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At least 325 records · Page 18

Erroneous predictions of auxotrophies by CarveMe

We report in their paper, D. Machado et al. claim to identify ‘cooperative’ communities with many amino acid auxotrophies1. A related paper, with many of the same authors, claims that 26% of bacteria from free-living communities are amino acid auxotrophs2. The putative amino acid auxotrophies were derived from genome sequences via the metabolic models of CarveMe3 but were not validated in any way. I checked the predictions of CarveMe for prototrophic bacteria and found a high rate of spurious auxotrophies.

59 BASIC BIOLOGICAL SCIENCES↗

Author Correction: US oil and gas system emissions from nearly one million aerial site measurements

Correction to: Naturehttps://doi.org/10.1038/s41586-024-07117-5 Published online 13 March 2024 In the version of the article initially published, several errors were present and have been corrected in the HTML and PDF versions of the article and Supplementary Information. The main results, conclusions, and our interpretations of the data remain unchanged. See the new Supplementary Information Section S15 for a more detailed description of the errors corrected and the resulting effects on the analysis. Data processing and methods corrections Overflight count correction: We previously used pre-computed source coverage data for some Carbon Mapper campaigns that was computed differently than was required for our analysis. We have re-computed Carbon Mapper source coverage based on flightline polygons and source coordinates. Transition point computation, well sites: The updated version now correctly compares the cumulative emissions distribution of simulated well site emissions with that of aerially detected sources (rather than plumes) when computing the transition point. Transition point computation, midstream: Additionally, the transition point calculation has been corrected to exclude aerially detected midstream emissions below the transition point, which was previously leading to double counting of these emissions. This error was not present for upstream (well site) emissions. Calculation errors Unit error: We corrected a specific unit conversion error affecting well site emissions in the Kairos Fort Worth dataset. Across all datasets, we also correct the conversion factor for converting from standard volume to mass for midstream emissions. Sorting error: We correct code that was applying incorrect sorting when computing correction factors to account for partial detection at well sites. Small typographical corrections were made in Fig. 1b and SI Section S4.1. Data processing and methods corrections Overflight count correction: We previously used pre-computed source coverage data for some Carbon Mapper campaigns that was computed differently than was required for our analysis. We have re-computed Carbon Mapper source coverage based on flightline polygons and source coordinates. Transition point computation, well sites: The updated version now correctly compares the cumulative emissions distribution of simulated well site emissions with that of aerially detected sources (rather than plumes) when computing the transition point. Transition point computation, midstream: Additionally, the transition point calculation has been corrected to exclude aerially detected midstream emissions below the transition point, which was previously leading to double counting of these emissions. This error was not present for upstream (well site) emissions. Calculation errors Unit error: We corrected a specific unit conversion error affecting well site emissions in the Kairos Fort Worth dataset. Across all datasets, we also correct the conversion factor for converting from standard volume to mass for midstream emissions. Sorting error: We correct code that was applying incorrect sorting when computing correction factors to account for partial detection at well sites. Small typographical corrections were made in Fig. 1b and SI Section S4.1. The following practices may help researchers conducting similar analyses avoid making similar errors: 1, Clear, accessible documentation explaining the interpretation of all columns in data input tables and all internal variables within the model, 2, Simple cross-check calculations computed before and after unit conversions.

Sherwin, Evan D↗

MetaFlux: Meta-learning global carbon fluxes from sparse spatiotemporal observations

We provide a global, long-term carbon flux dataset of gross primary production and ecosystem respiration generated using meta-learning, called MetaFlux. The idea behind meta-learning stems from the need to learn efficiently given sparse data by learning how to learn broad features across tasks to better infer other poorly sampled ones. Using meta-trained ensemble of deep models, we generate global carbon products on daily and monthly timescales at a 0.25-degree spatial resolution from 2001 to 2021, through a combination of reanalysis and remote-sensing products. Site-level validation finds that MetaFlux ensembles have lower validation error by 5–7% compared to their non-meta-trained counterparts. In addition, they are more robust to extreme observations, with 4–24% lower errors. We also checked for seasonality, interannual variability, and correlation to solar-induced fluorescence of the upscaled product and found that MetaFlux outperformed other machine-learning based carbon product, especially in the tropics and semi-arids by 10–40%. Overall, MetaFlux can be used to study a wide range of biogeochemical processes.

54 ENVIRONMENTAL SCIENCES↗

Electricity and natural gas tariffs at United States wastewater treatment plants

Abstract Wastewater treatment plants (WWTPs) are large electricity and natural gas consumers with untapped potential to recover carbon-neutral biogas and provide energy services for the grid. Techno-economic analysis of emerging energy recovery and management technologies is critical to understanding their commercial viability, but quantifying their energy cost savings potential is stymied by a lack of well curated, nationally representative electricity and natural gas tariff data. We present a dataset of electricity tariffs for the 100 largest WWTPs in the Clean Watershed Needs Survey (CWNS) and natural gas tariffs for the 54 of 100 WWTPs with on-site cogeneration. We manually collected tariffs from each utility’s website and implemented data checks to ensure their validity. The dataset includes facility metadata, electricity tariffs, and natural gas tariffs (where cogeneration is present). Tariffs are current as of November 2021. We provide code for technical validation along with a sample simulation.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

A dataset for understanding self-reported patterns influencing residential energy decisions

Household occupant behavior and decision-making dynamics substantially impact technology uptake and residential building energy performance. Although significant research underscores the importance of social science in energy studies, few public data with representative samples on household energy decision-making patterns are available. The dataset (UPGRADE-E: Understanding Patterns Guiding Residential Adoption and Decisions about Energy Efficiency) presents 9,919 responses from U.S. residents of single-family and small multifamily homes. Derived from a national-scale internet survey, the dataset contains 391 variables: demographics, building characteristics, home modifications, willingness to adopt new technologies, motivations for making changes, barriers, program participation, trusted information sources, and energy scenarios. Responses were validated via internal consistency checks and comparison with other U.S. national scale datasets. UPGRADE-E advances knowledge of household energy related decision-making, tying demographics, home modifications, and self-reported cognitive drivers together at a scale and breadth that has not been previously achieved. Policymakers and researchers at local, regional, and national levels may leverage this dataset to understand drivers influencing the adoption of key technologies in U.S. homes.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Effect of Thomas Rotation on the Lorentz Transformation of Electromagnetic fields

A relativistic particle undergoing successive boosts which are non collinear will experience a rotation of its coordinate axes with respect to the boosted frame. This rotation of coordinate axes is caused by a relativistic phenomenon called Thomas Rotation. We assess the importance of Thomas rotation in the calculation of physical quantities like electromagnetic fields in the relativistic regime. We calculate the electromagnetic field tensor for general three dimensional successive boosts in the particle’s rest frame as well as the laboratory frame. We then compare the electromagnetic field tensors obtained by a direct boost β δβ → + → and successive boosts β → and Δβ → and check their consistency with Thomas rotation. This framework might be important to situations such as the calculation of frequency shifts for relativistic spin1/2 particles undergoing Larmor precession in electromagnetic fields with small field non-uniformities.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Detecting operons in bacterial genomes via visual representation learning

Contiguous genes in prokaryotes are often arranged into operons. Detecting operons plays a critical role in inferring gene functionality and regulatory networks. Human experts annotate operons by visually inspecting gene neighborhoods across pileups of related genomes. These visual representations capture the inter-genic distance, strand direction, gene size, functional relatedness, and gene neighborhood conservation, which are the most prominent operon features mentioned in the literature. By studying these features, an expert can then decide whether a genomic region is part of an operon. We propose a deep learning based method named Operon Hunter that uses visual representations of genomic fragments to make operon predictions. Using transfer learning and data augmentation techniques facilitates leveraging the powerful neural networks trained on image datasets by re-training them on a more limited dataset of extensively validated operons. Our method outperforms the previously reported state-of-the-art tools, especially when it comes to predicting full operons and their boundaries accurately. Furthermore, our approach makes it possible to visually identify the features influencing the network’s decisions to be subsequently cross-checked by human experts.

59 BASIC BIOLOGICAL SCIENCES↗

Photosynthetic responses to light levels in drought-tolerant novel peanut (Arachis hypogaea L) genotypes

Abstract Drought is a significant abiotic stressor that reduces peanut production because it alters photosynthetic activity and impacts crop growth. Therefore, developing drought-tolerant peanut genotypes capable of maintaining higher photosynthetic rates (A) under stress is crucial. This study assessed changes in photosynthetic and chlorophyll fluorescence responses to light (photosynthetic photon flux density, PPFD) in newly bred drought-tolerant peanut genotypes. Ten genotypes [NM-3, NM-5, NM-6, NM-23, NM-69, NM-70, NM-74, NM-77, V-C, and C-76–16] were evaluated under full irrigation (FC 100 ) and deficit irrigation (FC 50 ) in a split-plot design with four replications in a greenhouse. Under high PPFD levels, genotype NM-5 with deficit irrigation exhibited significantly higherA, stomatal conductance (gs), quantum efficiency of photosystem II (ΦPSII), and electron transport rate (ETR) by 40–59%, 135–525%, 31–212%, and 31–102%, respectively, than check varieties (V-C and C-76–16) and other genotypes. The NM-74 and NM-77 genotypes also performed well under deficit irrigations but with slightly lowerA,gs, ΦPSII, and ETR. Genotypes NM-5, NM-23, NM-74, and NM-77 exhibited significantly higher quantum efficiency of photosystem II (Fv’/Fm’) and photochemical quenching (qP) with higher light intensities in the daily cycle under deficit irrigation. The decline in ETR at the same PPFD levels in NM-3, NM 69, NM-70, and C-76–16 indicated photoinhibition or saturation of the photosynthetic apparatus compared to other genotypes. Concurrently, FC 100 irrigation level minimizes photoinhibition, enhancingA,gs, ΦPSII, and ETR in the genotypes than FC 50 . Therefore, we conclude that NM-5, NM-74, and NM-77 genotypes can perform better under water deficit environments. As such, chlorophyll fluorescence parameters Fv’/Fm’ and qP can be considered for selective breeding to enhance photosynthetic efficiencies.

Science & Technology - Other Topics↗

Two-dimensional forms of robust CO 2 reduction photocatalysts

Photoelectrocatalysts that use sunlight to power the CO 2 reduction reaction will be crucial for carbon-neutral power and energy-efficient industrial processes. Scalable photoelectrocatalysts must satisfy a stringent set of criteria, such as stability under operating conditions, product selectivity, and efficient light absorption. Two-dimensional materials can offer high specific surface area, tunability, and potential for heterostructuring, providing a fresh landscape of candidate catalysts. From a set of promising bulk CO 2 reduction photoelectrocatalysts, we screen for candidate monolayers of these materials, then study their catalytic feasibility and suitability. For stable monolayer candidates, we verify the presence of visible-light band gaps, check that band edges can support CO 2 reduction, determine exciton binding energies, and compute surface reactivity. We find visible light absorption for SiAs, ZnTe, and ZnSe monolayers, and that due to a lack of binding, CO selectivity is possible. We thus identify SiAs, ZnTe, and ZnSe monolayers as targets for further investigation, expanding the chemical space for CO 2 photoreduction candidates.

36 MATERIALS SCIENCE↗

Opportunities in full-stack design of low-overhead fault-tolerant quantum computation

Quantum error correction provides a route to realizing large-scale quantum computation but incurs substantial resource overheads. Here, in this work, we highlight recent advances that reduce these overheads by co-designing different levels of the computational stack, including algorithms, quantum-error-correction strategies and hardware architecture. We then discuss opportunities for further optimization such as leveraging flexible qubit connectivity and quantum low-density parity check codes. These strategies can bring useful quantum computation closer to reality as experiments advance in the coming years.

quantum information↗

Resilient co-expansion planning between gas and electric distribution networks against natural disasters

Resiliently designed and constructed integrated gas-electric distribution networks (GEDNs) against natural disasters are crucial to social welfare. In this study, a two-stage robust optimisation-based co-expansion planning model is proposed to attain an integrated GEDN with a given resilience level, by optimising the investment strategies of hardening and selective expansion of power distribution feeders and natural gas pipelines, as well as the location and capacity of natural-gas-fired distributed generation. In the first stage, the overall annual investment and operation cost is minimised under normal operation conditions while in the second stage, the feasibility of the investment decisions under the identified worst-case natural disaster scenario is checked with an adjustable load shedding cost criterion. The proposed model is formulated as a mixed integer second-order cone programming problem with the column and constraint generation algorithm employed to seek the optimal solution. Case studies on two integrated GEDNs demonstrate the performance of the proposed methodology.

Zou, Bo↗

TDCOSMO. IX. Systematic comparison between lens modelling software programs: time delay prediction for WGD 2038-4008

The importance of alternative methods for measuring the Hubble constant, such as time-delay cosmography, is highlighted by the recent Hubble tension. It is paramount to thoroughly investigate and rule out systematic biases in all measurement methods before we can accept new physics as the source of this tension. In this study, we perform a check for systematic biases in the lens modelling procedure of time-delay cosmography by comparing independent and blind time-delay predictions of the system WGD 2038-4008 from two teams using two different software programs: GLEE and LENSTRONOMY. The predicted time delays from the two teams incorporate the stellar kinematics of the deflector and the external convergence from line-of-sight structures. The un-blinded time-delay predictions from the two teams agree within 1.2σ, implying that once the time delay is measured the inferred Hubble constant will also be mutually consistent. However, there is a ~4σ discrepancy between the power-law model slope and external shear, which is a significant discrepancy at the level of lens models before the stellar kinematics and the external convergence are incorporated. We identify the difference in the reconstructed point spread function (PSF) to be the source of this discrepancy. When the same reconstructed PSF was used by both teams, we achieved excellent agreement, within ~0.6σ<, indicating that potential systematics stemming from source reconstruction algorithms and investigator choices are well under control. We recommend that future studies supersample the PSF as needed and marginalize over multiple algorithms or realizations for the PSF reconstruction to mitigate the systematics associated with the PSF. A future study will measure the time delays of the system WGD 2038-4008 and infer the Hubble constant based on our mass models.

79 ASTRONOMY AND ASTROPHYSICS↗

The GAPS programme at TNG

Neptunes represent one of the main types of exoplanets and have chemical-physical characteristics halfway between rocky and gas giant planets. Therefore, their characterization is important for understanding and constraining both the formation mechanisms and the evolution patterns of planets. We investigate the exoplanet candidate TOI-1422 b, which was discovered by the TESS space telescope around the high proper-motion G2 V star TOI-1422 (V = 10.6 mag), 155 pc away, with the primary goal of confirming its planetary nature and characterising its properties. We monitored TOI-1422 with the HARPS-N spectrograph for 1.5 yr to precisely quantify its radial velocity (RV) variation. We analyse these RV measurements jointly with TESS photometry and check for blended companions through high-spatial resolution images using the AstraLux instrument. We estimate that the parent star has a radius of R$_\star$ = 1.019 -0.013 +0.014 R ⊙ , and a mass of M$_\star$ = 1.019 -0.013 +0.014 M ⊙ . Our analysis confirms the planetary nature of TOI-1422 b and also suggests the presence of a Neptune-mass planet on a more distant orbit, the candidate TOI-1422 c, which is not detected in TESS light curves. The inner planet, TOI-1422 b, orbits on a period of P b = 12.9972 ± 0.0006 days and has an equilibrium temperature of T eq,b = 867 ± 17 K. With a radius of R b = 3.96 -0.11 +0.13 R ⊕ , a mass of M b = 9.0 -2.0 +2.3 M ⊕ and, consequently, a density of ρ b = 0.795 -0.235 +0.290 g cm -3 , it can be considered a warm Neptune-sized planet. Compared to other exoplanets of a similar mass range, TOI-1422 b is among the most inflated, and we expect this planet to have an extensive gaseous envelope that surrounds a core with a mass fraction around 10% – 25% of the total mass of the planet. The outer non-transiting planet candidate, TOI-1422 c, has an orbital period of P c = 29.29 -0.20 +0.21 days, a minimum mass, M c sin i, of 11.1 -2.3 +2.6 M ⊕ , an equilibrium temperature of T eq,c = 661 ± 13 K and, therefore, if confirmed, could be considered as another warm Neptune.

79 ASTRONOMY AND ASTROPHYSICS↗

Discovering strongly lensed quasar candidates with catalogue-based methods from DESI Legacy Surveys

The Hubble tension, revealed by a ~5σ discrepancy between measurements of the Hubble-Lemaitre constant among observations of the early and local Universe, is one of the most significant problems in modern cosmology. In order to better understand the origin of this mismatch, independent techniques to measure H 0 , such as strong lensing time delays, are required. Notably, the sample size of such systems is key to minimising the statistical uncertainties and cosmic variance, which can be improved by exploring the datasets of large-scale sky surveys such as Dark Energy Spectroscopic Instrument (DESI). We identify possible strong lensing time-delay systems within DESI by selecting candidate multiply imaged lensed quasars from a catalogue of 24 440 816 candidate QSOs contained in the ninth data release of the DESI Legacy Imaging Surveys (DESI-LS). Using a friend-of-friends-like algorithm on spatial co-ordinates, our method generates an initial list of compact quasar groups. This list is subsequently filtered using a measure of the similarity of colours among a group’s members and the likelihood that they are quasars. A visual inspection finally selects candidate strong lensing systems based on the spatial configuration of the group members. We identified 620 new candidate multiply imaged lensed quasars (101 grade-A, 214 grade-B, 305 grade-C). This number excludes 53 known spectroscopically confirmed systems and existing candidate systems identified in other similar catalogues. When available, these new candidates will be further checked by combining the spectroscopic and photometric data from DESI.

79 ASTRONOMY AND ASTROPHYSICS↗

Cepheids with giant companions: II. Spectroscopic confirmation of nine new double-lined binary systems composed of two Cepheids

Context.Binary Cepheids with giant companions are crucial for studying the physical properties of Cepheid variables, in particular providing the best means to measure their masses. Systems composed of two Cepheids are even more important, but to date, only one such system has been identified, in the Large Magellanic Cloud (LMC). Aims.Our current aim is to increase the number of these systems known tenfold and to provide their basic characteristics. The final goal is to obtain the physical properties of the component Cepheids, including their masses and radii, and to learn about their evolution in the multiple systems, also revealing their origin. Methods.We started a spectroscopic monitoring campaign of nine unresolved pairs of Cepheids from the OGLE catalog to check if they are gravitationally bound. Two of these so-called double Cepheids are located in the LMC, five are in the Small Magellanic Cloud (SMC), and two are in the Milky Way (MW). Results.We report a spectroscopic detection of the binarity of all nine of these double Cepheids with orbital periods ranging from 2 to 18 years. This increases the number of known binary double (BIND) Cepheids from 1 to 10 and triples the number of all confirmed double-lined binary (SB2) Cepheids. For five BIND Cepheids, the disentangled pulsational light curves of the components show anti-correlated phase shifts due to orbital motion. We show the first empirical evidence that typical period–luminosity relations (PLRs) are rather binary Cepheid PLRs, as they include light of the companion. Conclusions.The statistics of pulsation period ratios of BIND Cepheids do not agree with those expected for pairs of Cepheids of the same age. These ratios together with the determined mass ratios far from unity suggest a merger origin of at least one component for about half of the systems. The SMC and MW objects are the first found in SB2 systems composed of giants in their host galaxies. The Milky Way BIND Cepheids are also the closest such systems, being located at about 11 and 26 kpc.

Astronomy & Astrophysics↗

Numerical challenges for energy conservation in N -body simulations of collapsing self-interacting dark matter halos

Dark matter (DM) halos can be subject to gravothermal collapse if the DM is not collisionless, but engaged in strong self-interactions instead. When the scattering is able to efficiently transfer heat from the centre to the outskirts, the central region of the halo collapses and reaches densities much higher than those for collisionless DM. This phenomenon is potentially observable in studies of strong lensing. Current theoretical efforts are motivated by observations of surprisingly dense substructures. However, a comparison with observations requires accurate predictions. One method to obtain such predictions is to use N-body simulations. Collapsed halos are extreme systems that pose severe challenges when applying state-of-the-art codes to model self-interacting dark matter (SIDM). In this work, we investigate the root of such problems, with a focus on energy non-conservation. Moreover, we discuss possible strategies to avoid them. We ran N-body simulations, both with and without SIDM, of an isolated DM-only halo and we adjusted the numerical parameters to check the accuracy of the simulation. We find that not only the numerical scheme for SIDM can lead to energy non-conservation, but also the modelling of gravitational interaction and the time integration are problematic. The main issues we find are: (a) particles changing their time step in a non-time-reversible manner; (b) the asymmetry in the tree-based gravitational force evaluation; and (c) SIDM velocity kicks breaking the time symmetry. Tuning the parameters of the simulation to achieve a high level of accuracy allows us to conserve energy not only at early stages of the evolution, but also later on. However, the cost of the simulations becomes prohibitively large as a result. Some of the problems that make the simulations of the gravothermal collapse phase inaccurate can be overcome by choosing appropriate numerical schemes. However, other issues still pose a challenge. Our findings motivate further works on addressing the challenges in simulating strong DM self-interactions.

dark matter↗

The DEHVILS in the details: Type Ia supernova Hubble residual comparisons and mass step analysis in the near-infrared

Measurements of type Ia supernovae (SNe Ia) in the near-infrared (NIR) have been used both as an alternate path to cosmology compared to optical measurements and as a method of constraining key systematics for the larger optical studies. With the DEHVILS sample, the largest published NIR sample with consistent NIR coverage of maximum light across three NIR bands ( Y, J , and H ), we check three key systematics: (i) the reduction in Hubble residual scatter as compared to the optical, (ii) the measurement of a “mass step” or lack thereof and its implications, and (iii) the ability to distinguish between various dust models by analyzing slopes and correlations between Hubble residuals in the NIR and optical. We produce SN Ia simulations of the DEHVILS sample and find that it is harder to differentiate between various dust models than previously understood. Additionally, we find that fitting with the current SALT3-NIR model does not yield accurate wavelength-dependent stretch-luminosity correlations, and we propose a limited solution for this problem. From the data, we see that (i) the standard deviation of Hubble residual values from NIR bands treated as standard candles are 0.007–0.042 mag smaller than those in the optical, (ii) the NIR mass step is not constrainable with the current sample size of 47 SNe Ia from DEHVILS, and (iii) Hubble residuals in the NIR and optical are correlated in the data. We test a few variations on the number and combinations of filters and data samples, and we observe that none of our findings or conclusions are significantly impacted by these modifications.

Astronomy & Astrophysics↗

Missing components in ΛCDM from DESI Y1 baryonic acoustic oscillation measurements: Insights from redshift remapping

We explore transformations of the Friedman-Lemaître-Robertson-Walker (FLRW) metric and cosmological parameters that align with observational data while aiming to gain insights into potential extensions of standard cosmological models. We modified the FLRW metric by introducing a scaling factor, e 2Θ(a) –the cosmological scaling function (CSF), which alters the standard relationship between cosmological redshift and the cosmic scale factor without affecting angular measurements or cosmic microwave background (CMB) anisotropies. Using data from DESI Year 1, Pantheon+ supernovae, and the Planck CMB temperature power spectrum, we constrained both the CSF and cosmological parameters through a Markov chain Monte Carlo approach. Our results indicate that the CSF model fits observational data with a lower Hubble constant (although it is compatible with the value given by Planck 2018 within 1σ) and is predominantly dark matter dominated. Additionally, the CSF model produces temperature and lensing power spectra similar to those predicted by the standard model, though with lower values in the CSF model at large scales. We also checked that when fitting a CSF model without dark energy to the data, we obtain a more negative conformal function. This suggests that the CSF model may offer hints about missing elements and opens up a new avenue for exploring physical interpretations of cosmic acceleration.

79 ASTRONOMY AND ASTROPHYSICS↗