@article{20814,
  abstract     = {We characterize all semigroups sandwiched between the semigroup of a Dirichlet form and the semigroup of its active main part. In case the Dirichlet form is regular, we give a more explicit description of the quadratic forms of the sandwiched semigroups in terms of pairs consisting of an open set and a measure on an abstract boundary.},
  author       = {Keller, Matthias and Lenz, Daniel and Schmidt, Marcel and Schwarz, Michael and Wirth, Melchior},
  issn         = {1572-929X},
  journal      = {Potential Analysis},
  publisher    = {Springer Nature},
  title        = {{Boundary representations of intermediate forms between a regular Dirichlet form and its active main part}},
  doi          = {10.1007/s11118-025-10251-y},
  volume       = {64},
  year         = {2025},
}

@article{20816,
  abstract     = {Background: DNA methylation (DNAm) can regulate gene expression, and its genome-wide patterns (epigenetic scores or EpiScores) can act as biomarkers for complex traits. The relative stability of methylation profiles may enable better assessment of chronic exposures compared to single time-point protein measures. We present the first large-scale epigenetic study of the highly-abundant serum proteome measured via ultra-high throughput mass spectrometry in 14,671 samples from the Generation Scotland cohort. We further demonstrate the first large-scale comparison of protein EpiScores and their respective proteins as predictors of incident cardiovascular disease.

Results: Marginal epigenome-wide association models, adjusting for age, sex, measurement batch, estimated white cell proportions, BMI, smoking and methylation principal components, reveal 15,855 significant CpG – protein associations across 125 of 133 proteins PBonferroni < 2.71 × 10-10. Bayesian epigenome-wide association studies of the same 133 proteins reveal 697 CpG-Protein associations (posterior inclusion probability > 0.95). 112 protein EpiScores correlate significantly with their respective protein in a holdout test-set. Of these, sixteen associate significantly with incident all-cause cardiovascular disease (Nevents=191) compared to one measured protein.

Conclusions: We highlight a complex interplay between the blood-based methylome and proteome. Importantly, we show that protein EpiScores correlate with measured proteins and demonstrate that the, as-yet understudied, high-abundance proteome may yield clinically relevant biomarkers. The protein EpiScores demonstrate more significant associations with cardiovascular disease than directly measured proteins, suggesting their potential as clinical biomarkers for monitoring or predicting disease risk. We suggest that biomarker development could be enhanced by the consideration of protein EpiScores alongside measured proteins.},
  author       = {Robertson, Josephine A. and Bajzik, Jakub and Vernardis, Spyros and Chybowska, Aleksandra D. and Mccartney, Daniel L. and Grauslys, Arturas and Mur, Jure and Smith, Hannah M. and Campbell, Archie and Drake, Camilla and Grant, Hannah and Pearce, Jamie and Russ, Tom C. and Adkin, Poppy and White, Matthew and Brigden, Charles and Messner, Christoph B. and Porteous, David J. and Hayward, Caroline and Cox, Simon R. and Zelezniak, Aleksej and Ralser, Markus and Robinson, Matthew Richard and Marioni, Riccardo E.},
  issn         = {1474-760X},
  journal      = {Genome Biology},
  publisher    = {Springer Nature},
  title        = {{Methylome-wide association studies and epigenetic biomarker development for 133 mass spectrometry-assessed circulating proteins in 14,671 Generation Scotland participants}},
  doi          = {10.1186/s13059-025-03892-0},
  volume       = {26},
  year         = {2025},
}

@inproceedings{20817,
  abstract     = {We present Mechanistic PDE Networks -- a model for discovery of governing partial differential equations from data. Mechanistic PDE Networks represent spatiotemporal data as space-time dependent linear partial differential equations in neural network hidden representations. The represented PDEs are then solved and decoded for specific tasks. The learned PDE representations naturally express the spatiotemporal dynamics in data in neural network hidden space, enabling increased modeling power. Solving the PDE representations in a compute and memory-efficient way, however, is a significant challenge. We develop a native, GPU-capable, parallel, sparse and differentiable multigrid solver specialized for linear partial differential equations that acts as a module in Mechanistic PDE Networks. Leveraging the PDE solver we propose a discovery architecture that can discovers nonlinear PDEs in complex settings, while being robust to noise. We validate PDE discovery on a number of PDEs including reaction-diffusion and Navier-Stokes equations.},
  author       = {Pervez, Adeel A and Gavves, Efstratios and Locatello, Francesco},
  booktitle    = {42nd International Conference on Machine Learning},
  issn         = {2640-3498},
  location     = {Vancouver, Canada},
  pages        = {48962--48973},
  publisher    = {ML Research Press},
  title        = {{Mechanistic PDE networks for discovery of governing equations}},
  volume       = {267},
  year         = {2025},
}

@article{20818,
  abstract     = {This study demonstrates that Marchantia non-canonical PINs are predominantly localized to the plasma membrane, with MpPINX and MpPINW exhibiting asymmetric distribution.
A newly identified miniW domain within the MpPINW hydrophilic loop governs subcellular trafficking and asymmetric PM localization of non-canonical PINs in Marchantia.},
  author       = {Tang, Han and Smoljan, Adrijana and Zou, Minxia and Zhang, Yuzhou and Lu, Kuan Ju and Friml, Jiří},
  issn         = {1365-3040},
  journal      = {Plant Cell and Environment},
  publisher    = {Wiley},
  title        = {{The miniW domain directs polarized membrane localization of non-canonical PINs in Marchantia polymorpha}},
  doi          = {10.1111/pce.70295},
  year         = {2025},
}

@article{18753,
  abstract     = {We continue a line of research which studies which hereditary families of digraphs have bounded dichromatic number. For a class of digraphs  C, a hero in  C  is any digraph  H
  such that  H -free digraphs in  C  have bounded dichromatic number. We show that if  F
  is an oriented star of degree at least five, the only heroes for the class of  F -free digraphs are transitive tournaments. For oriented stars  F  of degree exactly four, we show the only heroes in  F -free digraphs are transitive tournaments, or possibly special joins of transitive tournaments. Aboulker et al. characterized the set of heroes of  {H,K1+P2→} -free digraphs almost completely, and we show the same characterization for the class of  {H,rK1+P3→} -free digraphs. Lastly, we show that if we forbid two "valid" orientations of brooms, then every transitive tournament is a hero for this class of digraphs.},
  author       = {Carbonero, Alvaro and Koerts, Hidde and Moore, Benjamin and Spirkl, Sophie},
  issn         = {0195-6698},
  journal      = {European Journal of Combinatorics},
  publisher    = {Elsevier},
  title        = {{On heroes in digraphs with forbidden induced forests}},
  doi          = {10.1016/j.ejc.2024.104104},
  volume       = {125},
  year         = {2025},
}

@article{18754,
  abstract     = {Exploring the molecular correlates of metabolic health measures may identify their shared and unique biological processes and pathways. Molecular proxies of these traits may also provide a more objective approach to their measurement. Here, DNA methylation (DNAm) data were used in epigenome-wide association studies (EWASs) and for training epigenetic scores (EpiScores) of six metabolic traits: body mass index (BMI), body fat percentage, waist-hip ratio, and blood-based measures of glucose, high-density lipoprotein cholesterol, and total cholesterol in >17,000 volunteers from the Generation Scotland (GS) cohort. We observed a maximum of 12,033 significant findings (p < 3.6 × 10−8) for BMI in a marginal linear regression EWAS. By contrast, a joint and conditional Bayesian penalized regression approach yielded 27 high-confidence associations with BMI. EpiScores trained in GS performed well in both Scottish and Singaporean test cohorts (Lothian Birth Cohort 1936 [LBC1936] and Health for Life in Singapore [HELIOS]). The EpiScores for BMI and total cholesterol performed best in HELIOS, explaining 20.8% and 7.1% of the variance in the measured traits, respectively. The corresponding results in LBC1936 were 14.4% and 3.2%, respectively. Differences were observed in HELIOS for body fat, where the EpiScore explained ∼9% of the variance in Chinese and Malay -subgroups but ∼3% in the Indian subgroup. The EpiScores also correlated with cognitive function in LBC1936 (standardized βrange: 0.08–0.12, false discovery rate p [pFDR] < 0.05). Accounting for the correlation structure across the methylome can vastly affect the number of lead findings in EWASs. The EpiScores of metabolic traits are broadly applicable across populations and can reflect differences in cognition.},
  author       = {Smith, Hannah M. and Ng, Hong Kiat and Moodie, Joanna E. and Gadd, Danni A. and Mccartney, Daniel L. and Bernabeu, Elena and Campbell, Archie and Redmond, Paul and Taylor, Adele and Page, Danielle and Corley, Janie and Harris, Sarah E. and Tay, Darwin and Deary, Ian J. and Evans, Kathryn L. and Robinson, Matthew Richard and Chambers, John C. and Loh, Marie and Cox, Simon R. and Marioni, Riccardo E. and Hillary, Robert F.},
  issn         = {1537-6605},
  journal      = {American Journal of Human Genetics},
  number       = {1},
  pages        = {106--115},
  publisher    = {Elsevier},
  title        = {{DNA methylation-based predictors of metabolic traits in Scottish and Singaporean cohorts}},
  doi          = {10.1016/j.ajhg.2024.11.012},
  volume       = {112},
  year         = {2025},
}

@inbook{18765,
  abstract     = {Mosaic Analysis with Double Markers (MADM) represents a mouse genetic approach coupling differential fluorescent labeling to genetic manipulations in dividing cells and their lineages. MADM uniquely enables the generation and visualization of individual control or homozygous mutant cells in a heterozygous genetic environment. Among its diverse applications, MADM has been used to dissect cell-autonomous gene functions important for cortical development and neural development in general. The high cellular resolution offered by MADM also permits the analysis of transcriptomic changes of individual cells upon genetic manipulations. In this chapter, we describe an experimental protocol combining the generation and isolation of MADM-labeled cells with downstream single-cell RNA-sequencing technologies to probe cell-type specific phenotypes due to genetic mutations at single-cell resolution.},
  author       = {Cheung, Giselle T and Pauler, Florian and Hippenmeyer, Simon},
  booktitle    = {Lineage Tracing},
  editor       = {Garcia-Marques, Jorge and Lee, Tzumin},
  isbn         = {9781071643099},
  issn         = {1940-6029},
  pages        = {139--151},
  publisher    = {Springer Nature},
  title        = {{Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM)}},
  doi          = {10.1007/978-1-0716-4310-5_7},
  volume       = {2886},
  year         = {2025},
}

@article{18778,
  abstract     = {Transcription by RNA polymerase II (Pol II) can be repressed by noncoding RNA, including the human RNA Alu. However, the mechanism by which endogenous RNAs repress transcription remains unclear. Here we present cryogenic-electron microscopy structures of Pol II bound to Alu RNA, which reveal that Alu RNA mimics how DNA and RNA bind to Pol II during transcription elongation. Further, we show how distinct domains of the general transcription factor TFIIF control repressive activity. Together, we reveal how a noncoding RNA can regulate mammalian gene expression.},
  author       = {Tluckova, Katarina and Kaczmarek, Beata M and Testa Salmazo, Anita P and Bernecky, Carrie A},
  issn         = {1545-9985},
  journal      = {Nature Structural & Molecular Biology},
  pages        = {607--612},
  publisher    = {Springer Nature},
  title        = {{Mechanism of mammalian transcriptional repression by noncoding RNA}},
  doi          = {10.1038/s41594-024-01448-7},
  volume       = {32},
  year         = {2025},
}

@article{18820,
  abstract     = {Feature selection is essential in the analysis of molecular systems and many other fields, but several uncertainties remain: What is the optimal number of features for a simplified, interpretable model that retains essential information? How should features with different units be aligned, and how should their relative importance be weighted? Here, we introduce the Differentiable Information Imbalance (DII), an automated method to rank information content between sets of features. Using distances in a ground truth feature space, DII identifies a low-dimensional subset of features that best preserves these relationships. Each feature is scaled by a weight, which is optimized by minimizing the DII through gradient descent. This allows simultaneously performing unit alignment and relative importance scaling, while preserving interpretability. DII can also produce sparse solutions and determine the optimal size of the reduced feature space. We demonstrate the usefulness of this approach on two benchmark molecular problems: (1) identifying collective variables that describe conformations of a biomolecule, and (2) selecting features for training a machine-learning force field. These results show the potential of DII in addressing feature selection challenges and optimizing dimensionality in various applications. The method is available in the Python library DADApy.},
  author       = {Wild, Romina and Wodaczek, Felix and Del Tatto, Vittorio and Cheng, Bingqing and Laio, Alessandro},
  issn         = {2041-1723},
  journal      = {Nature Communications},
  publisher    = {Springer Nature},
  title        = {{Automatic feature selection and weighting in molecular systems using Differentiable Information Imbalance}},
  doi          = {10.1038/s41467-024-55449-7},
  volume       = {16},
  year         = {2025},
}

@article{18821,
  abstract     = {Even though the one-dimensional contact interaction requires no regularization, renormalization methods have been shown to improve the convergence of numerical calculations considerably. In this work, we compare and contrast these methods: “the running coupling constant” where the two-body ground-state energy is used as a renormalization condition, and two effective interaction approaches that include information about the ground as well as excited states. In particular, we calculate the energies and densities of few-fermion systems in a harmonic oscillator with the configuration-interaction method and compare the results based upon renormalized and bare interactions. We find that the use of the running coupling constant instead of the bare interaction improves convergence significantly. A comparison with an effective interaction, which is designed to reproduce the relative part of the energy spectrum of two particles, showed a similar improvement. The effective interaction provides an additional improvement if the center-of-mass excitations are included in the construction. Finally, we discuss the transformation of observables alongside the renormalization of the potential, and demonstrate that this might be an essential ingredient for accurate numerical calculations.},
  author       = {Brauneis, Fabian and Hammer, Hans Werner and Reimann, Stephanie M. and Volosniev, Artem},
  issn         = {2469-9934},
  journal      = {Physical Review A},
  number       = {1},
  publisher    = {American Physical Society},
  title        = {{Comparison of renormalized interactions using one-dimensional few-body systems as a testbed}},
  doi          = {10.1103/PhysRevA.111.013303},
  volume       = {111},
  year         = {2025},
}

@article{18822,
  abstract     = {Let N(X) be the number of integral zeros (mathematical equation). Works of Hooley and Heath-Brown imply (mathematical equation), if one assumes automorphy and grand Riemann hypothesis for certain Hasse–Weil L-functions. Assuming instead a natural large sieve inequality, we recover the same bound on N(X). This is part of a more general statement, for diagonal cubic forms in (mathematical equation) variables, where we allow approximations to Hasse–Weil L-functions.},
  author       = {Wang, Victor},
  issn         = {2041-7942},
  journal      = {Mathematika},
  number       = {1},
  publisher    = {London Mathematical Society},
  title        = {{Diagonal cubic forms and the large sieve}},
  doi          = {10.1112/mtk.70008},
  volume       = {71},
  year         = {2025},
}

@article{18823,
  author       = {Cao, Dechang and De Jaeger-Braet, Joke G},
  issn         = {1532-2548},
  journal      = {Plant Physiology},
  number       = {1},
  publisher    = {Oxford University Press},
  title        = {{Memory of maternal temperatures: DNA methylation alterations across generations}},
  doi          = {10.1093/plphys/kiae651},
  volume       = {197},
  year         = {2025},
}

@article{18848,
  abstract     = {Type II CRISPR endonucleases are widely used programmable genome editing tools. Recently, CRISPR-Cas systems with highly compact nucleases have been discovered, including Cas9d (a type II-D nuclease). Here, we report the cryo-EM structures of a Cas9d nuclease (747 amino acids in length) in multiple functional states, revealing a stepwise process of DNA targeting involving a conformational switch in a REC2 domain insertion. Our structures provide insights into the intricately folded guide RNA which acts as a structural scaffold to anchor small, flexible protein domains for DNA recognition. The sgRNA can be truncated by up to ~25% yet still retain activity in vivo. Using ancestral sequence reconstruction, we generated compact nucleases capable of efficient genome editing in mammalian cells. Collectively, our results provide mechanistic insights into the evolution and DNA targeting of diverse type II CRISPR-Cas systems, providing a blueprint for future re-engineering of minimal RNA-guided DNA endonucleases.},
  author       = {Ocampo, Rodrigo Fregoso and Bravo, Jack Peter Kelly and Dangerfield, Tyler L. and Nocedal, Isabel and Jirde, Samatar A. and Alexander, Lisa M. and Thomas, Nicole C. and Das, Anjali and Nielson, Sarah and Johnson, Kenneth A. and Brown, Christopher T. and Butterfield, Cristina N. and Goltsman, Daniela S.A. and Taylor, David W.},
  issn         = {2041-1723},
  journal      = {Nature Communications},
  publisher    = {Springer Nature},
  title        = {{DNA targeting by compact Cas9d and its resurrected ancestor}},
  doi          = {10.1038/s41467-024-55573-4},
  volume       = {16},
  year         = {2025},
}

@article{18849,
  abstract     = {Many biological systems operate near the physical limits to their performance, suggesting that aspects of their behavior and underlying mechanisms could be derived from optimization principles. However, such principles have often been applied only in simplified models. Here, we explore a detailed mechanistic model of the gap gene network in the Drosophila embryo, optimizing its 50+ parameters to maximize the information that gene expression levels provide about nuclear positions. This optimization is conducted under realistic constraints, such as limits on the number of available molecules. Remarkably, the optimal networks we derive closely match the architecture and spatial gene expression profiles observed in the real organism. Our framework quantifies the tradeoffs involved in maximizing functional performance and allows for the exploration of alternative network configurations, addressing the question of which features are necessary and which are contingent. Our results suggest that multiple solutions to the optimization problem might exist across closely related organisms, offering insights into the evolution of gene regulatory networks.},
  author       = {Sokolowski, Thomas R and Gregor, Thomas and Bialek, William and Tkačik, Gašper},
  issn         = {1091-6490},
  journal      = {Proceedings of the National Academy of Sciences},
  number       = {1},
  publisher    = {National Academy of Sciences},
  title        = {{Deriving a genetic regulatory network from an optimization principle}},
  doi          = {10.1073/pnas.2402925121},
  volume       = {122},
  year         = {2025},
}

@article{18851,
  abstract     = {We present volume-limited samples of cataclysmic variables (CVs) and AM CVn binaries jointly selected from SRG/eROSITA eRASS1 and Gaia DR3 using an X-ray + optical color–color diagram (the "X-ray Main Sequence"). This tool identifies all CV subtypes, including magnetic and low-accretion rate systems, in contrast to most previous surveys. We find 23 CVs, 3 of which are AM CVns, out to 150 pc in the Western Galactic Hemisphere. Our 150 pc sample is spectroscopically verified and complete down to LX = 1.3 × 1029 erg s−1 in the 0.2–2.3 keV band, and we also present CV candidates out to 300 pc and 1000 pc. We discovered two previously unknown systems in our 150 pc sample: the third nearest AM CVn and a magnetic period bouncer. We find the mean LX of CVs to be 〈LX〉 ≈ 4.6 × 1030 erg s−1, in contrast to previous surveys which yielded 〈LX〉 ∼ 1031−1032 erg s−1. We construct X-ray luminosity functions that, for the first time, flatten out at LX ∼ 1030 erg s−1. We infer average number, mass, and luminosity densities of ρN,CV = (3.7 ± 0.7) × 10−6pc−3, (math formular), and (math formular), respectively, in the solar neighborhood. Our uniform selection method also allows us to place meaningful estimates on the space density of AM CVns, ρN,AM CVn = (5.5 ± 3.7) × 10−7 pc−3. Magnetic CVs and period bouncers make up 35% and 25% of our sample, respectively. This work, through a novel discovery technique, shows that the observed number densities of CVs and AM CVns, as well as the fraction of period bouncers, are still in tension with population synthesis estimates.},
  author       = {Rodriguez, Antonio C. and El-Badry, Kareem and Suleimanov, Valery and Pala, Anna F. and Kulkarni, Shrinivas R. and Gaensicke, Boris and Mori, Kaya and Rich, R. Michael and Sarkar, Arnab and Bao, Tong and De Oliveira, Raimundo Lopes and Ramsay, Gavin and Szkody, Paula and Graham, Matthew and Prince, Thomas A. and Caiazzo, Ilaria and Vanderbosch, Zachary P. and Roestel, Jan Van and Das, Kaustav K. and Qin, Yu Jing and Kasliwal, Mansi M. and Wold, Avery and Groom, Steven L. and Reiley, Daniel and Riddle, Reed},
  issn         = {0004-6280},
  journal      = {Publications of the Astronomical Society of the Pacific},
  number       = {1},
  publisher    = {IOP Publishing},
  title        = {{Cataclysmic variables and AM CVn binaries in SRG/eROSITA + Gaia: Volume limited samples, X-ray luminosity functions, and space densities}},
  doi          = {10.1088/1538-3873/ada185},
  volume       = {137},
  year         = {2025},
}

@article{18852,
  abstract     = {Recent observations have found a growing number of hypervelocity stars with speeds of ≈1500 − 2500 km s−1 that could have only been produced through thermonuclear supernovae in white dwarf binaries. Most of the observed hypervelocity runaways in this class display a surprising inflated structure: their current radii are roughly an order of magnitude greater than they would have been as white dwarfs filling their Roche lobe. While many simulations exist studying the dynamical phase leading to supernova detonation in these systems, no detailed calculations of the long-term structure of the runaways have yet been performed. We used an existing AREPO hydrodynamical simulation of a supernova in a white dwarf binary as a starting point for the evolution of these stars with the one-dimensional stellar evolution code MESA. We show that the supernova shock is not energetic enough to inflate the white dwarf over timescales longer than a few thousand years, significantly shorter than the 105 − 6 year lifetimes inferred for observed hypervelocity runaways. Although they experience a shock from a supernova less than ≈0.02 R⊙ away, our models do not experience significant interior heating, and all contract back to radii of around 0.01 R⊙ within about 104 years. Explaining the observed inflated states requires either an additional source of significant heating or some other physics that is not yet accounted for in the subsequent evolution.},
  author       = {Bhat, Aakash and Bauer, Evan B. and Pakmor, Rüdiger and Shen, Ken J. and Caiazzo, Ilaria and Rajamuthukumar, Abinaya Swaruba and El-Badry, Kareem and Kerzendorf, Wolfgang E.},
  issn         = {1432-0746},
  journal      = {Astronomy & Astrophysics},
  number       = {1},
  publisher    = {EDP Sciences},
  title        = {{Supernova shocks cannot explain the inflated state of hypervelocity runaways from white dwarf binaries}},
  doi          = {10.1051/0004-6361/202451371},
  volume       = {693},
  year         = {2025},
}

@article{18853,
  abstract     = {Electrolyte additives are extensively validated effective in mitigating dendrite growth and parasitic reactions in aqueous zinc-ion batteries (AZIBs). Nonetheless, the mechanisms by which additives influence the formation and characteristics of the inorganic solid–electrolyte interphase (SEI) are not yet fully elucidated. Herein, we investigate how Zn(CF3COO)2 additives influence solvation structure and elucidate the mechanism by which these additives promote the dual reduction of anions. Through cryo-transmission electron microscopy analysis, we identified the SEI as a highly amorphous ZnS/ZnF2 phase. This amorphous hybrid SEI demonstrates exceptional stability, mechanical robustness, and high Zn2+ conductivity, effectively mitigating parasitic reactions and enhancing Zn plating/stripping reversibility. Even under elevated current densities, the Zn anode exhibits ultra-stable longevity and ultra-high reversibility. This study provides a comprehensive understanding of the intrinsic mechanisms governing solvation structure modulation that lead to the formation of amorphous hybrid SEI, underscoring their efficacy in enhancing the performance and durability of AZIBs.},
  author       = {Zeng, Guifang and Sun, Qing and Horta, Sharona and Martínez-Alanis, Paulina R. and Wu, Peng and Li, Jing and Wang, Shang and Ibáñez, Maria and Tian, Yanhong and Ci, Lijie and Cabot, Andreu},
  issn         = {1754-5706},
  journal      = {Energy and Environmental Science},
  number       = {4},
  pages        = {1683--1695},
  publisher    = {Royal Society of Chemistry},
  title        = {{Modulating the solvation structure to enhance amorphous solid electrolyte interface formation for ultra-stable aqueous zinc anode}},
  doi          = {10.1039/d4ee03750b},
  volume       = {18},
  year         = {2025},
}

@article{18854,
  abstract     = {Context. One of the surprising early findings with JWST has been the discovery of a strong “roll-over” or a softening of the absorption edge of Lyα in a large number of galaxies at z ≳ 6, in addition to systematic offsets from photometric redshift estimates and fundamental galaxy scaling relations. This has been interpreted as strong cumulative damped Lyα absorption (DLA) wings from high column densities of neutral atomic hydrogen (H I), signifying major gas accretion events in the formation of these galaxies.
Aims. To explore this new phenomenon systematically, we assembled the JWST/NIRSpec PRImordial gas Mass AssembLy (PRIMAL) legacy survey of 584 galaxies at z = 5.0 − 13.4, designed to study the physical properties and gas in and around galaxies during the reionization epoch.
Methods. We characterized this benchmark sample in full and spectroscopically derived the galaxy redshifts, metallicities, star formation rates, and ultraviolet (UV) slopes. We defined a new diagnostic, the Lyα damping parameter DLyα, to measure and quantify the net effect of Lyα emission strength, the H I fraction in the intergalactic medium, or the local H I column density for each source. The JWST-PRIMAL survey is based on the spectroscopic DAWN JWST Archive (DJA-Spec). We describe DJA-Spec in this paper, detailing the reduction methods, the post-processing steps, and basic analysis tools. All the software, reduced spectra, and spectroscopically derived quantities and catalogs are made publicly available in dedicated repositories.
Results. We find that the fraction of galaxies showing strong integrated DLAs with NHI > 1021 cm−2 only increases slightly from ≈60% at z ≈ 6 up to ≈65 − 90% at z > 8. Similarly, the prevalence and prominence of Lyα emission is found to increase with decreasing redshift, in qualitative agreement with previous observational results. Strong Lyα emitters (LAEs) are predominantly found to be associated with low-metallicity and UV faint galaxies. By contrast, strong DLAs are observed in galaxies with a variety of intrinsic physical properties, but predominantly at high redshifts and low metallicities.
Conclusions. Our results indicate that strong DLAs likely reflect a particular early assembly phase of reionization-era galaxies, at which point they are largely dominated by pristine H I gas accretion. At z = 8 − 10, this gas gradually cools and forms into stars that ionize their local surroundings, forming large ionized bubbles and producing strong observed Lyα emission at z < 8.},
  author       = {Heintz, K. E. and Brammer, G. B. and Watson, D. and Oesch, P. A. and Keating, L. C. and Hayes, M. J. and Abdurro'Uf, Unknown and Arellano-Córdova, K. Z. and Carnall, A. C. and Christiansen, C. R. and Cullen, F. and Davé, R. and Dayal, P. and Ferrara, A. and Finlator, K. and Fynbo, J. P.U. and Flury, S. R. and Gelli, V. and Gillman, S. and Gottumukkala, R. and Gould, K. and Greve, T. R. and Hardin, S. E. and Hsiao, T. Y.Y. and Hutter, A. and Jakobsson, P. and Killi, M. and Khosravaninezhad, N. and Laursen, P. and Lee, M. M. and Magdis, G. E. and Matthee, Jorryt J and Naidu, R. P. and Narayanan, D. and Pollock, C. and Prescott, M. K.M. and Rusakov, V. and Shuntov, M. and Sneppen, A. and Smit, R. and Tanvir, N. R. and Terp, C. and Toft, S. and Valentino, F. and Vijayan, A. P. and Weaver, J. R. and Wise, J. H. and Witstok, J.},
  issn         = {1432-0746},
  journal      = {Astronomy & Astrophysics},
  publisher    = {EDP Sciences},
  title        = {{The JWST-PRIMAL archival survey: A JWST/NIRSpec reference sample for the physical properties and Lyman-α absorption and emission of ∼600 galaxies at z = 5.0-13.4}},
  doi          = {10.1051/0004-6361/202450243},
  volume       = {693},
  year         = {2025},
}

@article{18855,
  abstract     = {A central problem in computational statistics is to convert a procedure for sampling combinatorial objects into a procedure for counting those objects, and vice versa. We consider sampling problems which come from Gibbs distributions, which are families of probability distributions over a discrete space Ω with probability mass function of the form μ^Ω_β(ω) ∝ e^{β H(ω)} for β in an interval [β_min, β_max] and H(ω) ∈ {0} ∪ [1, n]. Two important parameters are the partition function, which is the normalization factor Z(β) = ∑_{ω ∈ Ω} e^{β H(ω)}, and the vector of pre-image counts c_x=|H^-1(x)|.
We develop black-box sampling algorithms to estimate the counts roughly Õ(n²/ε²) samples for integer-valued distributions and Õ(q/ε²) samples for general distributions, where q = (log Z(β_max))/Z(β_min)  (ignoring some second-order terms and parameters). We show this is optimal up to logarithmic factors. We illustrate with improved algorithms for counting connected subgraphs, independent sets, and perfect matchings. As a key subroutine, we estimate all values of the partition function using Õ(n²/ε²) samples for integer-valued distributions and Õ(q/ε²) samples for general distributions. This improves over a prior algorithm of Huber (2015) which computes a single point estimate Z(β_max) and which uses a slightly larger amount of samples. We show matching lower bounds, demonstrating this complexity is optimal as a function of n and q up to logarithmic terms.},
  author       = {Harris, David G. and Kolmogorov, Vladimir},
  issn         = {1549-6333},
  journal      = {ACM Transactions on Algorithms},
  number       = {1},
  publisher    = {Association for Computing Machinery},
  title        = {{Parameter estimation for Gibbs distributions}},
  doi          = {10.1145/3685676},
  volume       = {21},
  year         = {2025},
}

@article{18866,
  abstract     = {Using JWST Near Infrared Camera (NIRCam) images of the globular cluster 47,Tucanæ, (or NGC,104), taken at two epochs just 7 months apart, we derived proper-motion membership down to F322W2 ∼ 27. We identified an intriguing feature at the very low-mass end of the main sequence, around ∼ 0.08,M_⋅, at magnitudes F322W2 ∼ 24 and m_ F150W2 ∼ 25. This feature, dubbed 'kink', is characterized by a prominent discontinuity in the slope of the main sequence. A similar discontinuity is seen in theoretical isochrones with oxygen-poor chemistries, related to the rapid onset of absorption. We therefore hypothesize that the cluster hosts disproportionately more oxygen-poor stars near the bottom of the main sequence compared to the upper main sequence and the red giant branch. Our results show no strong or conclusive evidence of a rise in the brown dwarf luminosity function at faint magnitudes, in contrast to previous findings likely affected by faint red background galaxies. In our analysis, we accounted for this contamination by using proper motion membership.},
  author       = {Scalco, M. and Gerasimov, R. and Bedin, L. R. and Vesperini, E. and Correnti, M. and Nardiello, D. and Burgasser, A. and Richer, H. and Caiazzo, Ilaria and Heyl, J. and Libralato, M. and Anderson, J. and Griggio, M.},
  issn         = {1432-0746},
  journal      = {Astronomy & Astrophysics},
  publisher    = {EDP Sciences},
  title        = {{JWST photometry and astrometry of 47 Tucanae. Discontinuity in the stellar sequence at the star--brown dwarf transition}},
  doi          = {10.1051/0004-6361/202452907},
  volume       = {694},
  year         = {2025},
}