bluuebunny/crossref_metadata_2025 huggingface dataset:
A Breath of Fresh Air: Pilot Testing Electronic Case Reporting for Public Health Surveillance of Occupational Lung Diseases in Wisconsin
Authors: Creswell Paul D. , Mader Sara , Modji Komi K.S. , McCoy Katherine E.
Published: February 2025

Context:

Public health surveillance plays a crucial role in evaluating disease risk and providing timely evidence to policymakers and the public. However, surveillance of many occupational diseases is limited by existing surveillance infrastructure, which is heavily dependent on laboratory tests.

Objective:

The present pilot study compared case data for 3 occupational lung diseases (ie, silicosis, asbestosis, and farmer’s lung disease) from electronic case reports (eCR) with existing hospital discharge data in the state of Wisconsin to see if eCR—which sends health records directly from clinics when specific criteria are met—provided previously undetected cases of these reportable diseases.

Design:

Case data for 3 reportable occupational lung diseases were pulled from eCR records within the Wisconsin Electronic Disease Surveillance System. In this retrospective cross-sectional study, a unique identifier was used to match eCR cases to hospital discharge data.

Setting and Participants:

This study was conducted using administrative data at a state health department to compare data systems and assess the utility of eCR for occupational health surveillance.

Main Outcome Measures:

The number and percentage of matched and unmatched cases were calculated to assess the overlap of the 2 data systems. For eCR cases, the median number of years since diagnosis was also assessed.

Results:

The percentage of eCR cases that could not be matched to hospital discharge data ranged from 55% to 81.2%, depending on the disease of interest. The median length of time since diagnoses for eCR cases was multiple years, suggesting that most had long been missing from existing surveillance.

Conclusions:

This study suggests that eCR creates new potential in occupational health surveillance. eCR was found to provide previously undetected cases of occupational lung disease at a state health department and stands to improve the timeliness of case reporting as well.
Understanding Vascular Complications Arising From Dermal Filler Injection
Authors: Yi Kyu-Ho
Published: February 2025

Soft tissue fillers are widely used in cosmetic procedures but carry inherent risks, especially vascular complications like tissue necrosis and vision loss due to retinal ischemia. Recent filler advancements beyond hyaluronic acid increase the risk of intravascular invasion during injections. Tissue necrosis follows distinct stages: initial blanching, skin mottling from tissue ischemia, discoloration, and possible necrosis. Direct injection into arteries or high-pressure techniques can cause embolisms, a significant cause of tissue necrosis. Vision loss occurs when critical arteries get blocked, leading to retinal or optic nerve ischemia. Studies show that even tiny filler amounts injected into specific arteries can result in blindness, challenging the idea of using smaller volumes in high-risk zones. While using cannulas for injections offers some advantages, it comes with risks. Hence, practitioners need to adopt meticulous injection techniques. An in-depth understanding of filler phases and potential vascular complications is crucial for ensuring practitioner safety and patient well-being during cosmetic procedures. This knowledge forms the basis for minimizing risks associated with filler injections.
Catatonia in a Patient With Lissencephaly Treated With ECT
Authors: Mahgoub Yassir , Khalid Moyyed , Sosal Wafa , Pathare Aum
Published: February 2025

Catatonia is a neuropsychiatric syndrome that occurs with several psychiatric and systemic medical conditions. Central nervous system abnormalities are believed to increase the risk of catatonia, with several cases reported in patients with neurodevelopmental and neurodegenerative disorders. Lissencephaly is a spectrum of neuronal migration disorders characterized by poorly defined or absent gyri and sulci, abnormally thick cortex, and a broad array of histopathological changes. Lissencephaly has a range of etiologies, clinical signs, symptoms, and degrees of severity. It is associated with comorbidities, such as epilepsy, visual, cardiac, and skeletal problems, as well as premature mortality.

In this article, we describe the case of a patient with lissencephaly who developed catatonia at 20 years of age. He was minimally responsive to treatment with a high dose of lorazepam, and catatonia subsided with the use of electroconvulsive therapy. This is the first case in our knowledge to describe the occurrence of catatonia among patients with lissencephaly and its treatment with electroconvulsive therapy.
Trait-environment interactions influence tree planting success in Peruvian tropical dry forests
Authors: Goossens W. , Fremout T. , Muys B. , Soto Quispe J.C. , Van Meerbeek K. , Maes S.L.
Published: February 2025

Tropical dry forests are among the most endangered ecosystems globally, despite their critical socio-ecological importance. In recent decades, various tree-planting initiatives have been undertaken to restore these forests, yielding mixed results. To enhance restoration effectiveness, it is imperative to adopt a predictive approach, focussing on the drivers of seedling performance and their interactions. This study explores how tree species traits and environmental conditions interact to influence survival and growth rates in the Tumbes-Piura tropical dry forests of northwestern Peru. Our findings support the widely acceptedgrowth-mortalityhypothesis, indicating that acquisitive species characterised by a high specific leaf area and low wood density achieve faster growth but experience higher mortality compared to conservative species. According to the general resource-use theory, these acquisitive species are also more sensitive to variations in water and nutrient availability, showing steep declines in growth and survival rates as site conditions become less favourable. Interestingly, we found that thegrowth-mortalityhypothesis holds along environmental gradients, with acquisitive species maintaining their high growth rates even under resource-poor conditions, but at the cost of greater vulnerability to mortality. In contrast, the growth rates of conservative species increase markedly when water and nutrients become less limiting. These insights underscore the importance of considering trait-environment interactions in planning tree-planting projects and adapting the management strategy to overall restoration objectives. By doing so, we can improve the outcomes and sustainability of restoration efforts in tropical dry forests.

Implications for practice

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Thegrowth-mortalityhypothesis holds along resource gradients in tropical dry forest restoration.

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Acquisitive species can exhibit high growth rates even in resource-poor sites, which comes at the cost of higher mortality. Increasing successful establishment through irrigation and fertilization will likely accelerate forest recovery in these restoration sites.

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Planting conservative species in less favourable sites is a more viable option when economic resources are limited, offering a more certain, albeit slower, forest establishment without the need for intensive management.

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Our findings highlight the importance of accounting for trait-environment interactions when evaluating restoration success in future studies.
A synthetic chlorophagy receptor promotes plant fitness by mediating chloroplast microautophagy
Authors: Liu Rui , Weng Xun , Li Xinjing , Cao Yongheng , Li Qiyun , Luan Lin , Tong Danqing , Kong Zhaosheng , Wang Hao , Wang Taotao , Gong Qingqiu
Published: February 2025

Chloroplasts are major photosynthetic and protein-containing organelles in green plants and algae. Unwanted chloroplast proteins and entire chloroplasts are cleared through various degradation pathways including autophagy. Nevertheless, canonical chlorophagy receptors remain unidentified, and whether and to what extent chlorophagy can be enhanced to benefect the plants remain unknown. Here we designed and validated a synthetic chloroplast autophagy receptor using biochemical, genetical, and imaging approaches. This synthetic receptor, LIR-SNT-BFP, was constructed by fusing a fragment containing the LC3-interacting region (LIR) of the selective autophagy receptor NBR1 and the N-terminal amphipathic α-helix of the chloroplast outer envelope protein SFR2. The fusion protein LIR-SNT-BFP coated the chloroplast and attracted ATG8ain planta. Upon induction, the synthetic receptor elicited vacuole-mediated microautophagy of entire chloroplasts independent of the ATG8 conjugation machinery proteins ATG5 or ATG7. Meanwhile, it induced chloroplast division; however the induced chlorophagy was independent of PDV2. Notably, moderate chlorophagy improves rosette growth, but excessive levels are detrimental. Furthermore, induced chlorophagy partially protects against herbicide-induced leaf chlorosis. This study demonstrates controlled chloroplast degradation using a synthetic chlorophagy receptor.
CDK9 degradation Inhibits Gastroesophageal Cancer growth and Overcomes Radiation Resistance by Increasing Chromatin Accessibility and Downregulating YAP1/TEAD signaling
Authors: Zhang Yan-ting , Ghelfi Mikel , Xue Yu , Chen Haiying , Calendo Gennaro , Grana Generosa , Li Yuan , Athavale Dipti , Balch Curt , Yao Xiaodan , Chung Woonbok , Wang Zhenning , Spitz Francis , Tang Tracy , Khazak Vladimir , Zhou Jia , Issa Jean-Pierre , Song Shumei
Published: February 2025

Background: Gastroesophageal cancer (GEAC) remains a major health burden and urgently needs novel therapeutic targets. The inhibition of CDK9 activity holds the potential to be a highly effective anti-cancer therapeutic. However, the functional role of CDK9, and its potential targeting in GEAC, remain largely unknown. Objective: We aim to evaluate the potential of degradation CDK9 in GEAC treatment and explore its mechanisms. Design: We evaluated the expression and distribution of CDK9 in GEAC tissue. We designed and synthesized novel CDK9 degraders using proteolysis targeting chimeras (PROTACs) strategy and selected the promising one for further anti-tumor activity evaluation both in vitro and in vivo. We evaluated the effects of CDK9 degradation on epigenetic reactivation, gene expression and chromatin accessibility. We evaluated the co-targeting of CDK9 and YAP/Tead signaling for GEAC treatment, especially for radiation-resistant tumor treatment. Results: We demonstrated significantly elevated CDK9 expression in primary GEAC tumor tissues compared to normal tissues, in association with poor survival. We developed a novel CDK9 degrader, YX0597, reducing RNA Pol II Serine 2 phosphorylation, and inhibition MCL-1; this was accompanied by potent inhibition of GEAC cell growth, especially in radiation-resistant tumor cells. Mechanistically, YX0597 strongly enhanced chromatin accessibility, activating epigenetically silenced genes; and dramatically inhibited YAP/TEAD signaling. CDK9 closely interacts with YAP/TEAD signaling, and co-targeting these two mediators could be a novel treatment strategy for the treatment of GEAC. Conclusion: Our studies reveal a new avenue for targeting CDK9-hyperactivated GEAC tumors, especially in combination with YAP1/TEAD inhibition in radiation-resistant GEAC tumors.
Luminos: open-source software for bidirectional microscopy
Authors: Itkis Daniel G. , Brooks Frederick Phillips , Davis Hunter C. , Hotter Raffi , Wong-Campos J. David , Qi Yitong , Jia Bill Z , Howell Madeleine , Xiong Marley , Hayward Rebecca Frank , Lee Byung Hun , Wang Yangdong , Perelman Rebecca T. , Cohen Adam Ezra
Published: February 2025

Bidirectional microscopy (BDM) combines simultaneous targeted optical perturbation and imaging of biophysical or biochemical signals (e.g. membrane voltage, Ca2+, or signaling molecules). A core challenge in BDM is precise spatial and temporal alignment of stimulation, imaging, and other experimental parameters. Here we present Luminos, an open-source MATLAB library for modular and precisely synchronized control of BDM experiments. The system supports hardware-triggered synchronization across stimulation, recording, and imaging channels with microsecond accuracy. Source code and documentation for Luminos are available online at https://www.luminosmicroscopy.com and https://github.com/adamcohenlab/luminos-microscopy. This library will facilitate development of bidirectional microscopy methods across the biological sciences.
When Less is MORE: Counterintuitive Stoichiometries and Cellular Abundances are Essential for ABC transporters function
Authors: Abdullah Hiba Qasem , Levanon Nurit Livnat , Perach Michal , Gruper Moti , Ziv Tamar , Lewinson Oded
Published: February 2025

Prokaryotes acquire essential nutrients primarily through ABC importers, consisting of an ATPase, a permease, and a substrate-binding protein. These importers are highly underrepresented in proteomic databases, limiting our knowledge about their cellular copy numbers, component stoichiometry, and the mechanistic implications of these parameters. We developed a tailored proteomic approach to compile the most comprehensive dataset to date of the E. coli 'ABC importome'. Functional assays and analysis of deletion strains revealed mechanistic features linking molecular mechanisms to cellular abundances, co-localization, and component stoichiometries. We observed 4-5 orders of magnitude variation in import system abundances, with copy numbers tuned to nutrient hierarchies essential for growth. Abundances of substrate-binding proteins are unrelated to their substrate binding affinities but are tightly, yet inversely, correlated with their interaction affinity with permeases. Counterintuitive component stoichiometries are crucial for function, offering insights into the design principles of multi-component protein systems, potentially extending beyond ABC importers.
High-Parameter Spatial Multi-Omics through Histology-Anchored Integration
Authors: Liu Yonghao , Wang Chuyao , Wang Zhikang , Chen Liang , Li Zhi , Song Jiangning , Zou Qi , Gao Rui , Qian Binzhi , Feng Xiaoyue , Guan Renchu , Yuan Zhiyuan
Published: February 2025

Recent advances in spatial omics technologies enable in situ molecular profiling while preserving spatial context but face fundamental challenges in achieving high-parameter and multi-omics co-profiling. Spatially resolving complementary panels or distinct omics layers across serial tissue sections circumvents technical trade-offs but introduces the spatial diagonal integration problem: reconstructing unified multi-omics states when datasets lack shared molecular features. To address this critical challenge, we present SpatialEx and its extension SpatialEx+, computational frameworks that leverage histology as a universal anchor to integrate spatial molecular data across tissue sections. The foundational SpatialEx model combines a pre-trained H&E foundation model with hypergraph learning and contrastive learning to predict single-cell omics profiles from histology, encoding multi-neighborhood spatial dependencies and global tissue context. Building upon SpatialEx, SpatialEx+ introduces an omics cycle module that encourages cross-omics consistency across adjacent sections via slice-invariant mapping functions, achieving seamless diagonal integration without requiring co-measured multi-omics data for training. Through rigorous validation across three key applications, we demonstrate: (1) H&E-to-omics prediction at single-cell resolution, characterizing tumor microenvironments beyond sequencing borders in breast cancer; (2) panel diagonal integration, merging non-overlapping spatial gene panels from different slices to resolve immune-stromal boundaries lost by individual panels; and (3) omics diagonal integration, revealing Parkinson's disease anatomical domains and context-specific tissue pathologies through integrated transcriptomic-metabolic analysis. The framework scales to datasets exceeding one million cells, maintains robustness with non-overlapping or heterogeneous sections, and supports unlimited omics layers in principle. By transforming highly feasible spatial single-omics assays with histology into a holistic spatial multi-omics map, our work democratizes systems-level tissue analysis, bridging fundamental spatial biology and scalable multi-omics research with minimal experimental overhead.
Expanding single-cell toolbox with a cost-effective full-length total RNA droplet-based sequencing technology
Authors: Sun Xue , Dadon Shir-Liya , Ennis Dena , Fan Wenpeng , Awawdy Muhammad , Reuveni Eli , Alajem Adi , Ram Oren
Published: February 2025

sc-rDSeq is a scalable, full-length total RNA droplet-based technology that captures both polyadenylated and non-polyadenylated RNAs, including histone-RNAs, small and long non-coding RNAs, and enhancer RNAs. It achieves a tenfold increase in UMIs per cell over inDrops while remaining simple and cost-efficient. Applied to lung cancer cells, sc-rDSeq revealed hidden heterogeneity, divergent signaling pathways, and non-polyA RNA variations undetectable with 3' end-based methods. In EGFR inhibitor-treated persister cells, it confirmed drug-induced cell cycle arrest based on histone mRNA expression, identified distinct resistance strategies. It also detected alternative splicing events and enabled single cell genotyping of SNVs linked to drug resistance. While SNVs act as drivers of drug resistance, additional layers of expression-based cellular states must be explored to fully understand and combat persister cells. These findings highlight the potential of sc-rDSeq to advance transcriptomic studies and personalized medicine by providing a comprehensive and scalable approach to cellular RNA analysis.
Nitric Oxide Inhibition of Glycyl Radical Enzymes and Their Activases
Authors: Cáceres Juan Carlos , Michellys Nathan G , Greene Brandon L
Published: February 2025

Innate immune response cells produce high concentrations of the free radical nitric oxide (NO) in response to pathogen infec-tion. The antimicrobial properties of NO include non-specific damage to essential biomolecules and specific inactivation of en-zymes central to aerobic metabolism. However, the molecular targets of NO in anaerobic metabolism are less understood. Here, we demonstrate that the Escherichia coli glycyl radical enzyme pyruvate formate lyase (PFL), which catalyzes the anaerobic metabolism of pyruvate, is irreversibly inhibited by NO. Using electron paramagnetic resonance and site-directed mutagenesis we show that NO destroys the glycyl radical of PFL. The activation of PFL by its cognate radical S-adenosyl-L-methionine-dependent activating enzyme (PFL-AE) is also inhibited by NO, resulting in the conversion of the essential iron-sulfur cluster to dinitrosyl iron complexes. Whole-cell EPR and metabolic flux analyses of anaerobically growing Escherichia coli show that PFL and PFL-AE are inhibited by physiologically relevant levels of NO in bacterial cell cultures, resulting in diminished growth and a metabolic shift to lactate fermentation. The class III ribonucleotide reductase (RNR) glycyl radical enzyme and its corre-sponding RNR-AE are also inhibited by NO in a mechanism analogous to those observed in PFL and PFL-AE, which likely contributes to the bacteriostatic effect of NO. Based on the similarities in reactivity of the PFL/RNR and PFL-AE/RNR-AE enzymes with NO, the mechanism of inactivation by NO appears to be general to the respective enzyme classes. The results implicate an immunological role of NO in inhibiting glycyl radical enzyme chemistry in the gut.
Likelihoods for a general class of ARGs under the SMC
Authors: Bisschop Gertjan , Ralph Peter L. , Kelleher Jerome
Published: February 2025

Ancestral recombination graphs (ARGs) are the focus of much ongoing research interest. Recent progress in inference has made ARG-based approaches feasible across of range of applications, and many new methods using inferred ARGs as input have appeared. This progress on the long-standing problem of ARG inference has proceeded in two distinct directions. First, the Bayesian inference of ARGs under the Sequentially Markov Coalescent (SMC), is now practical for tens-to-hundreds of samples. Second, approximate models and heuristics can now scale to sample sizes two to three orders of magnitude larger. Although these heuristic methods are reasonably accurate under many metrics, one significant drawback is that the ARGs they estimate do not have the topological properties required to compute a likelihood under models such as the SMC under present-day formulations. In particular, heuristic inference methods typically do not estimate precise details about recombination events, which are currently required to compute a likelihood. In this paper we present a backwards-time formulation of the SMC and derive a straightforward definition of the likelihood of a general class of ARG under this model. We show that this formulation does not require precise details of recombination events to be estimated, and is robust to the presence of polytomies. We discuss the possibilities for inference that this opens.
Accurate identification of medulloblastoma subtypes from diverse data sources with severe batch effects by RaMBat
Authors: Sun Mengtao , Wang Jieqiong , Wan Shibiao
Published: February 2025

As the most common malignant pediatric brain cancer, medulloblastoma (MB) accounts for around 20% of all pediatric central nervous system (CNS) neoplasms. MB includes a complex array of distinct molecular subtypes, mainly including SHH, WNT, Group 3 and Group 4. Accurate identification of MB subtypes enables improved downstream risk stratification and tailored therapeutic treatment design. Existing methods demonstrated the feasibility of leveraging transcriptomics data for identifying MB subtypes. However, their performance may be poor due to limited cohorts and severe batch effects when integrating various MB data sources. To overcome these limitations, we propose a novel and accurate approach called RaMBat for accurate MB subtype identification from diverse transcriptomics data sources with severe batch effects. Specifically, RaMBat leverages intra-sample gene expression ranking information instead of absolute gene expression levels, which can efficiently tackle batch effects across diverse transcriptomics data cohorts. By intra-sample gene rank analysis, reversal ratio analysis, and feature selection, RaMBat can select MB subtype-specific gene features and finally accurately identify MB subtypes. Benchmarking tests based on 13 datasets with severe batch effects suggested that RaMBat achieved a median accuracy of 99%, significantly outperforming other state-of-the-art MB subtyping approaches and conventional machine learning classifiers. In addition, in terms of visualization, RaMBat could efficiently remove the batch effects and clearly separate samples from diverse data sources according to MB subtypes, whereas conventional visualization methods like tSNE suffered from severe batch effects. We believe that RaMBat is a promising MB subtyping tool that would have direct positive impacts on downstream MB risk stratification and tailored treatment design. To facilitate the use of RaMBat, we have developed an R package which is freely available at https://github.com/wan-mlab/RaMBat.
Coronary bypass grafting in patients with three-vessel coronary artery disease in the setting of ST-elevation myocardial infarction and Cardiogenic shock is associated with substantially lower mortality compared to undergoing percutaneous coronary intervention
Authors: Movahed Mohammad Reza , McCoy Daniel , Hashemzadeh Mehrtash
Published: February 2025

Background: The shock trial was the first small, randomized trial revealing revascularization of patients presenting with ST-elevation myocardial infarction (STEMI) with coronary bypass surgery (CABG) have a better survival rate than percutaneous coronary intervention (PCI) The goal of this study was to use the largest inpatients database, to evaluate inpatients mortality of STEMI patients with three-vessel disease and cardiogenic shock undergoing CABG vs PCI. Methode: Using the Nationwide Inpatient Sample (NIS) database, and ICD-10 coding for cardiogenic shock, three-vessel CABG, and three-vessel PCI, we evaluate total inpatient mortality comparing three-vessel CABG vs three-vessel PCI in adults over age 18 years. Results: A total of 3,565 STEMI patients with 3 vessel disease and cardiogenic shock underwent PCI vs.3,950 undergoing CABG. CABG in the setting of STEMI-related cardiogenic shock and three-vessel CAD is associated with much lower mortality compared to three-vessel PCI despite multivariate adjustment. Mortality was more than twice in patients undergoing PCI vs CABG (68.27% vs 31.73%, P<0.001, OR for CABG patients: 0.32, CI: 0.25-0.42, P<0.001). After adjusting baseline characteristics and comorbidities in multivariate analysis, CABG remained significantly associated with lower mortality (CABG OR 0.34, CI:0.26-0.44, p<0.001). Conclusion: Our data confirms the finding of the Schock trial that three-vessel CABG is greatly superior to PCI in STEMI patients presenting with cardiogenic shock and three-vessel coronary artery disease.
Local Adaptation of Life-History Traits in a Seasonal Environment
Authors: Hall Rebekah Anna , MacPherson Ailene
Published: February 2025

Populations are often spread across a spatially heterogeneous landscape, connected by migration. Consequently, the question arises whether divergent selective forces created by spatial heterogeneity can overcome the homogenising force of migration and loss of diversity through genetic drift to favour different traits across space. Such spatial heterogeneity in the population due to divergent selection is known as local adaptation. While local adaptation has been studied in a variety of settings, it remains unclear whether local adaptation of certain life-history traits can arise. Life-history traits, such as those determining an organism's fecundity (the parameter r) and ability to compete for resources (the parameter K) demonstrate unique eco-evolutionary feedback loops due to their direct relationship to individual fitness. Classic theory holds that in a constant environment, evolution maximises the population's competitive ability. Divergent selective pressures on life-history traits requires complex environmental differences, such as heterogeneous patterns of seasonality. We consider life-history evolution in a Lotka-Volterra model with three types of seasonal perturbations: repeated, sudden crashes in population size, fluctuating death rates, and fluctuating resource levels. We show that fluctuating resources cannot change the evolutionary outcome, but that sufficiently harsh population crashes or fluctuating death rates favour increased fecundity over competitive ability. Finally, we apply deterministic and stochastic modelling to study local adaptation of an island population to periodic population crashes in an island-mainland model. We find that local adaptation favouring r-selected individuals again arises when conditions are sufficiently harsh, but not so harsh that the island population cannot be sustained in the absence of migration.
Put the frog in water: simple methods for improving individual identification as demonstrated with the agile frog
Authors: Nemeshazi Edina , Miko Zsanett , Ujhegyi Nikolett , Kasler Andrea , Lehofer Nadine , Bokony Veronika
Published: February 2025

Identification of individuals across time and space is required for investigating numerous evolutionary-ecology and conservation-related questions, and photo-based identification is commonly used for a broad taxonomic range. Systematic comparisons of available photo-matching software have been published for various taxa, and success of such software may greatly depend on image quality as well as the focal body parts. Yet, suitability assessments of images captured with different methods are missing. Here we tested the hypotheses that individual identification by color patterns can be facilitated by taking into account the natural medium surrounding the animals and the natural body posture they tend to take. We developed new photography methods to enable individual identification by whole-body assessment using the agile frog (Rana dalmatina), a species with common yet so-far neglected melanin-based pattern on its limbs and back. We compared the reliability of different photography methods for computer-assisted identification in the HotSpotter software as well as for observers operating it. We found that photographing either hand-restrained frogs with towel-dried skin, or frogs moving freely in clean water enabled comparison of the dorsal surface of the whole body including the hind legs, and HotSpotter identified matching images at rates similar to the relatively more successful of previously published anuran studies (>92% listed with rank≤10). By contrast, submerging hand-restrained frogs in water significantly improved identification: images of re-captured individuals were always ranked as the most likely match. We attribute this outstanding performance to the combination of advantageous effects of in-water light refractions that improve the visibility of melanin patterns, and uniform body postures facilitating comparison across individuals. Observers in general successfully identified matching images and ruled out non-matching ones, but some mistakes were recorded when images featured freely moving frogs. The photography methods developed in this study should be easily adapted to most frog and toad species for reliable individual identification. Our study highlights that taking into account features of the natural environment of the studied species can improve individual identification by photographs. Because such methods are non-invasive and inexpensive, they should be especially beneficial for population monitoring programs of endangered species.
Lead exposure positively affects coccidia abundance in feral pigeons (Columba livia)
Authors: JEANTET Aurélie , Audebert Fabienne , Agostini Simon , Decencière Beatriz , Gimeno Lou , Compain Tom , Federici Pierre , Lorang Camille , Rozen-Rechels David , Gasparini Julien
Published: February 2025

1. In urban environments, organisms are exposed to high levels of pollutants, including trace metals, whose concentrations can be increased by anthropogenic activities. Numerous studies have shown the toxic effects of pollutants on exposed organisms. However, due to their life within the host, parasites can also be affected by exposure to these pollutants. Overall, previous correlative findings reveal that the effects of parasite exposure to pollutants through the host can vary, from positive to negative, highlighting the complexity of host-parasite-environment interactions in relation to pollution. 2. In this study, we experimentally tested whether lead exposure affects the abundance of ecto-, meso-, and endoparasites in wild pigeons (Columba livia), which host a wide variety of parasites and are naturally exposed to trace metals in urban environments. As we had previously reported the toxic effects of lead on the immune system of pigeons, we expected lead exposure to be indirectly beneficial for the parasites. 3. To test this, we used a sample of wild pigeons captured in Paris, half of which were experimentally exposed to lead concentrations similar to those found in Paris. We then measured the abundance of several parasites: blood parasites (hemosporidian parasites), ectoparasites (Columbicola columbaeandCampanulote compar), coccidia and helminths. Additionally, we measured the intensity of the pigeons′ antiparasitic behavioral response (grooming) through behavioral analyses. 4. Our results did not reveal toxic effects of lead exposure on the parasites. On the contrary, we found positive effects of this exposure on coccidia abundance in male pigeons. This result could be explained by a toxic effect of lead on the host′s antiparasitic immune strategy, making the hosts less hostile to parasites. However, we found no effect of lead exposure on the abundance of lice, blood parasites and helminths. This could be explained by the lack of impact of lead exposure on grooming antiparasitic activity in our experiment, and by seasonal variations in the activity of blood parasite vectors, which may have masked potential effects of our treatment. 5. In conclusion, our study highlights the importance of considering the host environment, particularly pollutants, to understand parasite dynamics.
A Change of Heart: The Effect of High Flow Arteriovenous Fistulas on Cardiovascular Outcomes - a Systematic Review and Synthesis without Meta-analysis (SWiM)
Authors: Shah Nasir A , Hind Morgan E , Endre Zoltan H , Cochran Blake J. , Barber Tracie , Erlich Jonathan
Published: February 2025

Background: Although arteriovenous fistulas (AVF) are widely accepted as the gold standard form of dialysis access for hemodialysis patients, high AVF flow may impose significant hemodynamic stress, potentially contributing to adverse cardiovascular events, including heart failure (HF). Understanding this relationship is crucial for improving patient care. Aim: To describe the relationship between AVF flow and cardiac outcomes. Methods: A comprehensive search of the PubMed, EMBASE, and Cochrane databases was used to identify observational studies and randomized controlled trials reporting an effect of AVF flow on cardiac outcomes (clinical, echocardiographic, and biomarker). Due to study heterogeneity, meta-analysis was not feasible. Synthesis without meta-analysis (SWiM) was performed using vote counting of direction of effect as the primary outcome. Results: Higher AVF flow rates were consistently associated with increased incidence of HF and worsening HF symptoms. Cardiac imaging revealed left ventricular dilation and reduced left ventricular ejection fraction in patients with high-flow AVFs. Elevated biomarkers, such as natriuretic peptides, corroborated the adverse cardiovascular effects of high AVF flow. Conclusions: This systematic review and synthesis without meta-analysis showed a positive relationship between AVF flow and clinical, echocardiographic, and biomarker cardiovascular outcomes, but an inverse relationship between AVF flow and mortality. The methodological heterogeneity of studies highlights the need for well-designed prospective research with standardised definitions of high flow AVFs and measures for reporting of cardiovascular outcomes.
Artificial Intelligence in Healthcare: 2024 Year in Review
Authors: Awasthi Raghav , Ramachandran Sai Prasad , Mishra Shreya , Mahapatra Dwarikanath , Arshad Hajra , Atreja Aarit , Bhattacharyya Anirban , Bhattad Atharva , Singh Nishant , Cywinski Jacek B. , Khanna Ashish K. , Maheshwari Kamal , Dave Chintan , Khare Avneesh , Papay Francis A. , Mathur Piyush
Published: February 2025

Background: With over a thousand FDA-approved artificial intelligence/machine learning-enabled medical devices, research and publications is maturing from focusing on the development and internal validation of models to the external validation of models and implementation trials. Foundation models, especially Large Language Models, have spurred additional aspects of AI research related to healthcare, especially with the use of text-based data to address healthcare education and administrative tasks related to patient care. Methods: We performed a PubMed search using the terms 'machine learning' or 'artificial intelligence' and '2024', restricted to English language and human subject research on January 1, 2025. Utilizing a deep learning-based approach, we assessed the maturity of publications. Following this, we manually annotated the healthcare specialty, data utilized, and models employed for the identified mature articles. Subsequently, empirical data analysis was performed to elucidate trends and statistics. We also performed a detailed analysis of the distribution of foundation model-based publications amongst the healthcare specialties. Results: For the year 2024, the PubMed search yielded 28,180 articles, of which 1,693 were classified as mature using a BERT model. Following exclusions, 1,551 articles were selected for the final data analysis. Amongst these, the highest number of articles in each specialty originated from Imaging (407), Head and Neck (127), and General (122). The analysis of data types revealed that image data (903 [57.0%]) was still the predominant data type, but the use of text data (525 [33.1%]) had substantially increased. Additionally, we also found that LLMs (479) and AI General (448) category models have overtaken deep learning models (372) in healthcare AI research. For LLM-related publications, we are seeing increasing trends in research related to healthcare education and administrative tasks. Conclusion: With the introduction of foundation models, healthcare research trends are changing. The adoption of LLMs and text data types amongst various healthcare specialties, especially for education and administrative tasks, is unlocking new potential for AI applications in healthcare.
Pseudomonads coordinate innate defense against viruses and bacteria with a single regulatory system
Authors: Brinkley David M , Bertolli Savannah K , Gallagher Larry A , Tan Yongjun , Motha de Silva Minola , Brockman Ainsley , Zhang Dapeng , Peterson S. Brook , Mougous Joseph D.
Published: February 2025

Bacterial cells live under the constant existential threats imposed by other bacteria and viruses. Their mechanisms for contending with these threats are well documented; however, the regulation of these diverse defense elements remains poorly understood. Here we show that bacteria can mount a genome-wide, coordinated, and highly effective immune response against bacterial and viral threats using a single regulatory pathway. Bioinformatic analyses revealed thatPseudomonasspecies broadly possess a specialized form of the Gac/Rsm regulatory pathway (GRP), which our prior work inPseudomonas aeruginosaimplicated in activating interbacterial antagonism defense mechanisms in response to neighbor cell death. Proteomic studies comparing GRP-activated and -inactivated strains derived from diversePseudomonasspecies showed that the pathway regulates a large and variable suite of factors implicated in defense against both bacterial and phage threats. Focusing onP. protegens, we identify profound phenotypic consequences of these factors against multiple forms of bacterial antagonism and several phage. Together, our results reveal that bacteria, like more complex organisms, couple danger sensing to the activation of an immune system with antibacterial and antiviral arms.
Dual role of Arabidopsis SRS2 helicase in meiotic recombination
Authors: PETIOT Valentine , CHÉRON Floriane , WHITE Charles I , Da Ines Olivier
Published: February 2025

Helicases are enzymes that use the energy derived from ATP hydrolysis to translocate along and unwind nucleic acids. Accordingly, helicases are instrumental in maintaining genomic integrity and ensuring genetic diversity. Srs2 is a multi-functional DNA helicase that dismantles Rad51 nucleofilaments and regulates DNA strand invasion to prevent excessive or inappropriate homologous recombination in yeast. Consistently, the deletion of Srs2 has significant consequences for the maintenance of genome integrity in mitotic cells. In contrast, its role in meiotic recombination remains less clear. We present here substantial evidence that SRS2 plays an important role in meiotic recombination in the model plant Arabidopsis thaliana. Arabidopsis srs2 mutants exhibit moderate defects in DNA damage-induced RAD51 focus formation, but SRS2 is dispensable for DNA repair and RAD51-dependent recombination in somatic cells. Meiotic progression and fertility appear unaffected in srs2 plants but strikingly, the absence of SRS2 leads to increased genetic interference accompanied by increased numbers of Class I COs and a reduction in MUS81-dependent Class II COs. SRS2 thus has both anti- and pro-CO roles during meiosis in Arabidopsis thaliana - acting as an anti-CO factor by influencing the stability and/or the dissociation of early recombination intermediates, while playing a pro-CO role by promoting MUS81-mediated resolution of meiotic recombination intermediates.
Enhancing Medical Science Engagement through International Research Exchange: Objectives, Activities, and Outcomes
Authors: Jurgenson Monika , Garcia Llorca Andrea , Sarv Anu , Eysteinsson Thor , Hickey Miriam A.
Published: February 2025

The global decline in the number of physician-scientists, despite an increase in practicing physicians, underscores a critical need for integrating research training into medical education. Addressing this issue, we established an international research exchange program between the University of Tartu (UT) and the University of Iceland (UI). This initiative aimed to enhance scientific literacy, foster transferable skills, and align curricula with European standards through collaborative research experiences. The program enabled reciprocal student mobility, involving 11 medical undergraduates (6 from UT, 5 from UI), who conducted month-long basic science research projects. Participants completed comprehensive pre-training in scientific communication, safety protocols, and ethics before earning 6 ECTS credits for fulfilling laboratory requirements and submitting final reports. Students were also required to participate in local public engagement events. Despite challenges and delays due to the COVID-19 pandemic, the program met its objectives, demonstrating adaptability and effective resource management. Key outcomes included the development of an online learning platform, and multilingual guidelines and validated survey instruments to evaluate program impact, which we provide here to support similar initiatives. Feedback from pre-, post-, and post-1-year questionnaires revealed significant improvements in participants confidence in research methodologies, critical appraisal of scientific literature, and motivation for future research involvement. This project highlights the potential of structured international exchange programs to address gaps in medical education, enhance scientific training, and cultivate the next generation of physician-scientists.
Assessing wheat growth promotion potential of Delftia lacustris strain NSC through genomic and physiological characterization
Authors: Sharma Pinki , Pandey Rajesh , Chauhan Nar S
Published: February 2025

Background: Delftia sp. has gained considerable attention for its biocontrol and biofertilizer potential to promote the growth of crops such as Oryza sativa, Brassica campestris, and Solanum lycopersicum. However, Delftia sp. supporting wheat plants is yet to be explored. Methods: Delftia strain was cultured from wheat rhizosphere using different growth conditions. The biofertilizer potential of Delftia strain was assessed through physiological, biochemical, genomic, and field experiments. Results and Discussion: Phylogenetic and phylogenomic analysis confirmed taxonomic affiliation with Delftia lacustris. In vitro phosphate solubilization (0.325IU), nitrate reduction (0.401 IU), IAA production (0.485 IU), ACC deaminase activity (0.512 EU), siderophore synthesis properties, and strong antifungal activity against Fusarium oxysporum and Rhizoctonia solani indicated its potential as an effective biofertilizer and biocontrol agent. Drought stress tolerance (up to 40% PEG), metal stress tolerance, salt stress tolerance (up to 11.69% NaCl (w/v), 11.18% KCl (w/v), 4.24% LiCl (w/v)) indicated its survivability even in hostile conditions. Genes for phosphate solubilization (PhoR, PhoB, PhoU, PstABCD), nitrogen fixation (nifC, nifU), auxin production, siderophore biosynthesis, rhizosphere colonization and antifungal properties (chitinase, PhnZ) explains Delftia lacustris bioactivities. Significantly enhanced seed germination (93.33%), seedling growth, and biomass (P <0.05), particularly under stress conditions, indicated plant growth promotion properties of the Delftia strain. Significantly improved plant growth and yield parameters (P=0.0001) in field experiments, highlighting its potential as a biofertilizer and biocontrol agent. Conclusion: Delftia lacustris strain NSC1 exhibits multifaceted biofertilizer and biocontrol potential, promoting plant growth, suppressing pathogens, and enhancing stress resilience. Its eco-friendly properties and field efficacy make it a promising alternative to chemical fertilizers for sustainable wheat production.
Towards Scalable Biomarker Discovery in Posttraumatic Stress Disorder: Triangulating Genomic and Phenotypic Evidence from a Health System Biobank
Authors: Lee Younga Heather , Zhang Yingzhe , Espinosa Dice Ana Lucia , Li Josephine H , Tubbs Justin D , Feng Yen-Chen Anne , Ge Tian , Maihofer Adam X , Nievergelt Caroline M , Smoller Jordan W , Koenen Karestan C , Roberts Andrea L , Slopen Natalie
Published: February 2025

Importance.Biomarkers can potentially improve the diagnosis, monitoring, and treatment of posttraumatic stress disorder (PTSD). However, PTSD biomarkers that are scalable and easily integrated into real-world clinical settings have not been identified.Objective.To triangulate phenotypic and genomic evidence from a health system biobank with a goal of identifying scalable and clinically relevant biomarkers for PTSD.Design, setting, and participants.The analysis was conducted between June to November 2024 using genomic samples and laboratory test results recorded in the Mass General Brigham (MGB) Health System. The analysis included 23,743 European ancestry participants from the nested MGB Biobank study.Exposures.The first exposure was polygenic risk score (PRS) for PTSD, calculated using the largest available European ancestry genome-wide association study (GWAS), employing a Bayesian polygenic scoring method. The second exposure was a clinical diagnosis of PTSD, determined by the presence of two or more qualifying PTSD phecodes in the longitudinal electronic health records (EHR).Main outcomes and measures.The primary outcomes were the inverse normal quantile transformed, median lab values of 241 laboratory traits with non-zeroh2SNPestimates.Results.Sixteen unique laboratory traits across the cardiometabolic, hematologic, hepatic, and immune systems were implicated in both genomic and phenotypic lab-wide association scans (LabWAS). Two-sample Mendelian randomization analyses provided evidence of potential unidirectional causal effects of PTSD liability on five laboratory traits.Conclusion and relevance.These findings demonstrate the potential of a triangulation approach to uncover scalable and clinically relevant biomarkers for PTSD.