, while bacteria, such as SAR11, were able to adapt to the entire salinity gradient. We propose that the large differences in central metabolism required at high and low salinities dictate the striking divide between freshwater and marine microbiomes, and that the ability to inhabit different salinity regimes evolved early during bacterial phylogenetic differentiation. These findings significantly advance our understanding of microbial distributions and stress the need to incorporate salinity in future climate change models that predict increased levels of precipitation and a reduction in salinity.
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| 6. |
- Elmhagen, Bodil, et al.
(författare)
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Interacting effects of change in climate, human population, land use, and water use on biodiversity and ecosystem services
- 2015
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Ingår i: Ecology & Society. - 1708-3087. ; 20:1
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Tidskriftsartikel (refereegranskat)abstract
- Human population growth and resource use, mediated by changes in climate, land use, and water use, increasingly impact biodiversity and ecosystem services provision. However, impacts of these drivers on biodiversity and ecosystem services are rarely analyzed simultaneously and remain largely unknown. An emerging question is how science can improve the understanding of change in biodiversity and ecosystem service delivery and of potential feedback mechanisms of adaptive governance. We analyzed past and future change in drivers in south-central Sweden. We used the analysis to identify main research challenges and outline important research tasks. Since the 19th century, our study area has experienced substantial and interlinked changes; a 1.6 degrees C temperature increase, rapid population growth, urbanization, and massive changes in land use and water use. Considerable future changes are also projected until the mid-21st century. However, little is known about the impacts on biodiversity and ecosystem services so far, and this in turn hampers future projections of such effects. Therefore, we urge scientists to explore interdisciplinary approaches designed to investigate change in multiple drivers, underlying mechanisms, and interactions over time, including assessment and analysis of matching-scale data from several disciplines. Such a perspective is needed for science to contribute to adaptive governance by constantly improving the understanding of linked change complexities and their impacts.
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| 7. |
- Iwaszkiewicz-Eggebrecht, Elzbieta, et al.
(författare)
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FAVIS : Fast and versatile protocol for nondestructive metabarcoding of bulk insect samples
- 2023
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 18:7, s. e0286272-
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Tidskriftsartikel (refereegranskat)abstract
- Insects are diverse and sustain essential ecosystem functions, yet remain understudied. Recent reports about declines in insect abundance and diversity have highlighted a pressing need for comprehensive large-scale monitoring. Metabarcoding (high-throughput bulk sequencing of marker gene amplicons) offers a cost-effective and relatively fast method for characterizing insect community samples. However, the methodology applied varies greatly among studies, thus complicating the design of large-scale and repeatable monitoring schemes. Here we describe a non-destructive metabarcoding protocol that is optimized for high-throughput processing of Malaise trap samples and other bulk insect samples. The protocol details the process from obtaining bulk samples up to submitting libraries for sequencing. It is divided into four sections: 1) Laboratory workspace preparation; 2) Sample processing-decanting ethanol, measuring the wet-weight biomass and the concentration of the preservative ethanol, performing non-destructive lysis and preserving the insect material for future work; 3) DNA extraction and purification; and 4) Library preparation and sequencing. The protocol relies on readily available reagents and materials. For steps that require expensive infrastructure, such as the DNA purification robots, we suggest alternative low-cost solutions. The use of this protocol yields a comprehensive assessment of the number of species present in a given sample, their relative read abundances and the overall insect biomass. To date, we have successfully applied the protocol to more than 7000 Malaise trap samples obtained from Sweden and Madagascar. We demonstrate the data yield from the protocol using a small subset of these samples.
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| 8. |
- Lundén, Daniel, 1993-, et al.
(författare)
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Automatic Alignment in Higher-Order Probabilistic Programming Languages
- 2023
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Ingår i: Programming Languages and Systems. ; , s. 535-563
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Konferensbidrag (refereegranskat)abstract
- Probabilistic Programming Languages (PPLs) allow users to encode statistical inference problems and automatically apply an inference algorithm to solve them. Popular inference algorithms for PPLs, such as sequential Monte Carlo (SMC) and Markov chain Monte Carlo (MCMC), are built around checkpoints—relevant events for the inference algorithm during the execution of a probabilistic program. Deciding the location of checkpoints is, in current PPLs, not done optimally. To solve this problem, we present a static analysis technique that automatically determines checkpoints in programs, relieving PPL users of this task. The analysis identifies a set of checkpoints that execute in the same order in every program run—they are aligned. We formalize alignment, prove the correctness of the analysis, and implement the analysis as part of the higher-order functional PPL Miking CorePPL. By utilizing the alignment analysis, we design two novel inference algorithm variants: aligned SMC and aligned lightweight MCMC. We show, through real-world experiments, that they significantly improve inference execution time and accuracy compared to standard PPL versions of SMC and MCMC.
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| 9. |
- Lundén, Daniel, 1993-, et al.
(författare)
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Compiling Universal Probabilistic Programming Languages with Efficient Parallel Sequential Monte Carlo Inference
- 2022
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Ingår i: Programming Languages and Systems. - Cham : Springer. - 9783030993351 - 9783030993368 ; 13240, s. 29-56
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Konferensbidrag (refereegranskat)abstract
- Probabilistic programming languages (PPLs) allow users to encode arbitrary inference problems, and PPL implementations provide general-purpose automatic inference for these problems. However, constructing inference implementations that are efficient enough is challenging for many real-world problems. Often, this is due to PPLs not fully exploiting available parallelization and optimization opportunities. For example, handling probabilistic checkpoints in PPLs through continuation-passing style transformations or non-preemptive multitasking—as is done in many popular PPLs—often disallows compilation to low-level languages required for high-performance platforms such as GPUs. To solve the checkpoint problem, we introduce the concept of PPL control-flow graphs (PCFGs)—a simple and efficient approach to checkpoints in low-level languages. We use this approach to implement RootPPL: a low-level PPL built on CUDA and C++ with OpenMP, providing highly efficient and massively parallel SMC inference. We also introduce a general method of compiling universal high-level PPLs to PCFGs and illustrate its application when compiling Miking CorePPL—a high-level universal PPL—to RootPPL. The approach is the first to compile a universal PPL to GPUs with SMC inference. We evaluate RootPPL and the CorePPL compiler through a set of real-world experiments in the domains of phylogenetics and epidemiology, demonstrating up to 6 × speedups over state-of-the-art PPLs implementing SMC inference.
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| 10. |
- Marquina, Daniel, et al.
(författare)
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New mitochondrial primers for metabarcoding of insects, designed and evaluated using in silico methods
- 2019
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Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 19:1, s. 90-104
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Tidskriftsartikel (refereegranskat)abstract
- Insect metabarcoding has been mainly based on PCR amplification of short fragments within the barcoding region of the gene cytochrome oxidase I (COI). However, because of the variability of this gene, it has been difficult to design good universal PCR primers. Most primers used today are associated with gaps in the taxonomic coverage or amplification biases that make the results less reliable and impede the detection of species that are present in the sample. We identify new primers for insect metabarcoding using computational approaches (ecoprimers and degeprime) applied to the most comprehensive reference databases of mitochondrial genomes of Hexapoda assembled to date. New primers are evaluated in silico against previously published primers in terms of taxonomic coverage and resolution of the corresponding amplicons. For the latter criterion, we propose a new index, exclusive taxonomic resolution, which is a more biologically meaningful measure than the standard index used today. Our results show that the best markers are found in the ribosomal RNA genes (12S and 16S); they resolve about 90% of the genetically distinct species in the reference database. Some markers in protein-coding genes provide similar performance but only at much higher levels of primer degeneracy. Combining two of the best individual markers improves the effective taxonomic resolution with up to 10%. The resolution is strongly dependent on insect taxon: COI primers detect 40% of Hymenoptera, while 12S primers detect 12% of Collembola. Our results indicate that amplicon-based metabarcoding of insect samples can be improved by choosing other primers than those commonly used today.
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