bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enhanced atmospheric oxidation toward carbon neutrality reduces methane’s climate forcing
Authors: Liu Mingxu , Song Yu , Matsui Hitoshi , Shang Fang , Kang Ling , Cai Xuhui , Zhang Hongsheng , Zhu Tong 
Published: April 2024

AbstractThe hydroxyl radical (OH), as the central atmospheric oxidant, controls the removal rates of methane, a powerful greenhouse gas. It is being suggested that OH levels would decrease with reductions of nitrogen oxides and ozone levels by climate polices, but this remains unsettled. Here, we show that driven by the carbon neutrality pledge, the global-mean OH concentration, derived from multiple chemistry-climate model simulations, is projected to be significantly increasing with a trend of 0.071‒0.16% per year during 2015–2100. The leading cause of this OH enhancement is dramatic decreases in carbon monoxide and methane concentrations, which together reduce OH sinks. The OH increase shortens methane’s lifetime by 0.19‒1.1 years across models and subsequently diminishes methane’s radiative forcing. If following a largely unmitigated scenario, the global OH exhibits a significant decrease that would exacerbate methane’s radiative forcing. Thus, we highlight that targeted emission abatement strategies for sustained oxidation capacity can benefit climate change mitigation in the Anthropocene.
Spatiotemporal immune atlas of a clinical-grade gene-edited pig-to-human kidney xenotransplant
Authors: Cheung Matthew D. , Asiimwe Rebecca , Erman Elise N. , Fucile Christopher F. , Liu Shanrun , Sun Chiao-Wang , Hanumanthu Vidya Sagar , Pal Harish C. , Wright Emma D. , Ghajar-Rahimi Gelare , Epstein Daniel , Orandi Babak J. , Kumar Vineeta , Anderson Douglas J. , Greene Morgan E. , Bell Markayla , Yates Stefani , Moore Kyle H. , LaFontaine Jennifer , Killian John T. , Baker Gavin , Perry Jackson , Khan Zayd , Reed Rhiannon , Little Shawn C. , Rosenberg Alexander F. , George James F. , Locke Jayme E. , Porrett Paige M. 
Published: April 2024

AbstractPig-to-human xenotransplantation is rapidly approaching the clinical arena; however, it is unclear which immunomodulatory regimens will effectively control human immune responses to pig xenografts. Here, we transplant a gene-edited pig kidney into a brain-dead human recipient on pharmacologic immunosuppression and study the human immune response to the xenograft using spatial transcriptomics and single-cell RNA sequencing. Human immune cells are uncommon in the porcine kidney cortex early after xenotransplantation and consist of primarily myeloid cells. Both the porcine resident macrophages and human infiltrating macrophages express genes consistent with an alternatively activated, anti-inflammatory phenotype. No significant infiltration of human B or T cells into the porcine kidney xenograft is detectable. Altogether, these findings provide proof of concept that conventional pharmacologic immunosuppression may be able to restrict infiltration of human immune cells into the xenograft early after compatible pig-to-human kidney xenotransplantation.
Splice modulators target PMS1 to reduce somatic expansion of the Huntington’s disease-associated CAG repeat
Authors: McLean Zachariah L. , Gao Dadi , Correia Kevin , Roy Jennie C. L. , Shibata Shota , Farnum Iris N. , Valdepenas-Mellor Zoe , Kovalenko Marina , Rapuru Manasa , Morini Elisabetta , Ruliera Jayla , Gillis Tammy , Lucente Diane , Kleinstiver Benjamin P. , Lee Jong-Min , MacDonald Marcy E. , Wheeler Vanessa C. , Mouro Pinto Ricardo , Gusella James F. 
Published: April 2024

AbstractHuntington’s disease (HD) is a dominant neurological disorder caused by an expanded HTT exon 1 CAG repeat that lengthens huntingtin’s polyglutamine tract. Lowering mutant huntingtin has been proposed for treating HD, but genetic modifiers implicate somatic CAG repeat expansion as the driver of onset. We find that branaplam and risdiplam, small molecule splice modulators that lower huntingtin by promoting HTT pseudoexon inclusion, also decrease expansion of an unstable HTT exon 1 CAG repeat in an engineered cell model. Targeted CRISPR-Cas9 editing shows this effect is not due to huntingtin lowering, pointing instead to pseudoexon inclusion in PMS1. Homozygous but not heterozygous inactivation of PMS1 also reduces CAG repeat expansion, supporting PMS1 as a genetic modifier of HD and a potential target for therapeutic intervention. Although splice modulation provides one strategy, genome-wide transcriptomics also emphasize consideration of cell-type specific effects and polymorphic variation at both target and off-target sites.
A hemoprotein with a zinc-mirror heme site ties heme availability to carbon metabolism in cyanobacteria
Authors: Grosjean Nicolas , Yee Estella F. , Kumaran Desigan , Chopra Kriti , Abernathy Macon , Biswas Sandeep , Byrnes James , Kreitler Dale F. , Cheng Jan-Fang , Ghosh Agnidipta , Almo Steven C. , Iwai Masakazu , Niyogi Krishna K. , Pakrasi Himadri B. , Sarangi Ritimukta , van Dam Hubertus , Yang Lin , Blaby Ian K. , Blaby-Haas Crysten E. 
Published: April 2024

AbstractHeme has a critical role in the chemical framework of the cell as an essential protein cofactor and signaling molecule that controls diverse processes and molecular interactions. Using a phylogenomics-based approach and complementary structural techniques, we identify a family of dimeric hemoproteins comprising a domain of unknown function DUF2470. The heme iron is axially coordinated by two zinc-bound histidine residues, forming a distinct two-fold symmetric zinc-histidine-iron-histidine-zinc site. Together with structure-guided in vitro and in vivo experiments, we further demonstrate the existence of a functional link between heme binding by Dri1 (Domain related to iron 1, formerly ssr1698) and post-translational regulation of succinate dehydrogenase in the cyanobacterium Synechocystis, suggesting an iron-dependent regulatory link between photosynthesis and respiration. Given the ubiquity of proteins containing homologous domains and connections to heme metabolism across eukaryotes and prokaryotes, we propose that DRI (Domain Related to Iron; formerly DUF2470) functions at the molecular level as a heme-dependent regulatory domain.
CoPoP liposomes displaying stabilized clade C HIV-1 Env elicit tier 2 multiclade neutralization in rabbits
Authors: Koornneef Annemart , Vanshylla Kanika , Hardenberg Gijs , Rutten Lucy , Strokappe Nika M. , Tolboom Jeroen , Vreugdenhil Jessica , Boer Karin Feddes-de , Perkasa Aditya , Blokland Sven , Burger Judith A. , Huang Wei-Chiao , Lovell Jonathan F. , van Manen Danielle , Sanders Rogier W. , Zahn Roland C. , Schuitemaker Hanneke , Langedijk Johannes P. M. , Wegmann Frank 
Published: April 2024

AbstractOne of the strategies towards an effective HIV-1 vaccine is to elicit broadly neutralizing antibody responses that target the high HIV-1 Env diversity. Here, we present an HIV-1 vaccine candidate that consists of cobalt porphyrin-phospholipid (CoPoP) liposomes decorated with repaired and stabilized clade C HIV-1 Env trimers in a prefusion conformation. These particles exhibit high HIV-1 Env trimer decoration, serum stability and bind broadly neutralizing antibodies. Three sequential immunizations of female rabbits with CoPoP liposomes displaying a different clade C HIV-1 gp140 trimer at each dosing generate high HIV-1 Env-specific antibody responses. Additionally, serum neutralization is detectable against 18 of 20 multiclade tier 2 HIV-1 strains. Furthermore, the peak antibody titers induced by CoPoP liposomes can be recalled by subsequent heterologous immunization with Ad26-encoded membrane-bound stabilized Env antigens. Hence, a CoPoP liposome-based HIV-1 vaccine that can generate cross-clade neutralizing antibody immunity could potentially be a component of an efficacious HIV-1 vaccine.
Multiplicative joint coding in preparatory activity for reaching sequence in macaque motor cortex
Authors: Wang Tianwei , Chen Yun , Zhang Yiheng , Cui He 
Published: April 2024

AbstractAlthough the motor cortex has been found to be modulated by sensory or cognitive sequences, the linkage between multiple movement elements and sequence-related responses is not yet understood. Here, we recorded neuronal activity from the motor cortex with implanted micro-electrode arrays and single electrodes while monkeys performed a double-reach task that was instructed by simultaneously presented memorized cues. We found that there existed a substantial multiplicative component jointly tuned to impending and subsequent reaches during preparation, then the coding mechanism transferred to an additive manner during execution. This multiplicative joint coding, which also spontaneously emerged in recurrent neural networks trained for double reach, enriches neural patterns for sequential movement, and might explain the linear readout of elemental movements.
Reciprocating RNA Polymerase batters through roadblocks
Authors: Qian Jin , Cartee Allison , Xu Wenxuan , Yan Yan , Wang Bing , Artsimovitch Irina , Dunlap David , Finzi Laura 
Published: April 2024

AbstractRNA polymerases must transit through protein roadblocks to produce full-length transcripts. Here we report real-time measurements of Escherichia coli RNA polymerase passing through different barriers. As intuitively expected, assisting forces facilitated, and opposing forces hindered, RNA polymerase passage through lac repressor protein bound to natural binding sites. Force-dependent differences were significant at magnitudes as low as 0.2 pN and were abolished in the presence of the transcript cleavage factor GreA, which rescues backtracked RNA polymerase. In stark contrast, opposing forces promoted passage when the rate of RNA polymerase backtracking was comparable to, or faster than the rate of dissociation of the roadblock, particularly in the presence of GreA. Our experiments and simulations indicate that RNA polymerase may transit after roadblocks dissociate, or undergo cycles of backtracking, recovery, and ramming into roadblocks to pass through. We propose that such reciprocating motion also enables RNA polymerase to break protein-DNA contacts that hold RNA polymerase back during promoter escape and RNA chain elongation. This may facilitate productive transcription in vivo.
The deepwater oxygen deficit in stratified shallow seas is mediated by diapycnal mixing
Authors: Rippeth Tom , Shen Sijing , Lincoln Ben , Scannell Brian , Meng Xin , Hopkins Joanne , Sharples Jonathan 
Published: April 2024

AbstractSeasonally stratified shelf seas are amongst the most biologically productive on the planet. A consequence is that the deeper waters can become oxygen deficient in late summer. Predictions suggest global warming will accelerate this deficiency. Here we integrate turbulence timeseries with vertical profiles of water column properties from a seasonal stratified shelf sea to estimate oxygen and biogeochemical fluxes. The profiles reveal a significant subsurface chlorophyll maximum and associated mid-water oxygen maximum. We show that the oxygen maximum supports both upward and downwards O2 fluxes. The upward flux is into the surface mixed layer, whilst the downward flux into the deep water will partially off-set the seasonal O2 deficit. The results indicate the fluxes are sensitive to both the water column structure and mixing rates implying the development of the seasonal O2 deficit is mediated by diapcynal mixing. Analysis of current shear indicate that the downward flux is supported by tidal mixing, whilst the upwards flux is dominated by wind driven near-inertial shear. Summer storminess therefore plays an important role in the development of the seasonal deep water O2 deficit.
Metavalently bonded tellurides: the essence of improved thermoelectric performance in elemental Te
Authors: An Decheng , Zhang Senhao , Zhai Xin , Yang Wutao , Wu Riga , Zhang Huaide , Fan Wenhao , Wang Wenxian , Chen Shaoping , Cojocaru-Mirédin Oana , Zhang Xian-Ming , Wuttig Matthias , Yu Yuan 
Published: April 2024

AbstractElemental Te is important for semiconductor applications including thermoelectric energy conversion. Introducing dopants such as As, Sb, and Bi has been proven critical for improving its thermoelectric performance. However, the remarkably low solubility of these elements in Te raises questions about the mechanism with which these dopants can improve the thermoelectric properties. Indeed, these dopants overwhelmingly form precipitates rather than dissolve in the Te lattice. To distinguish the role of doping and precipitation on the properties, we have developed a correlative method to locally determine the structure-property relationship for an individual matrix or precipitate. We reveal that the conspicuous enhancement of electrical conductivity and power factor of bulk Te stems from the dopant-induced metavalently bonded telluride precipitates. These precipitates form electrically beneficial interfaces with the Te matrix. A quantum-mechanical-derived map uncovers more candidates for advancing Te thermoelectrics. This unconventional doping scenario adds another recipe to the design options for thermoelectrics and opens interesting pathways for microstructure design.
The rule of four: anomalous distributions in the stoichiometries of inorganic compounds
Authors: Gazzarrini Elena , Cersonsky Rose K. , Bercx Marnik , Adorf Carl S. , Marzari Nicola 
Published: April 2024

AbstractWhy are materials with specific characteristics more abundant than others? This is a fundamental question in materials science and one that is traditionally difficult to tackle, given the vastness of compositional and configurational space. We highlight here the anomalous abundance of inorganic compounds whose primitive unit cell contains a number of atoms that is a multiple of four. This occurrence—named here the rule of four—has to our knowledge not previously been reported or studied. Here, we first highlight the rule’s existence, especially notable when restricting oneself to experimentally known compounds, and explore its possible relationship with established descriptors of crystal structures, from symmetries to energies. We then investigate this relative abundance by looking at structural descriptors, both of global (packing configurations) and local (the smooth overlap of atomic positions) nature. Contrary to intuition, the overabundance does not correlate with low-energy or high-symmetry structures; in fact, structures which obey the rule of four are characterized by low symmetries and loosely packed arrangements maximizing the free volume. We are able to correlate this abundance with local structural symmetries, and visualize the results using a hybrid supervised-unsupervised machine learning method.
Computed entropy spectra for grain boundary segregation in polycrystals
Authors: Tuchinda Nutth , Schuh Christopher A. 
Published: April 2024

AbstractGrain boundary solute segregation influences most bulk material properties, and understanding solute thermodynamics at grain boundaries is critical for engineering them. However, the vast grain boundary space in polycrystals is challenging to evaluate due to its size, especially for the intrinsically hard-to-compute segregation excess entropy. Here data science methods are used to generate a database of site-wise grain boundary segregation entropy spectra for 155 dilute binary alloys within the harmonic approximation. The spectral framework allows scale bridging between the calculated atomistic site-wise energy-entropy spectra and macroscopic segregation entropy estimates. The results affirm that macroscopic averaging is not sufficient: a spectral treatment of grain boundary segregation is needed to accurately model bulk temperature dependence of grain boundary solute segregation. The calculated spectral entropy database and thermodynamic framework can be applied for both understanding segregation experiments and alloy design exercises, paving the way to a finite-temperature grain boundary genome.
JWST detection of a supernova associated with GRB 221009A without an r-process signature
Authors: Blanchard Peter K. , Villar V. Ashley , Chornock Ryan , Laskar Tanmoy , Li Yijia , Leja Joel , Pierel Justin , Berger Edo , Margutti Raffaella , Alexander Kate D. , Barnes Jennifer , Cendes Yvette , Eftekhari Tarraneh , Kasen Daniel , LeBaron Natalie , Metzger Brian D. , Muzerolle Page James , Rest Armin , Sears Huei , Siegel Daniel M. , Yadavalli S. Karthik 
Published: April 2024

AbstractIdentifying the sites of r-process nucleosynthesis, a primary mechanism of heavy element production, is a key goal of astrophysics. The discovery of the brightest gamma-ray burst (GRB) to date, GRB 221009A, presented an opportunity to spectroscopically test the idea that r-process elements are produced following the collapse of rapidly rotating massive stars. Here we present James Webb Space Telescope observations of GRB 221009A obtained +168 and +170 rest-frame days after the gamma-ray trigger, and demonstrate that they are well described by a SN 1998bw-like supernova (SN) and power-law afterglow, with no evidence for a component from r-process emission. The SN, with a nickel mass of approximately 0.09 M⊙, is only slightly fainter than the brightness of SN 1998bw at this phase, which indicates that the SN is not an unusual GRB-SN. This demonstrates that the GRB and SN mechanisms are decoupled and that highly energetic GRBs are not likely to produce significant quantities of r-process material, which leaves open the question of whether explosions of massive stars are key sources of r-process elements. Moreover, the host galaxy of GRB 221009A has a very low metallicity of approximately 0.12 Z⊙ and strong H2 emission at the explosion site, which is consistent with recent star formation, hinting that environmental factors are responsible for its extreme energetics.
Magnetic origin of the discrepancy between stellar limb-darkening models and observations
Authors: Kostogryz Nadiia M. , Shapiro Alexander I. , Witzke Veronika , Cameron Robert H. , Gizon Laurent , Krivova Natalie A. , Ludwig Hans-G. , Maxted Pierre F. L. , Seager Sara , Solanki Sami K. , Valenti Jeff 
Published: April 2024

AbstractStars appear darker at their limbs than at their disk centres because at the limb we are viewing the higher and cooler layers of stellar photospheres. Yet, limb darkening derived from state-of-the-art stellar atmosphere models systematically fails to reproduce recent transiting exoplanet light curves from the Kepler, TESS and JWST telescopes—stellar brightness obtained from measurements drops less steeply towards the limb than predicted by models. Previous models assumed stellar atmospheres devoid of magnetic fields. Here we use stellar atmosphere models computed with the three-dimensional radiative magnetohydrodynamic code MURaM to show that a small-scale concentration of magnetic fields on the stellar surface affects limb darkening at a level that allows us to explain the observations. Our findings provide a way forward to improve the determination of exoplanet radii and especially the transmission spectroscopy analysis for transiting planets, which relies on a very accurate description of stellar limb darkening from the visible to the infrared. Furthermore, our findings imply that limb darkening allows estimates of the small-scale magnetic field strength on stars with transiting planets.
Homogenized gridded dataset for drought and hydrometeorological modeling for the continental United States
Authors: Erhardt Robert , Di Vittorio Courtney A. , Hepler Staci A. , Lowman Lauren E. L. , Wei Wendy 
Published: April 2024

AbstractWe present a novel data set for drought in the continental US (CONUS) built to enable computationally efficient spatio-temporal statistical and probabilistic models of drought. We converted drought data obtained from the widely-used US Drought Monitor (USDM) from its native geo-referenced polygon format to a 0.5 degree regular grid. We merged known environmental drivers of drought, including those obtained from the North American Land Data Assimilation System (NLDAS-2), US Geological Survey (USGS) streamflow data, and National Oceanic and Atmospheric Administration (NOAA) teleconnections data. The resulting data set permits statistical and probabilistic modeling of drought with explicit spatial and/or temporal dependence. Such models could be used to forecast drought at short-range, seasonal to sub-seasonal, and inter-annual timescales with uncertainty, extending the reach and value of the current US Drought Outlook from the National Weather Service Climate Prediction Center. This novel data product provides the first common gridded dataset that includes critical variables used to inform hydrological and meteorological drought.
New ridge parameter estimators for the quasi-Poisson ridge regression model
Authors: Shahzad Aamir , Amin Muhammad , Emam Walid , Faisal Muhammad 
Published: April 2024

AbstractThe quasi-Poisson regression model is used for count data and is preferred over the Poisson regression model in the case of over-dispersed count data. The quasi-likelihood estimator is used to estimate the regression coefficients of the quasi-Poisson regression model. The quasi-likelihood estimator gives sub-optimal estimates if regressors are highly correlated—multicollinearity issue. Biased estimation methods are often used to overcome the multicollinearity issue in the regression model. In this study, we explore the ridge estimator for the quasi-Poisson regression model to mitigate the multicollinearity issue. Furthermore, we propose various ridge parameter estimators for this model. We derive the theoretical properties of the ridge estimator and compare its performance with the quasi-likelihood estimator in terms of matrix and scalar mean squared error. We further compared the proposed estimator numerically through a Monte Carlo simulation study and a real-life application. We found that both the simulation and application results show the superiority of the ridge estimator, particularly with the best ridge parameter estimator, over the quasi-likelihood estimator in the presence of multicollinearity issue.
The importance of continents, oceans and plate tectonics for the evolution of complex life: implications for finding extraterrestrial civilizations
Authors: Stern Robert J. , Gerya Taras V. 
Published: April 2024

AbstractWithin the uncertainties of involved astronomical and biological parameters, the Drake Equation typically predicts that there should be many exoplanets in our galaxy hosting active, communicative civilizations (ACCs). These optimistic calculations are however not supported by evidence, which is often referred to as the Fermi Paradox. Here, we elaborate on this long-standing enigma by showing the importance of planetary tectonic style for biological evolution. We summarize growing evidence that a prolonged transition from Mesoproterozoic active single lid tectonics (1.6 to 1.0 Ga) to modern plate tectonics occurred in the Neoproterozoic Era (1.0 to 0.541 Ga), which dramatically accelerated emergence and evolution of complex species. We further suggest that both continents and oceans are required for ACCs because early evolution of simple life must happen in water but late evolution of advanced life capable of creating technology must happen on land. We resolve the Fermi Paradox (1) by adding two additional terms to the Drake Equation: foc(the fraction of habitable exoplanets with significant continents and oceans) and fpt(the fraction of habitable exoplanets with significant continents and oceans that have had plate tectonics operating for at least 0.5 Ga); and (2) by demonstrating that the product of focand fptis very small (< 0.00003–0.002). We propose that the lack of evidence for ACCs reflects the scarcity of long-lived plate tectonics and/or continents and oceans on exoplanets with primitive life.