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At least 55 records · Page 3Linked to original sources
PubMed2005

Nanophotonic crescent moon structures with sharp edge for ultrasensitive biomolecular detection by local electromagnetic field enhancement effect.

We present novel gold nanophotonic crescent moon structures with a sub-10 nm sharp edge, which can enhance local electromagnetic field at the edge area. The formation of unconventional nanophotonic crescent moon structure is accomplished by using a sacrificial nanosphere template and conventional thin film deposition method, which allows an effective batch nanofabrication and precise controls of nanostructure shapes. Unique multiple scattering peaks are observed in a single gold nanocrescent moon with dark-field white light illumination. A 785 nm near-infrared (NIR) diode laser was used as the excitation source to induce the amplified scattering field on the sharp edge of the single gold nanocrescent moon. The Raman scattering spectrum of Rhodamine 6G molecules adsorbed on the single gold nanocrescent moon are characterized, and the Raman enhancement factor of single gold nanocrescent moon is estimated larger than 10(10), which suggests the potential applications of gold nanocrescent moons in ultrasensitive biomolecular detection and cellular imaging using surface enhanced Raman spectroscopy.

Electromagnetic Fields↗
PubMedDate not supplied

In situ quantification of aberrant p53 in colorectal neoplasia.

Aberrant p53 protein accumulation was measured immunohistologically in 342 colorectal paraffin-embedded tissue sections from 115 patients (24 with adenocarcinoma, 59 with adenoma and 32 'hospital controls'). Subjective scoring was compared with quantitative cell imaging, including dichotomous (p53+/p53-) status, ng p53mut mg(-1) enterocyte protein, and tumour burden and patient body 'burden' of aberrant p53. A total of 62.5% cancer patients, 23.7% adenoma patients and 3.1% hospital controls were accorded p53+ status on the basis of p53 quantification. Quantitative p53+/p53- assignment had a stronger inverse association with survival (chi2=6.17, p=0.013, Kaplan-Meier test) than subjective 'visual estimation' (chi2=0.57, p=0.449). There was a strong inverse relationship between the p53 'body burden' and the months of post-diagnosis survival (hazard ratio=1.42, p=0.0004, Cox proportional hazards). Absolute quantification for inactivated p53 permits objective and reproducible scoring, adjusts for intra-laboratory immunostaining 'batch effects', corrects for fixation artefacts, and standardizes for inter-laboratory differences in fixation, antibody selection and staining method. Clinically, in situ quantification of p53 will permit more accurate survival prognoses and will inform therapy selection and dose. Ultimately, accurate quantitative tissue/blood p53 correlations may provide a minimally invasive and systemic surrogate measure for these same clinical purposes.

Adenocarcinoma↗
PubMed2026

NoisyFlow: differentially private optimal transport using neural networks for secure biomedical data sharing across multiple institutions.

MOTIVATION: Biomedical models improve when trained on data pooled across institutions, but sensitive patient records (e.g. genomics, clinical data, and medical images) are difficult to share due to privacy constraints. Moreover, data collected at different sites often have shifted distributions because of covariate differences (including batch effects), so privacy-preserving sharing alone cannot simply resolve cross-site mismatch. Methods that protect individuals while explicitly aligning distributions are needed to enable reliable multi-institutional analyses. RESULTS: We present NoisyFlow, a three-stage differentially private framework for cross-institutional harmonization under distribution shift. In stage I, each site learns a differentially private flow-based generator of its local labeled distribution. In stage II, it learns a neural optimal transport map to a shared reference distribution. In stage III, a central server composes the released models to generate reference-aligned pseudo-data for downstream analysis without accessing raw records. Across four biomedical settings spanning single-cell genomics, histopathology, neurogenomics, and wearable sensing, NoisyFlow reduces distribution shift while preserving downstream utility under formal differential privacy guarantees. AVAILABILITY AND IMPLEMENTATION: The implementation of NoisyFlow is available at https://github.com/gersteinlab/NoisyFlow.

Information Dissemination↗
PubMed2026

RAREsim2: flexible simulation of rare variant genetic data using real haplotypes.

MOTIVATION: Realistic simulated data is critical for advancing methodological development and optimizing study design in genetics research. However, many genetic simulation tools are unable to replicate the distribution of rare variants or incorporate key genetic information, such as functional annotations and linkage disequilibrium. RAREsim, an accurate rare variant simulation algorithm that uses real genetic haplotypes, was developed to address these limitations. Here, we introduce RAREsim2, an update that provides both streamlined software and new functionalities for simulating individual-level differences (e.g., case-control status, technological or batch effects) and variant-level differences to represent a variety of causal models. RESULTS: We demonstrate RAREsim2's utility with three rare variant association methods (Burden, SKAT, and SKAT-O) across several simulation scenarios, including various genetic ancestries, gene sizes, strengths of association, and proportions of risk variants. Type I Error was maintained and the test with the highest power matched previously known patterns. Importantly, real genetic regions can be simulated to include known variant functions and disease associations. Ultimately, RAREsim2 offers additional flexibility and ease in simulating a multitude of realistic genetic scenarios. AVAILABILITY AND IMPLEMENTATION: The RAREsim2 Python package is publicly available on Github (https://github.com/Hendricks-Research-Team/RAREsim2), PyPI (https://pypi.org/project/raresim/), and Zenodo (https://doi.org/10.5281/zenodo.19442523). Code for the example demonstration can be found at https://github.com/JessMurphy/RAREsim2-demo.

Software↗
PubMed2025

Identification of key genes related to bone metastasis of breast cancer using bioinformatics methods and construction of a prognostic model.

Breast cancer (BC) ranks among the most prevalent cancers in females, with bone metastasis significantly compromising patients' quality of life and survival rates. Enhancing our comprehension of BC bone metastasis mechanisms at the molecular level holds promise for improving BC treatment and prognosis. Leveraging bioinformatics tools, we integrated multiple datasets, conducted comprehensive analyses across various databases, identified biomarkers associated with BC bone metastasis, and constructed a prognostic model. Firstly, 3 BC bone metastasis-related datasets were downloaded from gene expression omnibus, the data were merged, and batch effects were removed, followed by identification of differentially expressed genes (DEGs). Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed on the DEGs. A protein-protein interaction network was constructed using the STRING database to screen hub genes. Then, survival analysis of hub genes was performed using the Cancer Genome Atlas (TCGA) database. A prognostic model was constructed using key genes with survival differences, and the model was evaluated. Two hundred ninety-two DEGs were identified. Gene ontology and KEGG pathway enrichment analysis yielded 769 biological processes (BPs), 78 cellular components, 43 molecular functions, and 50 KEGG pathways. Fifteen hub genes were selected from the protein-protein interaction network. Survival analysis revealed 6 genes related to BC survival. The prognostic model identified 4 genes with important predictive value for BC prognosis. Our study utilized bioinformatics analysis to identify a series of DEGs related to BC bone metastasis. Based on further selection of hub genes, we constructed a relatively ideal prognostic model for BC, and identified 4 genes (DLGAP5, TPX2, PLK1, and CENPN) with valuable predictive value for BC prognosis.

Humans↗
PubMed2025

simPIC:flexible simulation of paired-insertion counts for single-cell ATAC sequencing data.

Single-cell Assay for Transposase Accessible Chromatin (scATAC-seq) is increasingly used at population scale to study how genetic variation shapes chromatin accessibility across diverse cell types. This widespread adoption of the assay has created a need for computational methods that can handle complex biological and technical variation. Yet method development is limited by the lack of flexible simulation tools with known ground truth. Here, we present simPIC, a simulation framework for generating realistic single-cell ATAC-seq data across individuals and cell types. simPIC supports both population-scale and single-individual simulations, with the ability to model cell groups, batch effects, and genotype-dependent variation in accessibility. These features enable realistic benchmarking for tasks such as chromatin accessibility quantitative trait locus (caQTL) mapping. simPIC generates data that closely match real datasets and better captures inter-individual and experimental variation compared to existing tools.

simulation↗
PubMed2026

A pan-cancer single-cell atlas uncovers the role of sex hormones and chromosomes in sex-divergent reprogramming of the tumor microenvironment.

BACKGROUND: Sex bias is pervasive in tumors; however, how sex chromosomes and hormone-responsive signaling shape the tumor microenvironment (TME) remains insufficiently characterized. Considering the critical impact of the TME on tumor progression and response to immunotherapy, a pan-cancer investigation of sex-specific and cancer-context-dependent TME features is warranted. METHOD: Based on stringent inclusion criteria, we constructed a high-resolution pan-cancer single-cell sequencing atlas by integrating 31 publicly available single-cell RNA-seq datasets, comprising a total of 1,831,436 cells by integrating 468 samples from eight types of non-sex-specific solid tumors (282 males and 186 females). After correcting for batch effects, we identified major and minor cellular subsets. Multiple computational approaches were applied to investigate sex-associated differences in cellular composition, gene expression, pathway activity, malignant cell states and intercellular communication. RESULTS: We systematically compared sex-specific TME features across eight common solid malignancies. Male-biased CD8+ T cell exhaustion emerged as a recurrent but non-uniform feature, with its magnitude varying across cancer types and being modified by tissue-specific contexts. This pattern was associated with androgen-response signature scores and expression-based loss of the Y chromosome (LOY) scores. M2-like macrophage polarization showed a more cancer-type-dependent pattern; although female-biased enrichment was observed in selected malignancies, it did not represent a uniform pan-cancer feature. Expression-based X chromosome inactivation (XCI)/XCI escape-related programs, estrogen-response signature scores and stromal components, including fibroblasts and endothelial cells, were associated with macrophage and immune-regulatory states in specific tumor contexts. Tumor cells of male origin displayed higher genomic instability and more aggressive phenotypes, with androgen-response signatures and LOY contributing to the development of a male biased malignant state. Furthermore, expression-based LOY scores in malignant cells were associated with CD8+ T cell exhaustion based on transcriptomic proxies. CONCLUSION: Our study uncovers extensive but heterogeneous sex-specific differences in the TME across multiple cancer types. We propose a regulatory framework linking sex chromosomes, hormone-responsive signaling and TME interactions, which is consistent with recurrent male-biased CD8⁺ T cell exhaustion and context-dependent M2-like macrophage polarization. Importantly, the magnitude and, in some cancers, the direction of these sex-biased features are modified by tissue-specific contexts. These findings underscore the need to include sex chromosome and hormone status as essential biological variables in studies of the tumor microenvironment and the design of immunotherapies.

Tumor Microenvironment↗
PubMed2026

Identification of mitochondrial energy metabolism-related candidate genes UQCR10 and NDUFA6 in pediatric tetralogy of fallot: an exploratory bioinformatics study.

BACKGROUND: Tetralogy of Fallot (TOF) is one of the most common cyanotic congenital heart diseases in infants and young children. Its molecular basis remains incompletely understood. This study aimed to identify mitochondrial energy metabolism-related candidate genes associated with pediatric TOF using public heart tissue transcriptomic datasets from the GEO database. METHODS: Datasets GSE146218 and GSE217772 were downloaded and merged, followed by batch-effect correction. Differential expression analysis was performed to identify differentially expressed genes (DEGs). Functional enrichment analysis, weighted gene co-expression network analysis (WGCNA), and protein-protein interaction (PPI) network analysis were used to prioritize candidate genes. The Comparative Toxicogenomics Database (CTD) was used as an exploratory literature-based tool to summarize gene-disease associations. RESULTS: A total of 960 DEGs were identified. Functional enrichment analyses showed that these genes were mainly enriched in mitochondrial energy metabolism-related pathways, including oxidative phosphorylation and the mitochondrial respiratory chain. WGCNA and PPI network analyses further prioritized UQCR10 and NDUFA6 as candidate genes, and both genes showed increased expression in TOF heart tissue samples. CTD analysis suggested literature-based associations between these genes and cardiovascular or developmental disease-related terms. CONCLUSION: This exploratory bioinformatics study identified UQCR10 and NDUFA6 as mitochondrial energy metabolism-related candidate genes upregulated in pediatric TOF heart tissue. These findings suggest that mitochondrial respiratory chain-related transcriptional alterations may be involved in TOF-associated myocardial remodeling or stress responses. Further experimental and clinical validation is required to confirm their biological relevance.

Humans↗
PubMed2026

ZBTB16-associated NK cell alterations reveal shared immunometabolic signatures linking primary Sjögren's syndrome and type 1 diabetes mellitus.

BACKGROUND: Primary Sjögren's syndrome (pSS) and type 1 diabetes mellitus (T1DM) share immune-inflammatory features, yet conserved pathogenic signatures linking these autoimmune disorders remain incompletely understood. The present research sought to uncover common molecular markers and dissect the underlying immune-metabolic cross-talk underlying pSS and T1DM. METHODS: Gene expression profiles of patients with pSS and T1DM were retrieved from the Gene Expression Omnibus database, normalized, and corrected for batch effects prior to downstream analyses. Overlapping potential biomarkers were screened by integrating differential expression analysis, weighted gene co-expression network analysis and least absolute shrinkage and selection operator regression. Functional enrichment based on Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases was implemented to interpret gene biological properties, and a protein-protein interaction network was further established afterwards. Diagnostic performance was evaluated using receiver operating characteristic analysis. Experimental validation was conducted in non-obese diabetic (NOD) mice using quantitative PCR, immunohistochemistry, and flow cytometry. The CIBERSORT algorithm was adopted to quantify immune cell infiltration levels. RESULTS: ZBTB16 was identified as a shared hub biomarker in both pSS and T1DM and exhibited favorable diagnostic performance. Experimental validation confirmed significantly reduced ZBTB16 expression in peripheral blood mononuclear cells, salivary gland tissues, and pancreatic tissues of NOD mice. Gene Set Enrichment Analysis indicated that ZBTB16-associated signatures were enriched in mitochondrial-related processes, neuroactive ligand-receptor interactions, and ribosome-related pathways. Immune infiltration analysis revealed that resting natural killer (NK) cells were positively correlated with ZBTB16 expression in both diseases. Flow cytometric analysis further confirmed a reduced proportion of resting NK cells in peripheral blood of NOD mice, consistent with the CIBERSORT-based prediction. CONCLUSION: This study identifies ZBTB16 as a shared biomarker linking pSS and T1DM. Reduced resting NK-cell abundance was consistently observed in both computational and experimental analyses, and bioinformatic correlation analysis suggested a positive association with ZBTB16 expression. These findings provide evidence for shared molecular and immunological signatures underlying the two autoimmune disorders and support further investigation of the biological role and diagnostic value of ZBTB16 in pSS and T1DM.

Sjogren's Syndrome↗
PubMed2025

Multi-omics technologies: Novel tools and methods for assessing nerve injury and regeneration.

Recently, with the rapid advancement of multi-omics technologies, including genomics, transcriptomics, proteomics, and metabolomics, new tools and approaches have been introduced for studying nerve injury and regeneration. This review highlights the application and progress of multi-omics in uncovering the mechanisms of nerve injury, guiding the development of regenerative strategies, and promoting clinical translation. By integrating multi-omics datasets, researchers can comprehensively track dynamic molecular changes following nerve injury, including abnormal gene expression, disrupted protein signaling, altered metabolic programs, and shifts in the immune microenvironment. Single-cell multi-omics technologies resolve cellular heterogeneity, revealing the distinct functions of neurons, glial cells, and immune cell subpopulations during the injury response. Spatially resolved transcriptomics maintain the spatial context of lesion and regeneration sites, enabling precise localization for targeted interventions. Multi-omics technologies not only identify key molecular players involved in nerve regeneration but also create opportunities for personalized medicine. Nonetheless, integrating multi-omics data poses technical challenges, including high dimensionality, batch effects, and algorithmic constraints, while ethical concerns related to stem cell therapy and gene editing require stringent oversight. To transition from structural reconstruction to functional remodeling, future research should emphasize artificial intelligence-driven data integration, organ-on-a-chip modeling, and cross-disciplinary collaboration to overcome existing technical barriers and accelerate the clinical application of neuroregenerative therapies.

artificial intelligence↗
PubMed2005

Dialysate partitioning in the Genius batch hemodialysis system: effect of temperature and solute concentration.

BACKGROUND: The Genius batch system contains a 75-L closed reservoir from which fresh dialysate is extracted at the top, and to which spent dialysate is returned at the bottom. In vivo studies have demonstrated that almost the entire amount of dialysate can be used before contamination of fresh with spent dialysate occurs. The question is raised whether density differences cause this separation, and what the relative contributions of temperature and solute content are. METHODS: As patient substitute, a container filled with dialysate was loaded with various amounts of urea. Temperature differences between spent and fresh dialysate were imposed by not heating the dialysate at the outlet line from the dialyzer (A), heating the outlet to obtain continuously equal temperatures at inlet and outlet (B), or to temperatures as in vivo (C). With a dialysate flow set at 300 mL/min, urea is not expected at the inlet before 250 minutes. RESULTS: With a urea concentration of 33 mg/dL, urea contamination at the dialysate inlet line occurred after 185 +/- 20 (A), 122 +/- 11 (B), and 175 +/- 12 minutes (C) of dialysis, whereas with 67 mg/dL, this happened at 219 +/- 5 (A), 162 +/- 11 (B), and 202 +/- 8 minutes (C). With 100 and 150 mg/dL, urea contamination appeared at 224 +/- 2 (A) and 204 +/- 14 minutes (B), and 227 +/- 5 (A) and 232 +/- 3 minutes (B), respectively. CONCLUSION: Both temperature differences between spent and fresh dialysate and solute content of spent dialysate contribute to dialysate partitioning in the Genius dialysis system.

Dialysis Solutions↗
PubMed2005

Anaerobic whey treatment by a stirred sequencing batch reactor (ASBR): effects of organic loading and supplemented alkalinity.

An assessment was made of cheese whey treatment in a mechanically stirred anaerobic sequencing batch reactor (ASBR) containing granular biomass. The effect of increasing organic load and decreasing influent alkalinity supplementation (as sodium bicarbonate) was analyzed. The reactor operated on 8-h cycles with influent COD concentrations of 500, 1000, 2000 and 4000 mg/L, corresponding to volumetric organic loads of 0.6 to 4.8 mgCOD/L.d. Organic COD removal efficiencies were always above 90% for filtered samples. These results were obtained with an optimized alkalinity supplementation of 50% (ratio between mass of NaHCO3 added and mass of influent mgNaHCO3/mgCOD) in the assays with 500 and 1000 mgCOD/L and of 25% in the assays with 2000 and 4000 mgCOD/L. Initial alkalinity supplementation was equal to the mass of influent COD (100%). The system showed formation of viscous polymer-like substances. These were probably of microbiological origin occurring mainly at influent CODs of 2000 and 4000 mg/L and caused some biomass flotation. This could, however be controlled to enable efficient and stable reactor operation.

Animals↗
PubMed2002

Effect of agitation and aeration on bioconversion of domestic wastewater sludge in a batch fermenter.

Effects of agitation and aeration rate on microbial treatment of domestic wastewater sludge were investigated in a batch fermenter using mixed culture of Penicillium corylophilum and Aspergillus niger. It was found that liquid state bioconversion (LSB) of wastewater sludge was highly influenced by the effects of agitation and aeration. The maximum production of sludge cake and reduction of organic substances in treated sludge were recorded at 150-200 rpm of agitation speed and 0.5 vvm of aeration rate after 72 h of treatment. No effective results were observed at higher rate of agitation (300 rpm) and aeration (1.5 vvm) as compared to optimum values. The results showed that the minimum level of air saturation (pO2) was adequate to maintain the bioconversion process.

Aspergillus niger↗
PubMed1996

The effect of antibiotics on nitrification processes. Batch assays.

The effect of different antibiotics at several concentrations of ampicillin (0-250 mg/L), benzylpenicillin (0-250 mg/L), novobiocine (0-150 mg/L), oxytetracycline (0-250 mg/L), and chloramphenicol (0-50 mg/L) on a stabilized nitrifying sludge was evaluated under aerated and lithoautotrophic conditions. No effect resulting from the presence of antibiotics on the biomass and nitrate production was noticed. The specific growth rate and volumetric nitrification rate average values for the controls were 8.28 x 10-3/h-1 and 2.74 x 10-3 g/L.h, respectively. Similar rate values were found when different kinds of antibiotic and concentrations were tested. These results may be explained by the nature of the floc or the instability of the antibiotics.

Aerobiosis↗
PubMed1988

Evaluation of carcinogenic effect of jute batching oil (JBO-P) fractions following topical application to mouse skin.

Jute batching oil (JBO-P), a mineral oil fraction used in the processing of jute fibers, was, as reported in our earlier studies, found to be tumorigenic following repeated topical application to mouse skin. In the present investigation an attempt has been made to identify the carcinogenic constituents of this oil. The JBO was fractionated into (1) PAH free fraction, (2) fraction containing two- and three-ring PAHs and (3) more than three-ring PAH fractions by an enrichment procedure. These three JBO fractions along with unfractionated and reconstituted oil were then subjected to the in vivo assay of complete carcinogenic activity of JBO-P and its fractions following its topical application to mouse skin. The results showed that only unfractionated and reconstituted JBO-P samples per se were able to produce benign skin tumours, while all the other three fractions, i.e. PAH-free fraction, two- and three-ring PAH-containing fraction and more than three-ring PAH-containing fraction failed to produce tumours up to 40 weeks after application. In an extended study, mice belonging to the groups exposed to various fractions of JBO were promoted with 12-O-tetradecanoyl phorbol-13-acetate (TPA), a potent skin tumour promoter, for the two stage initiation-promotion protocol for skin carcinogenesis. After 14 weeks of promotion with TPA, all the surviving animals exposed to the fraction having more than three-ring PAHs developed benign tumours on their backs, while the other two fractions failed to do so.(ABSTRACT TRUNCATED AT 250 WORDS)

Administration, Topical↗
PubMed1987

Effects of different batches of 125iodine on properties of 125I-hFSH and characteristics of radioligand-receptor assays.

Radioiodination of highly purified human follicle-stimulating hormone (hFSH) (4000 IU/mg) was performed every other week for 23 weeks using 2 mCI carrier free Na125I (Amersham Corp., 15 mCi/micrograms I2) in the presence of lactoperoxidase. Incorporation of 125I into hFSH was determined by the method of R. C. Greenwood, W. M. Hunter, and J. S. Grover (1963) Biochem. J. 89, 114). Hormone binding was studied in vitro under steady-state conditions (16 h, 20 degrees C) using different calf testis membrane preparations having similar receptor characteristics. Each 125I-hFSH preparation was characterized for maximum bindability, specific activity of bindable radioligand as determined by self-displacement analysis, and by determination of Ka and Rt. Incorporation of 125I into FSH was relatively constant over the large number of experiments (62.4 +/- 6.4 microCi/micrograms; n = 23). By comparison, however, specific radioactivity of the receptor bindable fraction of 125I-hFSH was related to the lot of 125I utilized, and was significantly (P less than or equal to 0.01) lower and more variable (28.7 +/- 10.5 microCi/micrograms). Maximum bindability of 125I-hFSH was not correlated to specific activity (r = 0.06) but was negatively correlated to hFSH 125I incorporation (r = -0.47; P less than or equal to 0.05). These observations demonstrate the need to assess the quality of each batch of radioligand before undertaking radioligand-receptor assays and suggest that differences in Na125I lots affect specific radioactivity of the radioligand and its receptor binding characteristics.

Follicle Stimulating Hormone↗
PubMed1985

Quantification of tumour initiating effect of jute batching oil and its distillates over mouse skin.

In order to identify the tumour initiating constituent(s) of a mineral oil, jute batching oil (JBO), used in the processing of jute fibres, it was fractionally distilled in various boiling range fractions. The latter were then subjected to in vivo assessment of their aryl hydrocarbon hydroxylase (AHH) inducing potential in mouse epidermis. Fractions with almost similar AHH inducing potential were regrouped and studied for their tumour initiating potential over mouse skin following two-stage initiation-promotion protocol and using 12-O-tetradecanoyl phorbol-13-acetate (TPA) as tumour promoter. It was noticed that: (1) JBO as initiator, provoked local development of benign skin tumours over mouse back; (2) fractions of JBO boiling below 335 degrees C and above 399 degrees C accounted for most of the tumour initiating potential of the oil; (3) the histological features of the tumours (i.e. benign papillomas and keratoacanthomas) initiated by these fractions were similar to those developed after being initiated with unfractionated or reconstituted JBO; (4) removal of these fractions from JBO may be attempted which could decontaminate the batch oil from most of its tumorigenic components and make it safer for industrial use.

Animals↗