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exoALMA. XXIII. Estimating Disk and Planet Properties from Dust Morphologies with DBNets 2.0
No full textThe exoALMA large program provided an unprecedented view of the morphologies and kinematics of 15 circumstellar disks, offering a biased but homogenous and well-characterized sample for population-level analysis. Continuum observations revealed numerous dust substructures, known to be potential signatures of embedded planets. We analyze the observed dust morphologies with the simulation-based inference tool DBNets2.0, assuming these are due to embedded planets at fixed locations, to infer the system’s properties. We estimate the putative planet mass, the disk α viscosity, scale height, and dust Stokes number that would reproduce 19 substructures in 13 of the 15 exoALMA disks. We compare our results with literature estimates derived with different methods, and find good agreement in most cases. We further explore the implications of the inferred disk properties for accretion, showing that for the Herbig stars in our sample, the implied viscous accretion timescales are too long to account for their observed stellar accretion rates. Regarding planet migration, our results favor inward migration, with only three putative planets expected to migrate outward. Finally, we check for correlations of the inferred disk and planet properties with the disks’ gas-to-dust mass ratio, nonaxisymmetry index, and masses of the gas, dust, and host stars, finding no remarkable trends
Soft cells, Kelvin's foam and the minimal surfaces of Schwarz
No full textWe study a class of geometric shapes termed soft cells tiling three-dimensional space without sharp corners. A special class of soft tilings, called standard soft tilings can be obtained by an algorithm transforming any convex polyhedral tiling into at least one combinatorially equivalent soft tiling. Natural examples of such shapes include, among others, cell tissues, corals, and chambers in nautilus shells. However, this construction leads to sharp, highly curved edges. Here we generalize this construction to produce not just a single standard soft tiling, but all soft tilings corresponding to a given polyhedral configuration. Unlike standard soft cells, these non-standard soft cells do not exhibit protruding edges. Notably, some non-standard soft cells are the fundamental building blocks within triply periodic minimal surfaces such as Schwarz surfaces and gyroid structures, which are critical in modeling the nanoscale architecture of various polymers and carbon-based materials. These shapes also appear at the nanoscale as fundamental models of biological structures. Finally, we identify a family of intermediate space-filling cells that bridge two distinct softcell morphologies, providing a previously unrecognized connection between Schwarz surfaces and encompassing the Kelvin cell, a structure of enduring importance in materials science
Medical negligence in the age of statistically superior AI
No full textAs artificial intelligence (AI) systems increasingly outperform human clinicians in specific diagnostic tasks, legal debates have turned to whether such statistical superiority should create new obligations in medical practice. This article proposes a two-stage transparency framework, distinguishing ‘pre-deployment transparency’ from ‘post-deployment interpretability’, to clarify when clinicians may, must, or must not use or rely upon AI systems. It argues that duties to adopt or rely on AI arise only where institutional endorsement and meaningful transparency enable doctors to make informed, context-sensitive judgments. Legal responsibility in AI-assisted care must rest on institutional validation and explainability, not on statistical performance alone. The article further shows that, consistent with existing case law, courts may draw adverse inferences from evidentiary gaps created by AI opacity, particularly when a party fails to preserve or disclose information within its control. This framework preserves clinical judgment and patient trust while ensuring that overall statistical gains do not mask systematic harms to minority groups. It concludes with recommendations for adapting medico-legal standards to the growing role of AI without displacing the clinician’s role as the legally accountable decision-maker
Colonic biopsy-associated microbial signatures are predictive of response to anti-TNFα biological therapy in Crohn’s disease
No full textIntroduction: Crohn’s disease (CD) is commonly treated with biologic therapies, including anti-TNFα agents, vedolizumab (VDZ), and ustekinumab (USTE), yet only a subset of patients respond to these treatments. This study aimed to evaluate the potential of the gut microbiome to predict treatment response. Methods: Adult CD patients initiating anti-TNFα (infliximab or adalimumab), VDZ or USTE were enrolled. Pre-treatment ileal and/or colonic biopsies were collected endoscopically. Treatment response after 26–52 weeks was defined by ≥50% reduction in the simple endoscopic score for CD and either a corticosteroid-free clinical response (≥3-point HBI decrease or remission [HBI ≤4] without systemic steroids) or a biochemical response (≥50% or ≤5 mg/L CRP reduction and ≥50% or ≤250 μg/g faecal calprotectin reduction) versus baseline. Mucosal microbiota was profiled by 16S rRNA gene sequencing of biopsies. Machine learning models predicting treatment response were trained using ASV-level count data. The impact of heat-killed bacteria on anti-TNFα–induced CD14+CD206+ macrophages was tested in mixed lymphocyte reactions (MLRs). Results: A total of 125 patients were included: 39 on anti-TNFα, 47 on VDZ, and 39 on USTE. Clinical features were similar between responders and non-responders, aside from sex (USTE-colon) and CRP (USTE-ileum). No major microbial differences were observed in VDZ, USTE ileal or colon samples. However, in colonic biopsies, anti-TNFα responders had significantly higher pre-treatment α-diversity, and 3.9% of β-diversity variation associated with response. Among six models, the anti-TNFα colonic model performed significantly better than random (AUC = 0.90) to predict response. Mediterraneibacter gnavus ASVs associated with non-response, whereas Blautia ASVs associated with response, to anti-TNFα. When tested in MLRs, pretreatment with M. gnavus and B. luti led to a reduction in macrophage polarization, with a significantly stronger effect observed for M. gnavus compared with B. luti. Discussion: Taken together, this study demonstrates that the colonic mucosal microbiome prior to anti-TNFα treatment can distinguish responders from non-responders in CD, supporting its potential as a predictive biomarker
Global Biodiversity Framework Targets Can Drive Action on Insect Declines, but Lack Robust Indicators to Prove Their Effectiveness
No full textInsects are the most diverse and functionally important animals on Earth. In at least some regions, terrestrial populations are declining. Despite this, insects are often overlooked in conservation policy, and it is difficult to assess how anthropogenic threats and conservation actions affect insect populations. The Kunming‐Montreal Global Biodiversity Framework (GBF) aims to reduce pressures on biodiversity, increase conservation efforts, and reverse losses. At the International Congress on Conservation Biology in 2023, we convened a round table of specialist scientists and practitioners in insect ecology and conservation to explore how well the GBF addresses insect declines. We discussed and evaluated: (1) how well GBF targets could deliver for insects, and (2) whether the indicators proposed for monitoring progress would detect changes in the status of insects. We found that although the GBF's targets can drive action for insect recovery, almost none of the indicators can effectively measure progress for insects. We propose four principles to enhance the effectiveness of biodiversity policy for insects, and recommend the establishment of a global working group to develop insect‐focused indicators. If implemented effectively, such indicators could provide evidence of whether restoration and conservation actions are putting us on a path to recovery of global biodiversity
Antibacterial properties of experimentally produced birch tar and its medicinal affordances in the Pleistocene
No full textBirch tar is well-documented for its use as an adhesive in the Middle Palaeolithic of Europe, but other uses remain poorly explored. Drawing from recent arguments suggesting multimodal uses of products such as ochre and birch tar, this study tests the antibiotic properties of birch tar produced experimentally with methods reconstructed from Middle Palaeolithic birch tar finds from Europe. Made from the bark of Betula pendula and Betula pubescens, widely documented for the European Late Pleistocene, we produced birch tar samples using an underground pit method, a condensation method, and a modern tin can method. The birch tar samples were tested for antibiotic properties using the modified Kirby-Bauer disc diffusion antibiotic assay. The resulting inhibition zones, ranging from no effect to 10.5 ± 0.7 mm with a mean of 7.5 ± 0.17 mm, indicate a moderate effect against the Gram-positive Staphylococcus aureus, a bacterium widely known for its role in wound infections. We further establish that the efficacy of antibiotic properties is not related to the production method, with all methods showing a degree of variation. This supports a coevolutionary relationship between medicinal and technological use and production of birch tar during the Pleistocene. The antibiotic properties documented in this study are consistent with the use of birch tar as a wound dressing and skin ointment in Mi’kmaq communities in Eastern Canada, and the use of birch tar in Saami communities of Lapland. Arguing from an underexplored angle between experimental archaeology and ethnopharmacology, we suggest that similar to the ethnographic examples, a use of birch tar beyond exclusively technological contexts must be considered for the Middle Palaeolithic
Investigating the functional and transcriptional regulation of human macrophages
No full textMacrophages are essential innate immune cells that maintain tissue homeostasis and defend the host against pathogens. During my DPhil, I investigated the functions and transcriptional regulation of macrophages under different physiological and pathological contexts.In the first part of my research, I explored several previously described in vitro models of tumor-associated macrophages (TAMs) that mimic distinct features of the tumor microenvironment, including exposure to soluble factors secreted by cancer cells, mixed immune-stimulatory and -suppressive cytokine signals, and metabolites characteristic of highly glycolytic tumors.Subsequently, I focused on developing a new method for pooled CRISPR screening in primary human macrophages. Using this approach, I systematically interrogated known human transcription factors in the context of M-CSF-mediated macrophage survival and identified ZNF207 as a novel negative regulator. Functional characterization revealed that ZNF207 plays a pleiotropic role in macrophage survival, polarization, and efferocytosis, with important implications for tissue homeostasis and the resolution of inflammation.Following submission of this thesis, I intend to further elucidate the mechanisms by which ZNF207 regulates macrophage survival, differentiation, and function
Amazonian materialisms: The life of machines among the Yagua people
No full textThis article presents different vignettes on the life of matter and machines among the Yagua people in northwestern Amazonia. Based on an extended period of ethnographic fieldwork, it highlights the potential ubiquity, plurality and complexity of life-forces in matter and machines among the Yagua people. It shows how Yaguan materialisms differ from existing materialisms in anthropology, archaeology and the wider social sciences. The article advocates for an ontologically open attitude towards the life of matter, which is rooted in the belief that we can never be certain about the underlying fabric of our world
Some fast algorithms for curves in surfaces
No full textWe present some algorithms that provide useful topological information about curves in surfaces. One of the main algorithms computes the geometric intersection number of two properly embedded 1-manifolds C1 and C2 in a compact orientable surface S. The surface S is presented via a triangulation or a handle structure, and the 1-manifolds are given in normal form via their normal coordinates. The running time is bounded above by a polynomial function of the number of triangles in the triangulation (or the number of handles in the handle structure), and the logarithm of the weight of C1 and C2. This algorithm represents an improvement over previous work, since its running time depends polynomially on the size of the triangulation of S and it can deal with closed surfaces, unlike many earlier algorithms. Another algorithm, with similar bounds on its running time, can determine whether C1 and C2 are isotopic. We also present a closely related algorithm that can be used to place a standard 1-manifold into normal form
Combinatorics, Probability and Computing
No full textThe main theme of the workshop was the use of probabilistic methods in combinatorics and related fields. This area is evolving extremely quickly, with the introduction of powerful new methods and the development of increasingly sophisticated techniques, and there have been a number of very significant breakthroughs in the area in recent years. The workshop emphasized several of these recent breakthroughs, which include foundational results in the theory of random graphs and processes, and also applications of probabilistic techniques in Ramsey theory, design theory, and group theory, and of combinatorial techniques to problems in number theory, functional analysis, and high-dimensional geometry