@article{SmithFoxSchwanghartetal.2022, author = {Smith, Adam G. G. and Fox, Matthew and Schwanghart, Wolfgang and Carter, Andrew}, title = {Comparing methods for calculating channel steepness index}, series = {Earth science reviews : the international geological journal bridging the gap between research articles and textbooks}, volume = {227}, journal = {Earth science reviews : the international geological journal bridging the gap between research articles and textbooks}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0012-8252}, doi = {10.1016/j.earscirev.2022.103970}, pages = {20}, year = {2022}, abstract = {Channel steepness index, k(s), is a metric derived from the stream power model that, under certain conditions, scales with relative rock uplift rate. Channel steepness index is a property of rivers, which can be relatively easily extracted from digital elevation models (DEMs). As DEM data sets are widely available for Earth and are becoming more readily available for other planetary bodies, channel steepness index represents a powerful tool for interpreting tectonic processes. However, multiple approaches to calculate channel steepness index exist. From this several important questions arise; does choice of approach change the values of channel steepness index, can values be so different that choice of approach can influence the findings of a study, and are certain approaches better than others? With the aid of a synthetic river profile and a case study from the Sierra Nevada, California, we show that values of channel steepness index vary over orders of magnitude according to the methodology used in the calculation. We explore the limitations, advantages and disadvantages of the key approaches to calculating channel steepness index, and find that choosing an appropriate approach relies on the context of a study. Given these observations, it is important that authors acknowledge the methodology used to calculate channel steepness index, to ensure that results can be contextualised and reproduced.}, language = {en} } @article{PotenteLeveilleBourretYousefietal.2022, author = {Potente, Giacomo and L{\´e}veill{\´e}-Bourret, {\´E}tienne and Yousefi, Narjes and Choudhury, Rimjhim Roy and Keller, Barbara and Diop, Seydina Issa and Duijsings, Dani{\"e}l and Pirovano, Walter and Lenhard, Michael and Sz{\"o}v{\´e}nyi, P{\´e}ter and Conti, Elena}, title = {Comparative genomics elucidates the origin of a supergene controlling floral heteromorphism}, series = {Molecular biology and evolution : MBE}, volume = {39}, journal = {Molecular biology and evolution : MBE}, number = {2}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0737-4038}, doi = {10.1093/molbev/msac035}, pages = {16}, year = {2022}, abstract = {Supergenes are nonrecombining genomic regions ensuring the coinheritance of multiple, coadapted genes. Despite the importance of supergenes in adaptation, little is known on how they originate. A classic example of supergene is the S locus controlling heterostyly, a floral heteromorphism occurring in 28 angiosperm families. In Primula, heterostyly is characterized by the cooccurrence of two complementary, self-incompatible floral morphs and is controlled by five genes clustered in the hemizygous, ca. 300-kb S locus. Here, we present the first chromosome-scale genome assembly of any heterostylous species, that of Primula veris (cowslip). By leveraging the high contiguity of the P. veris assembly and comparative genomic analyses, we demonstrated that the S-locus evolved via multiple, asynchronous gene duplications and independent gene translocations. Furthermore, we discovered a new whole-genome duplication in Ericales that is specific to the Primula lineage. We also propose a mechanism for the origin of S-locus hemizygosity via nonhomologous recombination involving the newly discovered two pairs of CFB genes flanking the S locus. Finally, we detected only weak signatures of degeneration in the S locus, as predicted for hemizygous supergenes. The present study provides a useful resource for future research addressing key questions on the evolution of supergenes in general and the S locus in particular: How do supergenes arise? What is the role of genome architecture in the evolution of complex adaptations? Is the molecular architecture of heterostyly supergenes across angiosperms similar to that of Primula?}, language = {en} } @article{WenderingNikoloski2022, author = {Wendering, Philipp and Nikoloski, Zoran}, title = {COMMIT}, series = {PLoS Computational Biology : a new community journal / publ. by the Public Library of Science (PLoS) in association with the International Society for Computational Biology (ISCB)}, volume = {18}, journal = {PLoS Computational Biology : a new community journal / publ. by the Public Library of Science (PLoS) in association with the International Society for Computational Biology (ISCB)}, number = {3}, publisher = {Public Library of Science}, address = {San Fransisco}, issn = {1553-734X}, doi = {10.1371/journal.pcbi.1009906}, pages = {24}, year = {2022}, abstract = {Composition and functions of microbial communities affect important traits in diverse hosts, from crops to humans. Yet, mechanistic understanding of how metabolism of individual microbes is affected by the community composition and metabolite leakage is lacking. Here, we first show that the consensus of automatically generated metabolic reconstructions improves the quality of the draft reconstructions, measured by comparison to reference models. We then devise an approach for gap filling, termed COMMIT, that considers metabolites for secretion based on their permeability and the composition of the community. By applying COMMIT with two soil communities from the Arabidopsis thaliana culture collection, we could significantly reduce the gap-filling solution in comparison to filling gaps in individual reconstructions without affecting the genomic support. Inspection of the metabolic interactions in the soil communities allows us to identify microbes with community roles of helpers and beneficiaries. Therefore, COMMIT offers a versatile fully automated solution for large-scale modelling of microbial communities for diverse biotechnological applications.
Author summaryMicrobial communities are important in ecology, human health, and crop productivity. However, detailed information on the interactions within natural microbial communities is hampered by the community size, lack of detailed information on the biochemistry of single organisms, and the complexity of interactions between community members. Metabolic models are comprised of biochemical reaction networks based on the genome annotation, and can provide mechanistic insights into community functions. Previous analyses of microbial community models have been performed with high-quality reference models or models generated using a single reconstruction pipeline. However, these models do not contain information on the composition of the community that determines the metabolites exchanged between the community members. In addition, the quality of metabolic models is affected by the reconstruction approach used, with direct consequences on the inferred interactions between community members. Here, we use fully automated consensus reconstructions from four approaches to arrive at functional models with improved genomic support while considering the community composition. We applied our pipeline to two soil communities from the Arabidopsis thaliana culture collection, providing only genome sequences. Finally, we show that the obtained models have 90\% genomic support and demonstrate that the derived interactions are corroborated by independent computational predictions.}, language = {en} } @article{ProlSmirnovHoqueetal.2022, author = {Prol, Fabricio S. and Smirnov, Artem G. and Hoque, M. Mainul and Shprits, Yuri Y.}, title = {Combined model of topside ionosphere and plasmasphere derived from radio-occultation and Van Allen Probes data}, series = {Scientific reports}, volume = {12}, journal = {Scientific reports}, number = {1}, publisher = {Macmillan Publishers Limited, part of Springer Nature}, address = {London}, issn = {2045-2322}, doi = {10.1038/s41598-022-13302-1}, pages = {11}, year = {2022}, abstract = {In the last years, electron density profile functions characterized by a linear dependence on the scale height showed good results when approximating the topside ionosphere. The performance above 800 km, however, is not yet well investigated. This study investigates the capability of the semi-Epstein functions to represent electron density profiles from the peak height up to 20,000 km. Electron density observations recorded by the Van Allen Probes were used to resolve the scale height dependence in the plasmasphere. It was found that the linear dependence of the scale height in the topside ionosphere cannot be directly used to extrapolate profiles above 800 km. We find that the dependence of scale heights on altitude is quadratic in the plasmasphere. A statistical model of the scale heights is therefore proposed. After combining the topside ionosphere and plasmasphere by a unified model, we have obtained good estimations not only in the profile shapes, but also in the Total Electron Content magnitude and distributions when compared to actual measurements from 2013, 2014, 2016 and 2017. Our investigation shows that Van Allen Probes can be merged to radio-occultation data to properly represent the upper ionosphere and plasmasphere by means of a semi-Epstein function.}, language = {en} } @article{PhamQuanMeietal.2022, author = {Pham, Duong Tung and Quan, Ting and Mei, Shilin and Lu, Yan}, title = {Colloidal metal sulfide nanoparticles for high performance electrochemical energy storage systems}, series = {Current opinion in green and sustainable chemistry}, volume = {34}, journal = {Current opinion in green and sustainable chemistry}, publisher = {Elsevier}, address = {Amsterdam}, issn = {2452-2236}, doi = {10.1016/j.cogsc.2022.100596}, pages = {11}, year = {2022}, abstract = {Transition metal sulfides have emerged as excellent replacement candidates of traditional insertion electrode materials based on their conversion or alloying mechanisms, facilitating high specific capacity and rate ability. However, parasitic reactions such as massive volume change during the discharge/ charge processes, intermediate polysulfide dissolution, and passivating solid electrolyte interface formation have led to poor cyclability, hindering their feasibility and applicability in energy storage systems. Colloidal metal sulfide nanoparticles, a special class that integrates the intrinsic chemical properties of metal sulfides and their specified structural features, have fairly enlarged their contribution due to the synergistic effect. This review highlights the latest synthetic approaches based on colloidal process. Their corresponding electrochemical outcomes will also be discussed, which are thoroughly updated along with their insight scientific standpoints.}, language = {en} } @article{Omel'chenkoLaing2022, author = {Omel'chenko, Oleh and Laing, Carlo R.}, title = {Collective states in a ring network of theta neurons}, series = {Proceedings of the Royal Society of London. Series A, Mathematical, physical and engineering sciences}, volume = {478}, journal = {Proceedings of the Royal Society of London. Series A, Mathematical, physical and engineering sciences}, number = {2259}, publisher = {Royal Society}, address = {London}, issn = {1364-5021}, doi = {10.1098/rspa.2021.0817}, pages = {23}, year = {2022}, abstract = {We consider a ring network of theta neurons with non-local homogeneous coupling. We analyse the corresponding continuum evolution equation, analytically describing all possible steady states and their stability. By considering a number of different parameter sets, we determine the typical bifurcation scenarios of the network, and put on a rigorous footing some previously observed numerical results.}, language = {en} } @article{AbramovaBatzelModesti2022, author = {Abramova, Olga and Batzel, Katharina and Modesti, Daniela}, title = {Collective response to the health crisis among German Twitter users}, series = {International Journal of Information Management Data Insights}, volume = {2}, journal = {International Journal of Information Management Data Insights}, number = {2}, publisher = {Elsevier}, address = {Amsterdam}, issn = {2667-0968}, doi = {10.1016/j.jjimei.2022.100126}, pages = {13}, year = {2022}, abstract = {We used structural topic modeling to analyze over 800,000 German tweets about COVID-19 to answer the questions: What patterns emerge in tweets as a response to a health crisis? And how do topics discussed change over time? The study leans on the goals associated with the health information seeking (GAINS) model, discerning whether a post aims at tackling and eliminating the problem (i.e., problem-focused) or managing the emotions (i.e., emotion-focused); whether it strives to maximize positive outcomes (promotion focus) or to minimize negative outcomes (prevention focus). The findings indicate four clusters salient in public reactions: 1) "Understanding" (problem-promotion); 2) "Action planning" (problem-prevention); 3) "Hope" (emotion-promotion) and 4) "Reassurance" (emotion-prevention). Public communication is volatile over time, and a shift is evidenced from self-centered to community-centered topics within 4.5 weeks. Our study illustrates social media text mining's potential to quickly and efficiently extract public opinions and reactions. Monitoring fears and trending topics enable policymakers to rapidly respond to deviant behavior, like resistive attitudes toward containment measures or deteriorating physical health. Healthcare workers can use the insights to provide mental health services for battling anxiety or extensive loneliness from staying home.}, language = {en} } @article{DamleSparreRichteretal.2022, author = {Damle, Mitali and Sparre, Martin and Richter, Philipp and Hani, Maan H. and Nuza, Sebastian and Pfrommer, Christoph and Grand, Robert J. J. and Hoffman, Yehuda and Libeskind, Noam and Sorce, Jenny and Steinmetz, Mathias and Tempel, Elmo and Vogelsberger, Mark and Wang, Peng}, title = {Cold and hot gas distribution around the Milky-Way - M31 system in the HESTIA simulations}, series = {Monthly notices of the Royal Astronomical Society}, volume = {512}, journal = {Monthly notices of the Royal Astronomical Society}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0035-8711}, doi = {10.1093/mnras/stac663}, pages = {3717 -- 3737}, year = {2022}, abstract = {Recent observations have revealed remarkable insights into the gas reservoir in the circumgalactic medium (CGM) of galaxy haloes. In this paper, we characterise the gas in the vicinity of Milky Way and Andromeda analogues in the hestia (High resolution Environmental Simulations of The Immediate Area) suite of constrained Local Group (LG) simulations. The hestia suite comprise of a set of three high-resolution arepo-based simulations of the LG, run using the Auriga galaxy formation model. For this paper, we focus only on the 𝑧 = 0 simulation datasets and generate mock skymaps along with a power spectrum analysis to show that the distributions of ions tracing low-temperature gas (H i and Si iii) are more clumpy in comparison to warmer gas tracers (O vi, O vii and O viii). We compare to the spectroscopic CGM observations of M31 and low-redshift galaxies. hestia under-produces the column densities of the M31 observations, but the simulations are consistent with the observations of low-redshift galaxies. A possible explanation for these findings is that the spectroscopic observations of M31 are contaminated by gas residing in the CGM of the Milky Way.}, language = {en} } @article{DahlkeSolbesMaturilli2022, author = {Dahlke, Sandro and Solb{\`e}s, Am{\´e}lie and Maturilli, Marion}, title = {Cold air outbreaks in fram strait: climatology, trends, and observations during an extreme season in 2020}, series = {Journal of geophysical research : atmospheres}, volume = {127}, journal = {Journal of geophysical research : atmospheres}, number = {3}, publisher = {American Geophysical Union}, address = {Washington}, issn = {2169-897X}, doi = {10.1029/2021JD035741}, pages = {18}, year = {2022}, abstract = {Fram Strait in the northern North Atlantic is a key region for marine cold air outbreaks (MCAOs), southward discharges of polar air under northerly air flow, which have a strong impact on air-sea heat fluxes, boundary layer processes and severe weather. This study investigates climatologies and decadal trends of Fram Strait MCAOs of different intensity classes based on the ERA5 reanalysis product for 1979-2020. Among striking interannual variability, it is shown that the main MCAO season is December through March, when MCAOs occur around 2/3 of the time. We report on significant decadal MCAO decreases in December and January, and a significant increase in March. While the mid-winter decrease is mainly related to the different paces of warming between the surface and the lower atmosphere, the increase in March can be related to changes in synoptic circulation patterns. As an explanation for the latter, a possible feedback between retreating Barents Sea sea ice, enhanced cyclonic activity and Fram Strait MCAOs is postulated. Exemplifying the trend toward stronger MCAOs during March, the study details the recordbreaking MCAO season in early 2020, and an observational case study of an extreme MCAO event in March 2020 is conducted. Thereby, radiosonde observations are combined with kinematic air back-trajectories to provide rare observational evidence for the diabatic cooling and drying during the MCAO preconditioning phase.}, language = {en} } @article{SieberYaxleyHermann2022, author = {Sieber, Melanie Jutta and Yaxley, Greg and Hermann, J{\"o}rg}, title = {COH-fluid induced metasomatism of peridotites in the forearc mantle}, series = {Contributions to Mineralogy and Petrology}, volume = {177}, journal = {Contributions to Mineralogy and Petrology}, number = {4}, publisher = {Springer}, address = {New York}, issn = {0010-7999}, doi = {10.1007/s00410-022-01905-w}, pages = {22}, year = {2022}, abstract = {Devolatilization of subducting lithologies liberates COH-fluids. These may become partially sequestered in peridotites in the slab and the overlying forearc mantle, affecting the cycling of volatiles and fluid mobile elements in subduction zones. Here we assess the magnitudes, timescales and mechanism of channelized injection of COH-fluids doped with Ca-aq(2+), Sr-aq(2+) and Ba-aq(2+) into the dry forearc mantle by performing piston cylinder experiments between 1-2.5 GPa and 600-700 degrees C. Cylindrical cores of natural spinel-bearing harzburgites were used as starting materials. Based on mineral assemblage and composition three reaction zones are distinguishable from the rim towards the core of primary olivine and orthopyroxene grains. Zone 1 contains carbonates + quartz +/- kyanite and zone 2 contains carbonates + talc +/- chlorite. Olivine is further replaced in zone 3 by either antigorite+ magnesite or magnesite +talc within or above antigorite stability, respectively. Orthopyroxene is replaced in zone 3 by talc + chlorite. Mineral assemblages and the compositions of secondary minerals depend on fluid composition and the replaced primary silicate. The extent of alteration depends on fluid CO2 content and fluid/rock-ratio, and is further promoted by fluid permeable reaction zones and reaction driven cracking. Our results show that COH-fluid induced metasomatism of the forearc mantle is self-perpetuating and efficient at sequestering Ca-aq(2+), Sr-aq(2+), Ba-aq(2+) and CO2aq into newly formed carbonates. This process is fast with 90\% of the available C sequestered and nearly 50\% of the initial minerals altered at 650 degrees C, 2 GPa within 55 h. The dissolution of primary silicates under high COH-fluid/rock-ratios, as in channelized fluid flow, enriches SiO2aq in the fluid, while CO2aq is sequestered into carbonates. In an open system, the remaining CO2-depleted, Si-enriched aqueous fluid may cause Si-metasomatism in the forearc further away from the injection of the COH-fluid into peridotite.}, language = {en} }