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PubMed2026

Spatial biology reveals altered macrophage states in immunosuppressed non-melanoma skin cancer.

Immunosuppressed patients with non-melanoma skin cancer experience worse clinical outcomes, yet the tumor immune microenvironment associated with systemic immunosuppression remains incompletely defined. Using integrated single-cell, spatial transcriptomic, multiplex immunofluorescence, and spatial epigenomic profiling across immunocompetent and immunosuppressed tumors, we found that overall immune-cell composition was largely preserved despite differences in immune-cell distribution, spatial organization, and T cell clonality. Immunosuppressed tumors demonstrated reduced intratumoral macrophage densities, decreased T cell clonal diversity, altered antigen-presenting cell and T cell spatial interactions, and distinct fibroblast- and macrophage-associated spatial niches. Multi-cohort validation across complementary spatial and single-cell platforms identified consistent alterations in innate-adaptive immune organization in immunosuppressed tumors. Together, these findings define spatial and functional remodeling of the tumor immune microenvironment under systemic immunosuppression and provide a framework for future therapeutic investigation in high-risk patients.

Humans↗
PubMed2026

Detection of antibiotic heteroresistance in clinical microbiology: current and emerging methodologies.

BACKGROUND: Antibiotic heteroresistance (HR) is characterised by the coexistence of susceptible and resistant subpopulations within an apparently isogenic bacterial isolate. Because routine antimicrobial susceptibility testing (AST) primarily assesses the dominant population, HR may escape detection, potentially leading to discrepancies between laboratory susceptibility categorisation and the underlying bacterial population structure. OBJECTIVES: To provide a critical and practice-oriented evaluation of current and emerging methodologies for HR detection and to discuss their strengths, limitations, and potential for clinical implementation. SOURCES: Narrative review based on PubMed searches, complemented by screening of key reference lists and relevant EUCAST and CLSI documents. Peer-reviewed literature was prioritised. CONTENT: Phenotypic approaches, particularly population analysis profiling, remain the reference method for HR definition, but their labour-intensive workflows, long turnaround times, and limited standardisation restrict routine implementation. Alternative strategies, including modified AST assays, metabolic assays, and single-cell platforms, offer gains in speed or throughput but require broader validation. Molecular approaches such as quantitative PCR, droplet digital PCR, targeted deep sequencing, and whole-genome sequencing improve detection of minority resistance determinants. Emerging computational frameworks, including machine learning models integrating phenotypic and genomic data, represent a promising frontier for scalable HR prediction. IMPLICATIONS: Available evidence supports the clinical relevance of HR, although its association with adverse outcomes varies across bacterial species and antibiotic classes. Harmonised methodologies and clinically validated interpretive criteria are needed to support integration of HR assessment into routine diagnostics. Prospective multicentre studies and further standardisation, including engagement with EUCAST and CLSI, will be important to advance clinical implementation.

Antimicrobial resistance↗
PubMed2006

Moderate alterations in lower limbs muscle temperature do not affect postural stability during quiet standing in both young and older women.

Older adults demonstrate increased amounts of postural sway, which may ultimately lead to falls. Temperature is known to have a profound effect on the performance of the neuromuscular system which could have important implications on motor control. It is, therefore, of interest to investigate if the age-related decline in postural stability could be affected by changes in local limbs temperature. The present study investigated the effects of localized warming and cooling on postural sway in nine young (22+/-3 years) and nine older (73+/-3 years) women. Postural sway was assessed, using a single force platform, during quiet standing at three muscle temperature conditions: control (34.2+/-0.2 degrees C), cold (31.3+/-0.3 degrees C) and warm (37.0+/-0.1 degrees C). Two stances were evaluated, the Romberg (large support base) and modified Tandem (narrow support base), under both eyes-open and eyes-closed conditions. Root mean square (RMS), mean velocity (MV), sway area (SA) and mean power frequency (MPF) were calculated from the centre of pressure (COP) displacement. Neither warming nor cooling significantly affected any of the postural parameters which were, however, all higher (P<0.05) in the older group than the young group in all conditions. This study demonstrated that, in quiet standing conditions, a moderate variation (+/-3 degrees C) in lower limbs temperature does not affect postural steadiness in either young or older women.

Adult↗
PubMed2006

Relationship between static and dynamic balance tests among elite Australian Footballers.

Research assessing the direct relationship between static and dynamic balance ability of athletes is sparse. The aim of this project was to determine the relationship between a static balance task on a firm surface with a stepping balance task on an unstable surface. Thirty-seven Australian male professional footballers participated in the study. The static test involved maintaining single limb stance on a force platform. The other balance test involved stepping on to a balance mat on top of the force platform and maintaining single limb stance. The centre of pressure was monitored and the maximum excursion in the medial-lateral direction was recorded and used as the balance value. It was found that the magnitude of the maximum centre of pressure excursion was significantly greater (53%) for the stepping balance task. There were significant but low correlations for the centre of pressure excursion values between the two balance tests for the right limb and average of both limbs. There was no significant correlation between the test values for the left limb. Only a small proportion of the variance could be explained by each test: 16% for right limb values, 7% for left limb values and 11% for the average of both limbs. Given the overall weak associations between the two balance test values, it was concluded that performance in the static balance test was not reflective of performance in the dynamic balance test. Attempting to infer dynamic balance ability based on static balance ability should be avoided.

Adult↗
PubMed2000

Multivariate analysis of near-infrared spectra using the G-programming language

"Real-time" chemometrics as envisioned by the union of instrument control, data acquisition, and chemometric analysis with a single software platform can provide substantial benefits to manufacturing concerns that require process control. Some of these benefits include faster generation of information and improved quality control. This paper describes a series of chemometric routines written in LabVIEW and demonstrates their use in predicting six properties of diesel fuel. In particular, near-infrared spectral data were used to predict the boiling point at 50% recovery, cetane number, density, freezing temperature, total aromatics, and viscosity for a series of diesel fuels.

Journal Article↗
PubMed2003

A novel mode of RBD-protein recognition in the Y14-Mago complex.

Y14 and Mago are conserved eukaryotic proteins that associate with spliced mRNAs in the nucleus and remain associated at exon junctions during and after nuclear export. In the cytoplasm, Y14 is involved in mRNA quality control via the nonsense-mediated mRNA decay (NMD) pathway and, together with Mago, is involved in localization of osk (oskar) mRNA. We have determined the crystal structure of the complex between Drosophila melanogaster Y14 and Mago at a resolution of 2.5 A. The structure reveals an atypical mode of protein-protein recognition mediated by an RNA-binding domain (RBD). Instead of binding RNA, the RBD of Y14 engages its RNP1 and RNP2 motifs to bind Mago. Using structure-guided mutagenesis, we show that Mago is also a component of the NMD pathway, and that its association with Y14 is essential for function. Heterodimerization creates a single structural platform that interacts with the NMD machinery via phylogenetically conserved residues.

Amino Acid Sequence↗
PubMed2006

A Web-based data warehouse on gene expression in human malignant melanoma.

The identification of melanoma-specific dysregulated genes could identify new molecular markers. By applying bioinformatic tools for screening of biomedical databases, a melanoma-specific gene expression profile "data warehouse" was constructed. Utilizable data sets of global gene expression analyses were available from nine studies that applied different technology platforms. A single study used cell lines, five investigations analyzed cell lines and tissues obtained from patients, two studies used exclusively specimens obtained from patients, and one study analyzed blood cells prepared from patients. The total number of investigated patients was 116. From 815 differential-regulated genes, 772 (95%) were identified merely in a single study, 37 in at least two studies, five (RAB33A, ERBB3, ADRB2, MERTK, SNF1LK, and ITPKB) in at least three studies, and a single gene, RAB33A, in four studies. These data show that the accuracy, reproducibility, and comparability among different gene expression profile studies are low in melanoma. In conclusion, the study demonstrates the high diversity of gene expression profiles associated with melanoma, the necessity to include a sufficient number of samples regarding clinical standards, for the design of standardized sample collecting and preparation, for the development of common standards for microarray data processing, and for developing standardized bioinformatic tools.

Cell Line↗
PubMed2006

A gene-expression signature to predict survival in breast cancer across independent data sets.

Prognostic signatures in breast cancer derived from microarray expression profiling have been reported by two independent groups. These signatures, however, have not been validated in external studies, making clinical application problematic. We performed microarray expression profiling of 135 early-stage tumors, from a cohort representative of the demographics of breast cancer. Using a recently proposed semisupervised method, we identified a prognostic signature of 70 genes that significantly correlated with survival (hazard ratio (HR): 5.97, 95% confidence interval: 3.0-11.9, P = 2.7e-07). In multivariate analysis, the signature performed independently of other standard prognostic classifiers such as the Nottingham Prognostic Index and the 'Adjuvant!' software. Using two different prognostic classification schemes and measures, nearest centroid (HR) and risk ordering (D-index), the 70-gene classifier was also found to be prognostic in two independent external data sets. Overall, the 70-gene set was prognostic in our study and the two external studies which collectively include 715 patients. In contrast, we found that the two previously described prognostic gene sets performed less optimally in external validation. Finally, a common prognostic module of 29 genes that associated with survival in both our cohort and the two external data sets was identified. In spite of these results, further studies that profile larger cohorts using a single microarray platform, will be needed before prospective clinical use of molecular classifiers can be contemplated.

Breast Neoplasms↗
PubMed1998

Increased ACTH and corticosterone secretion induced by different methods of paradoxical sleep deprivation.

The methods used to induce paradoxical sleep (PS) deprivation are believed to be stressful. In the present study, two methods were compared in regard to their ability to activate the hypothalamic-pituitary-adrenal (HPA) axis. Animals were placed on multiple large (MLP) or small (MSP) platforms or on single large (SLP) or small (SSP) platforms and blood sampled at the end of a 4-day period of PS deprivation (experiment 1) or on Days 1 (short-term) and 4 (long-term) of PS deprivation (experiment 2). ACTH and corticosterone (CORT) levels were determined by RIA. The results of experiment 1 showed that all experimental animals presented increased ACTH response, compared to controls. CORT levels, however, were only elevated in MSP animals, suggesting increased adrenal sensitivity. Experiment 2 showed that ACTH levels of MSP animals were higher than MLP and SSP animals, and that animals placed on the multiple platform tanks showed the highest ACTH levels on Day 4 of manipulation. CORT levels were elevated in the animals kept over small platforms, and these levels where higher on Day 1 than basal and further elevated on Day 4 of PS deprivation. These results indicate that the multiple platform technique induces a distinct activation of the HPA axis, and that PS deprivation may act as an additional stressor.

Adrenocorticotropic Hormone↗
PubMed2024

Simultaneous targeting of peripheral and brain tumors with a therapeutic nanoparticle to disrupt metabolic adaptability at both sites.

Brain metastasis of advanced breast cancer often results in deleterious consequences. Metastases to the brain lead to significant challenges in treatment options, as the blood-brain barrier (BBB) prevents conventional therapy. Thus, we hypothesized that creation of a nanoparticle (NP) that distributes to both primary tumor site and across the BBB for secondary brain tumor can be extremely beneficial. Here, we report a simple targeting strategy to attack both the primary breast and secondary brain tumors utilizing a single NP platform. The nature of these mitochondrion-targeted, BBB-penetrating NPs allow for simultaneous targeting and drug delivery to the hyperpolarized mitochondrial membrane of the extracranial primary tumor site in addition to tumors at the brain. By utilizing a combination of such dual anatomical distributing NPs loaded with therapeutics, we demonstrate a proof-of-concept idea to combat the increased metabolic plasticity of brain metastases by lowering two major energy sources, oxidative phosphorylation (OXPHOS) and glycolysis. By utilizing complementary studies and genomic analyses, we demonstrate the utility of a chemotherapeutic prodrug to decrease OXPHOS and glycolysis by pairing with a NP loaded with pyruvate dehydrogenase kinase 1 inhibitor. Decreasing glycolysis aims to combat the metabolic flexibility of both primary and secondary tumors for therapeutic outcome. We also address the in vivo safety parameters by addressing peripheral neuropathy and neurobehavior outcomes. Our results also demonstrate that this combination therapeutic approach utilizes mitochondrial genome targeting strategy to overcome DNA repair-based chemoresistance mechanisms.

Brain Neoplasms↗
PubMed2006

Metabolic activation of chemicals: in-silico simulation.

The role of metabolism in prioritising chemicals according to their potential adverse health effects is extremely important given the fact that innocuous parents can be transformed into toxic metabolites. Our recent efforts in simulating metabolic activation of chemicals are reviewed in this work. The application of metabolic simulators to predict biodegradation (microbial degradation pathways), bioaccumulation (fish liver metabolism), skin sensitisation (skin metabolism), mutagenicity (rat liver S-9 metabolism) are discussed. The ability of OASIS approach to predict metabolism (toxicokinetics) and toxicity (toxicodynamics) of chemicals resulting from their metabolic activation in a single modelling platform is an important advantage of the method. It allows prioritisation of chemicals due to predicted toxicity of their metabolites.

Animals↗
PubMed2005

Detection of immunoglobulin M antibody to hepatitis A virus in Alaska residents without other evidence of hepatitis.

During a 38-month period, 13 of 41 persons with test results positive for IgM antibody to hepatitis A virus did not meet the case definition for hepatitis A or have a clear indication for testing, which suggests that test results were falsely positive. No single testing platform or kit was used. Health care providers should restrict serologic testing for hepatitis A to patients with clinical or epidemiologic indications.

Adult↗
PubMed2026

MACS3: A Peak-calling Platform for Bulk and Single-cell Regulatory Genomics.

Since the original publication of Model-based Analysis for ChIP-Seq (MACS), the software has been widely used to identify enriched genomic regions in ChIP-seq, ATAC-seq, CUT&RUN, DNase-seq, and related regulatory genomics assays. Over the years, MACS has evolved substantially, with MACS version 3 (MACS3) now serving as the actively maintained implementation. MACS3 preserves the core MACS framework for fragment pileup, dynamic local background noise, statistical enrichment testing, and peak refinement, while adding functionality needed for contemporary bulk and single-cell workflows. It supports conventional bulk peak calling, paired-end and fragment-based file formats, modular signal processing, direct analysis of single-cell ATAC-seq fragment files, barcode-restricted pseudobulk and cluster-level peak calling, specialized ATAC-seq and variant-calling modules, as well as command-line and programmatic interfaces. MACS3 is distributed through standard software channels and supported by continuous testing across operating systems, Python versions, and CPU architectures. Here we describe the architecture, current capabilities, and recommended use of MACS3, providing an updated reference for applying the MACS framework in contemporary bulk and single-cell regulatory genomics workflows. MACS3 is open-source software available at https://github.com/macs3-project/MACS.

Bioinformatics software↗
PubMed2006

Development of non-agglutination microarray blood grouping.

Microarray technology provides an opportunity to monitor multiple parameters simultaneously. High-throughput applications such as blood donation screening could greatly benefit from performing various tests on a single testing platform. Blood grouping represents one part of the donation testing complementing the screening for blood-borne pathogens. Blood group serology traditionally exploited agglutination as the detection method. In this investigation, we have adapted blood grouping reactions to a solid-phase microarray substrate in a non-agglutination reaction format as an initial step in the development of a combined microarray testing platform. We have investigated immobilization of proprietary antibodies on multiple surfaces and monitored their performance under various reaction conditions. For the first time, highly specific blood grouping has been achieved on a planar microarray using directly labelled erythrocytes or a secondary labelled reagent using fluorescent signal end point readout. We have also complemented microarray data with a label-free, surface plasmon resonance-based Biacore platform data and used the real time quantitative measurement to rank anti-A antibodies according to the strength of reaction with the immobilized synthetic blood group antigen A.

Blood Grouping and Crossmatching↗
PubMed2006

Diagnostic applications of microarrays.

Microarrays were designed to monitor the expression of many genes in parallel, providing substantially more information than Northern blots or reverse transcription polymerase chain reaction analysing one or few genes at a time. The large sequencing projects provided the content for detailed expression studies under a variety of stimuli and conditions. The human genome project identified around 30 000 human genes. Estimated number of protein products is, however, 10-30 times higher, mainly due to the alternative splicing and post-translational modifications. The identification of gene functions requires both genomic and proteomic approaches, including protein microarrays, and numerous current microarray projects focus on deciphering gene expression patterns under a variety of conditions. Establishing the key genes and gene products for particular conditions opens the way for diagnostic applications using multiparameter, high-throughput assays. This format can also accommodate existing blood screening assays, potentially providing a single testing platform. This review considers the progress in diagnostic microarrays in a wider context of in vitro diagnostics field.

Diagnostic Techniques and Procedures↗
PubMed2004

Developing DNA vaccines that call to dendritic cells.

DNA vaccination is a novel immunization strategy that has great potential for the development of vaccines and immune therapeutics. This strategy has been highly effective in mice, while less immunogenic in nonhuman primates and humans. Enhancing DNA vaccine potency remains a challenge. It is likely that APCs, and especially DCs, play a paramount role in the presentation of vaccine antigen to the immune system. A new study reports the synergistic recruitment, expansion, and activation of DCs in vivo in a mouse model through covaccination with plasmids encoding macrophage inflammatory protein-1alpha (MIP-1alpha), fms-like tyrosine kinase 3 ligand (Flt3L), and the DNA vaccine. Such cooperative strategies delivering vaccine in a single, simple platform result in improved cellular immunity in vivo, including enhanced tetramer responses and IFN-gamma secretion by antigen-specific cells.

Animals↗
PubMed2025

Exome-wide association study of bleeding events in patients receiving direct oral anticoagulants.

BackgroundDirect oral anticoagulants (DOACs) are first-line medications for stroke prevention in non-valvular atrial fibrillation (AF). However, variability in drug response poses risks of hemorrhagic or thromboembolic events.ObjectivesAlthough genetic influences on DOACs safety are increasingly recognized, robust evidence directly linking specific polymorphisms to bleeding risk remains limited.DesignMulti-center observational case-control study including exome-wide association analysis of 196 non-valvular AF patients treated with rivaroxaban or apixaban, comprising 97 with bleeding complications and 99 without.MethodsDOAC plasma concentrations, urinary 6-&#x3b2;-hydroxycortisol and cortisol levels were measured for CYP3A4 phenotyping. Sequencing was performed on the DNBSEQ G-400 platform. Single-nucleotide variant (SNV) associations with bleeding risk were assessed using logistic regression with additive, dominant, and recessive genetic models. Polygenic risk scores (PRSs) were calculated to evaluate cumulative genetic effects.ResultsNo SNVs reached Bonferroni-corrected significance under any model. PRSs showed weak predictive ability for bleeding with apixaban. For rivaroxaban, regression indicated that ln&#x2005;Css min/D&#x2009;+&#x2009;1 index increased with PRS, age, and 6-&#x3b2;-hydroxycortisol/cortisol ratio, but decreased with higher 6-&#x3b2;-hydroxycortisol and coronary heart disease presence. No statistically significant differences were found for the PharmGKB Level 3 variants rs1045642 (rivaroxaban) and rs2231142 (apixaban). Trends toward statistical significance were observed for the rs2472304-G variant in rivaroxaban users, rs6977165-C in apixaban users, and for the CYP3A4*1/*36 diplotype.ConclusionResidual equilibrium concentration of DOACs, including dose-adjusted, did not independently predict bleeding risk in non-valvular AF patients. Variants rs2472304 and rs6977165 may warrant further investigation as potential contributors to bleeding risk.

Humans↗