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Integrative Transcriptomic and Proteomic Profiling Identifies S100P as a Potential Functional Biomarker for Sessile Serrated Lesions.

BACKGROUND: Sessile serrated lesions (SSLs) account for 15% of colorectal cancers (CRCs) but detection remains difficult due to flat morphology, mucinous features, and subtle histology. AIMS: This study aimed to identify novel and functionally relevant biomarkers of SSLs using transcriptomic screening and multi-omics validation. METHODS: Paired SSL and normal mucosa specimens (n = 6) underwent RNA sequencing. Differentially expressed genes (DEGs) were filtered for membrane or secretory proteins and validated across TCGA and adenoma transcriptomes. Functional significance was assessed using CRISPR dependency profiling, proteotranscriptomic concordance, pharmacogenomic sensitivity, and connectivity map analysis. RESULTS: We identified 216 upregulated genes in SSLs, including 68 encoding secretory/membrane proteins that better discriminated SSLs from controls and were enriched for adhesion and neuronal signaling while suppressing TNFα-NFκB inflammatory pathways. Cross-cohort comparison revealed five overlapping candidates between SSLs and TCGA CMS1 tumors. Among them, S100P emerged as the primary biomarker candidate, showing consistent upregulation in SSLs and CMS1 tumors while remaining low in normal mucosa and conventional adenomas. TFF1 also showed RNA-level upregulation but appeared more context-dependent. S100P demonstrated strong RNA-protein concordance in CRC cell-line profiling, supporting its detectability as a biomarker candidate. Pharmacogenomic profiling of LS411N cells revealed marked sensitivity to SN-38 and fluoropyrimidines, consistent with serrated CRC vulnerabilities. Connectivity map analysis identified perturbations, including MAPK1 and histone acetyltransferase suppression, that may reverse parts of the SSL transcriptional program. CONCLUSION: These findings prioritize S100P as a promising biomarker candidate for SSLs that warrants further validation in larger cohorts and clinically applicable platforms.

Humans

Anatomical mapping of retino-tectal connections in developing and metamorphosed Xenopus: evidence for changing connections.

Neural connections between the eye and optic tectum in Xenopus laevis were anatomically traced by observing the tectal location of Wallerian degeneration after discrete retinal lesion. These retinotectal connections were mapped in postmetamorphic frogs and tadpoles at stage 51, the stage at which retinal axons have grown into about the rostral one-half of the tectum. The course of the experimental degeneration was the same in frogs and tadpoles, but degeneration proceeded faster in the younger animals. In the frogs, connections were ordered, with nasal retina mapping to the caudal part of the tectum and temporal retina mapping to the rostral tectum. In the tadpoles, within the innervated area at the rostral tectum, the retino-tectal connections were generally organized as in the adults, with the temporal retina mapping to the rostral part of the innervated tectum and nasal retina mapping primarily to the caudal part. But a portion of the nasal fibers consistently mapped to the far rostral tectum as well. Electron microscopic observations showed degenerating synaptic terminals at both rostral and caudal portions of the innervated tectum after lesion of just the nasal retina. Degeneration was not seen in control animals. These results indicate that some fibers (particularly from nasal retina) may shift their terminals caudally on the tectum to match tectal growth and produce the adult pattern of connections. If there is such connection readjustment, the 'aberrant' connections from nasal retina in tadpoles may be an indication of this process.

Animals

AI-driven multi-omics modeling of myalgic encephalomyelitis/chronic fatigue syndrome.

Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a chronic illness with a multifactorial etiology and heterogeneous symptomatology, posing major challenges for diagnosis and treatment. Here we present BioMapAI, a supervised deep neural network trained on a 4-year, longitudinal, multi-omics dataset from 249 participants, which integrates gut metagenomics, plasma metabolomics, immune cell profiling, blood laboratory data and detailed clinical symptoms. By simultaneously modeling these diverse data types to predict clinical severity, BioMapAI identifies disease- and symptom-specific biomarkers and classifies ME/CFS in both held-out and independent external cohorts. Using an explainable AI approach, we construct a unique connectivity map spanning the microbiome, immune system and plasma metabolome in health and ME/CFS adjusted for age, gender and additional clinical factors. This map uncovers altered associations between microbial metabolism (for example, short-chain fatty acids, branched-chain amino acids, tryptophan, benzoate), plasma lipids and bile acids, and heightened inflammatory responses in mucosal and inflammatory T cell subsets (MAIT, γδT) secreting IFN-γ and GzA. Overall, BioMapAI provides unprecedented systems-level insights into ME/CFS, refining existing hypotheses and hypothesizing unique mechanisms-specifically, how multi-omics dynamics are associated to the disease's heterogeneous symptoms.

Humans

Stochastic epigenetic mutation profiles as biomarkers of clinical activity in juvenile idiopathic arthritis: a multi-omic machine learning approach for gene prioritization.

BACKGROUND: Juvenile idiopathic arthritis (JIA) is a rare autoimmune disease arising from a complex interplay between genetic and environmental factors. Epigenetic modifications such as DNA methylation (DNAm) have been described as potential mediators in gene-environment interactions, contributing to immune system dysregulation. Emerging evidence suggests that DNAm profiles also predict therapeutic responses in autoimmune diseases. This study aims to identify epigenetic biomarkers and epigenetic-driven gene expression changes associated with JIA clinical activity. METHODS: We reanalyzed a publicly available dataset of 44 JIA patients, with whole-genome DNAm and gene expression from CD4 + T cells measured at two points: at anti-TNF therapy withdrawal (T0) and eight months later (Tend). At Tend, 30 patients maintained inactive disease (ID) while 14 did not (NO ID). We investigated differences between ID and NO ID patients in the epigenetic mutation load and various epigenetic clocks through linear regression models, and prioritized genomic regions with significantly higher number of epimutations in NO ID patients through machine learning. RESULTS: We found a higher mutation load in NO ID than ID patients, both at T0 and at Tend, with the differences at Tend reaching statistical significance (p = 0.02). In contrast, we found no evidence of association between epigenetic clocks and JIA clinical activity. Using a multi-omic approach, we identified a List of candidate epigenetically-driven differentially expressed genes, 80 up-regulated and 77 down-regulated, in NO ID patients. Finally, comparing our candidate gene list with the Connectivity Map database, we identified new candidate potential therapeutic targets. Key findings were validated in independent datasets: DNAm profiles from CD4 + T cells (56 JIA patients, 57 controls) and transcriptomic data from PBMCs of JIA patients with active or inactive disease, confirming dysregulation of pathways such as TNF-α signaling via NF-kB and TGF-β signaling among others. CONCLUSIONS: We described a significant association of epigenetic mutations with JIA clinical activity, indicating that epigenetic changes might precede clinical symptoms and may serve as biomarkers for early disease monitoring. Further, our results shed light on biomolecular mechanisms of JIA, supporting the development of more effective treatments.

Humans

Construction of a molecular diagnostic system for neurogenic rosacea by combining transcriptome sequencing and machine learning.

Patients with neurogenic rosacea (NR) frequently demonstrate pronounced neurological manifestations, often unresponsive to conventional therapeutic approaches. A molecular-level understanding and diagnosis of this patient cohort could significantly guide clinical interventions. In this study, we amalgamated our sequencing data (n = 46) with a publicly accessible database (n = 38) to perform an unsupervised cluster analysis of the integrated dataset. The eighty-four rosacea patients were partitioned into two distinct clusters. Neurovascular biomarkers were found to be elevated in cluster 1 compared to cluster 2. Pathways in cluster 1 were predominantly involved in neurotransmitter synthesis, transmission, and functionality, whereas cluster 2 pathways were centered on inflammation-related processes. Differential gene expression analysis and WGCNA were employed to delineate the characteristic gene sets of the two clusters. Subsequently, a diagnostic model was constructed from the identified gene sets using linear regression methodologies. The model's C index, comprising genes PNPLA3, CUX2, PLIN2, and HMGCR, achieved a remarkable value of 0.9683, with an area under the curve (AUC) for the training cohort's nomogram of 0.9376. Clinical characteristics from our dataset (n = 46) were assessed by three seasoned dermatologists, forming the NR validation cohort (NR, n = 18; non-neurogenic rosacea, n = 28). Upon application of our model to NR diagnosis, the model's AUC value reached 0.9023. Finally, potential therapeutic candidates for both patient groups were predicted via the Connectivity Map. In summation, this study unveiled two clusters with unique molecular phenotypes within rosacea, leading to the development of a precise diagnostic model instrumental in NR diagnosis.

Humans

FOSB is a key factor in the genetic link between inflammatory bowel disease and acute myocardial infarction: multiple bioinformatics analyses and validation.

BACKGROUND: Inflammatory Bowel Disease (IBD), which includes Crohn's disease and ulcerative colitis, is associated with an increased risk of Acute Myocardial Infarction (AMI). The genetic mechanisms underlying this link are not well understood. METHODS: We downloaded IBD and AMI-related microarray datasets from the NCBI Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were identified and analyzed using enrichment analysis and Weighted Gene Co-expression Network Analysis (WGCNA). Machine learning techniques, including LASSO, random forest, and Boruta, were employed to screen for hub genes. These genes were validated through qRT-PCR and Western blotting. Single-cell sequencing was used to confirm findings. Additionally, potential therapeutic targets were identified using the Connectivity Map (CMap) database. RESULTS: Five key hub genes-THBD, FOSB, ADGPR3, IL1R2, and PLAUR-were identified as significantly involved in both IBD and AMI pathogenesis. A diagnostic model for AMI constructed using these hub genes demonstrated high predictive accuracy. Single-cell sequencing analysis and several potential drugs targeting these hub genes were identified, offering new therapeutic avenues. CONCLUSION: This study highlights the crucial role of FOSB and other hub genes in the comorbidity of IBD and AMI. The findings provide novel insights for early diagnosis and potential therapeutic strategies, emphasizing the importance of further investigation into these genetic links.

Humans

Identification of Drug-resistant Cell Subpopulations in Colorectal Cancer Through Single-cell Analysis and Exploration of Potential Therapeutic Strategies.

INTRODUCTION: The therapeutic efficacy of Colorectal Cancer (CRC) is often compromised by resistance to the standard chemotherapy agent oxaliplatin. METHODS: This study obtained single-cell RNA sequencing (scRNA-seq) data from the Gene Expression Omnibus (GEO) database. Differentially Expressed Genes (DEGs) between resistant and sensitive epithelial subpopulations were identified, followed by enrichment analysis. Pseudotemporal trajectory and cell-cell communication were analyzed using Monocle2 and CellChat, respectively. The candidate drug was predicted by Connectivity Map (cMAP) analysis. External validation included assessment of the EpC2 signature in an oxaliplatin-resistant cell line dataset (GSE76092), survival analysis using The Cancer Genome Atlas (TCGA) cohorts, and re-analysis of the GSE179784 dataset to assess the reproducibility of EpC2-like subpopulations and their DNA Damage Repair (DDR) scores. RESULTS: Cell subpopulations were divided into 10 clusters. Among them, epithelial cells comprised 5 subpopulations, with EPC2 identified as a potential oxaliplatin-resistant subset. DEGs were enriched in the TNF and IL-17 pathways. External validation confirmed the enrichment of EpC2 in resistant cell lines and its association with poor survival. Pseudotemporal trajectory revealed that epithelial cells underwent state transitions, forming two distinct branches. The resistant group exhibited enrichment in RNA splicing and NF-κB pathways. Cell-cell communication analysis revealed interactions involving MDK- NCL and PPIA-BSG. Dasatinib was predicted as a candidate drug. DISCUSSION: We identified an oxaliplatin-resistant subpopulation of Epithelial Cells (EpC2) in CRC, elucidated its multi-layered resistance mechanisms, and integrated multi- omics and cMAP database analyses to predict a potential intervention drug. CONCLUSION: This study provided potential therapeutic possibilities for oxaliplatin resistance, contributing to CRC treatment.

Humans

Connections and visual-field mapping in cat's tectoparabigeminal circuit.

1. The aim of these experiments was to analyze the organization of the reciprocal connections between the cat's superior colliculus and parabigeminal nucleus. Both physiological and anatomical techniques were employed. 2. A population of cells in the superficial gray and upper optic layers of the colliculus was labeled retrogradely by horseradish peroxidase injections into the parabigeminal nucleus. No other sources of input to the nucleus were found in the brain stem or diencephalon. 3. A map of the visual field within the parabigeminal nucleus was reconstructed by plotting visual receptive fields at 350 parabigeminal sites with microelectrodes. The map resembled that found in the colliculus, although it was considerably less orderly. The entire contralateral visual field was represented and, in addition, roughly the central 40 degrees of the ipsilateral hemifield was included; futhermore, the expansion of the central visual field was similar to that of the tectal map. 4. The return parabigeminal projections to the caudal parts of the two colliculi, representing the contralateral hemifields, were in register with the tectal visual-field maps. In contrast, the parabigeminal pathways to the anterior segments of the two colliculi, representing part of the ipsilateral visual fields, were not clearly topographic. The projection to this part of the contralateral colliculus showed little order, while that to the ipsilateral colliculus was extremely sparse. 5. A single site in the colliculus can be the target of axons from nonhomologous locations in the two parabigeminal nuclei; so that both parabigeminal inputs are in register with the tectal map.

Animals

Drug repurposing using transcriptomics: principles and unmet needs in cardiovascular disease.

Although cardiovascular disease is the leading cause of death globally, therapeutic development in this field is slow. Given the high cost of developing new drugs and running clinical trials for cardiovascular disease, repurposing of drugs with approved safety profiles is an attractive strategy for therapeutic development that can significantly reduce the time and cost investment before phase II clinical trials. In the era of "Omics," various new methods and several large databases have been developed to enable the use of transcriptomics data for drug repurposing. This review summarizes the principles and workflow of signature mapping, which forms the foundation of statistical models used for transcriptome-based drug repurposing. We highlight the features of different analysis pipelines and databases that have been developed for signature mapping. These analysis pipelines prioritize genes that are statistically important, an approach that fundamentally differs from the pharmacological approach of identifying disease-driving and therapeutically targetable pathways. Outcomes of signature mapping pipelines are sensitive to the quality of input data, and results are not always reproducible. Moreover, all widely used RNA-seq databases are derived from cancer research and lack high-quality molecular data for cardiovascular disease. These unmet needs call for interdisciplinary collaboration and large networks of cardiovascular research-oriented biobanks to create the databases needed for transcriptomic-based signature mapping for drug repurposing efforts.

Drug Repositioning

A guide to the synaptic analysis of the neuropil.

A morphological analysis of the organization of the gray matter in the central nervous system depends on the discovery of consistent repetitive patterns. Without these, the gray matter remains a chaotic jungle. An hypothesis derived from the study of a few simple regions has been developed to serve as a guide in finding these patterns. It states that all nerve fibers and terminals arising from a particular group of nerve cells, or, more precisely, a particular nerve cell type, display similar axoplasmic configurations despite variations in size and shape of the terminations. This hypothesis is reminiscent of the so-called Dale's principle that a nerve cell makes use of the same transmitter at all of its branches or terminations. These apparent rules of uniformity or congruity merely reflect the functional integrity of the nerve cell and the role of its parts in the nervous system. But as an hypothesis, it needs to be tested, and it needs to be tested anew in each region, since exceptions to the assumed rule can be expected. It is therefore proposed as the first working hypothesis in each new region. If it should prove to be true in general, it will facilitate and rationalize the analysis of the gray matter, as it has already done in the cerebellar cortex and the deep cerebellar nuclei. If it should prove to be false in a few regions, the analysis will become more difficult, and additional modes of marking nerve endings will have to be used. Experimental methods for identifying nerve terminals can be translated from the light microscopic to the electron microscopic level, but there are significant drawbacks at both levels: lack of precision, destruction of fibers of passage, and rapid evolution of the degenerative process may greatly restrict their usefulness. Labeling with tritiated amino acids or transmitters, or with horseradish peroxidase, provide new methods for tracing interneuronal connections at the electron microscopic level. These have the advantages of high specificity, nondestructiveness and a physiological mode of selective marking. However, they do not offer a solution to the problem of short-range connections. For these, careful reconstructions of serial sections may prove necessary, as Sjöstrand (1974) has demonstrated in a remarkable paper on the retina. The aim of all these methods is to discover patterns of synaptic connectivity in order to map the cellular organization of the nervous system. In the foregoing, nothing was said about synapses other than those articulating axons with somata or dendrites and their appendages. Clearly the same principles of recognition apply to axo-axonal and dendro-dendritic synapses. Although the synapses that have been considered here are chemical synapses, the same questions regarding the identity of the partners in electrotonic junctions must be asked as well.

Amino Acids

A restriction map of cauliflower mosaic virus DNA (strain PV 147). Mapping of the cleavage sites of HhaI, SacI, AvaI, PvuII, PstI, XbaI, EcoRI, Bg/II, HincII, HpaII and HindII + III.

The virion-extracted DNA (Mr5 x 10(6)) of cauliflower mosaic virus (CaMV) has three single-stranded interruptions. The mapping of this DNA using eleven restriction endonucleases (HhaI, SacI, AvaI, PvuII, PstI, XbaI, EcoRI, Bg/II, HincII, HpaII and HindII + III) is reported here. The existence of the three single-stranded breaks complicates the identification and the molecular weight determination of fragments produced by HpaII, HindIII and HindII + III. Indeed the electrophoretic mobility of some fragments in which a single-stranded discontinuity is located is modified, and the fluorescence of ethidium bromide complexed with these fragments is reduced as compared to that observed for the other fragments existing in a molar ratio. These drawbacks were overcome by performing experiments of nick-translation of CaMV DNA with Escherichia coli DNA polymerase I. FRom the data it follows that the CaMV DNA molecule bears bears 1 site for HhaI and SacI, 2 for AvaI and PvuII, 3 for PstI, 4 for XbaI, 5 for EcoRI, 6 for Bg/II and HincII, 11 for HpaII and 15 for HindII + III. The corresponding fragments have all been ordered and precisely located providing a suitable map for further investigations connected with the study of the fine structure and the function of the CaMV genome.

DNA Restriction Enzymes

Origin, destination and mapping of tritocerebral neurons of locust.

The connectivities of the tritocerebrum of locust (Locusta migratoria L., Schistocerca gregaria (Forsk.)) were studied histologically and by means of cobalt chloride infusion. Its neuropil consists partly of fibers which traverse the tritocerebrum and areas consisting of neuropilar agglomerizations ("glomeruli"). The following direct connections between the tritocerebrum and other regions were observed: connections to 1) dorsal and lateral brain regions (mushroom body, optic lobe), 2) the ventral nerve cord, 3) the stomatogastric nervous system (here the protocerebrum and the subesophageal ganglion are also involved in these connections), 4) the retro-cerebral glands (corpora cardiaca, corpora allata), and 5) muscles of the foregut.

Animals

Formation of topographic maps and columnar microstructures in nerve fields.

Topographic connections are found in many parts of the vertebrate nervous systems, known for example as retinotopy. The self-organizing ability of Hebb type modifiable synapses plays an important role in forming, at least in refining, the topographic connections. We present a mathematical analysis of a revised version of the Willshaw-Malsburg model of topographic formation, solving the equations of synaptic self-organization coupled with the field equation of neural excitations. The equilibrium solutions are obtained and their stability is studied. It is proved that two cases exist depending on parameters. In one case, the smooth topographic organization is obtained as a stable equilibrium of the equations. In the other case, this solution becomes unstable, and instead the topographic organization with columnar microstructures appears. This might explain the columnar structures in the cerebrum. The theory is confirmed by computer simulated experiments.

Computers

Genomic and ecological systems-thinking framework for pathogenic Leptospira in Puerto Rico.

INTRODUCTION: Leptospirosis is a complex zoonotic disease requiring high-resolution surveillance. A systems-thinking framework was used to connect genomic and ecological data and map the geographic and host-based structuring of co-circulating pathogenic Leptospira lineages in Puerto Rico. METHODS: Forty-four core genomes of L. interrogans, L. borgpetersenii, and L. kirschneri from human, domestic, and wildlife hosts were analyzed. Spatiotemporal and landscape metadata were integrated using root-to-tip regression, isolation-by-distance profiling and calibrated single-nucleotide polymorphism (SNP) thresholds (≤1, ≤5, and ≤10 SNPs) to define transmission clusters. RESULTS: Leptospira species exhibited distinct ecological pathways partitioned by geography, explaining 56% of genomic variance for L. interrogans and 91% for L. borgpetersenii (PERMANOVA). L. interrogans displayed high landscape connectivity across multiple hosts, forming localized networks (≤1 to ≤10 SNPs) that capture active spillovers (human-to-rat linkages at ≤1 SNP) and resolved into rodent host-specific lineages (R2 = 0.34). Conversely, L. borgpetersenii showed spatial and temporal genomic homogeneity and a lack of host-associated structure within an unpartitioned transmission pool dominated by Mus musculus. As a result, fixed genomic thresholds yielded disparate outcomes: L. interrogans resolved into 4 to 5 discrete, expanding clusters, whereas L. borgpetersenii grouped into a single uniform population at the ≤10-SNP threshold. CONCLUSION: Co-circulating pathogenic leptospires occupy distinct ecological niches shaped by varying host restriction and environmental persistence. Fixed genomic thresholds lack universal applicability; effective genomic epidemiological surveillance must employ species-specific threshold calibration to accurately map transmission pathways.

Puerto Rico

Formation of sensory maps: New tools reveal novel insights into neural development.

The development of functional neural circuits depends on the navigation of neurites (axons and dendrites) through spatially complex and molecularly diverse environments to their appropriate targets. How these processes maneuver through dense surroundings to reach their targets is a long-standing question in neuroscience. Studies of sensory systems have been especially enlightening for identifying cues that underlie connectivity due to their organization as stereotyped neural maps. Recent advances in imaging, connectomics, and genomics have profoundly deepened our understanding of these processes and uncovered new mechanisms regulating circuit development. In this review, we discuss studies of Drosophila sensory systems that provide new insights into axon and dendritic targeting, partner identification and selection, and subcellular refinement. We highlight related or divergent findings in other systems and provide an outlook for future studies.

Animals

A research synthesis of humans, animals, and environmental compartments exposed to PFAS: A systematic evidence map and bibliometric analysis of secondary literature.

BACKGROUND: Per- and polyfluoroalkyl substances (PFAS) are a class of widely used anthropogenic chemicals. Concerns regarding their persistence and potential adverse effects have led to multiple secondary research publications. Here, we aim to assess the resulting evidence base in the systematic secondary literature by examining research gaps, evaluating the quality of reviews, and exploring interdisciplinary connections. METHODS: This study employed a systematic evidence-mapping approach to assess the secondary literature on the biological, environmental, and medical aspects of exposure to 35 fluorinated compounds. The inclusion criteria encompassed systematic reviews published in peer-reviewed journals, pre-prints, and theses. Comprehensive searches across electronic databases and grey literature identified relevant reviews. Data extraction and synthesis involved mapping literature content and narrative descriptions. We employed a modified version of the AMSTAR2 checklist to evaluate the methodological rigour of the reviews. A bibliometric data analysis uncovered patterns and trends in the academic literature. A research protocol for this study was previously pre-registered (osf.io/2tpn8) and published (Vendl et al., Environment International 158 (2022) 106973). The database is freely accessible through the interactive and user-friendly web application of this systematic evidence map at https://hi-this-is-lorenzo.shinyapps.io/PFAS_SEM_Shiny_App/. RESULTS: Our map includes a total of 175 systematic reviews. Over the years, there has been a steady increase in the annual number of publications, with a notable surge in 2021. Most reviews focused on human exposure, whereas environmental and animal-related reviews were fewer and often lacked a rigorous systematic approach to literature search and screening. Review outcomes were predominantly associated with human health, particularly with reproductive and children's developmental health. Animal reviews primarily focused on studies conducted in controlled laboratory settings, and wildlife reviews were characterised by an over-representation of birds and fish species. Recent reviews increasingly incorporated quantitative synthesis methodologies. The methodological strengths of the reviews included detailed descriptions of study selection processes and disclosure of potential conflicts of interest. However, weaknesses were observed in the critical lack of detail in reporting methods. A bibliometric analysis revealed that the most productive authors collaborate within their own country, leading to limited and clustered international collaborations. CONCLUSIONS: In this overview of the available systematic secondary literature, we map literature content, assess reviews' methodological quality, highlight data gaps, and draw research network clusters. We aim to facilitate literature reviews, guide future research initiatives, and enhance opportunities for cross-country collaboration. Furthermore, we discuss how this systematic evidence map and its publicly available database benefit scientists, regulatory agencies, and other stakeholders by providing access to current systematic secondary literature on PFAS exposure.

Bibliometrics