Pub Date : 2025-12-30DOI: 10.1016/j.isci.2025.114579
Seung-Taek Park , Jina Won , Siyeon Jin , Sujin Kim , Haeun Shin , Su Hyun Lim , Ye-Ji Bang , Hyun Jik Kim
The nasopharynx (NP) serves as a primary site for localized immune responses that restrict the spread of SARS-CoV-2 to the lower respiratory tract. The microbiome is increasingly recognized as a key modulator of antiviral immunity but whether it shapes immune responses in upper airway remains uncharacterized. Detailed microbial profiles revealed that S. aureus complex abundance was the primary discriminating factor of microbial community in the NP and the enhanced abundance of S. aureus complex correlated with higher frequencies of CD4+, CD8+ tissue-resident memory T (TRM), and BRM cells. The abundance of S. aureus complex was closely associated with distinct metabolic pathways, particularly those involved in nitrogen metabolism (e.g., arginine, ornithine, and proline interconversion) and the mevalonate pathway for carotenoid biosynthesis. These findings suggest that S. aureus complex may foster unique metabolic dynamics in the NP in enhancing the tissue-residency of memory cells and localized immune responses in upper airway.
{"title":"Distinct commensal bacteria in human nasopharyngeal lymphoid tissue associated with localized immunological memory","authors":"Seung-Taek Park , Jina Won , Siyeon Jin , Sujin Kim , Haeun Shin , Su Hyun Lim , Ye-Ji Bang , Hyun Jik Kim","doi":"10.1016/j.isci.2025.114579","DOIUrl":"10.1016/j.isci.2025.114579","url":null,"abstract":"<div><div>The nasopharynx (NP) serves as a primary site for localized immune responses that restrict the spread of SARS-CoV-2 to the lower respiratory tract. The microbiome is increasingly recognized as a key modulator of antiviral immunity but whether it shapes immune responses in upper airway remains uncharacterized. Detailed microbial profiles revealed that <em>S</em>. <em>aureus</em> complex abundance was the primary discriminating factor of microbial community in the NP and the enhanced abundance of <em>S</em>. <em>aureus</em> complex correlated with higher frequencies of CD4<sup>+</sup>, CD8<sup>+</sup> tissue-resident memory T (T<sub>RM</sub>), and B<sub>RM</sub> cells. The abundance of <em>S</em>. <em>aureus</em> complex was closely associated with distinct metabolic pathways, particularly those involved in nitrogen metabolism (e.g., arginine, ornithine, and proline interconversion) and the mevalonate pathway for carotenoid biosynthesis. These findings suggest that <em>S</em>. <em>aureus</em> complex may foster unique metabolic dynamics in the NP in enhancing the tissue-residency of memory cells and localized immune responses in upper airway.</div></div>","PeriodicalId":342,"journal":{"name":"iScience","volume":"29 2","pages":"Article 114579"},"PeriodicalIF":4.1,"publicationDate":"2025-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145975590","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-30DOI: 10.1016/j.isci.2025.114586
Francesca Giordano , Francesca Troilo , Martina Roberta Nastasi , Lorenzo Caruso , Marta Mellini , Carlo Travaglini-Allocatelli , Giorgio Giardina , João B. Vicente , Giordano Rampioni , Adele Di Matteo , Elena Forte , Alessandro Giuffrè
Hydrogen sulfide is an important signaling molecule, beneficial at physiological concentrations but harmful at higher levels, due to which a tight control of its bioavailability is essential. Here, we investigated persulfide dioxygenase, an enzyme involved in H2S catabolism, from the pathogen Pseudomonas aeruginosa (PaPDO). Deletion of the gene pdo led to a 4-fold increase in H2S concentration, confirming its physiological role. The recombinant enzyme was structurally characterized at 2.06 Å resolution and assigned to the metallo-β-lactamase superfamily. Compared with its human homolog, PaPDO displayed a different dimerization area and a larger active site, suggesting different substrate preferences. Functionally, PaPDO catalyzed glutathione persulfide dioxygenation with a high turnover rate, and its activity was enhanced by reduced glutathione. Interestingly, the results show that PaPDO binds to nitric oxide, which reversibly inhibits its catalytic activity. These findings reveal a novel mechanism of crosstalk between hydrogen sulfide and nitric oxide signaling and provide insights into redox regulation in a multidrug-resistant pathogen.
{"title":"Structure and function of persulfide dioxygenase from Pseudomonas aeruginosa: Implications on H2S homeostasis and interplay with nitric oxide","authors":"Francesca Giordano , Francesca Troilo , Martina Roberta Nastasi , Lorenzo Caruso , Marta Mellini , Carlo Travaglini-Allocatelli , Giorgio Giardina , João B. Vicente , Giordano Rampioni , Adele Di Matteo , Elena Forte , Alessandro Giuffrè","doi":"10.1016/j.isci.2025.114586","DOIUrl":"10.1016/j.isci.2025.114586","url":null,"abstract":"<div><div>Hydrogen sulfide is an important signaling molecule, beneficial at physiological concentrations but harmful at higher levels, due to which a tight control of its bioavailability is essential. Here, we investigated persulfide dioxygenase, an enzyme involved in H<sub>2</sub>S catabolism, from the pathogen <em>Pseudomonas aeruginosa</em> (<em>Pa</em>PDO). Deletion of the gene <em>pdo</em> led to a 4-fold increase in H<sub>2</sub>S concentration, confirming its physiological role. The recombinant enzyme was structurally characterized at 2.06 Å resolution and assigned to the metallo-β-lactamase superfamily. Compared with its human homolog, <em>Pa</em>PDO displayed a different dimerization area and a larger active site, suggesting different substrate preferences. Functionally, <em>Pa</em>PDO catalyzed glutathione persulfide dioxygenation with a high turnover rate, and its activity was enhanced by reduced glutathione. Interestingly, the results show that <em>Pa</em>PDO binds to nitric oxide, which reversibly inhibits its catalytic activity. These findings reveal a novel mechanism of crosstalk between hydrogen sulfide and nitric oxide signaling and provide insights into redox regulation in a multidrug-resistant pathogen.</div></div>","PeriodicalId":342,"journal":{"name":"iScience","volume":"29 2","pages":"Article 114586"},"PeriodicalIF":4.1,"publicationDate":"2025-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145975712","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-30eCollection Date: 2026-01-16DOI: 10.1016/j.isci.2025.114384
Elle Jingjing Xu, Dat Tien Trong Cao, Xin Xu, Judith J Rakowski, Luan Van Nguyen, Laure Joanny, James L Slade, Tamara D Herold, Trung Tien Cao, Meredith L Gore
Integrating local community knowledge can enhance understanding of conservation crimes when existing knowledge relies primarily on expert elicitation. We adapted place network investigations (PNI) to structure community and expert knowledge gathering about wildlife poaching around Pù Mát National Park, Vietnam. Using participatory mapping, we identified the distribution of PNI's four crime-associated place types: corruption spots, comfort spaces, convergence settings, and crime sites. We compared knowledge between conservation experts and local villagers, then explored spatial patterns of these locations. Analyses revealed previously neglected places extending beyond park boundaries. Communities contributed more extensive knowledge than experts, particularly regarding convergence settings and corruption spots. Three crime-associated place types showed positive spatial autocorrelation, with identified clusters indicating intervention priorities. This participatory approach facilitated stakeholder knowledge exchange and broadened understanding of poaching-associated spaces. Findings suggest theoretical advancements concerning spatial commonalities and distinctions between conservation and violent crime, offering a replicable model for conservation crime prevention.
{"title":"Exploring neglected places enabling conservation crime through place network investigations.","authors":"Elle Jingjing Xu, Dat Tien Trong Cao, Xin Xu, Judith J Rakowski, Luan Van Nguyen, Laure Joanny, James L Slade, Tamara D Herold, Trung Tien Cao, Meredith L Gore","doi":"10.1016/j.isci.2025.114384","DOIUrl":"10.1016/j.isci.2025.114384","url":null,"abstract":"<p><p>Integrating local community knowledge can enhance understanding of conservation crimes when existing knowledge relies primarily on expert elicitation. We adapted place network investigations (PNI) to structure community and expert knowledge gathering about wildlife poaching around Pù Mát National Park, Vietnam. Using participatory mapping, we identified the distribution of PNI's four crime-associated place types: <i>corruption spots</i>, <i>comfort spaces</i>, <i>convergence settings</i>, and <i>crime sites</i>. We compared knowledge between conservation experts and local villagers, then explored spatial patterns of these locations. Analyses revealed previously neglected places extending beyond park boundaries. Communities contributed more extensive knowledge than experts, particularly regarding <i>convergence settings</i> and <i>corruption spots</i>. Three crime-associated place types showed positive spatial autocorrelation, with identified clusters indicating intervention priorities. This participatory approach facilitated stakeholder knowledge exchange and broadened understanding of poaching-associated spaces. Findings suggest theoretical advancements concerning spatial commonalities and distinctions between conservation and violent crime, offering a replicable model for conservation crime prevention.</p>","PeriodicalId":342,"journal":{"name":"iScience","volume":"29 1","pages":"114384"},"PeriodicalIF":4.1,"publicationDate":"2025-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12834101/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146058389","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-30DOI: 10.1016/j.isci.2025.114578
Ruirui Zhu , Hao Tian , Fangfang Zou , Hongfang Mo , Yulian Xi , Xingrong Lu , Chunyan Yang , Deshun Shi , Jianghua Shang , Jieping Huang
The intramuscular fat content and the unsaturated fatty acid (UFA) composition are both critical indicators of buffalo meat quality. While microRNAs regulate fatty acid metabolism, their specific roles in buffaloes remain unclear. Our previous WGCNA identified bta-miR-30f as a hub miRNA positively correlated with UFA levels. In the present study, bta-miR-30f was found to be highly expressed in sternum subcutaneous adipose tissue and mature adipocytes. Functional studies indicated that bta-miR-30f increased lipid accumulation via enhanced adipogenesis and UFA levels, upregulating key genes including PPARG, C/EBPα, SCD, and FADS1/2. It also promoted cell proliferation. Mechanistically, the dual luciferase assay confirmed that bta-miR-30f interacted with RAD23B, whose knockdown similarly increased lipid deposition and UFA content in buffalo intramuscular preadipocytes. Thus, this study demonstrated that bta-miR-30f enhances adipogenesis differentiation and UFA accumulation by targeting RAD23B in buffalo intramuscular preadipocytes, which provides significant information for the genetic improvement of meat quality in buffaloes.
{"title":"Bta-miR-30f promotes adipogenesis and unsaturated fatty acid accumulation by targeting RAD23B in buffalo intramuscular preadipocytes","authors":"Ruirui Zhu , Hao Tian , Fangfang Zou , Hongfang Mo , Yulian Xi , Xingrong Lu , Chunyan Yang , Deshun Shi , Jianghua Shang , Jieping Huang","doi":"10.1016/j.isci.2025.114578","DOIUrl":"10.1016/j.isci.2025.114578","url":null,"abstract":"<div><div>The intramuscular fat content and the unsaturated fatty acid (UFA) composition are both critical indicators of buffalo meat quality. While microRNAs regulate fatty acid metabolism, their specific roles in buffaloes remain unclear. Our previous WGCNA identified bta-miR-30f as a hub miRNA positively correlated with UFA levels. In the present study, bta-miR-30f was found to be highly expressed in sternum subcutaneous adipose tissue and mature adipocytes. Functional studies indicated that bta-miR-30f increased lipid accumulation via enhanced adipogenesis and UFA levels, upregulating key genes including <em>PPARG</em>, <em>C/EBPα</em>, <em>SCD</em>, and <em>FADS1/2</em>. It also promoted cell proliferation. Mechanistically, the dual luciferase assay confirmed that bta-miR-30f interacted with <em>RAD23B</em>, whose knockdown similarly increased lipid deposition and UFA content in buffalo intramuscular preadipocytes. Thus, this study demonstrated that bta-miR-30f enhances adipogenesis differentiation and UFA accumulation by targeting <em>RAD23B</em> in buffalo intramuscular preadipocytes, which provides significant information for the genetic improvement of meat quality in buffaloes.</div></div>","PeriodicalId":342,"journal":{"name":"iScience","volume":"29 2","pages":"Article 114578"},"PeriodicalIF":4.1,"publicationDate":"2025-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145975114","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-30DOI: 10.1016/j.isci.2025.114580
Vanesa Jiménez-Amilburu , Hugo Ducuing , Nursen Balekoglu , Sneha Sukumaran , Patricia T. Yam , Frédéric Charron
During cerebellar development, granule cell precursors (GCPs) undergo a series of tightly regulated events, including proliferation, migration, and differentiation. Arhgef7, a guanine nucleotide exchange factor for Rac1 and Cdc42, plays a crucial role in these processes. This study investigates the role of Arhgef7 in cerebellar development using conditional knockout (cKO) mice. We demonstrate that Arhgef7 is expressed in GCPs. Loss of Arhgef7 in GCPs results in severe cerebellar hypoplasia and foliation defects, particularly affecting lobules VI/VII. Arhgef7 cKO mice exhibit reduced postnatal GCP proliferation, disorganized cell layers, delayed differentiation, and impaired tangential and radial migration of GCPs. Our findings highlight the essential role of Arhgef7 in regulating multiple aspects of GCP development, thereby ensuring proper cerebellar morphogenesis.
{"title":"Arhgef7 is essential for granule cell precursor proliferation and migration during cerebellum development","authors":"Vanesa Jiménez-Amilburu , Hugo Ducuing , Nursen Balekoglu , Sneha Sukumaran , Patricia T. Yam , Frédéric Charron","doi":"10.1016/j.isci.2025.114580","DOIUrl":"10.1016/j.isci.2025.114580","url":null,"abstract":"<div><div>During cerebellar development, granule cell precursors (GCPs) undergo a series of tightly regulated events, including proliferation, migration, and differentiation. Arhgef7, a guanine nucleotide exchange factor for Rac1 and Cdc42, plays a crucial role in these processes. This study investigates the role of Arhgef7 in cerebellar development using conditional knockout (cKO) mice. We demonstrate that Arhgef7 is expressed in GCPs. Loss of <em>Arhgef7</em> in GCPs results in severe cerebellar hypoplasia and foliation defects, particularly affecting lobules VI/VII. <em>Arhgef7</em> cKO mice exhibit reduced postnatal GCP proliferation, disorganized cell layers, delayed differentiation, and impaired tangential and radial migration of GCPs. Our findings highlight the essential role of Arhgef7 in regulating multiple aspects of GCP development, thereby ensuring proper cerebellar morphogenesis.</div></div>","PeriodicalId":342,"journal":{"name":"iScience","volume":"29 2","pages":"Article 114580"},"PeriodicalIF":4.1,"publicationDate":"2025-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145975584","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-30DOI: 10.1016/j.isci.2025.114577
Guoliang Luo , Xiangjin Ma , Jiaqi Han , Lihao Zhu , Rui Li , Haixia Liu , Long Li
Backscatter communication (BC) is a low-power technology that transmits data by reflecting ambient RF signals. Conventional BC, based on antenna impedance modulation, suffers from low data rates and poor interference resistance. Programmable information metasurface (IMS) offers a breakthrough by enabling precise wave control. This article presents a PIN-diode-based IMS for polarization-diversity backscatter transmission. It performs full-space secondary modulation, converting horizontally polarized incident waves into ±45° polarized signals. Operating at 5 GHz, the system uses two polarization channels with BPSK and BASK modulation to transmit the same data, achieving 2 Mbps with improved reliability through diversity. The proposed system exhibits low power consumption, strong interference resistance, and high stability, making it suitable for IoT applications such as smart healthcare and environmental monitoring.
{"title":"Polarization-diversity backscatter communication based on programmable information metasurface","authors":"Guoliang Luo , Xiangjin Ma , Jiaqi Han , Lihao Zhu , Rui Li , Haixia Liu , Long Li","doi":"10.1016/j.isci.2025.114577","DOIUrl":"10.1016/j.isci.2025.114577","url":null,"abstract":"<div><div>Backscatter communication (BC) is a low-power technology that transmits data by reflecting ambient RF signals. Conventional BC, based on antenna impedance modulation, suffers from low data rates and poor interference resistance. Programmable information metasurface (IMS) offers a breakthrough by enabling precise wave control. This article presents a PIN-diode-based IMS for polarization-diversity backscatter transmission. It performs full-space secondary modulation, converting horizontally polarized incident waves into ±45° polarized signals. Operating at 5 GHz, the system uses two polarization channels with BPSK and BASK modulation to transmit the same data, achieving 2 Mbps with improved reliability through diversity. The proposed system exhibits low power consumption, strong interference resistance, and high stability, making it suitable for IoT applications such as smart healthcare and environmental monitoring.</div></div>","PeriodicalId":342,"journal":{"name":"iScience","volume":"29 2","pages":"Article 114577"},"PeriodicalIF":4.1,"publicationDate":"2025-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145975589","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-30DOI: 10.1016/j.isci.2025.114582
Vijaya Charaka , Raj K. Pandita , Chi-Lin Tsai , Xiaoyan Wang , Sharmista Chakraborty , Kenneth S. Ramos , Sandhik Nandi , Fransisca Leonard , Vipin Singh , Partha S. Sarkar , Clayton R. Hunt , John A. Tainer , Chandrima Das , Tej K. Pandita
Efficient DNA double-strand break (DSB) repair by homologous recombination (HR), as initiated by BRCA1 recruitment orchestrated by histone and non-histone proteins, is critical to genome stability, replication, transcription, and cancer avoidance. Here we reveal Heterochromatin Protein1 beta (HP1β) promotes BRCA1 enrichment at DNA DSB sites in gene-rich regions, and this is impaired by HP1β depletion. We find that HP1β is specifically enriched at DSBs within gene-rich regions via its Chromo Shadow Domain (CSD) that interacts with both Chromatin Assembly Factor 1 and the RING1A ubiquitinase component of Polycomb Repressor Complex 1. The resulting protein complex facilitates BRCA1 recruitment by promoting H2A lysine 119 ubiquitination. Collective findings reveal a novel mechanism whereby HP1β interactions, mediated through its CSD of HP1β interaction with RING1A, promotes H2AK119 ubiquitination to facilitate BRCA1 recruitment and orchestrate efficient HR and CtIP-dependent DNA resection at DSB sites in gene-rich active chromatin.
{"title":"HP1β recruits RING1A to ubiquitinate histone H2A for BRCA1-mediated resection of double-stand breaks","authors":"Vijaya Charaka , Raj K. Pandita , Chi-Lin Tsai , Xiaoyan Wang , Sharmista Chakraborty , Kenneth S. Ramos , Sandhik Nandi , Fransisca Leonard , Vipin Singh , Partha S. Sarkar , Clayton R. Hunt , John A. Tainer , Chandrima Das , Tej K. Pandita","doi":"10.1016/j.isci.2025.114582","DOIUrl":"10.1016/j.isci.2025.114582","url":null,"abstract":"<div><div>Efficient DNA double-strand break (DSB) repair by homologous recombination (HR), as initiated by BRCA1 recruitment orchestrated by histone and non-histone proteins, is critical to genome stability, replication, transcription, and cancer avoidance. Here we reveal Heterochromatin Protein1 beta (HP1β) promotes BRCA1 enrichment at DNA DSB sites in gene-rich regions, and this is impaired by HP1β depletion. We find that HP1β is specifically enriched at DSBs within gene-rich regions via its Chromo Shadow Domain (CSD) that interacts with both Chromatin Assembly Factor 1 and the RING1A ubiquitinase component of Polycomb Repressor Complex 1. The resulting protein complex facilitates BRCA1 recruitment by promoting H2A lysine 119 ubiquitination. Collective findings reveal a novel mechanism whereby HP1β interactions, mediated through its CSD of HP1β interaction with RING1A, promotes H2AK119 ubiquitination to facilitate BRCA1 recruitment and orchestrate efficient HR and CtIP-dependent DNA resection at DSB sites in gene-rich active chromatin.</div></div>","PeriodicalId":342,"journal":{"name":"iScience","volume":"29 2","pages":"Article 114582"},"PeriodicalIF":4.1,"publicationDate":"2025-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146035926","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-30DOI: 10.1016/j.isci.2025.114589
Ali Nouri , Ming Hu
The construction sector contributes significantly to greenhouse gas emissions, yet designers often lack tools that make life cycle assessment (LCA) accessible during routine decision-making. This study presents an AI-augmented framework that embeds automated, interpretable LCA within the building information modeling environment. The system links material quantities extracted from Revit with programmatic inventory modeling and an endpoint module that allows users to adjust time horizons to reflect different cultural risk perspectives. A conversational interface enables designers and stakeholders to explore trade-offs, visualize environmental impacts, and receive plain-language interpretations of results. Using a residential building model, the framework reproduced expert SimaPro outputs with less than 2.1% variation across indicators. By integrating environmental intelligence directly into early-stage design workflows, the approach supports more informed material choices, streamlines green permitting, and provides a foundation for policy tools that encourage lower-carbon construction.
{"title":"Democratizing environmental impact assessment: An AI-augmented framework for sustainable building design","authors":"Ali Nouri , Ming Hu","doi":"10.1016/j.isci.2025.114589","DOIUrl":"10.1016/j.isci.2025.114589","url":null,"abstract":"<div><div>The construction sector contributes significantly to greenhouse gas emissions, yet designers often lack tools that make life cycle assessment (LCA) accessible during routine decision-making. This study presents an AI-augmented framework that embeds automated, interpretable LCA within the building information modeling environment. The system links material quantities extracted from Revit with programmatic inventory modeling and an endpoint module that allows users to adjust time horizons to reflect different cultural risk perspectives. A conversational interface enables designers and stakeholders to explore trade-offs, visualize environmental impacts, and receive plain-language interpretations of results. Using a residential building model, the framework reproduced expert SimaPro outputs with less than 2.1% variation across indicators. By integrating environmental intelligence directly into early-stage design workflows, the approach supports more informed material choices, streamlines green permitting, and provides a foundation for policy tools that encourage lower-carbon construction.</div></div>","PeriodicalId":342,"journal":{"name":"iScience","volume":"29 2","pages":"Article 114589"},"PeriodicalIF":4.1,"publicationDate":"2025-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146035933","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-30DOI: 10.1016/j.isci.2025.114574
Jisheng Zhang , Yang Chen , Aijun Zhang , Yi Yang , Liqian Ma , Kewei Yu , Weitao Zhang , Xiaojing Ye , Jiangsong Zhang , Ke Lin , Xianming Lin
Long COVID is a chronic, multisystem disease with limited response to conventional treatments. While low-dose methylprednisolone has shown effectiveness in some patients, individual responses vary, and accurate predictive tools are lacking. This retrospective study included 330 long COVID patients who received low-dose methylprednisolone treatment across three hospitals. Patients were divided into training (n = 202), test (n = 33), and external validation sets (n = 53, n = 42). Using least absolute shrinkage and selection operator (LASSO) regression, 38 variables were analyzed to develop six machine learning models. The logistic regression (LR) model showed stable performance across all datasets (AUCs: 0.8715, 0.7198, 0.8419, and 0.8676), making it the final model selected. SHapley Additive exPlanations (SHAP) analysis identified seven key variables, which were used to construct a nomogram for predicting treatment efficacy. The LR model and nomogram demonstrated strong predictive performance and clinical interpretability, offering a valuable decision-support tool for individualized treatment of long COVID with low-dose methylprednisolone.
{"title":"Interpretable machine learning for predicting low-dose methylprednisolone effectiveness in long COVID","authors":"Jisheng Zhang , Yang Chen , Aijun Zhang , Yi Yang , Liqian Ma , Kewei Yu , Weitao Zhang , Xiaojing Ye , Jiangsong Zhang , Ke Lin , Xianming Lin","doi":"10.1016/j.isci.2025.114574","DOIUrl":"10.1016/j.isci.2025.114574","url":null,"abstract":"<div><div>Long COVID is a chronic, multisystem disease with limited response to conventional treatments. While low-dose methylprednisolone has shown effectiveness in some patients, individual responses vary, and accurate predictive tools are lacking. This retrospective study included 330 long COVID patients who received low-dose methylprednisolone treatment across three hospitals. Patients were divided into training (<em>n</em> = 202), test (<em>n</em> = 33), and external validation sets (<em>n</em> = 53, <em>n</em> = 42). Using least absolute shrinkage and selection operator (LASSO) regression, 38 variables were analyzed to develop six machine learning models. The logistic regression (LR) model showed stable performance across all datasets (AUCs: 0.8715, 0.7198, 0.8419, and 0.8676), making it the final model selected. SHapley Additive exPlanations (SHAP) analysis identified seven key variables, which were used to construct a nomogram for predicting treatment efficacy. The LR model and nomogram demonstrated strong predictive performance and clinical interpretability, offering a valuable decision-support tool for individualized treatment of long COVID with low-dose methylprednisolone.</div></div>","PeriodicalId":342,"journal":{"name":"iScience","volume":"29 2","pages":"Article 114574"},"PeriodicalIF":4.1,"publicationDate":"2025-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145975113","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-29DOI: 10.1016/j.isci.2025.114551
Tamara J.C. Schenk , Martijn Vos , Yannick van Sleen , Debbie van Baarle , Teun Guichelaar
Studying activation of antigen-specific T cells is essential for understanding adaptive immune response to pathogens, tumors, and vaccines. Flow cytometry is commonly used to identify antigen-specific T cells based on the induction of activation-induced markers (AIMs). However, these markers are also expressed on bystander T cells activated by cytokines produced by antigen-activated T cells. This complicates the distinction between true T cell receptor (TCR)-activated- and bystander T cells. We developed an approach to differentiate between these types of cells. We stimulated human PBMCs with anti-CD3 antibody (TCR-mediated) or supernatant of activated T cells, IL-2, or IL-15 (bystander activation). We analyzed AIM co-expression patterns on CD4+ and CD8+ T cells, and defined activation phenotypes that distinguish TCR-activated from bystander-activated T cells. In anti-viral responses, peptide stimulation mainly induced bystander activation, yet bystander T cells contributed minimally to cytokine production. Our findings provide a framework for identifying T cell response types in diverse clinical contexts.
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