SEARCH · PubMed Health

Results for “Accessibility”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 55 records · Page 3Linked to original sources

PubMed2025

Chromatin accessibility analysis reveals functional cis-regulatory regions related to fruit development and domestication in tomato.

Non-coding DNA sequences harbor vast regulatory programs that ensure the precise spatiotemporal control of gene expression, which is essential for proper plant development and trait formation. Chromatin accessibility analysis could identify functional DNA regions within the extensive non-coding sequences and infer regulatory elements, serving as a crucial approach to unravel the mysteries of non-coding DNA sequences. Tomato fruit, a fleshy organ, provides a special system for studying fruit development and trait formation. However, the role of cis-accessible chromatin regions (cis-ACRs) during tomato fruit development, particularly in comparison with protein-coding DNA sequences, remains poorly understood. Here, we used ATAC-seq to define the landscape of cis-ACRs during fruit development and domestication in tomato. Temporal differential analysis revealed the dynamic opening and closing of cis-ACRs during fruit development. Comparative analysis of cis-ACRs between cultivated and wild tomatoes highlighted their significant contributions to fruit domestication. Combining analysis with genomic structural variations (SVs) suggested that SVs are likely a key factor in the formation of specific accessible cis-ACRs in cultivated tomatoes. Moreover, using gene editing, we identified a functional cis-ACR within the intron of the MBP3 gene that regulates fruit development and size traits. Overall, our findings provide a comprehensive perspective on the roles of cis-ACRs in tomato fruit development and domestication.

Solanum lycopersicum↗

PubMed2023

H3.3 contributes to chromatin accessibility and transcription factor binding at promoter-proximal regulatory elements in embryonic stem cells.

BACKGROUND: The histone variant H3.3 is enriched at active regulatory elements such as promoters and enhancers in mammalian genomes. These regions are highly accessible, creating an environment that is permissive to transcription factor binding and the recruitment of transcriptional coactivators that establish a unique chromatin post-translational landscape. How H3.3 contributes to the establishment and function of chromatin states at these regions is poorly understood. RESULTS: We perform genomic analyses of features associated with active promoter chromatin in mouse embryonic stem cells (ESCs) and find evidence of subtle yet widespread promoter dysregulation in the absence of H3.3. Loss of H3.3 results in reduced chromatin accessibility and transcription factor (TF) binding at promoters of expressed genes in ESCs. Likewise, enrichment of the transcriptional coactivator p300 and downstream histone H3 acetylation at lysine 27 (H3K27ac) is reduced at promoters in the absence of H3.3, along with reduced enrichment of the acetyl lysine reader BRD4. Despite the observed chromatin dysregulation, H3.3 KO ESCs maintain transcription from ESC-specific genes. However, upon undirected differentiation, H3.3 KO cells retain footprinting of ESC-specific TF motifs and fail to generate footprints of lineage-specific TF motifs, in line with their diminished capacity to differentiate. CONCLUSIONS: H3.3 facilitates DNA accessibility, transcription factor binding, and histone post-translational modification at active promoters. While H3.3 is not required for maintaining transcription in ESCs, it does promote de novo transcription factor binding which may contribute to the dysregulation of cellular differentiation in the absence of H3.3.

Animals↗

PubMed1978

Health status indices and access to medical care.

This paper examines the uses of some health status indices in measuring equity of access to medical care. Empirical examples are provided using data from national surveys of the U.S. population conducted from 1964 through 1976. A simple indicator, mean number of physician visits, suggests that between 1963 and 1976 the poor improved their position relative to the rest of the population and, indeed, currently enjoy the highest level of access. However, a second measure, the use-disability ratio indicates that the poor may still receive less care relative to their need. A third measure, the symptoms-response ratio suggests how norms of appropriate behavior might be incorporated into an access measure.

Disability Evaluation↗

PubMed2026

Access to Guideline-Concordant Oncology Genomic Testing: A Qualitative Study of Black Cancer Patients and Oncology Providers.

Genomic testing is a key component of precision oncology; however, Black patients receive genomic testing at lower rates. The purpose of this qualitative study was to identify individual and health system drivers of genomic testing disparities at a National Cancer Institute-designated comprehensive cancer center. We conducted interviews with 15 oncology providers and 11 Black cancer patients between September 2023 and October 2024. These patients were eligible for genomic testing based on National Comprehensive Cancer Network (NCCN) guidelines, being diagnosed within last 10 years (2014-2023), at least 18 years old, and English-speaking. Providers included oncologists and oncology patient navigators. Topics included motivators, barriers, and knowledge of genomic testing and factors influencing decision-making. The Penchansky and Thomas theoretical framework of healthcare access (e.g., availability, accessibility, accommodation, affordability, and acceptability) guided thematic analysis. Among patients eligible for genomic testing, most participants (n = 7) received genomic testing as part of their cancer treatment based on EMRs, however many patients (n = 7) could not recall discussing genomic testing with their oncologist. Most patients and all providers highlighted affordability as a challenge: patients were concerned about unexpected costs associated with testing, while providers were concerned about costs of matched molecular targeted therapy. Both patients and providers highlighted patient-centered communication to mitigate mistrust and promote patient engagement in care. Despite limited awareness, Black patients view genomic testing positively. Addressing multiple dimensions of access is key to improving system-level processes and ensuring that more patients benefit from lifesaving targeted therapy.

Humans↗

PubMed1979

Vascular access: long-term results, new techniques.

Effective approaches to unique problems of vascular access in renal failure have evolved from a five-year experience with 840 angioaccess procedures. Standard techniques plus innovations have required only 0.62 operations per year per patient with an average access life of 1.6 years. Classical forearm external arteriovenous (AV) cannulas and internal AV fistulas provided vascular access in 392 patients, while 61 required more complex procedures due to failure of primary cannulas and fistulas, inherently small forearm vessels, and iatrogenic vessel loss. Secondary techniques include reverse fistula, vascular graft AV fistulas using expanded polytetrafluoroethylene (E-PTFE), and arterioarterial (AA) jump graft. Presently, the new renal failure patient receives a forearm radiocephalic AV fistula; the cannula is restricted to emergency or short-term hemodialysis and may later be converted to a subcutaneous fistula. The reverse fistula is attempted before using E-PTFE grafts. Upper extremity AV and AA loops can then be constructed de novo or from the reverse fistula.

Arm↗

PubMed1976

Prosthetic arteriovenous fistula for vascular access in hemodialysis.

Vascular access through subcutaneous prosthetic arteriovenous fistulas was studied in eighteen dogs. Dacron velour and woven Dacron grafts (6 mm diameter) were constructed across the lower abdomen between the common femoral artery and the opposite common femoral vein. In heparinized animals 197 percutaneous punctures were made with a "14 guage hemodialysis cannula at weekly intervals. Over a period of one and a half years there was no instance of infection. One of the fourteen Dacron velous and all four woven Dacron fistulas thrombosed. These data suggested the feasibility of achieving repetitive blood access through Dacron velour vascular prostheses. Nineteen Dacron velour fistula bypasses between the brachial artery and median basilic vein were performed in fifteen selected patients for a total dialysis period of ninety-six months. Failed standard subcutaneous fistulas or absence of suitable vessels in the upper extremity were indications for the primary procedure. Of three looped forearm fistulas, two thrombosed at twenty-two and two months. Complications among sixteen straight bypasses in the arm included two graft infections and one cannula tract infection. There were no instances of thrombosis in this group. The advantages of single needle dialysis in these high risk patients have been emphasized. Eleven grafts are presently functioning two to nine months postoperatively. Our preliminary results suggest that a Dacron velour fistula merits consideration as an alternative for vascular access in maintenance hemodialysis.

Adolescent↗

PubMed1978

Accessibility of phospholipids in the chromaffin granule membrane.

1. The accessibility of phospholipids in the membrane of the adrenomedullary storage vesicles (chromaffin granules) has been studied. 2. The reaction of 2,4,6-trinitrobenzenesulphonic acid with both intact granules and their ghosts, results in the labelling of 70% of the phosphatidylethanolamine. 3. The action of phospholipase A2 (from bee venom), phospholipase C (from Bacillus cereus) and sphingomyelinase C (from Staphylococcus aureus) on granules and their ghosts was followed as a function of time. No significant difference was observed between the intact granules and their ghosts. 4. In the intact granules the various treatments led to varying amounts of lysis although again no evidence was obtained that such lysis in any way increased the amount of accessible phospholipid. 5. Highly purified granule preparations were also compared with the so-called "large granule" fraction and no significant differences were detected. 6. Approx. 67% of phosphatidylethanolamine + phosphatidic acid, 50% of phosphatidylserine + phosphatidylinositol, 65% of phosphatidylcholine and 20% of sphingomyelin is accessible to enzymatic degradation. In total, approx. 50% of all the phospholipids reacted. 7. It is also shown that, unlike in enzymatic treatment, all the phosphatidylcholine can be exchanged in the presence of a phospholipid exchange protein (prepared from beef liver). 8. It is concluded that transmembrane movement of phosphatidylcholine is slow in isolated membranes of chromaffin granules. The presence of the exchange protein, however, in conjunction with membrane proteins and specific phospholipid arrangements may catalyse this transmembrane movement.

Animals↗

PubMed2026

The psychosocial supports and interventions accessed by family members of patients with developmental and epileptic encephalopathies: A systematic review.

AIM: Family members of patients with developmental and epileptic encephalopathies (DEEs) face profound emotional, social and practical challenges, yet little is known about how they access psychosocial support. We synthesised the literature on the psychosocial support accessed by family members of patients with DEEs, including evidence-based interventions. METHOD: Four databases were searched. Two reviewers independently screened and extracted data, appraised study quality (QualSyst Tool), and determined certainty of evidence (GRADE-CERQual Framework). Data were synthesised using inductive thematic analysis. RESULTS: 28 papers comprising 27 unique studies were included and methodological quality was high overall (median = 0.91, IQR = 0.85-1.00). Most studies focused on parent experiences; only two included siblings' perspectives. Families reported high psychological needs which were rarely met by psychological support. Clinicians rarely provided adequate information, quality communication or addressed mental health. Families valued respite care, but experienced barriers to access. Peer support was the most common and valued resource. Three studies tested interventions and appeared feasible and acceptable for parents. However, evidence for intervention effectiveness is preliminary and limited to small, uncontrolled pilot studies. INTERPRETATION: Gaps exist in psychosocial support provision for families of patients with DEEs, including insufficient research on siblings' and grandparents' needs, and lack of evidence-based interventions. We propose evidence-informed research and implementation strategies to address these gaps.

Humans↗

PubMed2026

Accessing Underexplored Biosynthetic Potential by Initiation Unit Engineering of Nonribosomal Peptide Synthetases in Proteobacteria.

Nonribosomal peptide synthetases (NRPSs) represent a valuable yet underexplored resource for producing bioactive natural products. However, most NRPSs remain silenced potentially due to factors such as dysfunction of the initiation unit. The starter condensation (Cs) domain of the initiation unit catalyzes the lipoinitiation of nonribosomal peptides via the incorporation of an N-terminal fatty acyl chain. The concept of initiation unit engineering introduced herein encompasses the replacement of the native initiation unit of NRPSs with a foreign and well-characterized Cs domain-containing initiation unit to activate the NRPS and optimize its expression. This strategy was employed herein to successfully access three of the six previously silent NRPS pathways in Mycetohabitans rhizoxinica HKI 454, a bacterium of the class β-proteobacteria, resulting in the identification of three classes of lipopeptides. This strategy was then extended to access two NRPS pathways in Pseudomonas syringae (γ-proteobacteria) and obtain novel lipopeptides, thereby establishing a feasible complement to existing genome mining strategies for natural product discovery. Furthermore, change of the initiation regions of biosynthetic pathways of nonlipidated chitinimide (β-proteobacteria) and pseudotetraivprolide (γ-proteobacteria) with heterologous Cs-containing initiation units enabled the successful incorporation of fatty acyl chains into the N-terminus of both peptide backbones, launching a workable approach to create artificial lipopeptides. Overall, this study provides a practical strategy for the rational recovery of silent BGCs and introduction of fatty acyl chains into nonribosomal peptides, at least in Proteobacteria, thereby enriching genome mining and combinatorial biosynthesis approaches for accessing the underexplored biosynthetic potential of NRPSs from various bacteria.

Proteobacteria↗

PubMed2026

Flexible use of conserved motifs constrains genome access in cell type evolution.

Cell types can be organized into related families, but the regulatory mechanisms that define and maintain these families across deep evolutionary time remain unknown. Here, combining single-nucleus multi-omic sequencing with deep learning to analyse the accessible genomes of two groups of vastly divergent animals including flatworms and vertebrates, we find that hundreds of accessibility-dictating sequence motifs partition into distinct yet conserved sets, or 'vocabularies', each associated with a specific cell type family. However, combinatorial relationships among these motifs preferred by individual cell types are largely species specific. Deep-learning models trained on one species accurately predict family-level chromatin accessibility in distantly related species, albeit frequently rely on different motifs from shared vocabularies to reach convergent predictions. By contrast, models trained on individual cell types within a family lose cross-species predictive power, indicating that the regulatory syntax governing cell type-level identity evolves rapidly. We propose a 'collective maintenance' model in which motif vocabularies defining cell type families are evolutionarily stable, while recombination of these motifs generates cell type-specific regulatory programmes. This suggests that family identity is maintained collectively by large, conserved pools of regulatory factors, analogous to the logic of developmental homology, where character identity persists through network-level conservation despite extensive rewiring.

Journal Article↗

PubMed2026

CIRCE: a scalable Python package to predict cis-regulatory DNA interactions from single-cell chromatin accessibility data.

MOTIVATION: Chromatin 3D folding creates numerous DNA interactions, participating in gene expression regulation. Single-cell chromatin-accessibility assays now profile hundreds of thousands of cells, challenging existing methods for mapping cis-regulatory interactions. RESULTS: We present CIRCE, a fast and scalable Python package to predict cis-regulatory DNA interactions from single-cell chromatin accessibility data. CIRCE re-implements the Cicero workflow to analyse single-cell atlases, cutting runtime and memory use by several orders of magnitude. We also provide new options to compute metacells, grouping similar cells to reduce data sparsity. We benchmarked CIRCE against Cicero on two datasets of different sizes and demonstrated the improvement from CIRCE's metacells' strategy with promoter capture Hi-C data. We also evaluated how DNA interaction predictions are impacted by different pre-processing. We observed a negative impact of Cicero's count normalization, and the best performance was obtained with the single-cell count matrix directly. Finally, we demonstrated the scalability of CIRCE by processing a dataset of more than 700 000 cells and 1 million DNA regions in less than an hour. CIRCE should greatly facilitate the prediction of DNA region interactions for scverse and Python users, while providing new and up-to-date pre-processing insights. AVAILABILITY AND IMPLEMENTATION: CIRCE is released as an open-source software under the AGPL-3.0 licence. The package source code is available on GitHub at https://github.com/cantinilab/CIRCE, and its documentation is accessible at https://circe.readthedocs.io. The code to reproduce the presented results is available as a Snakemake pipeline at https://github.com/cantinilab/circe_reproducibility.s.

Software↗

PubMed2026

Immune Checkpoint Inhibitor-related Adverse Events in Publicly Accessible United States Malpractice Records: A Systematic Legal Database Review, 2015 to 2026.

OBJECTIVES: By 2023, an estimated 56.7% of US patients with advanced or metastatic cancer were eligible for immune checkpoint inhibitor (ICI) therapy. Grade 3 to 4 immune-related adverse events (irAEs) occur in ∼14% to 21% of patients depending on regimen, yet publicly accessible malpractice records involving ICI administration or irAE management have not been systematically described. METHODS: We searched Lexis+ and Westlaw Advantage for publicly accessible US malpractice records filed from January 1, 2015, through March 31, 2026. Sources included jury verdicts and settlement databases, federal and state dockets, and briefs, pleadings, and motions databases. Cases were included only when ICI administration, indication selection, toxicity counseling, toxicity recognition, toxicity monitoring, or irAE management was causally central to the alleged negligence. RESULTS: Among 38 legal matters identified after cross-platform deduplication, 4 met eligibility criteria. These matters reflected 4 pleaded negligence theories: inappropriate ICI indication, toxicity counseling and informed-consent failure, irAE mismanagement, and treatment-related multiorgan toxicity. Publicly visible irAE-centered malpractice records were rare relative to the clinical burden, but the data do not support a national litigation incidence estimate. CONCLUSIONS: Publicly accessible irAE-centered malpractice records appear rare. As ICI use expands, litigation risk may increasingly focus on indication documentation, individualized toxicity counseling, and structured monitoring.

immune checkpoint inhibitors↗

PubMed2026

Quantitative trait loci mapping of gene expression and chromatin accessibility in primary fibroblasts reveals shared allelic effects between Latin American and European ancestries.

BACKGROUND: Quantitative Trait Locus (QTL) analysis of molecular data has identified genetic variants associated with traits such as gene expression, and colocalization of these functional QTL with GWAS risk loci has offered insights into the genetic basis of human disease. We employed gene expression (RNA-seq) and chromatin accessibility (ATAC-seq) obtained from human primary fibroblasts to investigate quantitative trait loci (QTLs) in cohorts ascertained for bipolar disorder of European (n = 150) and Latin American (n = 96) ancestries. RESULTS: Leveraging data from three countries of origin (The Netherlands, Colombia, Costa Rica) within our cohort, we characterized differences among individuals at the SNP, gene, and accessible-chromatin levels to compute ancestry-specific expression (e)QTLs and chromatin-accessibility (ca)QTLs. Across ancestries, we observed R2 ≥ 0.93 for eQTL effect sizes and R2 ≥ 0.95 for caQTLs, indicating a high degree of concordance. Integrating chromatin data with expression and genotype information enabled precise fine-mapping of eQTLs, yielding 203 genes with high-confidence (posterior probability > 90%) candidate regulatory pathways. In downstream analyses, transcriptome-wide (TWAS) and chromatin-wide (CWAS) association studies with brain- and skin-related GWAS identified 36 TWAS-significant genes and 77 CWAS-significant open chromatin regions. CONCLUSIONS: These findings underscore the shared genetic regulatory mechanisms across European and Latin American ancestries, while demonstrating that ancestry-specific reference panels enhance the accuracy of TWAS and CWAS in diverse populations. More broadly, this study highlights the value of paired multi-omic datasets from diverse cohorts for interpreting disease-associated genetic variation.

Humans↗

PubMed2025

iNOME-seq: in vivo simultaneous genome-wide mapping of chromatin accessibility, nucleosome positioning, DNA-binding protein sites, and DNA methylation in Arabidopsis.

We present iNOMe-seq, a novel method for in vivo simultaneous profiling of chromatin accessibility, nucleosome occupancy, DNA-binding protein sites, and DNA methylation in living tissues. iNOMe-seq utilizes an m5C methyltransferase to mark accessible cytosines in a GpC context, bypassing nucleosome-restricted regions. Using Arabidopsis thaliana, we demonstrate that iNOMe-seq improves chromatin accessibility quantification compared to existing methods. Furthermore, it allows for the spatial and temporal analysis of chromatin dynamics, transcription factor binding, and DNA methylation, offering insight into the role of epigenetic components in transcriptional regulation across tissues and genetic variations in natural populations.

Arabidopsis↗

PubMed1977

An analysis of the accessibility and nonaccessibility of patients in a follow-up study.

In a follow-up study of 184 emergency room patients experiencing acute drug reactions, several respondents were inaccessible. In this paper the 83 accessible and 101 nonaccessible patients are compared in order to determine why respondents are often difficult to locate in a follow-up study. Those patients who were the most accessible proved to be primarily young, White males who had been referred to a traditional drug treatment program from the hospital emergency room. Those patients who were the least accessible proved to be primarily White females between 24 and 29 years of age who had not been referred for further treatment.

Adolescent↗

PubMed2026

Genome-wide subgenome-resolved analysis validates chromosome 4 differentiation and prioritizes introgressed Coffea arabica accessions.

Chromosome 4 introgression in Timor hybrid-derived Coffea arabica is established, but the robustness of accession prioritization and the relative strength of cultivated-introgressed differentiation across the canephora-derived (sgC) and eugenioides-derived (sgE) subgenomes remained unclear under explicit subgenome filtering. We reanalyzed public genomic resources from 44 coffee accessions using strict contig-level subgenome filtering, Arabica-only population-structure analysis, SNP-panel sensitivity testing, genome-wide differentiation scans, permutation testing, and direct sequence alignment. Population structure and accession rankings were stable across marker densities and random seeds, and the same six introgressed references were retained throughout. Chromosome 4 ranked first in both subgenomes, with a strong sgC signal and a markedly weaker sgE signal; independent baseline-panel permutation tests supported both chromosome 4-associated signals. Direct alignment supported correspondence to the expected chromosome 4 pseudomolecules while showing incomplete source coverage and unresolved exact boundaries. Alignment-supported blocks contained 88 sgC and 62 sgE provisional defense-, signaling-, and regulatory-associated annotations. These results provide a genome-wide, quantitatively validated framework for prioritizing introgressed germplasm and candidate chromosome 4 regions for phenotype-linked coffee research without implying equivalent introgression, exact liftover, or causal resistance genes.

Coffea arabica↗

PubMed1979

Polytetrafluoroethylene grafts for vascular access for hyperalimentation.

A polytetrafluoroethylene (PTFE) graft from the brachial artery to the axillary vein may provide a safe and trouble-free means of vascular access in selected patients requiring long-term intravenous feeding in the hospital setting. This route for the administration of solutions supplying total parenteral nutrition (TPN) should be considered in persons whose requirement for parenteral feeding is likely to extend over many months and in whom there are other sources of bacteremia which can imitate or be confused with infection of a conventional central venous feeding line. In a 52-year-old man an 8-mm PTFE graft was anastomosed end-to-side to the brachial artery and the axillary vein and brought through a subcutaneous tunnel on the medial aspect of the upper arm. Access to it was obtained by intermittent puncture with a no. 21 butterfly needle. Hyperosmolar TPN solutions flowed easily by gravity drip into the shunt. The graft seemed resistant to infection. This form of vascular access appears to exclude parenteral feeding lines, solutions and catheters as sources of sepsis.

Arteriovenous Shunt, Surgical↗

PubMed1978

Hydrogen exchange kinetics of human hemoglobins. The pH dependence of solvent accessibility in cyanomet-, oxy-, and deoxyhemoglobin.

The hydrogen exchange kinetics of human oxy-, deoxy-, and cyanomethemoglobin have been measured as a function of pH by the tritium tracer method. At 5 degrees C and in phosphate buffer both liganded and unliganded forms of ferrohemoglobin exhibit deviations from the regular pH dependence of exchange that is characteristic of cyanomethemoglobin. In oxyhemoglobin, the deviation from the normal exchange pattern is centered at pH 7.4 and is in the direction of increased exchange or solvent accessibility. The effect in deoxyhemogloin, while occurring at the same pH and being of the same order of magnitude, is in the opposite direction, thus suggesting a pH-induced conformational transition leading to a less accessible structure. The width of these pH-induced deviations in solvent accessibility is approximately 1 pH unit in both cases. We propose a model in which specific interactions between charged groups in both froms of ferrohemoglobin account for these deviations.

Cyanides↗