bluuebunny/crossref_metadata_2025 huggingface dataset:
Pupillometry reveals autonomic adjustments during diving reflex in face immersion apnea
Authors: Rizzuto V. , Montanari R. , Mesin L. , Bortolozzo-Gleich M. H. , Laurino M. , Bonneh Y. , Yellin D. , Laganovska G. , Vanags J. , Gemignani A
Published: February 2025

The human diving reflex (DR), an innate defensive reflex triggered during periods of apnea, concurrently activates both the sympathetic and parasympathetic branches of the autonomic nervous system to regulate physiology against challenging demands. Despite pupil dilation and constriction being antagonistically controlled by the two autonomic branches, the effect of the diving reflex on pupil diameter fluctuations is still unknown. Thus, we compared participants’ pupil diameter fluctuations while breathing or performing apnea either with (Wet) or without (Dry) face immersion in cold water. We found that pupil diameter fluctuations in both apneic conditions are associated with lower power in the low-frequency band (< 0.25 Hz) while in the Wet condition, a reallocation of power towards higher frequencies (> 0.25 Hz) occurs, together with an increased entropy, contrary to the remaining conditions. This indicates a shift in autonomic balance and an increased complexity of pupil fluctuations during the diving reflex. Our findings present pupil dynamics as a valuable entry point to the exploration of autonomic adjustments for this reflex.
Using artificial intelligence to optimize ecological restoration for climate and biodiversity
Authors: Silvestro Daniele , Goria Stefano , Groom Ben , Sterner Thomas , Antonelli Alexandre
Published: February 2025

The restoration of degraded ecosystems can provide important contributions to help mitigate climate change and bend the curve of biodiversity loss. Depending on the primary objective – such as maximizing carbon storage, protecting threatened species, or reducing overall costs – different spatial priorities have been identified at global and regional levels. Funding mechanisms to support such work comprise public sources, philanthropy, and the private sector, including the sales of carbon and biodiversity credits. However, effectively exploring tradeoffs between restoration objectives and estimating the price of biodiversity and carbon credits to design financially viable projects remain challenging. Here we harness the power of artificial intelligence in our software CAPTAIN, which we further develop to identify spatial priorities for ecological restoration that maximize multiple objectives at once and which allows a robust evaluation of biodiversity and climate outcomes. We find through a series of realistic simulations that even low to moderate consideration of biodiversity in restoration projects leads to the selection of restored areas that substantially improve the conservation of threatened species, while resulting in a relatively small decrease in total carbon captured. We propose a data-driven valuation of biodiversity credits in relation to carbon credits enabling the design of a blended financial model that could support restoration efforts even in areas previously excluded for economic reasons. This study shows how the use of a robust methodological framework can lead to significant improvements in outcomes for climate and nature, while minimizing costs.
Positive associations between growth and thermal tolerance in the reef-building coralMontipora capitata
Authors: Walker Nia S. , Luke Hayley , Miller Spencer , Kealoha Darienne , Caruso Carlo , Johnston Erika C. , Mujica Elena M. , Hancock Joshua R. , Drury Crawford
Published: February 2025

Relationships between ecologically important traits are increasingly important for the future of coral reefs, which are declining globally due to a variety of stressors. Corals that resist and recover from bleaching will be selected under future climates, which may negatively or positively impact a range of associated traits important for the structure and function of contemporary and future reefs. Using standardized assays, we investigated growth under ambient conditions, bleaching resistance and recovery after bleaching in a model population of 60Montipora capitatacolonies harboring diverse symbiont communities. We found significantly higher trait variance withinDurusdinium-dominated colonies, highlighting the interaction of host and symbiont. We also show that symbiont community impacted thermal tolerance and survivorship during the thermal stress assay, but not recovery or growth. There was also a positive relationship between thermal tolerance and change in surface area and thermal tolerance and recovery from equivalent amounts of stress. These results demonstrate limited tradeoffs to thermal tolerance and suggest that bleaching tolerant corals in this model system are suited to recover from stress and maintain high growth rates under ambient conditions, providing insight into the adaptive capacity of thermally tolerant corals in the Anthropocene.
In Silico Discovery of Small Molecule Modulators Targeting Ebola Virus VP 35 and VP 40 protein
Authors: Liu Yang , Zhu Chen , chen Mei , Guo Daoyu
Published: February 2025

Ebola virus (EBoV) proteins VP35 and VP40 are acknowledged as significant pharmacological targets for disrupting viral replication, virion assembly, and the budding process from host cells. We employed molecular docking based throughput virtual screening (HTVS), standard precision (SP), and extra precision (XP) docking to discover candidate compounds. Subsequently, molecular dynamics simulations, and ADMET analyses to identify potential small molecular compounds that could inhibit the Ebola virus. Among 210,590 compounds from the SPECS database, we found the compounds AO-022/43452438, AN-465/43369333, and AN-465/43369198 were optimal candidates for the EBOV-VP35 protein, while AN-465/43369160, AN-465/4341136, and AN-465/43369952 also emerged as optimal compounds for the EBOV-VP40 protein. Furthermore, we employed the energy decomposition technique, MM-GB/SA, to identify the top ten amino acids that significantly contribute to the binding interactions. ADMET result implicated that the six compounds have potential druggability, but special attention should be given to AN-465/43369333 due to potential cardiac toxicity. In conclusions, the six compounds and their key interacting amino acid sites identified in this study may serve as a valuable platform for the future development of novel therapeutics targeting the Ebola virus.
A simple method to classify behaviours of aerial predators using tri-axial high-frequency accelerometers
Authors: García-Silveira D. , Benhamou S. , Lopez-Ricaurte L. , Hernández-Pliego J. , Duriez O. , Bustamante J.
Published: February 2025

Background

Remote monitoring of animals has opened new avenues in behavioural research. The advent of animal-borne accelerometers makes it possible to derive the body posture and activity level, and thereby to identify fine-scale behaviours with no need for direct observation. This is particularly useful for species that forage or hunt beyond human sight in sometimes hard-to-access or remote areas. However, the complexity of numerous methods developed for this purpose may discourage researchers from effectively using acceleration data.

Results

We present a simple and straightforward approach to identify and classify behaviours based on tri-axial high-frequency (25 Hz) acceleration data. This method relies on constructing a decision tree to assign predefined behaviours to time series of acceleration data using four accelerometer-based parameters that are biologically relevant and easy to interpret. Initially, we manually labelled sequences of acceleration data with the behaviours using paired high-frequency (i.e. 1 Hz) GPS tracking data as ground-truth. Then, threshold values of the acceleration-based parameters were objectively determined based on receiver operating characteristic (ROC) analysis. Finally, we built the decision tree to automatically classify the behaviours of the whole dataset and tested further improvements. As a case study, we used two falcon species (lesser kestrelFalco naumanniand common kestrelF. tinnunculus). Our simple method achieved an overall accuracy of 97.6% in classifying the following behaviours: perching (99.9%), soaring-gliding (99.3%), flapping (93.1%) and hovering (86.4%). We also showed that kestrels’ prey capture attempts can be identified from the tri-axial high-frequency accelerometers due to diagnostic signatures (the so-called ‘spikes’).

Conclusions

Our simple method has broad applicability to free-ranging aerial predators. We show that behavioural categories can be accurately classified from a relatively small subset of manually labelled acceleration data (43,075 seconds). Although quantifying hunting success needs further investigation, the detection of prey capture attempts opens new possibilities for studying the hunting behaviour of aerial predators.
Reconstructing the three-dimensional architecture of extrachro-mosomal DNA with ec3D
Authors: Chowdhury Biswanath , Zhu Kaiyuan , Li Chaohui , Luebeck Jens , Chapman Owen S. , Kraft Katerina , Zhang Shu , Chavez Lukas , Henssen Anton G. , Mischel Paul S. , Chang Howard Y. , Bafna Vineet
Published: February 2025

Extrachromosomal DNAs (ecDNAs) are large, acentric, circular DNA molecules that occur pervasively across many human cancers. EcDNA can drive tumor formation and evolution, contribute to drug resistance, and associate with poor patient survival outcomes. Beyond mediating high copy numbers, the circular topology and dynamic conformational changes of ecDNA disrupt topological domains and rewire regulatory networks, thereby conferring an important role in the transcriptional regulation of oncogenes. Here, we develop ec3D, a computational method for reconstructing the three-dimensional structures of ecDNA and analyzing significant interactions from high-throughput chromatin capture (Hi-C) data. Given a candidate ecDNA sequence and the corresponding whole-genome Hi-C as input, ec3D reconstructs the spatial structure of ecDNA by maximizing the Poisson likelihood of observed interactions. Ec3D’s performance was validated using both simulated ecDNA structures with varying conformations, and Hi-C data from previously-characterized cancer cell lines. Our reconstructions reveal that ecDNAs occupy spherical configurations and mediate unique long-range interactions involved in gene regulation. Through algorithmic innovations, ec3D can resolve complex ecDNA structures with duplicated copies of large genomic segments, identify multi-way interactions, distinguish between interactions arising from direct spatial proximity and secondary interactions resulting from alternative folding patterns or intermolecular (trans) contacts of ecDNA molecules. Our findings provide insights into how the spatial organization of ecDNA may influence gene regulation and contribute to increased oncogene expression.

Code availability

https://github.com/AmpliconSuite/ec3D
Viral kinetics of H5N1 infections in dairy cattle
Authors: Eales Oliver , McCaw James M. , Shearer Freya M.
Published: February 2025

Since early-2024 unprecedented outbreaks of highly pathogenic avian influenza H5N1 clade 2.3.4.4b have been ongoing in dairy cattle in the United States with significant consequences for the dairy industry and public health. Estimation of key epidemiological parameters is required to support outbreak response, including predicting the likely effectiveness of interventions and testing strategies. Here we pool limited publicly available data from three studies of naturally and experimentally infected dairy cattle. We quantify Ct value trajectories of infected dairy cattle and the relationship between Ct value and the log-titre of infectious virus, β2a proxy for infectiousness. We estimate that following infection peak Ct values are rapidly reached within 1–2 days with a population mean Ct value of 16.9 (13.2, 20.5). We identify a critical threshold Ct value of 21.5 (20.1, 23.6), with values of Ct value above this threshold representing little-to-no infectious viral load. Finally, we estimate the distribution of the duration of infectiousness for dairy cattle (i.e. the duration their Ct value remains above the critical threshold) with a population median of 6.2 (2.8, 13.1) days.
Adaptive selection of p53 mutation metaplastic phenotypes in estrogen-independent progression of ER+ tumors: A mechanism for acquired resistance to hormonal therapy
Authors: Moon Hyeongsun , Mori Hidetoshi , Chen Jane , Patino Alejandra , Penzvalto Zsofia , Ramamurthy Kavya , Choi Jaeyong , McPherson John D. , Snyder Joshua C. , Cardiff Robert D. , Borowsky Alexander D.
Published: February 2025

Estrogen receptor positive (ER+) subtypes of mammary adenocarcinoma comprise 79% of all breast cancer diagnosis and 67% of all breast cancer mortality. The paucity of models of ER+mammary cancer that mimic human disease and response to treatment has limited critical preclinical study of mechanisms and new therapies for ER+breast cancer. TheStat1knockout, 129S6/SvEvTac-Stat1tm1Rds(Stat1-/-), females develop luminal type FoxA1+, ER+, and PR+mammary carcinomas after prolonged latencies. Initial studies showed that a cell line derived from a Stat1-/- mammary carcinoma was tumorigenic in syngeneic mice, but non-tumorigenic in ovariectomized (Ovx) mice. Here, data shows that Ovx performed after SSM2 tumors establish growth results in ovarian hormone independent growth. The viable post-Ovx tumors were primarily composed of metaplastic CK14+basal type cells with a high percentage p53 immunohistochemistry (IHC) positive “mutation pattern”, rather than the original luminal type tumors with low percent “wild type” pattern p53. Comparing whole exome sequences of ER+Stat1-/-mammary tumors before and after Ovx, revealed basal keratins, mesenchymal (EMT) phenotypes, and unique mutation profiles in genes, includingTrp53andPrlr,in the estrogen-independent tumors. Our experimental findings are consistent with the clinical evidence of tumor heterogeneity of ER+breast cancers in patients in recent whole genome sequencing studies. Similarly, spontaneous Stat1-/- tumors with high percentage p53 “mutation pattern” were more basaloid and grew rapidly after Ovx, while retaining high expression of ER and FoxA1. This study demonstrates that the STAT1-/-, ER+estrogen dependent breast cancers can become resistant to through clonal selection of mammary cells comprised of metaplastic p53+/CK14+basaloid cells.
Vaccine Hesitancy, Coercion and Regret: Post-Pandemic Lessons on COVID-19 Vaccine Policies and Outreach among Newcomer Communities in Alberta, Canada
Authors: Antonio Minnella , Ramirez-Cerino Edna , Sahilie Adanech , Yemane Mussie , Youssef Michael , Nielssen Ingrid , Holdbrook Linda , Essar Mohammad Yasir , Santana Maria , Spitzer Denise , Pottie Kevin , Fabreau Gabriel E.
Published: February 2025

Background

Since the COVID-19 pandemic routine vaccination rates have dropped in Canada. Many newcomers and refugees experience significant vaccine inequities despite wide vaccine availability and COVID-19 pandemic vaccination campaigns. We aimed to investigate post-pandemic vaccine hesitancy, acceptance, and vaccine outreach strategies among newcomers’ communities.

Methods

We conducted a prospective community-based-participatory research (CBPR) qualitative study with self-identified newcomers in Alberta between October 2022 - January 2023. Community Scholars, leaders representing various ethnocultural communities trained in community-engaged research conducted semi-structured interviews and focus groups in English and first languages. Scholars collected and translated detailed qualitative notes and sociodemographic data with a standardized survey. Qualitative data was thematically analyzed and coded using a consensus-based approach.

Results

We conducted two focus groups and five semi-structured interviews with 12 participants, 50% who identified as female and originated from the Philippines, Ethiopia, Eritrea, Mexico, Burundi, and Egypt. We identified three main themes, each with two subthemes: (1) vaccine hesitancy due to lack of reliable information and religious and cultural beliefs, (2) access to COVID-19 vaccines and information, and (3) vaccine acceptance as voluntary or coerced. Employer mandated vaccination emerged as a critical issue with potential long-term negative public health implications, leading to vaccine regret and loss of trust of public health authorities and healthcare systems.

Conclusion

During population-wide COVID-19 vaccination campaigns newcomers perceived their communities’ circumstances were overlooked, potentially increasing vaccine hesitancy. Perceived coercive vaccination policies had unintended negative public health consequences. These findings may help inform future emergency and routine public health vaccination policies.
Prognostic Implications of Codon-SpecificKRASMutations in Localized and Advanced Stages of Pancreatic Cancer
Authors: Raji Sara , Zaribafzadeh Hamed , Jones Tyler , Kanu Elishama , Tong Kunling , Fletcher Ashley , Howell T. Clark , McCall Shannon J. , Marks Jeffrey R. , Rogers Bruce , Niedzwiecki Donna , Allen Peter J. , Nussbaum Daniel P. , Kabiri Zahra
Published: February 2025

Introduction

WhileKRASmutations represent the primary oncogenic driver in pancreatic ductal adenocarcinoma (PDAC), the association between codon-specific alterations and patient outcomes remains poorly elucidated, largely due to a lack of datasets coupling genomic profiling with rich clinical annotations across disease stages.

Patients and Methods

We utilized AACR’s GENIE Biopharma Consortium Pancreas v1.2 dataset to test the associating of codon-specificKRASmutations with clinicogenomic features and patient outcomes in PDAC patients diagnosed with localized (stages I-III) and advanced disease (stage IV). Overall survival was compared using Kaplan–Meier and multivariable Cox proportional hazards methods.

Results

Among 1,032 eligible patients, 949 (92%) exhibited mutantKRAS. These mutations were predominantly observed at G12D (n=390, 41%), G12V (n=305, 32%), and G12R (n=149, 16%). In the group of patients who presented with localized disease, those with G12V mutation had notably longer survival compared to G12D mutation (P= 0.002). In contrast, patients with G12V mutation who presented with metastatic disease experienced shorter overall survival compared to those with G12R (P= 0.005), and G12D mutations (P= 0.009). Furthermore, no significant differences were observed in the frequencies of co-altered driver genes, includingTP53,CDKN2A, andSMAD4, across the differentKRASmutations.

Conclusions

These findings demonstrated that codon-specificKRASmutations impact PDAC outcomes differently based on disease stage at diagnosis. As studies testingKRASinhibitors continue to emerge and mature, these data offer important contextual insights regarding survival outcomes associated with codon-specificKRASmutations based on existing therapeutic approaches.
A Binary Prototype for Time-Series Surveillance and Intervention
Authors: Olejarz Jason , Hoffmann Till , Zapf Alex , Mugahid Douaa , Molinaro Ross , Brown Chadwick , Boltyenkov Artem , Dudykevych Taras , Gupta Ankit , Lipsitch Marc , Atun Rifat , Onnela Jukka-Pekka , Fortune Sarah , Sampath Rangarajan , Grad Yonatan H.
Published: February 2025

Despite much research on early detection of anomalies from surveillance data, a systematic framework for appropriately acting on these signals is lacking. We addressed this gap by formulating a hidden Markov-style model for time-series surveillance, where the system state, the observed data, and the decision rule are all binary. We incur a delayed cost,c, whenever the system is abnormal and no action is taken, or an immediate cost,k, with action, wherek<c. If action costs are too high, then surveillance is detrimental, and intervention should never occur. If action costs are sufficiently low, then surveillance is detrimental, and intervention should always occur. Only when action costs are intermediate and surveillance costs are sufficiently low is surveillance beneficial. Our equations provide a framework for assessing which approach may apply under a range of scenarios and, if surveillance is warranted, facilitate methodical classification of intervention strategies. Our model thus offers a conceptual basis for designing real-world public health surveillance systems.
Loss of an uncharacterized mitochondrial methionine tRNA-synthetase induces mitochondrial unfolded protein response inCaenorhabditis elegans
Authors: Thapa Bharat Vivan , Das Mohit , Held James P , Patel Maulik R
Published: February 2025

Aminoacyl-tRNA synthetases (aaRSs) are essential for translation, as they charge tRNA molecules with their corresponding amino acids. Alterations in aaRSs can significantly disrupt both cytosolic and mitochondrial translation. Through a forward genetic screen for mitochondrial unfolded protein response (UPRmt) activators inC. elegans, we identified a missense mutation (P447V) in the previously uncharacterized gene Y105E8A.20, which encodes a dually localized methionine tRNA synthetase (MetRS). Here, we characterize the UPRmtinduction by Y105E8A.20, which we callmars-2, and demonstrate that the P447V allele is a loss-of-function mutation. Furthermore, we show impairedmars-2activity in the mitochondria triggers UPRmt. This strain provides a valuable tool for studying mitochondrial translation and understanding how aaRSs are involved in mitochondrial homeostasis.
Clinical Evaluation of an AI System for Streamlined Variant Interpretation in Genetic Testing
Authors: Ruzicka Jiri , Ravel Jean-Marie , Audoux Jérôme , Boulat Alexandre , Thévenon Julien , Yauy Kévin , Dancer Marine , Raymond Laure , Lombardi Yannis , Philippe Nicolas , Blum Michael GB , Duforet-Frebourg Nicolas , Mesnard Laurent
Published: February 2025

Background

The growing use of whole exome/genome sequencing for diagnosing hereditary diseases has increased the interpretive workload for clinical laboratories. Efficient methods are needed to identify pathogenic variants and maximize diagnostic yield without overwhelming resources.

Methods

We developed DiagAI, an AI-powered system trained on 2.5 million ClinVar variants to predict ACMG pathogenicity classes. DiagAI ranks variants, proposes diagnostic shortlists, and identifies probands likely to receive molecular diagnoses. It integrates molecular features, inheritance patterns, and phenotypic data when available. We retrospectively analyzed 966 exomes from a nephrology cohort, including 196 with causal variants and 770 undiagnosed cases.

Results

DiagAI identified 94.9% of causal variants in diagnostic exomes with HPO terms, compared to 90.8% without, with median shortlist sizes of 12 and 9 variants, respectively. It achieved a sensitivity of 57.1% and a specificity of 92.6% in tagging exomes likely to contain a diagnostic variant. With HPO terms, 74% of top-ranked (top 1) variants were diagnostic, versus 42% without, and DiagAI outperformed Exomiser and AIMARRVEL in this setting.

Conclusion

DiagAI generates accurate shortlists of variants that streamline the variant interpretation process. It provides a scalable solution for managing growing diagnostic test volumes without compromising quality.
Cervicovaginal inflammation and HIV target cell activation in adolescent girls and young women with asymptomaticChlamydia trachomatisinfections
Authors: Dabee Smritee , Barnabas Shaun , Kullin Brian , Versteeg Bart , Mkhize Nonhlanhla , Muller Etienne , Maseko Venessa , Lewis David A. , Dietrich Janan , Gray Glenda , Gill Katherine , Bekker Linda-Gail , Sinkala Musalula , Martin Darren P. , Bruisten Sylvia M. , Jaspan Heather B. , Passmore Jo-Ann S.
Published: February 2025

Background

Adolescent girls and young women (AGYW) in sub-Saharan Africa are disproportionately affected byChlamydia trachomatis(CT) infections, a leading cause of pelvic inflammatory disease (PID), infertility, and increased HIV susceptibility. CT-induced genital inflammation disrupts mucosal barriers and activates HIV target cells, compounding reproductive and immunological risks. We investigated the impact of CT infection in AGYW from two South African regions, focusing on genital inflammation and immune activation.

Methods

An observational cohort of 298 sexually active AGYW (16–22 years) from Cape Town and Johannesburg was enrolled. Those in Johannesburg attended one visit while those in Cape Town were followed for three visits over 6-8 months. Cytokine profiling of cervicovaginal samples assessed inflammatory responses, while cervical cytobrush-derived CD4+ T cells were analyzed for CD38, Ki67 and CCR5 expression. CTompAgenotyping examined strain diversity.

Results

CT prevalence was 2.4 times higher in Cape Town (41.6%) than in Johannesburg (17.4%). Infection with CT led to an upregulation of inflammatory cytokines, including IL-1β, IL-6, and TNF-α, with a stronger inflammatory response observed in Johannesburg. Genotypic analysis revealed regional variations: genovar D, which was predominant in Cape Town, was associated with lower IFN-γ levels, whereas genovar E, prevalent in Johannesburg, was linked to higher IFN-γ levels. AGYW who experienced CT infection across multiple study visits did not exhibit elevated genital tract cytokine levels compared to those with a single infection. However, they did show an increase in activated and proliferating cervical CD4+ T cells, which may contribute to heightened HIV susceptibility.

Conclusions

CT genotypic diversity and regional variations significantly influence immune responses in AGYW. Region-specific vaccines and integrated sexual health services would support mitigating STI and HIV risks in this vulnerable population.
Klebsiella pneumoniaedisrupts vasodilation by targeting eNOS post translational modifications via the type VI secretion system and the capsule polysaccharide
Authors: Rehman Safi , sa Pessoa Joana , Buckley Charlotte , Lancaster Rebecca , Ross Ciara , Zhang Xun , McCarron John G. , Curtis Tim M. , Bengoechea Jose A.
Published: February 2025

Vasodilation is a crucial protective response to inflammation and infection. Endothelial cells control vasodilation through the bioavailability of eNOS-produced nitric oxide (NO), and the generation of endothelium-dependent hyperpolarization (EDH). Here, we demonstrate thatKlebsiella pneumoniae, one of the most prevalent blood stream infection pathogens, inhibits agonist-induced vasodilation by blunting the NO-dependent pathway and attenuating the EDH pathway. The type VI secretion system (T6SS) effector VgrG4 licences the kinase PKCβ in an NLRX1-controlled mitochondria reactive oxygen species (mtROS)-dependent manner to phosphorylate the eNOS inhibitory site Thr495, effectively dampening eNOS activity. The capsule polysaccharide, on the other hand, limits the phosphorylation of the eNOS activation site Ser1177by inducing the phosphatase PP2Ac upon activation of an EGF receptor-dependent pathway. VgrG4-induced mtROS attenuates the EDH pathway. Overall, this work reveals a new anti-host activity of the T6SS and illustrates how pathogens can control vascular biology by targeting eNOS post translational modifications.
Neural mechanisms of flexible perceptual inference
Authors: Schwarcz John , Bauer Jan , Rajabi Haneen , Marmur Gabrielle , Lottem Eran , Kadmon Jonathan
Published: February 2025

What seems obvious in one context can take on an entirely different meaning if that context shifts. While context-dependent inference has been widely studied, a fundamental question remains: how does the brain simultaneously infer both the meaning of sensory input and the underlying context itself, especially when the context is changing? Here, we study flexible perceptual inference--the ability to adapt rapidly to implicit contextual shifts without trial and error. We introduce a novel change-detection task in dynamic environments that requires tracking latent state and context. We find that mice exhibit first-trial behavioral adaptation to latent context shifts driven by inference rather than reward feedback. By deriving the Bayes-optimal policy under a partially observable Markov decision process, we show that rapid adaptation emerges from sequential updates of an internal belief state. In addition, we show that artificial neural networks trained via reinforcement learning achieve near-optimal performance, implementing Bayesian inference-like mechanisms within their recurrent dynamics. These networks develop flexible internal representations that enable real-time adjustments to the inference model. Our findings establish flexible perceptual inference as a core principle of cognitive flexibility, offering computational and neural-mechanistic insights into adaptive behavior in uncertain environments.
Combined effects of mechanical loading and Piezo1 chemical activation on 22-months-old female mouse bone adaptation
Authors: Meslier Quentin A. , Oehrlein Robert , Shefelbine Sandra J.
Published: February 2025

With age, bones mechanosensitivity is reduced, which limits their ability to adapt to loading. The exact mechanism leading to this loss of mechanosensitvity is still unclear, making developing effective treatment challenging. Current treatments mostly focus on preventing bone mass loss (such as bisphosphonates) or promoting bone formation (such as Sclerostin inhibitors) to limit the decline of bones mass. However, treatments do not target the cause of bone mass loss which may be, in part, due to the bone’s inability to initiate a normal bone mechanapdatation response. In this work, we investigated the effects of 2 weeks of tibia loading, and Piezo1 agonist injectionin vivoon 22-month-old mouse bone adaptation response. We used an optimized loading profile, which induced high fluid flow velocity and low strain magnitude in adult mouse tibia. We found that tibia loading and Yoda2 injection have an additive effect on increasing cortical bone parameters in 22-month-old mice. This combination of mechanical and chemical stimulation could be a promising treatment strategy to help promote bone formation in patients who have low bone mass due to aging.
Diffusion in liquid metals is directed by competing collective modes
Authors: Demmel Franz , Jakse Noel
Published: February 2025

The self-diffusion process in a dense liquid is influenced by collective particle movements. Extensive molecular dynamics simulations for liquid aluminium and rubidium evidence a crossover in the diffusion coefficient at about 1.4 times the melting temperature Tm, indicating a profound change in the diffusion mechanism. The corresponding velocity autocorrelation functions demonstrate a decrease of the cage effect with a gradual set in of a power-law decay, they celebrate long time tail. This behavior is caused by a competition of density fluctuations near the melting point with vortex-type particle patterns from transverse currents in the hot fluid. The investigation of the velocity autocorrelation function evidences a gradual transition in dynamics with rising temperature. The competition between these two collective particle movements, one hindering and one enhancing the diffusion process, leads to a non-Arrhenius-type behavior of the diffusion coefficient around 1.4Tm, which signals the transition from a dense to a fluidlike liquid dynamics in the potential energy landscape picture.

Published by the American Physical Society
2025
Adaptive stratified mixture importance sampling for efficiently estimating extremely small failure probability with high-dimensional inputs and multiple failure domains
Authors: Yan Yuhua , Lu Zhenzhou
Published: February 2025

Purpose

This study aims to efficiently estimate the extremely small failure probability with high-dimensional inputs and multiple failure domains.

Design/methodology/approach

This paper proposed an adaptive stratified mixture importance sampling method. The proposed method first constructs an explicit and regular mixture importance sampling probability density function (M-IS-PDF) by taking the clustering centroids as the density centers. Then by the constructed M-IS-PDF, the proposed method explores the rare multiple failure domains by adaptively stratifying, thereby addressing the issue of estimating extremely small failure probability robustly and efficiently.

Findings

Compared with the existing cross-entropy based IS method, the constructed M-IS-PDF not only covers the domains significantly contributing to the failure probability through clustering centroids to reduce the variance of failure probability estimation, but also has no undetermined parameter set to optimize, enhancing the adaptability in high-dimensional problems. Compared with the subset simulation method, the adaptive stratified M-IS-PDF constructed is explicit, regular and easy sampling. It not only has high sampling efficiency but also avoids estimating conditional failure probabilities layer by layer, improving the algorithmic robustness for estimating extremely small failure probability.

Originality/value

Both numerical and engineering examples indicate that, under the similar failure probability estimation accuracy, the proposed method requires significantly smaller sample size and lower computational cost than subset simulation and cross-entropy based IS methods, demonstrating higher efficiency and robustness in addressing intractable reliability analysis problems with high-dimensional inputs, multiple failure domains and rare failure.
Stable isotope analysis reveals individual variations in feeding habits among wild Japanese macaques
Authors: Funakawa Kazuho , Suzumura Takafumi , Koba Keisuke
Published: February 2025

We employed stable isotope ratio analysis to quantitatively assess the feeding behaviors of individual macaques within a wild group of Japanese macaques (Macaca fuscata). The primary objective was to evaluate macaque's feeding habits at the individual scale and to clarify the relationship between feeding habits and social factors, including age, sex, and social rank. The study population consisted of the Main group of Japanese macaques on Koshima Island. We collected 78 body hair samples and 29 food resource samples for isotopic analysis. The variability in carbon, nitrogen, and sulfur isotope ratios among individuals in the Main group has ranges of 5.5‰, 6.5‰, and 6.8‰, respectively. Furthermore, the Bayesian mixture model revealed that there were individual differences in the utilization of forest‐derived (62.3%–90.5%), marine‐derived (6.1%–27.6%), and human‐derived (1.7%–23.4%) food resources, driven by the effect of sex, rank, and year. These findings particularly emphasize the utility of sulfur stable isotope ratios and demonstrate how the combined use of three stable isotope ratios enables effective analysis of the relationships between Japanese macaques and their food resources. Furthermore, our results provide a valuable opportunity for the advancement of future research that integrates stable isotope approaches with field investigations. This study not only highlights the applicability of sulfur isotope ratios as a tool for uncovering the use of marine resources by primates in other regions but also shows the potential of using isotopic techniques to distinguish human‐derived resources, such as wheat, and to develop strategies for managing crop‐raiding by macaques.
Nectar traits and their responses to herbivory in Solidago altissima as a dominant introduced flowering herb in Japan
Authors: Ikemoto Mito , Hashimoto Koya , Katayama Noboru
Published: February 2025

This study investigates the nectar characteristics of the tall goldenrod (Solidago altissima L.), an introduced dominant fall‐flowering herb in Japan. We found that the nectar volume of S. altissima peaked at approximately 13:00 before decreasing. Glucose and fructose were identified as the primary sugar components, followed by sucrose. The average sugar amount per panicle of naturally growing plants was estimated as 229.0 mg. Herbivory by the exotic lacebug (Corythucha marmorata) reduced the nectar volume per floret but did not affect the total sugar amount per floret. However, the sugar amount per panicle decreased substantially because C. marmorata reduced both the number of disc florets (i.e., nectar‐secreting florets) per head and the number of heads per panicle. Plant genotypes also influenced some nectar traits, interacting with the effects of herbivory. As the distribution of C. marmorata continues to expand across Japan, the nectar resources provided by S. altissima may be diminishing nationwide.
The views and course practices of science teachers on the psychological resilience of students with learning disabilities
Authors: Özen Altınkaynak Şenay , Erginsoy Osmanoğlu Devrim , Inaltekin Tufan , Kirman Bilgin Arzu , Erdağı Selma
Published: February 2025

It is crucial for students with learning disabilities (SLDs) to possess psychological resilience in order to pursue their careers as entrepreneurial individuals. One of the areas where entrepreneurship skills are taught in middle school is in science courses. This shows the importance of teaching psychological resilience in science courses. On the basis of this idea, the present study aims to determine the views and suggestions of science teachers on the psychological resilience of SLDs as well as the course processes they carry out in order to foster this trait. Individual and focus group interviews were conducted with 15 science teachers and observations were recorded with two science teachers. Interview and observation forms were developed, taking into account the indicators of the four dimensions of resilience: coping with stress, communication, assertiveness and problem‐solving skills. The study revealed that science teachers did not implement teaching processes to develop the psychological resilience of SLDs and that they considered themselves professionally inadequate in this regard. The science teachers suggested that activities based on learning by practice and experience, collaboration with different businesses and project‐based teaching could be effective in improving the psychological resilience of SLDs.
PRODUCING THE GHATS OF BANARAS AS WORLD‐CLASS SPACES: The Mobilization of Nishad Boatmen
Authors: Shahi Ishan
Published: February 2025

The mobilization of boatmen of the Nishad community on the riverfront of Varanasi, also known as Banaras, against the introduction of a cruise service between September 2018 and the initial months of 2019 reveals the confluence of forces such as Hindu nationalism and the neoliberal pursuit of a world‐class aesthetic, which articulate themselves in the urban developments in Banaras. These include the smart cities mission at the level of the city, which has a cruise service among its constituent world‐class practices, and the protest at the ghat (the riverfront steps that lead to the Ganga river) by the Nishads—the community of fishermen and boatmen in Varanasi, India—at a community level. Meanwhile, at the national and global level, the Hindu nationalist Bhartiya Janata Party (BJP) government has been trying to transform and showcase the city of Banaras as a world‐class city with a Hindu nationalist flavour since 2014. The article shows how different dimensions of Henri Lefebvre's dialectic of the production of space undergo changes through state interventions that are seemingly limited to one dimension, that of conceived space or representation of space.
Better Transcriptomic Stability and Broader Transcriptomic Thermal Response Range Drive the Greater Thermal Tolerance in a Global Invasive Turtle Relative to Native Turtle
Authors: Zhang Changyi , Jiang Shufen , Storey Kenneth B. , Zhang Wenyi
Published: February 2025

Greater thermal tolerance of invasive species benefits their survival and spread under extreme climate events, especially under global warming. Revealing the mechanisms underlying the interspecific differences in thermal tolerance between invasive and native species can help understand the invasion process and predict potential invaders. Here, we link the changes in global transcriptomics and antioxidant defense at multiple temperatures with the differences in thermal limits in the juveniles of a successful globally invasive turtle, Trachemys scripta elegans, and a native turtle in China, Mauremys reevesii. The two species show different thermal tolerances and have co‐existed in habitats with the risk of overheating. The majority of the transcriptional response to thermal stress is conserved in the two turtle species, including protein folding or DNA damage responses activated under relatively moderate thermal stress and regulation of the cell cycle and apoptosis during severe thermal stress. Greater thermal tolerance of T. scripta elegans can be associated with a more stable global transcriptome during thermal stress, except for necessary stress responses, and a broader thermal range of continuous up‐regulation of the core mechanisms promoting survival under thermal stress, mainly protein folding and negative regulation of apoptosis. Under extreme hot conditions, the opposite change trends of genes involved in survival mechanisms during thermal stress between invasive and native turtles can be due to differences in energy turnover. The present study provides insights into the mechanisms of physiological differences between invasive and native species given global transcriptional changes and helps understand successful invasion and predict potential invasive species.
Transparency and Policymaking with Endogenous Information Provision
Authors: Li Hanzhe
Published: February 2025

How does the politician's reputation concern affect information provision when the information is endogenously provided by a biased lobbyist? I develop a model to study this problem and show that the answer depends on the transparency design. When the lobbyist's preference is publicly known, the politician's reputation concern induces the lobbyist to provide more information. When the lobbyist's preference is unknown, the politician's reputation concern may induce the lobbyist to provide less information. One implication of the result is that given transparent preferences, the transparency of decision consequences can impede information provision by moderating the politician's reputational incentive.
Experiences of accessing injury prevention, treatment and rehabilitation services for older Māori
Authors: Hikaka Joanna , Ihimaera Louise , Vercoe Hariata , Parsons John
Published: February 2025

Objective

Unintentional injuries cause significant morbidity and mortality for older adults. Māori, the Indigenous people of Aotearoa New Zealand (NZ), experience inequitable access to injury treatment and care services; however, the extent to which this impacts older Māori is unknown. Our objective was to explore older Māori, family and stakeholders' perceptions and experiences of injury‐related care and access for older Māori.

Methods

Convenience sampling was used to recruit three participant groups: older Māori (aged ≥55, and living in two regional areas of NZ); family/support network members (whānau) of older Māori; stakeholders (roles in injury prevention/care, health professionals, injury policy, health navigators or Indigenous health service development). Data were collected through demographic questionnaires and in‐person interviews or focus groups. A general inductive approach to thematic analysis was utilised, guided by Māori research theory to situate the findings in the relevant social, political and cultural context for Māori.

Results

Forty‐four people participated between September and November 2021 (n = 23 older Māori; n = 21 stakeholders). The findings generated four themes. First, quality of care impacts holistic well‐being. Second, informed advocates and advocacy to access and connect injury‐related care. Third, culturally safe and Māori‐led care. Fourth, the role of family and self in injury‐related care.

Conclusions

Unintentional injury‐related care in older Māori is difficult to access and navigate, often not meeting the multidimensional well‐being needs of older Māori. Solutions that support advocacy and navigation through the health system are required to respond to mental health and social, as well as physical needs.
Smoking Cessation Practices in Australian Oncology Settings: A Cross‐Sectional Study of Who, How, and When
Authors: Young Alison Luk , McEnallay Melissa , Day Fiona , Vinod Shalini K. , Stone Emily , Morris Sarah , Stefanovska Elena , Devitt Bianca , Yip Po Yee , Kukard Craig , Pal Abhijit , Thawal Vaibhav , Wright Gavin , Hofman Alison , Sareen Heena , McLennan James , Wong Shuet Oi , Rubio Cassandra , Liu Jennifer , Smith Alexandra , Betts Dimity , Mack Jane , Donnelly Jennifer , Paul Christine
Published: February 2025

Purpose

Patients who smoke tobacco during and after a cancer diagnosis have poorer health outcomes. Oncology healthcare providers (HCPs) are crucial to providing smoking cessation support. The study examined the characteristics associated with differences in HCPs’ smoking cessation practices.

Methods

As part of the Care to Quit trial, a cross‐sectional survey exploring smoking cessation practices was completed by HCPs across nine cancer centers in New South Wales and Victoria, Australia.

Results

One hundred and seventy‐seven HCPs completed the survey. Over half of the HCP respondents reported asking patients their smoking status, but fewer than half advised patients about the benefits of quitting, referred patients to behavioral support such as Quitline, or offered pharmacotherapy medication. All components of the “3A's” model (Ask, Advise, Act) were more likely to be completed by doctors compared to registered nurses (OR: 7.86, 95% CI: 3.64, 16.95, p<0.001), by those with more years of practice (OR: 0.26, 95% CI: 0.07−0.93, p = 0.039), and those who had received smoking cessation training (OR: 3.91, 95% CI: 1.80, 8.48, p = 0.001). Multivariate analyses also identified differences in the amount of cancer‐specific advice provided between occupation type (p<0.001) and years of practice (p = 0.021).

Conclusion

The need for smoking cessation care training in oncology continues to be apparent. Training in prescribing pharmacotherapies (for doctors) or supporting the use of pharmacotherapies (for nurses) is a particular “gap.” Differences between the roles and engagement of doctors and nurses in relation to smoking cessation care should be carefully considered when developing site‐specific models of cessation care and providing training.
Association of First‐Trimester Combined Inflammatory Markers (NLR, SII, SIRI, and AISI) With Poor Obstetric Outcomes in Pregnancies With Ulcerative Colitis
Authors: Ozkavak Osman Onur , Tanacan Atakan , Serbetci Hakki , Karatas Esra , Haksever Murat , Basaran Ezgi , Atar Melike Busra , Sahin Dilek
Published: February 2025

Aim

To compare the first‐trimester combined inflammatory markers between pregnant women diagnosed with ulcerative colitis (UC) and healthy pregnant women. Furthermore, to investigate the predictive value of these markers for adverse obstetric outcomes in pregnant women affected by UC.

Methods

In this retrospective study, data were collected from pregnant women with UC who gave birth at our hospital between January 2021 and May 2024 and from a control group of healthy pregnant women. A comparison was made between the two groups in terms of their demographic characteristics, neonatal outcomes, and the values of the first‐trimester neutrophil‐to‐lymphocyte ratio (NLR), systemic inflammation index (SII), systemic inflammatory response index (SIRI), and aggregated index of systemic inflammation (AISI). Furthermore, the relationship between these combined inflammatory markers and adverse obstetric outcomes in pregnant women with UC was investigated.

Results

No notable discrepancy was observed between the UC group and the control group with respect to SIRI and AISI. The first‐trimester NLR and SII values were observed to be higher in the UC group in comparison to the control group. The data indicated that pregnant women with UC who experienced poor obstetric outcomes exhibited elevated levels of NLR, SII, SIRI, and AISI during the first trimester. In the ROC analysis, the predictive capacity of all four parameters for poor obstetric outcomes in UC patients was statistically significant.

Conclusion

There is an association between elevated combined inflammatory markers in the first trimester and poor obstetric outcomes in pregnant women with UC.