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Topology-guided rotational dynamics of magnetic soliton assemblies under pulsed current

FAVABEAN and FALAPhyl: Open-source pipelines for scalable 16s rRNA microbiome data processing and visualization

Reproducible and scalable analysis of 16S rRNA amplicon sequencing data remains a persistent challenge in microbiome research due to the complexity of available tools, incompatibilities between platforms, and the need for extensive bioinformatics expertise. We developed two containerized workflows—FAVABEAN (Fast Amplicon Variant Annotation, Binning, Error-correction And ANalysis) and FALAPhyl (Forays into Automating Laborious Analyses of Phylogeny)—to address these challenges. FAVABEAN and FALAPhyl are Snakemake-based pipelines designed for flexible execution across local, cluster, and cloud environments. FAVABEAN automates preprocessing, ASV inference, and taxonomic assignment using DADA2 and FIGARO, integration of taxonomic knowledge when samples are sequenced with multiple primers using SMURF. FALAPhyl supports downstream analysis including alpha/beta diversity, network analysis, and differential abundance testing, with integrated provenance tracking. We validated both pipelines using three case studies involving oral microbiome datasets. In Case Study 1, we compared oral microbiota across family members and niches, showing primer-dependent variability in ASV-based similarity and minimal reseeding from familial sources after prophylaxis. Case Study 2 analyzed dental aerosol samples, revealing no significant microbial differences between pre-, intra-, and post-procedure air. Case Study 3, a randomized trial of a nitrate mouthrinse, demonstrated no significant microbiome shifts, highlighting oral microbial stability. FALAPhyl’s integration of DAtest enabled empirical evaluation of multiple statistical tests, aiding robust differential abundance inference. FAVABEAN and FALAPhyl offer a reproducible, automated solution for 16S rRNA amplicon data analysis. Their modular design, containerization, and provenance tracking enhance accessibility and scientific rigor in microbiome research.

Response by Stepanian and Jaffe to Letters Regarding Article, “Ponatinib, but Not the New Abl-Kinase Inhibitor Asciminib, Activates Platelets, Leukocytes, and Endothelial Cell TNF Signaling to Induce Atherosclerotic Plaque Inflammation, Myocardial Infarction, and Stroke”

Intrinsic attraction driving the high temperature performance of additively manufactured aluminum alloys

Abstract Developing additive manufacturing (AM) aluminum alloys with high temperature strength remains a formidable scientific challenge, primarily due to the strengthening precipitates coarsening above 200°C. Conventional heat-resistant alloy design strategies aim to hinder the precipitate coarsening by incorporating low diffusive alloying elements. However, such approaches remain ineffective against thermally driven defect mobilization, especially for vacancy diffusion and dislocation climbing, which are dominant drivers of high temperature weakening. As a result, most AM Al alloys exhibit a rapid decline in strength within this critical temperature range. Through reverse-engineering of intrinsic atom-defect/atom attraction, we employ an intrinsic attraction (IA) strategy to trigger multi-dimensional defect confinement mechanisms. This approach achieves: divacancy clusters anchoring free vacancies; solute atmospheres capturing mobile dislocations and suppressing creep deformation; specific segregation forming nanostructures at precipitate interfaces and interiors to inhibit coarsening. The AM heat-resistant Al alloy demonstrates satisfactory high temperature performance, exhibiting yield strengths of ~305 MPa at 300°C, ~190 MPa at 400°C, coupled with creep resistance at 200-400°C ( $$\dot{\varepsilon }$$ ε °  < 10 -7 /s) and prominent processability for large-size bladed disk. This strategy transcends the conventional empirical paradigm by engineering elemental segregation tendencies at specific sites, provides a universal design approach for the development of aluminum alloys or other high temperature structural materials.

Spatial heterogeneity of the nonlinear impact of built environment on suburban railway commuting willingness: Taking Guiyang Loop Line Railway as an example

This study takes the Guiyang Loop Line Railway as a case study and, based on resident commuting survey data, applies an XGBoost model combined with Individual Conditional Expectation (ICE) analysis to examine the threshold effects and non-linear spatial characteristics of the built environment on residents’ willingness to commute via the Loop Line Railway. The results indicate that: (1) population density, distance to the nearest bus stop, road network density, and distance to the city center are key built environment factors influencing commuting willingness. Among them, population density and road network density exhibit overall positive effects, whereas distance to the nearest bus stop and distance to the city center show negative effects; (2) the spatial distributions of the threshold effect magnitude (Δy) and the non-linear effect intensity (m) display a heterogeneous pattern broadly characterized by a “city center–suburban–peripheral” gradient, suggesting pronounced spatial non-stationarity in the relationship between the built environment and commuting willingness; (3) compared with the central urban area, residents living around suburban and peripheral stations are more sensitive to changes in bus feeder conditions, road network connectivity, and commuting distance, exhibiting stronger threshold effects and non-linear responses. These findings suggest that enhancing residents’ willingness to commute via the Loop Line Railway requires context-sensitive strategies that account for the built environment characteristics of different areas, with targeted improvements in bus–rail integration and road network conditions, rather than adopting uniform development and supporting policies across all stations.

Letter by Xu et al Regarding Article, “Ponatinib, But Not the New Abl-Kinase Inhibitor Asciminib, Activates Platelets, Leukocytes, and Endothelial Cell TNF Signaling to Induce Atherosclerotic Plaque Inflammation, Myocardial Infarction, and Stroke”

Experimental investigation of sustainable concrete production using ceramic waste powder as partial fine aggregate replacement

Universal thiourea coupling enhances electron and ion transport in quinone cathodes for aqueous zinc batteries

Quadratic programming-based autonomous cruise control of an intelligent tugboat

To address the multi-objective control problem of autonomous cruising, collision avoidance, and input constraints in intelligent tugboats, a quadratic programming-based autonomous cruise control method is proposed. The method enables the tugboat to reach the target location with prescribed speed, heading, and path while rigorously avoiding collisions within its actuation limits. First, a desired control input is derived using back-stepping and sliding mode control to ensure asymptotic stability of the tracking error. Second, based on Nagumo’s theorem, the positional constraints for safe collision avoidance of the tugboat are equivalently transformed into input constraints, effectively preventing any collisions with other vessels. Third, a unified controller is synthesized using a quadratic programming approach to optimally balance cruising control, collision avoidance, and input limitations. Finally, simulation results demonstrate that the proposed quadratic programming-based autonomous cruise control method enforces the prescribed safety distance and actuator limits, while avoiding large or persistent deviations from the reference trajectory and allowing the desired speed and heading to be re-established rapidly after the avoidance maneuver.

Aortic and Iliac Calcifications as Predictors of Aortic Dissection, Aneurysm Rupture, and Peripheral Vascular Disease: A Prospective Cohort Study from the DANCAVAS Trials

BACKGROUND: There is limited evidence of the relationship between aortic and iliac calcification and aortic events (aortic dissection or aneurysm rupture) and major adverse limb events (MALEs; peripheral revascularization and lower limb amputation). The aim of this population-based prospective cohort study was to investigate the association of aortic and iliac calcifications with aortic events and MALEs. METHODS: All participants from the DANCAVAS (Danish Cardiovascular Screening) trials who received a full thoracoabdominal aortic computed tomography scan with recorded measurements of aortic and iliac calcification were included. The aorta and iliac artery calcifications were measured in a 5-segment model and categorized into quartiles, apart from the ascending aorta, which was categorized into 4 exposure groups, as the majority of participants had no calcification in the ascending aorta. The participants were followed from inclusion in the DANCAVAS trial until aortic events, MALE, death, or end of follow-up on May 1, 2025. We used a competing risk hazard regression model adjusted for demographics, cardiovascular risk factors, aortic diameter, and ankle-brachial index. RESULTS: In total, 13 065 participants were included in this study (94% men; mean age, 67±4 years). Participants were followed for a mean of 8 years, during which 42 experienced an aortic event, and 311 experienced a MALE. The analyses of the aortic event outcome showed significantly increased subdistribution hazard ratios (SHRs) when having calcification scores in the fourth group or quartile for the ascending and abdominal aorta (SHR, 3.06 [95% CI, 1.15–8.16]; SHR, 7.61 [95% CI, 1.44–40.22], respectively). Calcification scores in the fourth group or quartile were strongly associated with MALEs in all segments: ascending aorta (SHR, 2.20 (95% CI, 1.56–3.10]), aortic arch (SHR, 6.49 [95% CI, 3.10–13.56]), descending aorta (SHR, 2.43; [95% CI, 1.45–4.08]), abdominal aorta (SHR, 7.89 [2.95–21.15]), and iliac arteries (SHR, 13.52 [95% CI, 4.32–42.24]). CONCLUSIONS: Severe aortic and iliac calcification was associated with significantly higher risk of aortic events and MALEs, suggesting that quantifying aortic calcification may provide valuable prognostic information and potentially improve the risk stratification in patients with aortic aneurysm or peripheral artery disease.

Deep sleep slow wave–spindle coupling is selectively linked to plasma amyloid-β levels in older adults in clinical trials

Horticultural intensification and plant-based diets of 18th century CE Waikato Māori in Aotearoa New Zealand

Expanding the toolkit of LacI/GalR chimeras

When creating synthetic transcription circuits, multi-input regulation is desirable. However, the size and complexity of prokaryotic circuits are constrained by the number of transcription factors that can simultaneously bind a promoter region. This limitation has been circumvented by leveraging the conserved architecture of LacI/GalR transcription repressors: The DNA binding domain of one repressor can be fused to paralogous ligand binding domains that bind different allosteric ligands; function can be optimized by mutating domain interfaces. When such chimeras were used in prior studies to co-regulate transcription, their set of allosteric ligands conveyed Boolean “AND”, “NOT”, and “NOR” logic from a single DNA operator. Here, we report construction and characterization of additional chimeras that can be used to expand the LacI/GalR toolkit. For both novel and previously reported chimeras, we assessed (and in most cases ruled out) cross reactivity among their ligands. As such, we propose that three of the novel chimeras, along with a previously uncharacterized fourth chimera, could be co-expressed in engineered systems to expand the options available for Boolean “AND” logic. Gratuitous inducers were identified for another prior chimera that would allow “OR” logic using a single transcription factor. Surprisingly, another novel chimera was anti-induced by the ligand that induces its parent protein. This allosteric switch illustrates what may be a general feature of the LacI/GalR proteins: they appear poised to switch between induction and anti-induction via changes in ligands or amino acid mutations. Practically speaking, this anti-induced chimera could be co-expressed with a previous anti-induced chimera to perform “NOR” logic.

Correction to: 2025 ACC/AHA/HRS/ISACHD/SCAI Guideline for the Management of Adults With Congenital Heart Disease: A Report of the American College of Cardiology/American Heart Association Joint Committee on Clinical Practice Guidelines

Evaluation and analysis of brittleness and acoustic emission characteristics of tight sandstone under the influence of acid-treatment

Abstract Acid treatment has been proven to effectively reduce reservoir fracture pressure, but the variation pattern of sandstone brittleness after acid treatment remains unclear. To effectively evaluate the characteristics of brittleness changes, uniaxial compression tests were conducted on tight sandstone subjected to acid treatment for different durations, and a brittleness index evaluation method based on radial strain response was established. The results show that sandstone uniaxial compressive strength decreases stepwise with prolonged acid treatment. Elastic modulus decreases slowly initially, drops sharply after 24 h of acid treatment, and stabilizes between 120 and 168 h. Poisson’s ratio decreases linearly after 6 h of acid treatment. The brittleness index first increases and then decreases, peaking at 12–24 h of acid treatment—consistent with AE results showing more high-intensity signals during the elastic compression stage of axial stress-strain curves. After acid treatment, sandstone crack initiation stress first increases slowly, then gradually decreases, and finally drops rapidly. This is attributed to acid-rock reaction-induced dissolution of minerals and cementing materials, which detaches fine-grained matrix particles, increases porosity, and reduces crack initiation stress. The findings provide a reference for engineering design and construction of high fracture pressure tight sandstone reservoirs.

High-resolution mapping reveals features of bacterial NAD-capped RNAs and stress-responsive transcription initiation

Determinants of tuberculosis presentation and successful treatment outcome among tuberculosis patients in Geita, Tanzania

The Geita Region of Tanzania is known as critical focal point for tuberculosis (TB) control due to its persistently high disease burden and unique socio-economic landscape. Despite this, limited research has explored how sociodemographic and clinical factors influence TB presentation (pulmonary versus extrapulmonary) and successful treatment outcome. This study aimed to identify these factors within this community to inform targeted interventions. We conducted a retrospective cohort study of TB cases aged 15 years and above, who were notified in Geita Region from January 2017 to December 2020. Data were obtained from the national TB program registers, and included sociodemographic, clinical, and treatment information. The primary outcomes were TB presentation (Pulmonary vs. Extrapulmonary) and treatment outcome, categorized as successful (a composite of “cured” and “treatment completed”) or unsuccessful (death, failure, and loss to follow-up). Multivariable binary logistic regression was applied to assess associations with TB presentation and treatment outcomes, including potential interaction effects between factors. Statistical analyses were performed using SAS OnDemand for initial data cleaning, and Stata 17.0 for all statistical modeling. A total of 13,107 TB cases were included, of which 12,032 (91.9%) pulmonary TB and 1,058 (8.1%) extrapulmonary TB. Logistic regression showed workplace significantly associated with presentation: prisoners had lower odds of pulmonary TB compared to miners (OR 0.26, 95% CI 0.12–0.58). Community-referred cases had higher odds of pulmonary TB than self-referred cases (OR 1.24, 95% CI 1.06–1.45). New TB cases had lower odds of pulmonary TB compared with relapse (OR 0.33, 95% CI 0.15–0.75). Age × sex and HIV × sex interactions associated with differential presentation risks. Treatment success was achieved in 12,385 patients (95.5%), while 581 (4.5%) experienced unsuccessful outcomes. Predictors of successful treatment included age < 60 years (OR 1.31, 95% CI 1.05–1.65), new TB status (OR 2.45, 95% CI 1.53–3.93), and HIV-negative status (OR 1.90, 95% CI 1.53–2.37). Workplace, referral source, and HIV status significantly influence TB presentation and treatment outcomes. Implementation targeted interventions, including strengthened occupational health policies, enhanced community-based screening, and focused strategies for high-risk groups is essential to improving TB control in Tanzania.

Local shear mechanical behavior of rock joint under constant normal load

Dissecting PGE2-driven inhibition of T cell activation using single-cell multi-omic and inflammatory bowel disease genetic association analysis

State impulsivity and substance use: A systematic review and meta-analysis protocol

The association between substance use and impulsivity has been documented extensively in the literature. More recently, there has been a shift from viewing impulsivity solely as a stable trait toward examining its moment-to-moment expression in everyday life and how these fluctuations influence substance use. Despite this growing interest, there has not yet been a comprehensive meta-analysis synthesizing findings across studies. Existing reviews have largely focused on trait-level impulsivity, which limits our understanding of how impulsivity operates across real-world contexts. The aim of this proposed meta-analysis is to integrate these findings and quantify the strength of the association between everyday impulsivity and substance use, specifically alcohol, cannabis, and tobacco use. In addition, we aim to identify key moderators of this relationship. For example, we will evaluate whether the strength of association differs by substance (e.g., alcohol vs. cannabis vs. tobacco), by sample characteristics (substance-dependent vs. community), and by methodological factors. We will search major databases (e.g., PsycINFO, PubMed, Web of Science) for peer-reviewed studies as well as unpublished studies reporting associations between everyday impulsivity and substance use. Random-effects models will estimate pooled effect sizes, and subgroup/meta-regression analyses will test moderators. Overall, this proposed meta-analysis aims to provide a comprehensive estimate of the association between everyday impulsivity and alcohol, cannabis, and tobacco use.