julilili42/papers huggingface dataset:
MITE: the Minimum Information about a Tailoring Enzyme database for capturing specialized metabolite biosynthesis
2025-09-26

Abstract Secondary or specialized metabolites show extraordinary structural diversity and potent biological activities relevant for clinical and industrial applications. The biosynthesis of these metabolites usually starts with the assembly of a core ‘scaffold’, which is subsequently modified by tailoring enzymes to define the molecule’s final structure and, in turn, its biological activity profile. Knowledge about reaction and substrate specificity of tailoring enzymes is essential for understanding and computationally predicting metabolite biosynthesis, but this information is usually scattered in the literature. Here, we present MITE, the Minimum Information about a Tailoring Enzyme database. MITE employs a comprehensive set of parameters to annotate tailoring enzymes, defining substrate and reaction specificity by the expressive reaction SMARTS (Simplified Molecular Input Line Entry System Arbitrary Target Specification) chemical pattern language. Both human and machine readable, MITE can be used as a knowledge base, for in silico biosynthesis, or to train machine-learning applications, and tightly integrates with existing resources. Designed as a community-driven and open resource, MITE employs a rolling release model of data curation and expert review. MITE is freely accessible at https://mite.bioinformatics.nl/.
Spyglass: a framework for reproducible and shareable neuroscience research
2025-09-26

Abstract Scientific progress depends on reliable and reproducible results. Progress can be accelerated when data are shared and re-analyzed to address new questions. Current approaches to storing and analyzing neural data involve bespoke formats and software that make replication and reuse of data difficult. To address these challenges, we created Spyglass, an open-source data management and analysis framework written in Python. Spyglass provides reproducible pipelines for common neuroscience analyses and sharing of raw data, intermediate analyses and final results within and across labs. Spyglass uses the Neurodata Without Borders (NWB) standard and includes pipelines for spectral filtering, spike sorting, pose tracking, and neural decoding. Spyglass can be extended to apply existing and newly developed pipelines to datasets from multiple sources. We demonstrate these features in the context of a cross-laboratory replication by applying advanced state space decoding algorithms to publicly available data. New users can try out Spyglass on a Jupyter Hub hosted by HHMI and 2i2c: https://spyglass.hhmi.2i2c.cloud/.
Risking your Tail: Modeling Individual Differences in Risk-sensitive Exploration using Bayes Adaptive Markov Decision Processes
2025-09-26

Abstract Novelty is a double-edged sword for agents and animals alike: they might benefit from untapped resources or face unexpected costs or dangers such as predation. The conventional exploration/exploitation tradeoff is thus coloured by risk-sensitivity. A wealth of experiments has shown how animals solve this dilemma, for example using intermittent approach. However, there are large individual differences in the nature of approach, and modeling has yet to elucidate how this might be based on animals’ differing prior expectations about reward and threat, and differing degrees of risk aversion. To capture these factors, we built a Bayes adaptive Markov decision process model with three key components: an adaptive hazard function capturing potential predation, an intrinsic reward function providing the urge to explore, and a conditional value at risk (CVaR) objective, which is a contemporary measure of trait risk-sensitivity. We fit this model to a coarse-grain abstraction of the behaviour of 26 animals who freely explored a novel object in an open-field arena (Akiti et al. Neuron 110, 2022). We show that the model captures both quantitative (frequency, duration of exploratory bouts) and qualitative (with distinguished, cautious, tail-behind approach) features of behavior, including the substantial idiosyncrasies that were observed. Some animals begin with cautious exploration, and quickly transition to confident approach to maximize exploration for reward; we classify them as potentially more risk neutral, and enjoying a flexible hazard prior. By contrast, other animals only ever approach in a cautious manner and display a form of self-censoring; they are characterized by potential risk aversion and high and inflexible hazard priors. Explaining risk-sensitive exploration using factorized parameters of reinforcement learning models could aid in the understanding, diagnosis, and treatment of psychiatric abnormalities such as anxiety disorders.
Salicylic acid inhibits V-ATPase activity and restricts cell elongation
2025-09-26

Abstract While the role of salicylic acid (SA) in plant defence has been investigated for decades, its role in regulating plant growth and development has only come into focus recently. SA application inhibits growth independently of the established “Nonexpressor of Pathogenesis Related” (NPR) receptors. However, the underlying mechanism at the cellular level remains largely elusive. Here, we show that SA induces changes in vacuolar morphology and a significant increase in vacuolar pH in Arabidopsis (Arabidopsis thaliana). We demonstrate SA-mediated inhibition of V-ATPase activity, which is confirmed by experiments using the V-ATPase mutant vha-a2 vha-a3. The observed effects seem to be independent of the phytohormone auxin, which has been reported to crosstalk with SA. By inhibiting V-ATPase activity, SA impacts basic cellular functions such as vesicle trafficking and/or nutrient storage, affecting cell size and growth. Our results reveal a NPR-independent mechanism that attenuates growth, potentially reallocating resources to enhance plant robustness and promote endurance during environmental stresses.
Rift‐Related Sedimentary Basin and Deeper‐Seated Mafic Intrusions Modeled Beneath Thwaites Glacier, West Antarctica: Influence on Glacier Dynamics
2025-09-26

Abstract Thwaites Glacier in West Antarctica has been identified as a route to destabilization of the whole West Antarctic Ice Sheet, potentially leading to several meters of sea‐level rise. However, future evolution of Thwaites Glacier remains uncertain due to a lack of detailed knowledge about its basal boundary that will affect how its retreat proceeds. Here we aim to improve understanding of the basal boundary in the lower part of Thwaites Glacier by modeling the crustal structures that are related to the bed‐type distribution and therefore influence the basal slip. We combine long‐offset seismic, and gravity‐ and magnetic‐anomaly data to model the crustal structures along two 120 km lines roughly parallel to ice flow. We find a sedimentary basin 40 km in length in the along‐flow direction, with a maximum thickness of 1.7 0.2 km, and two mafic intrusions at 5–10 km depth that vary in maximum thickness between 3.8 and 8.6 km. The sedimentary basin and major mafic intrusions we modeled are likely related to the multi‐stage tectonic evolution of the West Antarctic Rift System. Thwaites Glacier flows across a tectonic boundary within our study site, indicating it flows across tectonically formed structures. The varying geology and resulting variations in bed types demonstrate the influence of tectonics on Thwaites Glacier dynamics.
The N‐Bromo‐Hammick Intermediate
2025-09-26

Abstract We report the characterization of bromopyridin‐2‐ylidene, the N‐bromo‐Hammick intermediate, isolated in solid neon at 4.4 K. Computations (B2PLYP, NEVPT2), IR, and UV/vis spectroscopy characterize this intermediate as a singlet carbene with a vacant σ*‐type frontier orbital. This unusual electronic structure (σ 2 σ* 0 ) allows the carbene to isomerize to its more stable pyridine tautomer via a planar transition state, avoiding the deviation from planarity seen in other singlet carbenes. The compound's reaction with molecular hydrogen faces a minor but prohibitive barrier (8.4 kcal mol −1 ) at the low temperatures of the experiment.
On-site plant-wax biomarker analysis for assessing soil-organic-microbial degradation in archaeological contexts: A case study from Southern India
2025-09-27

Stable carbon isotope (δ<sup>13</sup>C) analysis of soil organic matter (SOM) from archaeological contexts is widely employed as a proxy for palaeovegetation and palaeoenvironmental reconstruction. However, the reliability of δ<sup>13</sup>C<sub>SOM</sub> as a palaeovegetation proxy is influenced by issues of physico-chemical diagenesis and isotopic fractionation, prompting increased interest in source-specific biomarker approaches. In this study, we present a case study from the Palaeolithic site of Jwalapuram (India), where plant-wax biomarker data indicate the degradation of plant-derived lipids, raising concerns about the reliability of δ<sup>13</sup>C<sub>SOM</sub> as a palaeovegetation proxy in this context. To further investigate SOM degradation, topsoil samples from central Andhra Pradesh were analyzed, revealing variable levels of SOM preservation across the region, strongly correlated with sedimentary and vegetation contexts. Our research highlights the importance of integrating source-specific proxies, such as plant-wax biomarkers, with bulk proxies such as δ<sup>13</sup>C<sub>SOM</sub> to mitigate preservation biases and ensure the integrity of palaeovegetation reconstructions.
MRC2 expression modulates metabolism in acute myeloid leukemia stem cells
2025-09-27

Leukemic stem cells (LSC) are well recognized for their essential roles in acute myeloid leukemia (AML) initiation and relapse. LSC can be distinguished from non-LSC AML cells by the expression of specific cell surface markers, but there is considerable phenotypic heterogeneity among LSC in AML. Here, using primary patient samples, we report that mannose receptor C-type 2 (MRC2) can be used to enrich for LSC across various AML subtypes. When compared to MRC2- AML cells isolated from the same patient samples, MRC2+ leukemic subpopulations show increased in vitro clonogenic capacity, a stemness transcriptomic signature, and enhanced leukemic capacity in mouse xenograft models. Further, we find that MRC2 is functional on AML cells, and enables their robust uptake of collagen, which supports their glycolytic metabolism. In sum these data highlight the use of functional surface markers to distinguish LSC in AML, and how they can yield insight into their unique characteristics.
Investigating Factors Associated with Employees’ Attitudes Towards Work-Related Infection Control Measures During the COVID-19 Pandemic: An Exploratory Cross-Sectional Study from Seven Different Companies in Germany, July–August 2021
2025-09-27

Background/Objectives: This study is part of an exploratory mixed-methods project investigating how companies and their employees in Germany dealt with adapted working conditions during the COVID-19 pandemic. Here, we identify predictive factors for employees’ attitudes towards the suitability of work-related technical, organisational, and personal SARS-CoV-2 infection control measures. Methods: In July 2021, when there was little evidence to suggest that the risk of work-related exposure to SARS-CoV-2 differed between occupations and workplaces, a standardised online and an optional paper-and-pencil survey were distributed across seven companies in southern Germany. Multivariate linear regression was used for analysis. Results: A total of 821 employees participated (average response rate: 24.5%). Most of the respondents (93%) worked in large companies, in the production industry (82%), with most of them having office jobs (82%). Around 29% reported doing most of their office work remotely during the pandemic. The perceived suitability of workplace infection control measures was rated quite high, with an overall mean score of 4.11 (SD 0.60) out of a possible 5. Workplace characteristics related to the COVID-19 pandemic as well as individual perception of SARS-CoV2 and COVID-19 in general were the most prominent predictors of attitudes towards the suitability of work-related SARS-CoV-2 infection control. For example, a higher COVID-19-specific reactance was negatively associated with attitudes towards technical (ß = −0.16), organisational (ß = −0.14), and personal (ß = −0.17) infection control measures (all p-values &lt; 0.001). Furthermore, a higher rating of the employer’s commitment to occupational safety and health related to SARS-CoV-2, a higher individual disease perception, and a higher individual COVID-19-specific resilience had a positive association with attitudes towards the suitability of infection control measures. Finally, professional activity as well as company affiliation had statistically significant associations with employees’ attitudes towards the suitability of infection control measures. Conclusions: The results provide insight into factors relevant to pandemic prevention and control. In particular, our findings highlight the potential to implement organisational measures alongside compulsory technical occupational health measures. This could inform the development of pandemic preparedness strategies that prioritise adherence to established occupational infection control measures.
Determination of Chemical Mixtures in Environmental, Food, and Human Samples Using High-Resolution Mass Spectrometry-Based Suspect Screening Approaches
2025-09-28

Chemical contaminants are widely dispersed in the environment in all its dimensions, posing significant public health problems. Comprehensive knowledge of these stressors is a prerequisite for assessing the associated risk and implementing public policy measures to reduce the level of population exposure. Nontargeted suspect screening approaches broaden the knowledge of the chemical human exposome. We developed and used a suspect screening method based on large spectral libraries. Chemical profiling was based on a combined LC- and GC-HRMS approach. The methodology was applied to 16 samples spanning the environment, food, and health continuum. Using a combination of matching and scoring data, a total of 547 compounds were likely identified, from which the chemical structure of 63 molecules was confirmed to the highest level of certainty. Wastewater, and more generally environmental samples, had the highest number of chemicals detected, while fish samples had a lower number. Pharmaceuticals, pesticides, and personal care product-related compounds were found to be the most common compounds in and between the extracts, particularly in water and serum samples. Many natural and endogenous compounds were consistently annotated in the samples submitted for analysis, regardless of the compartment investigated.
Complete attenuation of Plasmodium falciparum sporozoites by atovaquone–proguanil
2025-09-29

Abstract To develop a Plasmodium falciparum (Pf) vaccine that precludes replication inside the host for improved vaccine safety, we tested chemo-attenuation (CVac) of sporozoites (SPZ) with atovaquone–proguanil (AP). In mice, P. berghei sporozoites administered with AP invaded hepatocytes, arrested early, and induced robust protection, which correlated with parasite-specific effector-memory CD8+ T cell responses. In a clinical trial of PfSPZ-CVac (AP), in which three doses of 5.12 × 10 4 or 1.5 × 10 5 PfSPZ were administered by direct venous inoculation combined with oral single-dose AP (1000/400 mg), blood stage infections were fully prevented during immunisation. 2/8 and 2/10 of vaccinees, respectively, were protected when challenged with 3.2 × 10 3 PfSPZ 10 weeks later, inferior to PfSPZ-CVac (chloroquine/CQ) that allows in-host replication. Comparative analysis of responses to 228 Pf proteins revealed that protection with PfSPZ-CVac (CQ) was associated with antibodies to two liver-stage antigens (LISP2, LSA1) and a multi-stage antigen (PfMSP5), but not to the major surface protein PfCSP. The complete arrest of high numbers of Pf sporozoites by single-dose AP should allow a significant dose-frequency reduction of the current daily AP malaria chemoprophylaxis regimen.
Prevention of type 2 diabetes through prediabetes remission without weight loss
2025-09-29

Abstract Clinical practice guidelines recommend defined weight loss goals for the prevention of type 2 diabetes (T2D) in those individuals with increased risk, such as prediabetes. However, achieving prediabetes remission, that is, reaching normal glucose regulation according to American Diabetes Association criteria, is more efficient in preventing T2D than solely reaching weight loss goals. Here we present a post hoc analysis of the large, multicenter, randomized, controlled Prediabetes Lifestyle Intervention Study (PLIS), demonstrating that prediabetes remission is achievable without weight loss or even weight gain, and that it also protects against incident T2D. The underlying mechanisms include improved insulin sensitivity, β-cell function and increments in β-cell-GLP-1 sensitivity. Weight gain was similar in those achieving prediabetes remission (responders) compared with nonresponders; however, adipose tissue was differentially redistributed in responders and nonresponders when compared against each other—while nonresponders increased visceral adipose tissue mass, responders increased adipose tissue in subcutaneous depots. The findings were reproduced in the US Diabetes Prevention Program. These data uncover essential pathways for prediabetes remission without weight loss and emphasize the need to include glycemic targets in current clinical practice guidelines to improve T2D prevention.
Strong Decay of Correlations for Gibbs States in Any Dimension
2025-09-29

Abstract Quantum systems in thermal equilibrium are described using Gibbs states. The correlations in such states determine how difficult it is to describe or simulate them. In this article, we show that if the Gibbs state of a quantum system satisfies that each of its marginals admits a local effective Hamiltonian with short-range interactions, then it satisfies a mixing condition, that is, for any regions A , C the distance of the reduced state <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msub> <mml:mi>ρ</mml:mi> <mml:mrow> <mml:mi>AC</mml:mi> </mml:mrow> </mml:msub> </mml:math> on these regions to the product of its marginals, <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:mfenced> <mml:msub> <mml:mi>ρ</mml:mi> <mml:mrow> <mml:mi>AC</mml:mi> </mml:mrow> </mml:msub> <mml:msubsup> <mml:mi>ρ</mml:mi> <mml:mi>A</mml:mi> <mml:mrow> <mml:mo>-</mml:mo> <mml:mn>1</mml:mn> </mml:mrow> </mml:msubsup> <mml:mo>⊗</mml:mo> <mml:msubsup> <mml:mi>ρ</mml:mi> <mml:mi>C</mml:mi> <mml:mrow> <mml:mo>-</mml:mo> <mml:mn>1</mml:mn> </mml:mrow> </mml:msubsup> <mml:mo>-</mml:mo> <mml:msub> <mml:mn>1</mml:mn> <mml:mrow> <mml:mi>AC</mml:mi> </mml:mrow> </mml:msub> </mml:mfenced> <mml:mspace/> <mml:mo>,</mml:mo> </mml:mrow> </mml:math> decays exponentially with the distance between regions A and C . This mixing condition is stronger than other commonly studied measures of correlation. In particular, it implies the exponential decay of the mutual information between distant regions. The mixing condition has been used, for example, to prove positive log-Sobolev constants. On the way, we prove that the the condition regarding local effective Hamiltonian is satisfied if the Hamiltonian only has commuting interactions which also commute with every marginal of their products. The proof of these results employs a variety of tools such as Araki’s expansionals, quantum belief propagation and cluster expansions.
The earliest evidence of blue pigment use in Europe
2025-09-29

Blue pigments are absent in Palaeolithic art. This has been ascribed to a lack of naturally occurring blue pigments or low visual salience of these hues. Using a suite of archaeometric approaches, the authors identify traces of azurite on a concave stone artefact from the Final Palaeolithic site of Mühlheim-Dietesheim, Germany. This represents the earliest use of blue pigment in Europe. The scarcity of blue in Palaeolithic art, along with later prehistoric uses of azurite, may indicate that azurite was used for archaeologically invisible activities (e.g. body decoration) implying intentional selectivity over the pigments used for different Palaeolithic artistic activities.
Early Pleistocene rhinoceroses (Mammalia, Perissodactyla, Rhinocerotidae) from Northern Greece: biochronological and paleobiogeographic implications
2025-09-29

Abstract Rhinoceroses were well-distributed across Southern Europe during the Early Pleistocene with abundant remains, but they are rather scarce in the Greek record and even less studied from a systematic point of view. In this article, we study a total of 124 specimens from eight fossil-bearing Lower Pleistocene localities of Northern Greece, spanning from ~ 2.3 to ~ 1.2 Ma. The localities of Tsiotra Vryssi and Krimni in the Mygdonia Basin provided the best material in terms of both number and preservation of specimens, whereas in the rest of the sites from Mygdonia, Drama and Neapolis-Grevena Basins less than ten specimens for each site are known. The present study documents the first occurrence in Greece of Stephanorhinus cf. S. hundsheimensis in the localities of Riza-1, Krimni-1, 3 and Tsiotra Vryssi, which suggests that the species may have entered earlier than the rest of the Europe. Additionally, the last occurrence of Stephanorhinus jeanvireti in Greece is recorded in Dafnero-3. The presence of Stephanorhinus etruscus is confirmed in several localities including Volax, Tsiotra Vryssi, Libakos and Apollonia-1, and indicates a chronological range from ~ 2.3 to ~ 1.2 Ma. At the beginning of this time frame both S. jeanvireti and S. etruscus co-occur in Greece, whereas the presence of both S. etruscus and Stephanorhinus cf . S. hundsheimensis at Tsiotra Vryssi testifies their first local co-occurrence.
Vortices without inflow: Bound spectra in horizonless rotational analogs
2025-09-29

Analog gravity experiments are making remarkable strides in unveiling both the classical and quantum nature of black holes. By harnessing diverse states of matter, contemporary tabletop setups now replicate strong-field phenomena typically confined to the enigmatic regions surrounding black holes. Through these modern gravity simulators, physical processes once considered elusive may finally be brought into experimental reach. In this work, we investigate the spectrum of massless scalar excitations propagating within the effective geometry of a rotating acoustic metric. Specifically, we build an analog vortex-like spacetime endowed with a tunable parameter that emulates the geometry of a rotating gravitational background. This model accommodates both the presence of a sonic horizon, characteristic of an acoustic black hole for non-zero tuning parameters, and its absence when the parameter vanishes, yielding a horizonless, purely rotational vortex flow devoid of radial inflow. We focus on the case where the vortex flow is purely rotational. The resulting spectral properties is found to be qualitatively consistent with that observed in recent experimental realizations of giant multiply quantum vortices featuring solid or hollow cores. This correspondence suggests that the analog spacetime used here holds significant potential to replicate, qualitatively, the phenomenology of cutting-edge laboratory experiments. In doing so, it offers new insight into the intricate landscape of analog black-hole spectroscopy and, potentially, the resonant topography of bounded, rotating astrophysical environments around black holes.