Search Results (108)

Reactive transport in porous media exists ubiquitously in natural and industrial systems—reformation of geological energy repository, carbon dioxide (CO${}_2$) sequestration, CO${}_2$ storage via mineralization, and soil remediation are just some examples where geo-/bio-chemical reactions play a key role. Reactive transport models are expected to provide assessments of (1) the effective property variation and (2) the reaction capability. However, the synergy among flow, solute transport, and reaction undermines the predictability of the existing model. In recent decades, the Micro-Continuum Approach (MCA) has demonstrated advantages for modeling pore-scale reactive transport and high accuracy compared with experiments. In this study, we present an MCA-based numerical framework that simulates dissolution/erosion or precipitation in digital rocks. The framework imports two- or three-dimensional digital rock samples, conducts reactive transport simulations, and evaluates dynamic changes in porosity, surface area, permeability tensor, tortuosity, mass change, and reaction rate. The results show that samples with similar effective properties, e.g., porosity or permeability, may exhibit different reaction abilities, suggesting that the pore-scale geometry has a strong impact on reactive transport. Additionally, the numerical framework demonstrates the advantage of conducting multiple reaction studies on the same sample, in contrast to reality, where there is often only one physical experiment. This advantage enables the identification of the optimal condition, quantified by the dimensionless P$\acute{\mathrm{e}}$clet number and Damk$\ddot{\mathrm{o}}$hler number, to reach the maximum reaction. We believe that the newly developed framework serves as a toolbox for evaluating reactivity capacity and predicting effective properties of digital samples. Full article

Chromophobe renal cell carcinoma (chRCC) is a distinct subtype of non–clear cell renal cell carcinoma (ncRCC), arising from intercalated cells of the distal nephron collecting ducts. No standard treatments are specifically approved for chRCC, which is further hindered by lack of a universally accepted grading system. This study sought to find molecular drivers that may aid in the diagnosis or development of treatments for chRCC. A retrospective analysis of chRCC was conducted using data from the American Association for Cancer Research (AACR) Project Genomics Evidence Neoplasia Information Exchange (GENIE) repository, accessed through cBioPortal (version 17.0-public) on 21 July 2025. The study examined recurrent somatic mutations and assessed co-occurrence with Benjamini–Hochberg False Discovery Rate (FDR) correction. Additional analyses evaluated mutation by sex and race, with significance set at p < 0.05. The cohort included 180 tumor samples from 170 chRCC patients. Most patients were adults (n = 167, 98.2%) and White (n = 115, 67.6%). Recurrent alterations occurred in genes part of the p53, PI3K/mTOR, Hippo, and NOTCH signaling pathway. Exploratory demographic analyses identified isolated single-patient mutations in select genes across sex and race; however, these rare events are not interpretable as population-level differences. This study provides a comprehensive genomic profile of chRCC across multiple demographic categories. Full article

Biodegradable polyesters have gained attention due to their sustainability benefits, considering the escalating environmental challenges posed by synthetic polymers. Advances in artificial intelligence (AI), including machine learning (ML) and deep learning (DL), are expected to significantly accelerate research in polymer science. This review article explores “bio” polymer informatics by harnessing insights from the AI techniques used to predict structure–property relationships and to optimize the synthesis of bioplastics. This review also discusses PolyID, a machine learning-based tool that employs message-passing graph neural networks to provide a framework capable of accelerating the discovery of bioplastics. An extensive literature review is conducted on explainable AI (XAI) and generative AI techniques, as well as on benchmarking data repositories in polymer science. The current state-of-the art in ML methods for ring-opening polymerizations and the synthesizability of biodegradable polyesters is also presented. This review offers an in-depth insight and comprehensive knowledge of current AI-based models for polymerizations, molecular descriptors, structure–property relationships, predictive modeling, and open-source benchmarked datasets for sustainable polymers. This study serves as a reference and provides critical insights into the capabilities of AI for the accelerated design and discovery of green polymers aimed at achieving a sustainable future. Full article

This paper presents a methodology for extracting and simulating arterial pulse waveform signals from Fabry–Perot interferometric measurements, emphasizing a practical approach for noninvasive cardiovascular assessment. A key novelty of this work is the presentation of a complete Python-based processing pipeline, which is made publicly available as open-source code on GitHub (git version 2.39.5). To the authors’ knowledge, no such repository for demodulating these specific interferometric signals to obtain a raw arterial pulse waveform previously existed. The proposed system utilizes accessible Python-based preprocessing steps, including outlier removal, Butterworth high-pass filtering, and min–max normalization, designed for robust signal quality even in settings with common physiological artifacts. Key features such as the rate of change, the Hilbert transform of the rate of change (envelope), and detected extrema guide the signal reconstruction, offering a computationally efficient pathway to reveal its periodic and phase-dependent dynamics. Visual analyses highlight amplitude variations and residual noise sources, primarily attributed to sensor bandwidth limitations and interpolation methods, considerations critical for real-world deployment. Despite these practical challenges, the reconstructed arterial pulse waveform signals provide valuable insights into arterial motion, with the methodology’s performance validated on measurements from three subjects against synchronized ECG recordings. This demonstrates the viability of Fabry–Perot sensors as a potentially cost-effective and readily implementable tool for noninvasive cardiovascular diagnostics. The results underscore the importance of precise yet practical signal processing techniques and pave the way for further improvements in interferometric sensing, bio-signal analysis, and their translation into clinical practice. Full article

Background/Objectives: Iron stores accrued in utero are critical for fetal and infant neurodevelopment. Low neonatal hemoglobin (Hb) may indicate inadequate iron capture and storage. Prior studies differ on whether and under what conditions maternal anemia predicts neonatal Hb; whether sex differences are present is unknown. Methods: Maternal and neonatal Hb and sociodemographic and health characteristics were abstracted from electronic medical records for biorepository participants at a tertiary academic medical center. Maternal anemia was defined as Hb < 11 g/dL in trimesters T1 and T3 and Hb < 10.5 g/dL in T2. Adjusted linear regression models were used to estimate associations of maternal anemia with neonatal Hb. Sex differences were evaluated with product terms and stratification. Results: In 228 participants with maternal Hb measured, the prevalence of prenatal (pre-delivery) and delivery anemia was 54% and 44%, respectively. Maternal race and ethnicity but no other sociodemographic characteristics were associated with maternal anemia. Neonatal hematology was available for 114 newborns < 7 days old (50%; 52% male). The median (IQR) neonatal Hb was 16.7 g/dL (14.9, 18.0) and did not differ by sex, but it was lower among infants of mothers with vs. without delivery anemia (15.9 vs. 17.1, p = 0.032) and those identifying as Black vs. Hispanic or other (16.0, 17.9, 17.0, respectively; p = 0.003). Independent associations of maternal anemia and race and ethnicity with neonatal Hb were stronger in males and attenuated to null in females. Conclusions: Maternal anemia was highly prevalent and associated sex-specifically with neonatal Hb independent of maternal race and ethnicity. Future studies to replicate these findings with a more comprehensive panel of iron biomarkers are needed. Functional consequences of greater susceptibility to risk factors for low neonatal Hb in male infants need to be further investigated. Full article

The major objective was to investigate the protective capabilities of endophytic bacterial strains isolated from a number of medicinal plant species towards Aspergillus spp. secured from the internal tissues of fungi-infected peanuts. Among 32 fungal isolates surveyed for mycotoxin production in various culture media (PDA, RBCA, YES, CA), 10 isolates qualitatively producing AFB₁, besides 10 OTA-producers, were assayed by HPLC for quantitative toxin production. Aspergillus spp. isolate Be 13 produced an extraordinary quantity of 1859.18 μg mL⁻¹ AFB₁, against the lowest toxin level of 280.40 μg mL⁻¹ produced by the fungus isolate IS 4. The estimated amounts of OTA were considerably lower and fell in the range 0.88–6.00 μg mL⁻¹; isolate Sa 1 was superior, while isolate Be 7 seemed inferior. Based on ITS gene sequencing, the highly toxigenic Aspergillus spp. isolates Be 13 and Sa 1 matched the description of A. novoparasiticus and A. ochraceus, respectively, ochraceus, respectively, which are present in GenBank with identity exceeding 99%. According to 16S rRNA gene sequencing, these antagonists labeled Ar6, Ma27 and So34 showed the typical characteristics of Pseudomonas aeruginosa, Bacillus subtilis and Bacillus velezensis, respectively, with similarity percentages of 99–100. The plant growth-promoting activity measurements of the identified endophytes indicated the production of 16.96–80.00 μg/100 mL culture medium of IAA. Phosphate-solubilizing capacity varied among endophytes from 2.50 to 21.38 μg/100 mL. The polysaccharide production pool of bacterial strains ranged between 2.74 and 6.57 mg mL⁻¹. P. aeruginosa Ar6 and B. velezensis successfully produced HCN, but B. subtilis failed. The in vitro mycotoxin biodegradation potential of tested bacterial endophytes indicated the superiority of B. velezensis in degrading both mycotoxins (AFB₁-OTA) with average percentage of 88.7; B. subtilis ranked thereafter (85.6%). The 30-day old peanut (cv. Giza 6) seedlings grown in gnotobiotic system severely injured due to infection with AFB₁/OTA-producing fungi, an effect expressed in significant reductions in shoot and root growth traits. Simultaneous treatment with the endophytic antagonists greatly diminished the harmful impact of the pathogens; B. velezensis was the pioneer, not P. aeruginosa Ar6. In conclusion, these findings proved that several endophytic bacterial species have the potential as alternative tools to chemical fungicides for protecting agricultural commodities against mycotoxin-producing fungi. Full article

Many endodontic procedures within the pediatric population are performed with patients aged 12 years and older, using intracanal irrigants to complement mechanical debridement for the removal of debris and to disinfect the root canal system. The use of antimicrobial irrigants that limit damage to the dental pulp are the goals of endodontic biomaterials research. Using an existing biorepository of dental pulp stem cells (DPSCs), Endocyn was evaluated in varying concentrations in proliferation and viability assays, and compared with positive (sodium hypochlorite or bleach) and negative (phosphate-buffered saline) controls. The DPSC viability was reduced in the range of −8.3% to −15.8%, p = 0.22 to p = 0.042, while the growth inhibition varied between −29.7% and −63%, p = 0.041 to p = 0.022. However, the RNA analysis revealed that no significant changes in biomarker mRNA expression (Nestin, NANOG, Sox2, Oct4, CD73, CD90, and CD105) were observed. These data demonstrated that all of the concentrations of Endocyn inhibited the DPSC viability and growth, although only high concentrations were statistically significant. Moreover, the administration of Endocyn did not alter the DPSC biomarker expression, which are novel and important findings not previously observed or reported that may assist with the development of clinical decision protocols and methods for the treatment of vital pulp tissue. Full article

Background/Objectives: Tuberculosis (TB) remains a major global health issue, further complicated by the COVID-19 pandemic. This study assesses the clinical outcomes of TB-COVID-19-coinfected patients compared to those with TB disease alone at an Italian infectious disease hospital during the pandemic’s first two years. Methods: Retrospective data analysis was conducted on TB patients hospitalized from March 2020 to June 2022. Data included demographics, comorbidities, clinical characteristics, and outcomes. Coinfection was defined as concurrent TB disease and SARS-CoV-2 infection. Statistical methods included Fisher’s exact test and Mann–Whitney statistics. Results: Of 267 TB patients, 25 (9.4%) had concurrent COVID-19 infection. The TB-COVID-19 group showed higher rates of diabetes and cough. Acute respiratory failure was more prevalent in coinfected patients (odds ratio, 5.99), and coinfection was associated with worse outcomes compared to TB alone (odds ratio, 0.15). Despite similar socio-demographic factors, the coexistence of TB and COVID-19 led to exacerbated respiratory failure and increased mortality. Conclusions: Coinfection with TB and COVID-19 significantly increases the risk of acute respiratory failure and poor outcomes. Clinicians should be aware of this risk, especially in patients with pulmonary involvement. Although specific protocols are unavailable, prompt diagnosis and management may enhance outcomes. Additional research is necessary to understand the long-term effects of TB-COVID-19 coinfection, particularly as COVID-19 becomes endemic. Full article

APOL1 Renal Risk Variants (APOL1RRVs, G1, and G2) are known to be toxic to glomerular podocytes and causally associated with an enhanced prevalence and progression of many different etiologies of chronic kidney disease (CKD), leading to the delineation of a new disease designation of APOL1-Mediated Kidney Disease (AMKD). Notably, APOL1RRVs have not consistently been shown to increase the prevalence or severity of diabetic kidney disease (DKD) progression, which is the most common cause of End-Stage Kidney Disease (ESKD). While this apparent discrepancy seems perplexing, its clarification should provide important mechanistic and therapeutic insights. Activation of the Renin–Angiotensin System (RAS) plays a critical role in the development and progression of DKD. Recent in vitro and in vivo studies also demonstrated that RAS activation contributes to kidney cell injury in AMKD experimental models. Both high glucose, as well as APOL1RRVs escalate the podocyte expression of miR193a, a known mediator of glomerulosclerosis, including idiopathic Focal Segmental Glomerular Sclerosis (FSGS) and DKD. We propose that either the RAS and/or miR193a levels in the diabetic milieu are already maximally conducive to kidney target cell injury and, therefore, are agnostic to further injury in response to APOL1RRVs. Similarly, the contributory role of hypertension (which is frequently reported as the second most common cause of ESKD) in the progression of AMKD remains a controversial issue. Since several clinical reports have shown that controlling hypertension does not consistently slow the progression of AMKD, this has led to a formulation wherein APOL1-RRVs primarily lead to kidney injury with accompanying hypertension. Notably, half a decade later, the notion that hypertension is not a cause but rather a consequence of kidney injury was contested by investigators analyzing the Mount Sinai BioMe repository, a comprehensive clinical and genetic database including participants with APOL1RRVs. These investigators observed that hypertension predated the observed decline in GFR in individuals with APOL1RRVs by ten years. In the present study, we discuss the mechanistic forces that may underpin the gaps in these clinical manifestations, which did not allow the temporal association of hypertension with AMKD to be translated into causation and may also dissociate DKD and AMKD. We have hypothesized models that need to be validated in future experimental studies. Full article

Reproductive technologies, including sperm cryopreservation, offer conservationists enhanced capacity to genetically manage populations and improve the outcomes of conservation breeding programs (CBPs). Despite this potential, the post-thaw quality of amphibian sperm is highly variable following cryopreservation, and research focused on protocol refinement is needed. The aim of this study was twofold: (1) to investigate the effect of the addition of bovine serum albumin (BSA) to the cryopreservation medium (pre-freeze), and (2) the effect of the addition of caffeine to the activation medium (post-thaw), on post-thaw sperm characteristics in the critically endangered Booroolong frog (Litoria booroolongensis). Spermic urine samples were collected from 14 male frogs following hormonal induction of spermiation, and each sample was split among three cryopreservation treatments, where the cryopreservation medium contained either 0 (control), 0.5, or 1% BSA (w/v). Samples were cryopreserved and thawed, and sperm motility was then activated in one of two activation treatments: Milli-Q water (control) or Milli-Q water plus 4.5 mM caffeine. Sperm viability (proportion live/dead) was assessed using fluorescent microscopy, and sperm motility metrics were evaluated using computer-assisted sperm analysis (CASA). Results from this study showed that BSA concentration had no effect on post-thaw sperm viability. Additionally, neither BSA concentration nor activation in caffeine influenced post-thaw sperm motility characteristics (total motility, forward progressive motility, and velocity). Assessment time of sperm motility varied from 5 to 13 min post-activation and was significantly correlated with each motility measure, with motility and velocity metrics decreasing as time post-activation increased. The results reported herein provide no evidence for an effect of BSA or caffeine at the concentrations tested on post-thaw sperm characteristics in the Booroolong frog, but they highlight the time-sensitive nature of sperm assessment post-thaw and implications for the timing of sperm handling during assisted fertilisation efforts. Full article

Background/Objectives: Hemolysis has been associated with acute kidney injury (AKI) in infants and neonates after surgery involving cardiopulmonary bypass (CPB). Erythrocyte hemolysis and subsequent end-organ injury have been shown to be a complex process involving the liberation of multiple molecules that mediate the loss of nitric oxide and oxidative damage. This study assesses the association of multiple products of erythrocyte hemolysis with the evolution of AKI in neonates and infants undergoing CPB surgery. Methods: Blood and urine samples were collected at multiple time points before and after CPB and stored within an institutional biorepository. Twenty-one patients with AKI were matched with twenty-one non-Aki patients based on demographic and case complexity data. Results: Samples were analyzed for cell-free hemoglobin, heme, non-transferrin-bound iron, haptoglobin, hemopexin, and nitrite/nitrate. NGAL and KIM-1 were measured to index AKI. Cell-free hemoglobin was higher, haptoglobin was lower, and haptoglobin:hemoglobin ratio was lower in AKI compared to non-AKI patients. Conclusions: AKI in neonates and infants after CPB is associated with a pre and postoperative decrease in serum haptoglobin. These results confirm the need for future studies to prevent injury from hemolysis during CPB and potentially identify at-risk patients with decreased haptoglobin levels before surgery if delay is an option. Full article

Background: Pregnancy is a unique stage of the life course characterized by trade-offs between the nutritional, immune, and metabolic needs of the mother and fetus. The Camden Study was originally initiated to examine nutritional status, growth, and birth outcomes in adolescent pregnancies and expanded to study dietary and molecular predictors of pregnancy complications and birth outcomes in young women. Methods: From 1985–2006, 4765 pregnant participants aged 12 years and older were recruited from Camden, NJ, one of the poorest cities in the US. The cohort reflects a population under-represented in perinatal cohort studies (45% Hispanic, 38% non-Hispanic Black, 17% White participants; 98% using Medicaid in pregnancy). Study visits, including questionnaires, dietary assessments, and biospecimen collection, occurred in early and late pregnancy as well as at delivery. Medical records were abstracted, and a subset of mothers and infants participated in a six-week postpartum visit. Results: Findings from the Camden Study have added to the understanding of adolescent and young adult maternal health and perinatal outcomes. These include associations of adolescent linear growth while pregnant with smaller neonatal birth size, low dietary zinc intake in early pregnancy with increased risk of delivery <33 gestational weeks, and higher circulating fatty acid levels with greater insulin resistance. More recent analyses have begun to unpack the biochemical pathways in pregnancy that may be shaped by race as an indicator of systemic racism. Conclusions: The Camden Study data and biorepositories are well-positioned to support future research aimed at better understanding perinatal health in under-represented women and infants. Linkages to subsequent health and administrative records and the potential for recontacting participants over 18–39 years after initial participation may provide key insights into the trajectories of maternal and child health across the life course. Full article

The Chinese sturgeon (Acipenser sinensis) is an ancient, complex autooctoploid fish species that is currently facing conservation challenges throughout its distribution. To comprehensively characterize the expression profiles of genes and their associated biological functions across different tissues, we performed a transcriptome-scale gene expression analysis, focusing on housekeeping genes (HKGs), tissue-specific genes (TSGs), and co-expressed gene modules in various tissues. We collected eleven tissues to establish a transcriptomic repository, including data from Pacific Biosciences isoform sequencing (PacBio Iso-seq) and RNA sequencing (RNA-seq), and then obtained 25,434 full-length transcripts, with lengths from 307 to 9515 bp and an N50 of 3195 bp. Additionally, 20,887 transcripts were effectively identified and classified as known homologous genes. We also identified 787 HKGs, and the number of TSGs varied from 25 in the liver to 2073 in the brain. TSG functions were mainly enriched in certain signaling pathways involved in specific physiological processes, such as voltage-gated potassium channel activity, nervous system development, glial cell differentiation in the brain, and leukocyte transendothelial migration in the spleen and pronephros. Meanwhile, HKGs were highly enriched in some pathways involved in ribosome biogenesis, proteasome core complex, spliceosome activation, elongation factor activity, and translation initiation factor activity, which have been strongly implicated in fundamental biological tissue functions. We also predicted five modules, with eight hub genes in the brown module, most of which (such as rps3a, rps7, rps23, rpl11, rpl17, rpl27, and rpl28) were linked to ribosome biogenesis. Our results offer insights into ribosomal proteins that are indispensable in ribosome biogenesis and protein synthesis, which are crucial in various cell developmental processes and neural development of Chinese sturgeon. Overall, these findings will not only advance the understanding of fundamental biological functions in Chinese sturgeon but also supply a valuable genetic resource for characterizing this extremely important species. Full article

With the rapid expansion of cloud computing and the pervasive growth of IoT across industries and educational sectors, the need for efficient remote data management and service orchestration has become paramount. Web services, facilitated by APIs, offer a modular approach to integrating and streamlining complex business processes. However, real-time monitoring and optimal service selection within large-scale, cloud-based repositories remain significant challenges. This study introduces the novel Improved Eagle Strategy (IES) hybrid model, which uniquely integrates bio-inspired optimization with clustering techniques to drastically reduce computation time while ensuring highly accurate service selection tailored to specific user requirements. Through comprehensive NetLogo simulations, the IES model demonstrates superior efficiency in service selection compared to existing methodologies. Additionally, the IES model’s application through a web dashboard system highlights its capability to manage both functional and non-functional service attributes effectively. When deployed on real-time IoT devices, the IES model not only enhances computation speed but also ensures a more responsive and user-centric service environment. This research underscores the transformative potential of the IES model, marking a significant advancement in optimizing cloud computing processes, particularly within the IoT ecosystem. Full article