Journal Articles, BioMed Central and SpringerOpen

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Engaging communities in public health practice: lived experience or lived expertise?
Lee, Lisa M.; Metzler, Marilyn (BioMed Central, 2026-04-10)
Use of the term ‘expert’ implies specialized knowledge, which is the case for scientists as well as people immersed in communities. Naming this expertise signals to all parties the essential value of understanding the context in which public health decisions are implemented. We outline arguments for and concerns about viewing lived experience as a complementary expertise akin to scientific expertise.
Beyond linearity: reimagining AI as a participant in circular bioeconomies
Muthukumar, Aarthi; Rashid, Barira; Yang, Lihong (2026-03-27)
As artificial intelligence transitions from industry-exclusive tool to public-facing technology, society faces critical decisions about its integration into socioecological systems. This paper proposes a reimagining of AI as a synthetic participant in the circular bioeconomy (CBE)—a regenerative model emphasizing cyclical flows of resources, information, and energy. Drawing on Bruno Latour’s Actor-Network Theory and Donna Haraway’s posthumanism, we reconceptualize AI as a non-living organism capable of functioning within multispecies systems, analogous to viruses that shape ecosystems without conventional life. Conventional, in that it meets the standard biological criteria for like: metabolism, reproduction, and homeostasis. AI, like viruses, does not meet this biological criteria. Current AI applications in CBE—from biowaste recycling to precision agriculture—demonstrate both transformative potential and ethical concerns. While AI enables unprecedented efficiency through advanced algorithms and embodied robotics, it risks perpetuating extractive logics that treat information as a resource to be mined rather than circulated. Critical ethical challenges emerge including algorithmic bias amplifying inequalities, epistemic opacity eroding stakeholder trust, blurred accountability for AI-driven harm, displacement of human labor, and marginalization of indigenous and local ecological knowledge. Through examples in medicine and remote sensing, we argue that AI becomes a “friend” to the Circular Bioeconomy (CBE) only when designed as circular and relational rather than linear and extractive. This requires synthetic datasets preserving privacy, multimodal architectures enabling dimensional understanding, and human-machine-ecosystem feedback loops replacing terminal outputs with ongoing accountability. Ultimately, AI’s role depends on intentional design grounded in justice and multispecies dignity—transforming it from extractive tool into participant in shared regenerative futures.
Wheel–rail-induced derailment analysis: a comprehensive literature review of experimental and simulation-based approaches
Kumar, Nikhil; Ahmadian, Mehdi; Marquis, Brian (Springer, 2026-03-16)
This paper offers a comprehensive review of the literature on the role of wheel–rail contact mechanics in train derailments. Using experimental and simulation methods, this review examines various research efforts that analyze how contact forces influence wheel climb and derailment dynamics. The related studies are summarized, and insights are provided on how they have contributed to understanding derailments and enhancing overall rolling stock safety. The review shows significant progress across different specialized areas within the broader topic of derailments. This includes advanced, state-of-the-art testing rigs, high-fidelity models that accurately replicate field conditions, materials that help prevent derailments, and wheel and rail profiles that reduce derailment risks. However, the accuracy of testing and modeling often requires more complex setups, sophisticated data analysis techniques, and greater resources. Despite these advances over the past few decades, further scientific research is necessary to understand better the root causes of events like wheel climb derailments under controlled and repeatable conditions.
Understanding health systems thinking in medical education: qualitative interviews with expert clinicians
Norris, Matthew B.; Grohs, Jacob R.; Mutcheson, R. Brock; Karp, Natalie; Katz, Andrew; Musick, David W.; Lane, Heidi; Parker, Sarah; Gonzalo, Jed (2026-01-31)
Background: Health systems science (HSS) education is an increasingly important component of undergraduate medical education. Despite curricular advances, the ways in which clinicians implement health systems science knowledge in everyday clinical practice, health systems thinking, remains understudied. A better understanding of how clinicians engage in health systems thinking to address everyday problems in clinical contexts is needed. Methods: We conducted semi-structured interviews with 10 expert clinicians experienced in undergraduate medical education, health systems science, and curriculum development to identify components of competent health systems thinking. Interview questions were informed by ecological systems theory and literature on learning professional competencies. Results: Through interviews with experts, we have come to define health systems thinking (HST) as “an approach to solving problems in healthcare systems that utilizes a deeper understanding of interconnections and behavior of the entire system. As a skill, it coordinates the application of clinical and HSS knowledge and skills toward solving a contextual problem in the healthcare environment.” Clinician comments support the idea that HST is a metacognitive process rather than a specific subset of knowledge domains or affective attributes. This process requires that clinicians understand and navigate pressures on patient care originating from surrounding meso- and macro-systems. Conclusions: Medical students require more explicit exposure to HSS knowledge being implemented in clinical environments, and varied examples highlighting how meso- and macro-system patterns can impact individual patient care. This metacognitive integration of HSS knowledge into everyday clinical practice is critical for preparing medical students to meet the requirements of the accreditation council for graduate medical education (ACGME) core competencies in residency programs. Health systems thinking requires a method of operational assessment to provide students feedback and highlight targeted interventions for further development.
The effect of flooding on low birthweight and preterm birth: a systematic review and meta-analysis
Mendrinos, Antonia; Loyd, Elly; Jagger, Meredith; Comer, C. Cozette; Gohlke, Julia M. (2026-03-05)
Background: Numerous studies have examined pregnancy outcomes following flood events, with the majority focusing on two related outcomes: preterm birth (PTB) and low birthweight (LBW). Summarizing the results of these previous studies and determining remaining data gaps is the main objective of this systematic review and meta-analysis. Methods: We included publications in English that examined birthweight and/or gestational length related to exposure to floods, or events typically causing flooding (e.g. tropical cyclones). Seven academic databases were searched: CAB Abstracts (CABI), Academic Search Complete and Environment Complete (EBSCOhost), Environmental Science Index & Database (ProQuest), PubMed, Scopus, and Web of Science Core Collection. Searches were updated on February 23, 2025. For inclusion in meta-analyses, quantitative estimates of effect size and variance were required, and quality was assessed using the Quality Assessment Tool for Observational Cohort and Cross-Sectional Studies. Random effects regression was used for meta-analyses, and results are presented in forest plots, with potential for publication bias assessed in funnel plots and Egger’s test results. Results: Overall, data from 34 studies were extracted, and 25 studies across 13 countries were included in meta-analyses. Most studies (N = 18) examined tropical cyclone exposure. Meta-analyses indicate increases in LBW (RR = 1.03, 95% CI: 1.00, 1.05) and PTB (RR = 1.10, 95% CI: 1.00, 1.22). The LBW result was not significantly influenced by quality rating, while the PTB result is non-significant when all studies, regardless of quality rating, were included in the meta-analysis (RR = 1.01, 95% CI: 0.97, 1.05). Additionally, the PTB estimate is strongly influenced by one study with a large and highly significant effect size. Additional sub-analyses suggest no decreasing effect following more recent events (after 2005). Conclusions: Results are limited by the range of methods used across studies to estimate exposure to flooding and potential co-exposures related to events that caused the flooding (e.g. wind damage-related health outcomes during tropical cyclones). Regardless, results indicate that adverse pregnancy outcomes may increase following in utero exposure to flood events. Future studies incorporating finer spatiotemporally resolved estimates of exposure to flooding will improve estimates of effect. The study is registered in PROSPERO (CRD42024514540).
Sensitivity of the Hyper-Kamiokande experiment to neutrino oscillation parameters using accelerator neutrinos
Hyper-Kamiokande Collaboration; Vogelaar, R. Bruce (2026-02-23)
This paper presents the expected sensitivity to the neutrino oscillation parameters of the Hyper-Kamiokande long-baseline program. The Hyper-Kamiokande experiment, currently under construction in Japan, will measure the oscillations of accelerator-produced neutrinos with thousands of selected events per sample: this corresponds to an increase of statistics of a factor 25–100 with respect to recent results from the currently-running long-baseline neutrino oscillation experiment in Japan, T2K. In the most favorable scenario we will achieve the discovery of Charge-Parity (CP) violation in neutrino oscillation at 5 σ C.L. in less than 3 years. With 10 years of data-taking, and assuming a neutrino : antineutrino beam running ratio of 1:3, a CP violation discovery at 5 σ C.L. is possible for more than 60% of the actual values of the CP-violating phase, δ CP . Moreover, we will measure δ CP with a precision ranging from 20 ∘ , in the case of maximal CP violation, to 6 ∘ , in the case of CP conservation. We aim to achieve a 0.5% resolution on the Δ m 32 2 parameter, and a resolution between 3% and 0.5% on the sin 2 θ 23 parameter, depending on its true value. These results are obtained by extending the analysis methods of T2K with dedicated tuning to take into account the Hyper-Kamiokande design: the larger far detector, the more powerful beam, the upgraded near detector ND280, and the planned additional Intermediate Water Cherenkov Detector.
Sample pooling approaches simulated under resource scarcity, lapses in testing capacity, and rapid processing demands for surveillance testing: a data-driven performance comparison
Burgess, Catharine; Curran, Alan; Ceci, Alessandro; Finkielstein, Carla V.; Lahmers, Kevin K. (2026-01-30)
Background: Sample pooling is a critical strategy to meet increased testing demand and conserve resources in surveillance testing. Much of its effectiveness depends on how well optimized the pool size is to the prevalence of infection in the sampled population, which can be difficult to anticipate in many circumstances. Multiple methods exist to better optimize pooling, with unique trade-offs. Methods: Pooling optimization methods were simulated to examine trade-offs between surveillance priorities and operational characteristics using SARS-CoV-2 surveillance data and workflows generated by the Virginia Tech Molecular Diagnostics Laboratory under varying capacity conditions. All in-house validation procedures were designed and established exclusively under CLIA to ensure full control of the analytical framework and to accurately reflect true capacity constraints. We used binary surveillance data to run Monte Carlo simulations (MCS) comparing conservative and large fixed pools, historical prevalence optimization (HPO), prevalence estimation testing (PET), truly optimized pooling, and individual testing. Median test counts from the MCS fed a discrete-event simulation (DES) that assessed processing time at different lab capacities under surveillance and outbreak conditions. We then used the combined performance results to build a classification tree to guide method selection under different testing priorities and constraints. Results: MCS results indicated that small pools (4 samples), HPO, and PET resulted in test counts that were not statistically different from truly optimized pooling (p > 0.05). The DES showed that pooling methods generally performed comparably to individual testing in processing time at low laboratory capacity, but individual testing became faster as capacity increased. Across capacity conditions, individual testing processed fewer than 500 daily samples more quickly, yet it demanded more hands-on time than pooling. Large-scale surveillance favored pooled methods, which were quicker under most conditions, while outbreak scenarios often favored individual testing when capacity wasn’t highly limited. Machine learning analysis highlighted surveillance priorities and sample intake as key determinants in selecting the best pooling optimization method for the given circumstance. Conclusion: This study demonstrates the importance of maintaining multiple pooling optimization approaches and adapting strategies to match evolving demands and potential constraints in surveillance testing.
Serum biochemical profiles are distinct between White Leghorn chicken lines selected for divergent antibody response to sheep red blood cells
Assumpcao, Anna L. F. V.; Caputi, Valentina; Ashwell, Christopher M.; Honaker, Christa F.; Siegel, Paul B.; Taylor, Robert L.; Lyte, Joshua M. (2026-01-13)
Background: For forty-nine generations, White Leghorn chickens have been selected for divergent responses to injection of sheep red blood cells (SRBCs), generating the high (HAS) or low (LAS) antibody response lines. The objective of this study was to determine if selection for systemic antibody concentrations would result in divergence in blood serum biochemistry profiles. Materials and methods: Blood serum samples were collected from the same birds at 4, 8, 12, 16, and 66 weeks to analyze several biochemical serum parameters, including total protein (TP), albumin, globulin, albumin: globulin (A: G) ratio, aspartate transferase (AST), creatine kinase (CK), uric acid, glucose, calcium, phosphorus, potassium, sodium, total bile acid (TBA), gamma-glutamyl transferase (GGT), alanine transferase (ALT), and total cholesterol (TC). Results: Our results showed that HAS chickens had higher globulin and potassium levels and lower albumin: globulin (A: G) ratio serum concentrations than LAS chickens at 8, 12, and 16 weeks. At 12 weeks, HAS had total protein (TP) higher than LAS. Additionally, at 16 and 66 weeks, HAS had a higher concentration of creatine kinase (CK) than LAS. At 8 weeks, alanine transferase (ALT) levels were lower in HAS than LAS, and at 12 weeks, LAS females’ ALT levels were higher than HAS females. Furthermore, HAS had higher gamma-glutamyl transferase (GGT) levels than LAS at 12 and 16 weeks. The TP, globulin, and A: G ratios are consistent with the selection of HAS for higher antibody concentration. Additionally, our data also showed a divergence in potassium and liver enzyme levels between HAS and LAS. Females at 66 weeks had a biochemistry profile consistent with egg production, including increased total cholesterol (TC), total bile acid (TBA), aspartate transferase (AST), calcium, and phosphorus levels, as well as decreased uric acid and GGT concentrations compared with their male counterparts. Conclusions: Our findings demonstrate that direct selection on the humoral immune system resulted in distinct serum biochemical profiles. These results are likely to serve as potential informative and diagnostic markers in poultry health, food safety, and performance.
Building research capacity in sub-Saharan Africa: findings from a pilot scientific writing workshop in Cameroon
Dabou, Solange; Ngo, Valery N.; Dongho, Ghyslaine B. D.; Nanseu, Evrard M. K.; Sinsai, Regina Y.; Asahngwa, Constantine T.; Kibu, Odette D.; Goupeyou-Youmsi, Jessy; Cheuyem, Fabrice Z. L.; Conner, Anna; Gobina, Ronald M.; Foretia, Denis A. (2026-01-24)
Objective: Sub-Saharan Africa produces less than 4% of global scientific output, despite significant health and development challenges. This study evaluated the effectiveness of a pilot scientific writing workshop in Cameroon aimed at building writing skills and publication readiness of early career researchers. We conducted two workshops’ sessions in Yaoundé, Cameroon, in April and November 2023. A mixed-methods approach was used. Quantitative data were obtained via pre- and post-workshop questionnaires designed to capture participants’ self-assessed knowledge, skills, and confidence related to the workshop content. Qualitative data were gathered through in-depth interviews. Descriptive and inferential statistics were applied to the survey data, and thematic content analysis was used to assess qualitative responses. Results: A total of 86 participants completed both the pre- and post-workshop surveys (response rate: 86.9%). The majority had never published scientific papers (62.8%) nor had they received formal writing training (61.6%). The quantitative results showed statistically significant improvements in participants’ overall understanding of scientific writing and publishing (mean difference = 0.93, p < 0.001) and confidence regarding writing skills (mean difference = 0.94, p < 0.001). Thematic analysis of the interviews revealed high satisfaction with the learning environment, perceived knowledge gains, and a strong demand for mentorship and sustained training opportunities. Highlights: Most of the participants (61.6%) had never completed a scientific writing or publication course. Almost two thirds (62.8%) had never published a scientific paper before. Participants reported increased knowledge, skills and confidence in scientific communication. Junior researchers in Africa seek consistent mentorship and training opportunities.
AMSB in Sp(N_c) gauge theories
Varier, Digvijay R.; Gu, Zijian; Noether, Bea; Murayama, Hitoshi (2026-02-10)
We present a careful study of the chiral symmetry breaking minima and other potential minima in supersymmetric symplectic QCD (Sp(Nc) with Nf flavors) perturbed by Anomaly Mediated Supersymmetry Breaking (AMSB). Although the case of Nf = Nc + 1 requires particular care due to the inherently strongly coupled nature of the quantum modified moduli space, we are able to show that all Sp(Nc) theories to which AMSB can be applied (Nf < 3(Nc + 1)) possess stable chiral symmetry breaking minima, which are plausibly continuously connected to the vacua of QCD-like Sp(Nc) theories for large SUSY breaking, and are protected from runaways to incalculable minima.
How yoga interventions are operationalized and reported in the context of mental health and wellbeing RCTs: a systematic review and qualitative synthesis
Frazier, Mary C.; Remskar, Masha; Harden, Samantha M.; Barley, Karsen S.; David, Danielle E.; Guillen, Marina Z.; Olsen, Daryn E.; Markley, Kayla M.; Pullin, Megan J.; Brinsley, Jacinta (2025-12-22)
Background: Yoga is a popular intervention demonstrating promising impacts for mental health and wellbeing. Despite growing research interest, yoga remains poorly operationalized and inconsistently described in scientific literature, hindering dissemination, rigorous evaluation, and replication. This systematic review aims to address this critical knowledge gap by examining how yoga is operationalized in recent mental health and wellbeing research. Methods: We conducted a systematic review of literature from January 2013 to August 2024. Terms relating to yoga, mental health, wellbeing, and interventions were used to search MEDLINE, CINAHL, Embase, Emcare, PsycINFO, and Scopus. Randomized controlled trials that included yoga as the primary intervention and reported a validated measure of mental ill-health, mental wellbeing, or quality of life, were included. Inductive qualitative analyses of yoga definitions and descriptions were conducted. Results: Of 5206 studies identified, 129 were included with exclusion primarily due to study design. Qualitative analysis resulted in a total of 1291 meaning units (MU). Yoga definitions suggest that yoga is operationalized as a practice, complementary and alternative medicine, or system (e.g., encompassing philosophy and practices) with mind-body or mind-body-spirit aspects. Components of yoga included physical such as postures, mental such as meditation, and breath. Conclusions: This is the first systematic review to comprehensively analyze how yoga is operationalised and reported in recent experimental mental health and wellbeing research. Generally, yoga is operationalized as a mind-body or mind-body-spirit practice comprising mental, physical, and breathing components. We provide recommendations to improve the translation and implementation of yoga interventions. Trial registration This study was prospectively registered with PROSPERO (CRD42023455373). Clinical trial number: not applicable.
Metabarcoding-based characterization of the boxwood root-zone soil microbiome
Li, Xiaoping; Weiland, Jerry E.; Ohkura, Mana; Luster, Douglas G.; Kong, Ping; Hong, Chuanxue (2026-01-16)
Background: Soil microbiomes are important for plant growth and health. The objectives of this study were to characterize boxwood root-zone microbial community and understand their associations with plant disease resistance and other horticultural traits. Soil samples were collected from four cultivars with three distinct boxwood blight tolerance at two geographically distant nursery locations in May, August, and November of 2021. Bacterial and fungal communities were characterized through DNA metabarcoding. Results: The dominant bacteria in the boxwood root-zone soil included Bacillus and several unknown genera of the order Gaiellales and families Xanthobacteraceae and Gemmatimonadaceae; the dominant fungi included Clonostachys, an unknown genus, Solicoccozyma, and Fusarium. Ceratobasidium, Hyaloscypha, and Sistotrema were also the dominant genera within the presumptive mycorrhizal fungi (PMF) group. Fungal community structure was distinct among cultivars with different blight tolerance in May and August, but the divergence of the bacterial community structure was only significant in the August samples. Community composition-wise, greater numbers of genera differed in abundance between the intermediate and the susceptible cultivars. Moreover, cross-kingdom network analysis showed a more connected network constructed from the intermediate cultivars and identified more hub taxa as module connectors compared with the other two cultivars. Some of the hub taxa, including bacterial genera Gaiella, Streptomyces, and Sphingomonas, and fungal genera Solicoccozyma and Pseudonectria were also among the 27 bacterial and 6 fungal core genera identified from all samples across four cultivars, two locations, and three seasons. Further, Volutella and Pseudonectria were negatively associated with 10 bacterial genera and all identified PMF-PMF connections were positive across all networks. Conclusions: Boxwood root-zone soil harbored diverse plant-beneficial microbes, including PMFs. Fungal community and microbial network connectivity also differed among the cultivars, suggesting the regulatory roles of plant phenotype and genotype in fungi recruitment and microbial interactions. Several keystone taxa were identified and may be crucial in maintaining the structure and communication within the boxwood root-zone microbiome. The negative associations between bacteria and Volutella/Pseudonectria provide a new insight into managing the rise of the boxwood Volutella blight. Together, this study offers several leads to enhancing plant resilience to disease and environmental stress.
Geometry as Method and Generative System: A Virtual Reconstruction of Fernando Higueras’s Montecarlo Project
del Blanco García, Federico L.; Quintana, Anderson G.; Borunda, Luis (2026-01-13)
This paper presents a virtual reconstruction of Fernando Higueras’s unbuilt Montecarlo Building (Edificio polivalente de Montecarlo – Concurso Internacional restringido. Fundación Fernando Higueras, Madrid. (Audiovisual material, January 29, 2017). https://www.youtube.com/watch?v=dBwv2htnzUQ , 1969), a landmark in his exploration of radial-expansive systems. The project, conceived as a growing organism, employed a generative grammar based on the duplication of polygonal rings (n = 6·2x), producing modular slabs, large cantilevers, and a flexible spatial structure. Using archival documents and digital modeling, this research reconstructs the building’s geometry, structural hierarchy and active perimeter, showing how Higueras turned abstract principles into rational strategies. It reveals how practical solutions can be formalized as mathematical rules, bridging analog experimentation with digital parametric design. Results highlight its dual nature: organic yet rigorous, integrating prefabrication, scalability and bioclimatic performance. Though never built, Montecarlo emerges as a culmination of Higueras’s analog experiments and a precursor of contemporary computational design.
Blocking simple and complex social contagions using dominating set heuristics
Bao, Robert C.; Hancock, Matthew; Kuhlman, Chris J.; Ravi, S. S. (2025-12-11)
There are myriad real-life examples of contagion processes on human social networks, e.g., spread of viruses and mis/dis/information, joining groups, and social unrest. Also, there are many methods to control or block undesirable contagion spread on networks. In this work, we introduce a novel method of blocking contagions that uses nodes from dominating sets (DSs). This is the first work to use DS nodes to block contagions. Finding minimum dominating sets of graphs is an NP-Complete problem, so we generalize a well-known heuristic, enabling us to customize its execution. Our method produces a prioritized list of dominating nodes, which is, in turn, a prioritized list of blocking nodes. Given a network, we compute this list of blocking nodes and we use it to block contagions for all blocking node budgets, contagion seed sets, and parameter values of the contagion model. We provide examples to illustrate the issues associated with DS-based contagion blocking. We report on computational experiments of the blocking efficacy of our approach using seven mined networks. Among the results is that the heuristic generalization is important for improved blocking performance. We also demonstrate the effectiveness of our approach by comparing blocking results with those from the high degree heuristic, which is a common standard in blocking studies. We discuss how our general DS-based method recovers the high degree heuristic as a special case.
Lawsonia intracellularis infection induces changes in microbial community function and composition associated with reduced pig growth and feed efficiency
Helm, Emma T.; Burrough, Eric R.; Gabler, Nicholas K.; Leite, Fernando L. (2026-01-05)
Background: Lawsonia intracellularis and its resulting disease remains a troubling pathogen for pork producers worldwide. In the current experiment, we aimed to characterize the microbiome of pigs challenged with L. intracellularis through peak disease impact to better understand microbial community function and how microbial changes may contribute to disease and resulting decreased growth. Twenty-four L. intracellularis negative barrows were assigned to either L. intracellularis negative (NC) or L. intracellularis challenged (PC) treatment groups (n = 12 pigs/treatment). On days post-inoculation (dpi) 0, PC pigs were inoculated with L. intracellularis. Feed disappearance was monitored daily, body weights and fecal samples were collected weekly. At dpi 21, pigs were euthanized for sample collection and macroscopic lesion scoring. Results: Pigs challenged with L. intracellularis had sustained reductions in growth performance and feed intake throughout the 21-day period (P < 0.001). This was accompanied by changes to fecal microbial communities, particularly increased abundance of Chlamydia suis in challenged pigs at dpi 7, 14, and 21. Changes to microbial communities were also accompanied by differences in microbial metabolism, marked most notably by signatures of lesser amino acid biosynthesis and greater nucleotide synthesis in challenged pigs. Conclusions: In summary, L. intracellularis challenge produced reductions in growth and feed intake. This was accompanied by sustained changes to fecal microbial communities, particularly sustained increased abundance of C. suis in challenged pigs. Changes to microbial communities were also accompanied by differences in microbial metabolism which likely play a role disease.
Perinatal citalopram exposure alters the gut composition and microbial metabolic profiles of Sprague-Dawley rat dams and female offspring but not male offspring
Kropp, Dawson R.; Glover, Matthew E.; Samanta, Rupabali; Unroe, Keaton A.; Clinton, Sarah M.; Hodes, Georgia E. (2025-12-03)
Background: Selective serotonin reuptake inhibitors are widely prescribed during pregnancy. Their main route of administration is through the gut. However, their impact on the maternal and offspring gut microbiome and microbial metabolic pathways remains poorly understood. This study used metagenomic shotgun sequencing to examine the effects of perinatal citalopram exposure in rat dams and their offspring on gut composition and downstream metabolic pathways. Methods: We treated pregnant and nursing rat dams with either citalopram or vehicle (water). Their feces were collected, DNA from these samples was extracted and then sequenced using shotgun metagenomic sequencing. The BioBakery suite of microbiome analysis tools was utilized in tandem with RStudio to analyze the gut composition and microbial metabolic pathways of the rat dams and their offspring. Results: Pregnant and nursing dams treated with citalopram exhibited marked shifts in microbial community structure, including phylum-level alterations in Proteobacteria and Defferibacteria. Citalopram treated dams displayed significantly altered beta diversity. Species level alterations due to treatment were composed of five significantly altered microbes, two of which belong to the Proteobacteria phylum. These changes were highly diverse and were not congruent with microbe-level alterations observed in offspring. Alpha diversity of microbial metabolic pathways was compared using the Gini-Simpson index, which was significantly increased in dams suggesting greater metabolic functional diversity with age. Female offspring perinatally exposed to citalopram showed significant changes in gut beta diversity, with seven significant alterations at the microbe level. These microbial shifts were accompanied by twenty-one significantly altered microbial metabolic pathways. In contrast, male offspring showed no significant differences in microbial composition or beta diversity and only minor metabolic changes. Conclusions: These findings demonstrate that maternal citalopram exposure during pregnancy and lactation has lasting, sex-specific impacts on the offspring’s gut microbiome and microbial metabolic pathways. The pronounced alterations in female, but not male offspring, suggest that host sex may be a critical determinant in the developmental response to citalopram exposure. This work underscores the value of metagenomic approaches in uncovering complex host-microbiome interactions and highlights the need to consider offspring sex in evaluating the safety and long-term effects of antidepressant use during pregnancy.
Carbon stock, fluxes, and partitioning in Pinus taeda plantations are affected by genetic variation and stand density in Southeast Brazil
Campoe, Otávio C.; Cordeiro, Natielle G.; Rojas, Gerardo; Albaugh, Timothy J.; Cook, Rachel L.; Rubilar, Rafael A.; Carter, David R.; Alvares, Clayton A.; Maier, Chris A. (2025-12-06)
Background: To understand how genetic variation among varieties and stand density affect carbon (C), we assessed C stocks, fluxes, and partitioning in Pinus taeda L. plantations in Southeast Brazil. We measured the annual C balance in two consecutive years (from 7 to 9 years after planting) in four different clonal varieties with distinct crown structures (C1-medium, C2-broad, C3-narrow, and C4-broad) and an OP (open-pollinated) family. From age 7 to 8 years, the C balance was assessed for all five varieties at a stand density of 1894 trees ha− 1. From age 8 to 9 years, the C balance was assessed for three varieties (C2, C3, and OP) at two stand densities (low density (LD): 613 trees ha− 1 and high density (HD): 1894 trees ha− 1). Results: At age 7–8, the total C stock (above- and belowground plus the litter layer) among varieties ranged from 168 Mg C ha− 1 (C3) to 186 Mg C m− 2 (C1), with the bole as the largest pool (68%). Aboveground net primary production (ANPP) ranged from 1.9 to 3.1 kg C m− 2 year− 1, and total belowground carbon flux (TBCF) from 2.0 to 2.9 kg C m− 2 year− 1. The partitioning of GPP (Gross Primary Production) to ANPP and TBCF reached a maximum value of 35% and 41%, respectively. At age 8–9 years, the C stock was greater in the HD stands than in the LD stands across all varieties. Overall, C stock reached between 103.5 and 184.6 Mg C ha− 1. ANPP under HD was 1.9 kg C m−² year−¹ compared with 0.62 kg C m−² year−¹ under LD. There were no significant differences in TBCF between the HD and LD stands. The partitioning of GPP to ANPP was lower and to TBCF was higher under LD compared with HD. Conclusion: Relationship between crown structure and the C stock, fluxes, and partitioning is not clear and should be used with caution for management prescriptions related to C sequestration. Also, no differences in the bole C stock and sequestration were found across varieties within the same planting density. Finally, the genetic variation among varieties and stand density significantly affected stand productivity, with stand density showing greater effect.
Single-cell transcriptomic analysis suggests potential differences in the developmental stage and quantity of adipose progenitor cells between bovine intramuscular and subcutaneous fat
Tan, Zhendong; Lyu, Pengcheng; Jiang, Honglin (2025-11-27)
Background: Intramuscular fat (IMF), the white adipose tissue deposited between skeletal muscle fibers, is a key determinant of beef quality due to its contribution to meat flavor, juiciness, and tenderness. However, IMF develops later and grows more slowly, compared to other fat depots such as subcutaneous fat (SF) in cattle. The cellular and molecular mechanisms underlying the delayed development and slow growth of IMF remain poorly understood. We hypothesized that later development and slower growth of IMF compared to SF may, in part, arise from the differences in their progenitor cells. Results: We performed single-cell RNA sequencing (scRNA-seq) on the stromal vascular fractions (SVFs) from IMF and SF of adult Angus crossbred steers as well as the mononuclear cell fractions (MCFs) from skeletal muscles of newborn Angus crossbred bull calves, with each tissue type collected from two animals. A total of 14,802 cells from 6 animals were sequenced. Clustering analysis revealed that these cells comprised ten cell types, including adipose progenitor cells (APCs), muscle satellite cells (MuSCs), myoblasts, smooth muscle cells, and various immune cell populations. The SF-derived SVF from adult cattle harbored a significantly higher proportion of APCs than the IMF-derived SVF. The MCFs from newborn calves did not contain detectable APCs. Subclustering analysis revealed that the APCs comprised six subpopulations (C0–C5), among which C3 and C5 were absent in the IMF-derived SVF while C1 was markedly less abundant in the IMF-derived SVF than in the SF-derived SVF. Gene set variation analysis and pseudotime trajectory analysis showed that C1 and C3 represented more differentiated APCs, with higher expression of genes involved in adipogenesis, such as PPARG, ADAM12, and PPARGC1A, whereas subclusters C0 and C4 represented undifferentiated, uncommitted APCs, with higher expression of genes involved in DNA replication and cell adhesion, compared to the other subclusters. Conclusions Overall, this single-cell transcriptomics study suggests two potential differences in APCs between IMF and SF in adult cattle: (1) IMF contains fewer APCs than SF; (2) APCs in IMF are adipogenically less committed and less differentiated compared to APCs in SF. These differences may partially explain why IMF develops later and grows more slowly than SF in cattle. This study also suggests that, in cattle, intramuscular fat begins to develop postnatally, challenging the widely held belief that it forms during late gestation.
Gauge potentials on the M5 brane in twisted equivariant cohomotopy
Banerjee, Pinak (2025-12-22)
In this article, we work out some variations on the discussion of the C-field flux densities in the Sati-Schreiber program. We start by explaining the need for global completion of the field content: the fluxes, the gauge potentials and the gauge transformations on the worldvolume of a single M5 brane in eleven-dimensional supergravity, and how this is encoded by the choice of flux quantization law. Assuming Hypothesis H that the 4-flux in M-Theory is flux quantized in a non-abelian cohomology theory called 4-cohomotopy, and the three-flux on the M5 brane worldvolume in (twisted) 3-cohomotopy, we generalize some previous calculations known in the literature to include twisting by background gravity and placing M5 branes on orbifolds. We show that the null concordances of cohomotopically charged fluxes give rise to the traditional gauge potentials and the null concordances of concordances give rise to the corresponding gauge transformations via surjections, in the cases of tangentially twisted cohomotopy, twistorial cohomotopy and equivariant twistorial cohomotopy. We construct the surjections explicitly for these cases and check the consistency relations with the corresponding Bianchi identities. Thus, we show how the traditional formulas for the local gauge potentials on M5 brane worldvolume on curved spacetimes and orbifolds are indeed reproduced by the homotopy theory and, as such, become amenable to global completion in cohomotopical charge quantization.
Multiomics analysis revealed the temporally common and specific molecular changes in Arabidopsis thaliana (L.) under salt stress
Chen, Zixuan; Ye, Chanjuan; Zeng, Yuan; Guo, Jie; Zhou, Xinqiao; Chen, Dagang; Liu, Juan; Liu, Chuanguang; Jaremko, Mariusz; Chen, Ke; Fan, Guoqiang (2025-11-19)
Salt stress is a major abiotic constraint that limits plant growth and productivity worldwide. In this study, we performed a comprehensive temporal analysis using transcriptomics (6 h), ribosome profiling (12 h), proteomics and phytohormone quantification (24 h), and metabolomics (48 h) to uncover the regulatory mechanisms in Arabidopsis thaliana underlying salt stress adaptation. Novel transcriptional regulators, including JAZ7, CBF4, bHLH92, and NAC041 that responded rapidly to early salt stress, were identified. At the post-transcriptional level, TAS1C and TAS2, along with chloroplast tRNAs (AtTRNR.1, AtTRNC, AtTRNV.1), were found to be translationally upregulated, suggesting a previously unrecognized role of organellar translation in stress response. At the protein level, chloroplast functional proteins, AtPSBA, AtRBCL, AtPSAA, AtPSAB, were revealed to respond to salt stress. Some functional proteins, including AtCER1, AtGGL19, and AtLEA14, with opposite trends between transcription and translation, highlighting the complexity of salt stress adaptation. Abscisic acid (ABA) was significantly upregulated, while jasmonic acid (JA) was dramatically suppressed, with AtOPR3 and JAZ7 identified as key regulatory nodes. Metabolomics analysis further showed that d-proline and 1-pyrroline-2-carboxylate accumulated at later stages, potentially contributing to increased salt stress resistance. Overall, these findings provide new insights into the temporal regulation of stress adaptation and identify candidate genes and metabolites that may serve as targets for improving salt tolerance in crops.

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