Modeling the Impact of Baryons on Subhalo Populations with Machine Learning

We identify subhalos in dark matter-only (DMO) zoom-in simulations that are likely to be disrupted due to baryonic effects by using a random forest classifier trained on two hydrodynamic simulations of Milky Way (MW)-mass host halos from the Latte suite of the Feedback in Realistic Environments (FIRE) project. We train our classifier using five properties of each disrupted and surviving subhalo: pericentric distance and scale factor at first pericentric passage after accretion, and scale factor, virial mass, and maximum circular velocity at accretion. Our five-property classifier identifies disrupted subhalos in the FIRE simulations with an $85\%$ out-of-bag classification score. We predict surviving subhalo populations in DMO simulations of the FIRE host halos, finding excellent agreement with the hydrodynamic results; in particular, our classifier outperforms DMO zoom-in simulations that include the gravitational potential of the central galactic disk in each hydrodynamic simulation, indicating that it captures both the dynamical effects of a central disk and additional baryonic physics. We also predict surviving subhalo populations for a suite of DMO zoom-in simulations of MW-mass host halos, finding that baryons impact each system consistently and that the predicted amount of subhalo disruption is larger than the host-to-host scatter among the subhalo populations. Although the small size and specific baryonic physics prescription of our training set limits the generality of our results, our work suggests that machine-learning classification algorithms trained on hydrodynamic zoom-in simulations can efficiently predict realistic subhalo populations.Comment: 20 pages, 14 figures. Updated to published version. Code available at https://github.com/ollienad/subhalo_randomfores

Secoviridae: a proposed family of plant viruses within the order Picornavirales that combines the families Sequiviridae and Comoviridae, the unassigned genera Cheravirus and Sadwavirus, and the proposed genus Torradovirus

The order Picornavirales includes several plant viruses that are currently classified into the families Comoviridae (genera Comovirus, Fabavirus and Nepovirus) and Sequiviridae (genera Sequivirus and Waikavirus) and into the unassigned genera Cheravirus and Sadwavirus. These viruses share properties in common with other picornavirales (particle structure, positive-strand RNA genome with a polyprotein expression strategy, a common replication block including type III helicase, a 3C-like cysteine proteinase and type I RNA-dependent RNA polymerase). However, they also share unique properties that distinguish them from other picornavirales. They infect plants and use specialized proteins or protein domains to move through their host. In phylogenetic analysis based on their replication proteins, these viruses form a separate distinct lineage within the picornavirales branch. To recognize these common properties at the taxonomic level, we propose to create a new family termed “Secoviridae” to include the genera Comovirus, Fabavirus, Nepovirus, Cheravirus, Sadwavirus, Sequivirus and Waikavirus. Two newly discovered plant viruses share common properties with members of the proposed family Secoviridae but have distinct specific genomic organizations. In phylogenetic reconstructions, they form a separate sub-branch within the Secoviridae lineage. We propose to create a new genus termed Torradovirus (type species, Tomato torrado virus) and to assign this genus to the proposed family Secoviridae

Heterocyst placement strategies to maximize growth of cyanobacterial filaments

Under conditions of limited fixed-nitrogen, some filamentous cyanobacteria develop a regular pattern of heterocyst cells that fix nitrogen for the remaining vegetative cells. We examine three different heterocyst placement strategies by quantitatively modelling filament growth while varying both external fixed-nitrogen and leakage from the filament. We find that there is an optimum heterocyst frequency which maximizes the growth rate of the filament; the optimum frequency decreases as the external fixed-nitrogen concentration increases but increases as the leakage increases. In the presence of leakage, filaments implementing a local heterocyst placement strategy grow significantly faster than filaments implementing random heterocyst placement strategies. With no extracellular fixed-nitrogen, consistent with recent experimental studies of Anabaena sp. PCC 7120, the modelled heterocyst spacing distribution using our local heterocyst placement strategy is qualitatively similar to experimentally observed patterns. As external fixed-nitrogen is increased, the spacing distribution for our local placement strategy retains the same shape while the average spacing between heterocysts continuously increases.Comment: This is an author-created, un-copyedited version of an article accepted for publication in Physical Biology. IOP Publishing Ltd is not responsible for any errors or omissions in this version of the manuscript or any version derived from it. The definitive publisher-authenticated version will be available onlin

Endothelial Restoration of Receptor Activity-Modifying Protein 2 Is Sufficient to Rescue Lethality, but Survivors Develop Dilated Cardiomyopathy.

RAMPs (receptor activity-modifying proteins) serve as oligomeric modulators for numerous G-protein-coupled receptors, yet elucidating the physiological relevance of these interactions remains complex. Ramp2 null mice are embryonic lethal, with cardiovascular developmental defects similar to those observed in mice null for canonical adrenomedullin/calcitonin receptor-like receptor signaling. We aimed to genetically rescue the Ramp2(-/-) lethality in order to further delineate the spatiotemporal requirements for RAMP2 function during development and thereby enable the elucidation of an expanded repertoire of RAMP2 functions with family B G-protein-coupled receptors in adult homeostasis. Endothelial-specific expression of Ramp2 under the VE-cadherin promoter resulted in the partial rescue of Ramp2(-/-) mice, demonstrating that endothelial expression of Ramp2 is necessary and sufficient for survival. The surviving Ramp2(-/-) Tg animals lived to adulthood and developed spontaneous hypotension and dilated cardiomyopathy, which was not observed in adult mice lacking calcitonin receptor-like receptor. Yet, the hearts of Ramp2(-/-) Tg animals displayed dysregulation of family B G-protein-coupled receptors, including parathyroid hormone and glucagon receptors, as well as their downstream signaling pathways. These data suggest a functional requirement for RAMP2 in the modulation of additional G-protein-coupled receptor pathways in vivo, which is critical for sustained cardiovascular homeostasis. The cardiovascular importance of RAMP2 extends beyond the endothelium and canonical adrenomedullin/calcitonin receptor-like receptor signaling, in which future studies could elucidate novel and pharmacologically tractable pathways for treating cardiovascular diseases

Daphniaperformance on diets containing different combinations of high-quality algae, heterotrophic bacteria, and allochthonous particulate organic matter

Filter-feeding zooplankton in lakes feed on a mixture of phytoplankton, bacteria, and terrestrial particles and the proportions and nutritional value of these components can be highly variable. However, the extent to which food quality interacts with food quantity in affecting overall zooplankton performance is not yet fully resolved. Here we performed laboratory feeding experiments to test how the performance of the unselective filter feederDaphnia galeatawas affected if various quantities of high-quality food (the phytoplanktonRhodomonas) were diluted with low-quality food such as heterotrophic bacteria (Pseudomonas) or terrestrial detritus particles (t-POM) from the riparian zone of a boreal forest stream. We hypothesised: that increased proportions of bacteria and t-POM in the diet will lead to decreased survival, somatic growth; and reproduction ofDaphniadespite the presence of phytoplankton; that these effects are more pronounced for t-POM than for heterotrophic bacteria; and that this response is stronger when phytoplankton availability is low. Increasing the concentrations ofPseudomonasaffectedDaphniasurvival, growth, and reproduction negatively whenRhodomonaswas available at intermediate (0.37 mgC/L) and high (0.55 mgC/L) quantities. WhenRhodomonasquantity was low (0.22 mgC/L), the addition ofPseudomonasgenerally resulted in betterDaphniaperformance except at very high concentrations of the bacterium relative toRhodomonas. In contrast, the addition of t-POM was detrimental for overallDaphniaperformance at allRhodomonasconcentrations. Daphniaperformance was best described by a model including the interaction between food quality and quantity, with stronger negative effects onDaphniawhen high-quality food was supplemented with t-POM than withPseudomonas. The results indicate that the ability of zooplankton to use low-quality food is affected by the concurrent availability of high-quality food. Furthermore, food sources that can be used but do not fulfil dietary requirements of grazers (e.g. bacteria), may still provide nutritional benefits as long as other complementary food components are available in sufficient quantities to compensate for biochemical deficiencies. Therefore, we conclude that heterotrophic bacteria, but not peat layer t-POM, can be an important component of zooplankton diets in boreal lakes, especially if the concentration of phytoplankton is low

Matching functions for heavy particles

We introduce matching functions as a means of summing heavy-quark logarithms to any order. Our analysis is based on Witten's approach, where heavy quarks are decoupled one at a time in a mass-independent renormalization scheme. The outcome is a generalization of the matching conditions of Bernreuther and Wetzel: we show how to derive closed formulas for summed logarithms to any order, and present explicit expressions for leading order and next-to-leading order contributions. The decoupling of heavy quarks in theories lacking asymptotic freedom is also considered.Comment: Revised version to be published in Physical Review D; added section with application to decoupling of heavy particles in non-asymptotically free theorie

Ultrafast carrier relaxation in GaN, In_(0.05)Ga_(0.95)N and an In_(0.05)Ga_(0.95)/In_(0.15)Ga_(0.85)N Multiple Quantum Well

Room temperature, wavelength non-degenerate ultrafast pump/probe measurements were performed on GaN and InGaN epilayers and an InGaN multiple quantum well structure. Carrier relaxation dynamics were investigated as a function of excitation wavelength and intensity. Spectrally-resolved sub-picosecond relaxation due to carrier redistribution and QW capture was found to depend sensitively on the wavelength of pump excitation. Moreover, for pump intensities above a threshold of 100 microJ/cm2, all samples demonstrated an additional emission feature arising from stimulated emission (SE). SE is evidenced as accelerated relaxation (< 10 ps) in the pump-probe data, fundamentally altering the re-distribution of carriers. Once SE and carrier redistribution is completed, a slower relaxation of up to 1 ns for GaN and InGaN epilayers, and 660 ps for the MQW sample, indicates carrier recombination through spontaneous emission.Comment: submitted to Phys. Rev.

Comparison of SMILES ClO profiles with satellite, balloon-borne and ground-based measurements

We evaluate the quality of ClO profiles derived from the Superconducting Submillimeter-Wave Limb-Emission Sounder (SMILES) on the International Space Station (ISS). Version 2.1.5 of the level-2 product generated by the National Institute of Information and Communications Technology (NICT) is the subject of this study. Based on sensitivity studies, the systematic error was estimated as 5–10 pptv at the pressure range of 80–20 hPa, 35 pptv at the ClO peak altitude (~ 4 hPa), and 5–10 pptv at pressures ≤ 0.5 hPa for daytime mid-latitude conditions. For nighttime measurements, a systematic error of 8 pptv was estimated for the ClO peak altitude (~ 2 hPa). The SMILES NICT v2.1.5 ClO profiles agree with those derived from another level-2 processor developed by the Japan Aerospace Exploration Agency (JAXA) within the bias uncertainties, except for the nighttime measurements in the low and middle latitude regions where the SMILES NICT v2.1.5 profiles have a negative bias of ~ 30 pptv in the lower stratosphere. This bias is considered to be due to the use of a limited spectral bandwidth in the retrieval process of SMILES NICT v2.1.5, which makes it difficult to distinguish between the weak ClO signal and wing contributions of spectral features outside the bandwidth. In the middle and upper stratosphere outside the polar regions, no significant systematic bias was found for the SMILES NICT ClO profile with respect to data sets from other instruments such as the Aura Microwave Limb Sounder (MLS), the Odin Sub-Millimetre Radiometer (SMR), the Envisat Michelson Interferometer for Passive Atmospheric Sounding (MIPAS), and the ground-based radiometer at Mauna Kea, which demonstrates the scientific usability of the SMILES ClO data including the diurnal variations. Inside the chlorine-activated polar vortex, the SMILES NICT v2.1.5 ClO profiles show larger volume mixing ratios by 0.4 ppbv (30%) at 50 hPa compared to those of the JAXA processed profiles. This discrepancy is also considered to be an effect of the limited spectral bandwidth in the retrieval processing. We also compared the SMILES NICT ClO profiles of chlorine-activated polar vortex conditions with those measured by the balloon-borne instruments: Terahertz and submillimeter Limb Sounder (TELIS) and the MIPAS-balloon instrument (MIPAS-B). In conclusion, the SMILES NICT v2.1.5 ClO data can be used at pressures ≤ ~30 hPa for scientific analysis

Strong Coupling Constant with Flavour Thresholds at Four Loops in the MS-bar Scheme

We present in analytic form the matching conditions for the strong coupling constant alpha_s^(n_f)(mu) at the flavour thresholds to three loops in the modified minimal-subtraction scheme. Taking into account the recently calculated coefficient beta_3 of the Callan-Symanzik beta function of quantum chromodynamics, we thus derive a four-loop formula for alpha_s^(n_f)(mu) together with appropriate relationships between the asymptotic scale parameters Lambda^(n_f) for different numbers of flavours n_f.Comment: 10 pages (Latex), 3 figures (Postscript