@article{SandhageHofmannAngombeKindermannetal.2022, author = {Sandhage-Hofmann, Alexandra and Angombe, Simon and Kindermann, Liana and Linst{\"a}dter, Anja and M{\"o}rchen, Ramona}, title = {Conservation with elephants and agricultural intensification}, series = {Geoderma : an international journal of soil science}, volume = {425}, journal = {Geoderma : an international journal of soil science}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0016-7061}, doi = {10.1016/j.geoderma.2022.116009}, pages = {15}, year = {2022}, abstract = {Nature conservation is currently shaping many terrestrial ecosystems in Africa. This is particularly evident in Sub-Saharan Africa (SSA), where conservation is intended to recover wildlife populations, with special focus on elephants. Rising numbers of elephants induce woody biomass losses but increase soil organic carbon (SOC) stocks from decaying wood and dung. We hypothesized that these increases under wildlife conservation in SSA go along with rising contents of plant residues in SOC, traceable by the molecular markers lignin and n-alkanes. In contrast, agricultural intensification would reduce them due to lower C input and faster SOC turnover through tillage. To test this, we analyzed lignin by the CuO oxidation method and n-alkanes by fast pressurized solvent extraction in topsoils (0-10 cm) of Arenosols and corresponding plant samples (trees, grasses and crops). Sampling sites followed conservation gradients with low, medium and high elephant densities and intensification gradients with rangeland and cropland in the woodland savanna of the Namibian Zambezi Region. Patterns of lignin-derived phenols were retained in the soil, whereas n-alkanes showed shifts in chain lengths. n-Alkanes also showed no clear increase or decrease under conservation or intensification, respectively. Differently, lignin-derived phenols showed lower values under intensification than under conservation. Confirming our hypothesis, rising SOC contents with rising elephant densities (from 4.4 at low to 5.7 g kg(-1) SOC at high elephant densities) went along with an increasing accumulation of lignin-derived phenols (24.4-34.8 g kg(-1) VSCOC). This increase is associated with the input of woody debris to the soil, as indicated by V-units and carbon isotopes, modulated by clay and woody biomass. We conclude, that increasing input of woody residues into soil by browsing behaviour of elephants is an important mechanism for controlling SOC supply in the context of wildlife conservation and is traceable with lignin-derived phenols, but not with n-alkanes.}, language = {en} } @article{AransonPikovskij2022, author = {Aranson, Igor S. and Pikovskij, Arkadij}, title = {Confinement and collective escape of active particles}, series = {Physical review letters}, volume = {128}, journal = {Physical review letters}, number = {10}, publisher = {American Physical Society}, address = {College Park, Md.}, issn = {0031-9007}, doi = {10.1103/PhysRevLett.128.108001}, pages = {6}, year = {2022}, abstract = {Active matter broadly covers the dynamics of self-propelled particles. While the onset of collective behavior in homogenous active systems is relatively well understood, the effect of inhomogeneities such as obstacles and traps lacks overall clarity. Here, we study how interacting, self-propelled particles become trapped and released from a trap. We have found that captured particles aggregate into an orbiting condensate with a crystalline structure. As more particles are added, the trapped condensates escape as a whole. Our results shed light on the effects of confinement and quenched disorder in active matter.}, language = {en} } @article{KayaFreitag2022, author = {Kaya, Adem and Freitag, Melina A.}, title = {Conditioning analysis for discrete Helmholtz problems}, series = {Computers and mathematics with applications : an international journal}, volume = {118}, journal = {Computers and mathematics with applications : an international journal}, publisher = {Elsevier Science}, address = {Amsterdam}, issn = {0898-1221}, doi = {10.1016/j.camwa.2022.05.016}, pages = {171 -- 182}, year = {2022}, abstract = {In this paper, we examine conditioning of the discretization of the Helmholtz problem. Although the discrete Helmholtz problem has been studied from different perspectives, to the best of our knowledge, there is no conditioning analysis for it. We aim to fill this gap in the literature. We propose a novel method in 1D to observe the near-zero eigenvalues of a symmetric indefinite matrix. Standard classification of ill-conditioning based on the matrix condition number is not true for the discrete Helmholtz problem. We relate the ill-conditioning of the discretization of the Helmholtz problem with the condition number of the matrix. We carry out analytical conditioning analysis in 1D and extend our observations to 2D with numerical observations. We examine several discretizations. We find different regions in which the condition number of the problem shows different characteristics. We also explain the general behavior of the solutions in these regions.}, language = {en} } @article{ChoudhuryDeVineSinhaetal.2022, author = {Choudhury, Arnab and DeVine, Jessalyn A. A. and Sinha, Shreya and Lau, Jascha Alexander and Kandratsenka, Alexander and Schwarzer, Dirk and Saalfrank, Peter and Wodtke, Alec Michael}, title = {Condensed-phase isomerization through tunnelling gateways}, series = {Nature : the international weekly journal of science}, volume = {612}, journal = {Nature : the international weekly journal of science}, number = {7941}, publisher = {Macmillan Publishers Limited, part of Springer Nature}, address = {London}, issn = {0028-0836}, doi = {10.1038/s41586-022-05451-0}, pages = {691 -- 695}, year = {2022}, abstract = {Quantum mechanical tunnelling describes transmission of matter waves through a barrier with height larger than the energy of the wave(1). Tunnelling becomes important when the de Broglie wavelength of the particle exceeds the barrier thickness; because wavelength increases with decreasing mass, lighter particles tunnel more efficiently than heavier ones. However, there exist examples in condensed-phase chemistry where increasing mass leads to increased tunnelling rates(2). In contrast to the textbook approach, which considers transitions between continuum states, condensed-phase reactions involve transitions between bound states of reactants and products. Here this conceptual distinction is highlighted by experimental measurements of isotopologue-specific tunnelling rates for CO rotational isomerization at an NaCl surface(3,4), showing nonmonotonic mass dependence. A quantum rate theory of isomerization is developed wherein transitions between sub-barrier reactant and product states occur through interaction with the environment. Tunnelling is fastest for specific pairs of states (gateways), the quantum mechanical details of which lead to enhanced cross-barrier coupling; the energies of these gateways arise nonsystematically, giving an erratic mass dependence. Gateways also accelerate ground-state isomerization, acting as leaky holes through the reaction barrier. This simple model provides a way to account for tunnelling in condensed-phase chemistry, and indicates that heavy-atom tunnelling may be more important than typically assumed.}, language = {en} } @article{BouamraZouhalRateletal.2022, author = {Bouamra, Marwa and Zouhal, Hassane and Ratel, S{\´e}bastien and Makhlouf, Issam and Bezrati, Ikram and Chtara, Moktar and Behm, David George and Granacher, Urs and Chaouachi, Anis}, title = {Concurrent Training Promotes Greater Gains on Body Composition and Components of Physical Fitness Than Single-Mode Training (Endurance or Resistance) in Youth With Obesity}, series = {Frontiers in Physiology}, volume = {13}, journal = {Frontiers in Physiology}, publisher = {Frontiers}, address = {Lausanne, Schweiz}, issn = {1664-042X}, doi = {10.3389/fphys.2022.869063}, pages = {1 -- 16}, year = {2022}, abstract = {The prevalence of obesity in the pediatric population has become a major public health issue. Indeed, the dramatic increase of this epidemic causes multiple and harmful consequences, Physical activity, particularly physical exercise, remains to be the cornerstone of interventions against childhood obesity. Given the conflicting findings with reference to the relevant literature addressing the effects of exercise on adiposity and physical fitness outcomes in obese children and adolescents, the effect of duration-matched concurrent training (CT) [50\% resistance (RT) and 50\% high-intensity-interval-training (HIIT)] on body composition and physical fitness in obese youth remains to be elucidated. Thus, the purpose of this study was to examine the effects of 9-weeks of CT compared to RT or HIIT alone, on body composition and selected physical fitness components in healthy sedentary obese youth. Out of 73 participants, only 37; [14 males and 23 females; age 13.4 ± 0.9 years; body-mass-index (BMI): 31.2 ± 4.8 kg·m-2] were eligible and randomized into three groups: HIIT (n = 12): 3-4 sets×12 runs at 80-110\% peak velocity, with 10-s passive recovery between bouts; RT (n = 12): 6 exercises; 3-4 sets × 10 repetition maximum (RM) and CT (n = 13): 50\% serial completion of RT and HIIT. CT promoted significant greater gains compared to HIIT and RT on body composition (p < 0.01, d = large), 6-min-walking test distance (6 MWT-distance) and on 6 MWT-VO2max (p < 0.03, d = large). In addition, CT showed substantially greater improvements than HIIT in the medicine ball throw test (20.2 vs. 13.6\%, p < 0.04, d = large). On the other hand, RT exhibited significantly greater gains in relative hand grip strength (p < 0.03, d = large) and CMJ (p < 0.01, d = large) than HIIT and CT. CT promoted greater benefits for fat, body mass loss and cardiorespiratory fitness than HIIT or RT modalities. This study provides important information for practitioners and therapists on the application of effective exercise regimes with obese youth to induce significant and beneficial body composition changes. The applied CT program and the respective programming parameters in terms of exercise intensity and volume can be used by practitioners as an effective exercise treatment to fight the pandemic overweight and obesity in youth.}, language = {en} } @article{ThiekenMohorKreibichetal.2022, author = {Thieken, Annegret and Mohor, Guilherme Samprogna and Kreibich, Heidi and M{\"u}ller, Meike}, title = {Compound inland flood events}, series = {Natural hazards and earth system sciences : NHESS}, volume = {22}, journal = {Natural hazards and earth system sciences : NHESS}, number = {1}, publisher = {Copernicus}, address = {G{\"o}ttingen}, issn = {1561-8633}, doi = {10.5194/nhess-22-165-2022}, pages = {165 -- 185}, year = {2022}, abstract = {Several severe flood events hit Germany in recent years, with events in 2013 and 2016 being the most destructive ones, although dynamics and flood processes were very different. While the 2013 event was a slowly rising widespread fluvial flood accompanied by some severe dike breaches, the events in 2016 were fast-onset pluvial floods, which resulted in surface water flooding in some places due to limited capacities of the drainage systems and in destructive flash floods with high sediment loads and clogging in others, particularly in small steep catchments. Hence, different pathways, i.e. different routes that the water takes to reach (and potentially damage) receptors, in our case private households, can be identified in both events. They can thus be regarded as spatially compound flood events or compound inland floods. This paper analyses how differently affected residents coped with these different flood types (fluvial and pluvial) and their impacts while accounting for the different pathways (river flood, dike breach, surface water flooding and flash flood) within the compound events. The analyses are based on two data sets with 1652 (for the 2013 flood) and 601 (for the 2016 flood) affected residents who were surveyed around 9 months after each flood, revealing little socio-economic differences - except for income - between the two samples. The four pathways showed significant differences with regard to their hydraulic and financial impacts, recovery, warning processes, and coping and adaptive behaviour. There are just small differences with regard to perceived self-efficacy and responsibility, offering entry points for tailored risk communication and support to improve property-level adaptation.}, language = {en} } @article{WeithoffBell2022, author = {Weithoff, Guntram and Bell, Elanor Margaret}, title = {Complex Trophic Interactions in an Acidophilic Microbial Community}, series = {Microorganisms}, volume = {10}, journal = {Microorganisms}, edition = {7}, publisher = {MDPI}, address = {Basel, Schweiz}, issn = {2076-2607}, doi = {10.3390/microorganisms10071340}, pages = {1 -- 10}, year = {2022}, abstract = {Extreme habitats often harbor specific communities that differ substantially from non-extreme habitats. In many cases, these communities are characterized by archaea, bacteria and protists, whereas the number of species of metazoa and higher plants is relatively low. In extremely acidic habitats, mostly prokaryotes and protists thrive, and only very few metazoa thrive, for example, rotifers. Since many studies have investigated the physiology and ecology of individual species, there is still a gap in research on direct, trophic interactions among extremophiles. To fill this gap, we experimentally studied the trophic interactions between a predatory protist (Actinophrys sol, Heliozoa) and its prey, the rotifers Elosa woralli and Cephalodella sp., the ciliate Urosomoida sp. and the mixotrophic protist Chlamydomonas acidophila (a green phytoflagellate, Chlorophyta). We found substantial predation pressure on all animal prey. High densities of Chlamydomonas acidophila reduced the predation impact on the rotifers by interfering with the feeding behaviour of A. sol. These trophic relations represent a natural case of intraguild predation, with Chlamydomonas acidophila being the common prey and the rotifers/ciliate and A. sol being the intraguild prey and predator, respectively. We further studied this intraguild predation along a resource gradient using Cephalodella sp. as the intraguild prey. The interactions among the three species led to an increase in relative rotifer abundance with increasing resource (Chlamydomonas) densities. By applying a series of laboratory experiments, we revealed the complexity of trophic interactions within a natural extremophilic community.}, language = {en} } @article{GalhuberMichenthalerHeiningeretal.2022, author = {Galhuber, Markus and Michenthaler, Helene and Heininger, Christoph and Reinisch, Isabel and N{\"o}ssing, Christoph and Krstic, Jelena and Kupper, Nadja and Moyschewitz, Elisabeth and Auer, Martina and Heitzer, Ellen and Ulz, Peter and Birner-Gruenberger, Ruth and Liesinger, Laura and Lenihan-Geels, Georgia Ngawai and Oster, Moritz and Spreitzer, Emil and Chiozzi, Riccardo Zenezini and Schulz, Tim J. and Schupp, Michael and Madl, Tobias and Heck, Albert J. R. and Prokesch, Andreas}, title = {Complementary omics strategies to dissect p53 signaling networks under nutrient stress}, series = {Cellular and molecular life sciences}, volume = {79}, journal = {Cellular and molecular life sciences}, number = {6}, publisher = {Springer Nature}, address = {Basel}, issn = {1420-682X}, doi = {10.1007/s00018-022-04345-8}, pages = {22}, year = {2022}, abstract = {Signaling trough p53is a major cellular stress response mechanism and increases upon nutrient stresses such as starvation. Here, we show in a human hepatoma cell line that starvation leads to robust nuclear p53 stabilization. Using BioID, we determine the cytoplasmic p53 interaction network within the immediate-early starvation response and show that p53 is dissociated from several metabolic enzymes and the kinase PAK2 for which direct binding with the p53 DNA-binding domain was confirmed with NMR studies. Furthermore, proteomics after p53 immunoprecipitation (RIME) uncovered the nuclear interactome under prolonged starvation, where we confirmed the novel p53 interactors SORBS1 (insulin receptor signaling) and UGP2 (glycogen synthesis). Finally, transcriptomics after p53 re-expression revealed a distinct starvation-specific transcriptome response and suggested previously unknown nutrient-dependent p53 target genes. Together, our complementary approaches delineate several nodes of the p53 signaling cascade upon starvation, shedding new light on the mechanisms of p53 as nutrient stress sensor. Given the central role of p53 in cancer biology and the beneficial effects of fasting in cancer treatment, the identified interaction partners and networks could pinpoint novel pharmacologic targets to fine-tune p53 activity.}, language = {en} } @article{ThayumanasundaramRamanVenkatesanOussetetal.2022, author = {Thayumanasundaram, Savitha and Raman Venkatesan, Thulasinath and Ousset, Aymeric and Van Hollebeke, Kim and Aerts, Luc and Wubbenhorst, Michael and Van den Mooter, Guy}, title = {Complementarity of mDSC, DMA, and DRS Techniques in the Study of T-g and Sub-T-g Transitions in Amorphous Solids}, series = {Molecular pharmaceutics}, journal = {Molecular pharmaceutics}, publisher = {American Chemical Society}, address = {Washington}, issn = {1543-8384}, doi = {10.1021/acs.molpharmaceut.2c00123}, pages = {17}, year = {2022}, abstract = {Recently, glasses, a subset of amorphous solids, have gained attention in various fields, such as polymer chemistry, optical fibers, and pharmaceuticals. One of their characteristic features, the glass transition temperature (T-g) which is absent in 100\% crystalline materials, influences several material properties, such as free volume, enthalpy, viscosity, thermodynamic transitions, molecular motions, physical stability, mechanical properties, etc. In addition to T-g, there may be several other temperaturedependent transitions known as sub-T-g transitions (or beta-, gamma-, and delta-relaxations) which are identified by specific analytical techniques. The study of T-g and sub-T-g transitions occurring in amorphous solids has gained much attention because of its importance in understanding molecular kinetics, and it requires the combination of conventional and novel characterization techniques. In the present study, three different analytical techniques [modulated differential scanning calorimetry (mDSC), dynamic mechanical analysis (DMA), and dielectric relaxation spectroscopy (DRS)] were used to perform comprehensive qualitative/quantitative characterization of molecular relaxations, miscibility, and molecular interactions present in an amorphous polymer (PVPVA), a model drug (indomethacin, IND), and IND/PVPVA-based amorphous solid dispersions (ASDs). This is the first ever reported DMA study on PVPVA in its powder form, which avoids the contribution of solvent to the mechanical properties when a selfstanding polymer film is used. A good correlation between the techniques in determining the T-g value of PVPVA, IND, and IND/ PVPVA-based ASDs is established, and the negligible difference (within 10 degrees C) is attributed to the different material properties assessed in each technique. However, the overall T-g behavior, the decrease in T-g with increase in drug loading in ASDs, is universally observed in all the above-mentioned techniques, which reveals their complementarity. DMA and DRS techniques are used to study the different sub-T-g transitions present in PVPVA, amorphous IND, and IND/PVPVA-based ASDs because these transitions are normally too weak or too broad for mDSC to detect. For IND/PVPVA-based ASDs, both techniques show a shift of sub-T-g transitions (or secondary relaxation peaks) toward the high-temperature region from -140 to -45 degrees C. Thus, this paper outlines the usage of different solid-state characterization techniques in understanding the different molecular dynamics present in the polymer, drug, and their interactions in ASDs with the integrated information obtained from individual techniques.}, language = {en} } @article{SobhkhizMiandehiYamazakiArrasetal.2022, author = {Sobhkhiz-Miandehi, Sahar and Yamazaki, Yosuke and Arras, Christina and Miyoshi, Yasunobu and Shinagawa, Hiroyuki}, title = {Comparison of the tidal signatures in sporadic E and vertical ion convergence rate, using FORMOSAT-3/COSMIC radio occultation observations and GAIA model}, series = {Earth, planets and space : EPS}, volume = {74}, journal = {Earth, planets and space : EPS}, number = {1}, publisher = {Springer}, address = {Heidelberg}, issn = {1880-5981}, doi = {10.1186/s40623-022-01637-y}, pages = {13}, year = {2022}, abstract = {Sporadic E or Es is a transient phenomenon where thin layers of enhanced electron density appear in the ionospheric E region (90-120 km altitude). The neutral wind shear caused by atmospheric tides can lead ions to converge vertically at E-region heights and form the Es layer. This research aims to determine the role of atmospheric solar and lunar tides in Es occurrence. For this purpose, radio occultation data of FORMOSAT-3/COSMIC have been used, which provide complete global coverage of Es events. Moreover, GAIA model simulations have been employed to evaluate the vertical ion convergence induced by solar tides. The results show both migrating and non-migrating solar tidal signatures and the semidiurnal migrating lunar tidal signature mainly in low and mid-latitude Es occurrence. The seasonal variation of the migrating solar tidal components of Es is in good agreement with those in the vertical ion convergence derived from GAIA at higher altitudes. Furthermore, some non-migrating components of solar tides, including semidiurnal westward wavenumbers 1 and 3 and diurnal eastward wavenumbers 2 and 3, also significantly affect the Es occurrence rate.}, language = {en} } @article{HuangRichterKleickmannetal.2022, author = {Huang, Yizhen and Richter, Eric and Kleickmann, Thilo and Richter, Dirk}, title = {Comparing video and virtual reality as tools for fostering interest and self-efficacy in classroom management}, series = {British journal of educational technology / British Educational Communications and Technology Agency}, volume = {54}, journal = {British journal of educational technology / British Educational Communications and Technology Agency}, number = {2}, publisher = {Wiley-Blackwell}, address = {Oxford}, issn = {0007-1013}, doi = {10.1111/bjet.13254}, pages = {467 -- 488}, year = {2022}, abstract = {Video is a widely used medium in teacher training for situating student teachers in classroom scenarios. Although the emerging technology of virtual reality (VR) provides similar, and arguably more powerful, capabilities for immersing teachers in lifelike situations, its benefits and risks relative to video formats have received little attention in the research to date. The current study used a randomized pretest-posttest experimental design to examine the influence of a video- versus VR-based task on changing situational interest and self-efficacy in classroom management. Results from 49 student teachers revealed that the VR simulation led to higher increments in self-reported triggered interest and self-efficacy in classroom management, but also invoked higher extraneous cognitive load than a video viewing task. We discussed the implications of these results for pre-service teacher education and the design of VR environments for professional training purposes. Practitioner notes What is already known about this topic Video is a popular teacher training medium given its ability to display classroom situations. Virtual reality (VR) also immerses users in lifelike situations and has gained popularity in recent years. Situational interest and self-efficacy in classroom management is vital for student teachers' professional development. What this paper adds VR outperforms video in promoting student teachers' triggered interest in classroom management. Student teachers felt more efficacious in classroom management after participating in VR. VR also invoked higher extraneous cognitive load than the video. Implications for practice and/or policy VR provides an authentic teacher training environment for classroom management. The design of the VR training environment needs to ensure a low extraneous cognitive load.}, language = {en} } @article{Braun2022, author = {Braun, Jean}, title = {Comparing the transport-limited and ξ-q models for sediment transport}, series = {Earth surface dynamics}, volume = {10}, journal = {Earth surface dynamics}, number = {2}, publisher = {Copernicus}, address = {G{\"o}ttingen}, issn = {2196-6311}, doi = {10.5194/esurf-10-301-2022}, pages = {301 -- 327}, year = {2022}, abstract = {Here I present a comparison between two of the most widely used reduced-complexity models for the representation of sediment transport and deposition processes, namely the transport-limited (or TL) model and the under-capacity (or xi-q) model more recently developed by Davy and Lague (2009). Using both models, I investigate the behavior of a sedimentary continental system of length L fed by a fixed sedimentary flux from a catchment of size A(0) in a nearby active orogen through which sediments transit to a fixed base level representing a large river, a lake or an ocean. This comparison shows that the two models share the same steady-state solution, for which I derive a simple 1D analytical expression that reproduces the major features of such sedimentary systems: a steep fan that connects to a shallower alluvial plain. The resulting fan geometry obeys basic observational constraints on fan size and slope with respect to the upstream drainage area, A(0). The solution is strongly dependent on the size of the system, L, in comparison to a distance L-0, which is determined by the size of A(0), and gives rise to two fundamentally different types of sedimentary systems: a constrained system where L < L-0 and open systems where L > L-0. I derive simple expressions that show the dependence of the system response time on the system characteristics, such as its length, the size of the upstream catchment area, the amplitude of the incoming sedimentary flux and the respective rate parameters (diffusivity or erodibility) for each of the two models. I show that the xi-q model predicts longer response times. I demonstrate that although the manner in which signals propagates through the sedimentary system differs greatly between the two models, they both predict that perturbations that last longer than the response time of the system can be recorded in the stratigraphy of the sedimentary system and in particular of the fan. Interestingly, the xi-q model predicts that all perturbations in the incoming sedimentary flux will be transmitted through the system, whereas the TL model predicts that rapid perturbations cannot. I finally discuss why and under which conditions these differences are important and propose observational ways to determine which of the two models is most appropriate to represent natural systems.}, language = {en} } @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}, 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} }