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At least 19 recordsLinked to original sources
PubMed2026

AI-driven snapshot hyperspectral imaging for on-line sorting systems in food industry: From real-time sensing to intelligent decision-making.

High-throughput food sorting requires rapid, non-destructive detection of external defects, foreign materials, and internal quality attributes in heterogeneous food matrices. Conventional scanning hyperspectral imaging may suffer from motion-induced spatial-spectral mismatches, whereas snapshot hyperspectral imaging (S-HSI) captures spectral images within a single integration time. However, its advantage is limited by trade-offs in resolution, signal-to-noise ratio (SNR), reconstruction uncertainty, and calibration stability, which are further amplified by variable tissue structure, surface reflection, moisture, and fat distribution in foods. This review critically examines artificial intelligence (AI)-driven S-HSI for on-line food sorting within a sensing-representation-decision-execution framework. Compact architectures are compared according to their physical constraints, food-sorting suitability, and ability to support mapping between spectral responses and physicochemical quality attributes. AI strategies are reviewed for spectral reconstruction, image restoration, spatial-spectral representation, band selection, uncertainty-aware decision-making, and edge implementation. AI can partially compensate for snapshot-specific limitations, but current evidence remains largely limited to laboratory or prototype studies. Future work should link system performance to food safety and quality outcomes by reporting throughput, decision latency, calibration drift, missed-detection risk, false-rejection cost, and closed-loop sorting success.

Hyperspectral Imaging↗
PubMedDate not supplied

Differentiation between hepatoma and hemangioma with inversion-recovery snapshot FLASH MRI and Gd-DTPA.

Thirty-eight patients with focal liver tumors (20 hepatomas, 18 hemangiomas) were studied by dynamic sequential inversion recovery (IR) snapshot fast low angle shot (FLASH) MR imaging with Gd-DTPA. Immediately after 0.05 mmol/kg Gd-DTPA was administered intravenously for 2-3 s followed by flushing with normal saline for 4-5 s, 10 images were obtained in the first 20 s (time zero is the end of flush, early phase). Then, one image every 30 s from 1 to 3 min (late phase) and images at 5 min and 7 min (delayed phase) were obtained serially. Hepatomas showed total enhancement in 18 of 20 patients in the early phase, and isointense or low intensity enhancement with respect to the surrounding liver parenchyma in 18 patients in the late to delayed phases. Hemangiomas showed peripheral enhancement in 14 patients in the early phase, but did not show total enhancement (except for two hemangiomas less than 3 cm in size) in the early phase, and showed high intensity enhancement in 15 patients in the late phase. Ninety percent of hepatomas and 82% of hemangiomas showed their characteristic enhancement patterns in the early to delayed phases. We conclude that dynamic sequential IR snapshot FLASH MR images enhanced with Gd-DTPA can facilitate differentiation between hepatomas and hemangiomas.

Aged↗
PubMed1992

[Differentiation between hepatoma and hemangioma by inversion recovery snapshot FLASH MR imaging with variable TIs].

To differentiate hepatoma from hemangioma, MR studies were performed for 18 patients with 21 untreated liver tumors (hepatoma 10, hemangioma 11). We obtained inversion recovery snapshot FLASH images of liver tumors with variable TIs (50, 100, 150, 200, 250, 300, 400, and 500 msec). 8 hemangiomas showed higher intensity than liver parenchyma on the images at 150 msec and less of TI, and lower intensity at 200 msec or more TI. In 7, signal intensity of hepatoma became low at 150 msec or less of TI or remained high with prolonged TI. Inversion recovery snapshot FLASH imaging with variable TIs will be useful for differentiating between hepatoma and hemangioma.

Adult↗
PubMed2026

Four-dimensional molecular mapping from a spatial snapshot reveals the dynamics of hair follicle organogenesis.

Understanding organ formation requires capturing molecular information simultaneously in three-dimensional (3D) space and across developmental time. To this end, we developed 3D DNase-Enhanced Expression Profiling (3DEEP), a tissue-clearing approach that removes genomic DNA to extend spatial transcriptomic profiling hundreds of microns into intact tissues. We applied 3DEEP to neonatal mouse skin, capturing hundreds of developing hair follicles across their organogenesis trajectory. Ordering follicles by molecularly inferred developmental age transformed this single spatial snapshot into a four-dimensional (3D + time) molecular map of organogenesis. This map revealed developmental dynamics spanning stem cell compartment stratification, emergence of new cell subtypes within the follicle, and cascading structural transformations leading to hair canal formation. Comparative analysis of Foxn1-deficient nude mice, a hairlessness model, revealed organ-wide changes in developmental dynamics, including delayed molecular progression, reduced coordination, and increased developmental instability, preceding overt structural defects. This work demonstrates how deep-tissue spatial transcriptomics can uncover hidden dynamics of organ formation.

Animals↗
PubMed2025

HERV Modulation in Colorectal Carcinoma Patients: A Snapshot of Endogenous Retroviral Transcriptome.

Human endogenous retroviruses (HERVs) are proviral relics of infections that affected primates' germ line. Many HERV elements retain a residual capacity to encode transcripts and proteins that have been occasionally domesticated for the host physiology. In addition, HERV transcriptional modulation is of great interest to clarify the etiology of complex disorders such as cancer, even if a few studies assessed the specific HERV loci modulated in tumor tissues. In the present work, we used a transcriptomic approach to investigate the specific expression of ~3300 HERV loci in paired tumor and normal tissues of 7 colorectal cancer (CRC) patients. A total of 102 HERVs were significantly modulated in CRC, with a general tendency towards downregulation. Of note, among the 42 upregulated HERVs 23 belonged to the HERV-H group, that is the most investigated in CRC. De novo transcriptome reconstruction and qPCR validation allowed to identify a transcript from a HERV-H locus on chromosome Xp22.3 with high specific expression in CRC samples, potentially encoding for a partial Pol protein. These results provide a detailed description of HERV transcriptional variations in CRC and its interindividual variability, identifying a HERV-H transcript that deserves further investigation for its possible impact on tumor progression.

Endogenous Retroviruses↗
PubMed2026

A one‑year snapshot of pediatric regional anesthesia at a French Tertiary University Hospital.

BACKGROUND: Regional anesthesia (RA) is a major component of multimodal perioperative analgesia in children. Despite proven benefits, pediatric RA practice shows marked inter-institutional and international variability, with global practice patterns remaining largely underreported. This study aimed to characterize current RA practices in a pediatric anesthesia department of a French tertiary university hospital. METHODS: This retrospective observational study of prospectively collected data over one year included all children aged 0-18 years receiving at least one RA procedure. The data analyzed comprised demographics, surgical characteristics, RA techniques, guidance methods, and pharmacologic agents. Each RA procedure was considered an independent event, and patients were stratified into five age groups. RESULTS: Over the study period, 907 patients (6.0 [1.0; 12.0] years) underwent 1073 RA procedures: 894 peripheral blocks (83%) and 179 neuraxial blocks (17%). Peripheral blocks predominated in children >6 months (90%), while 59% of neuraxial RA were in infants <6 months. RA was conducted under general anesthesia in 90% of cases; awake spinal anesthesia in small infants comprised most neuraxial procedures. Ultrasound guidance was used in 98% of peripheral blocks, and pre-puncture scanning preceded 22% of neuraxial procedures. Clonidine was used as an adjuvant in >60% of cases. CONCLUSIONS: This single-center cohort reports one year of pediatric RA practice, characterized by high RA implementation rates. While ultrasound guidance was standard for peripheral blocks, pre-puncture scanning remains infrequently used for neuraxial techniques, highlighting a potential margin for improvement based on current practice. Results highlight selective neuraxial strategies in vulnerable infants and routine adjuvant use to optimize postoperative analgesia. Findings confirm RA feasibility in daily pediatric anesthesia and support multicenter studies evaluating inter-institutional variability and outcomes impact.

Humans↗
PubMed2025

Snapshot Genomic Surveillance Reveals Insights into Antimicrobial Resistance and Lineage Diversity of Uropathogens in Older Adults in Queensland.

BACKGROUND: Community-acquired urinary tract infections (UTIs) are a significant health concern in older adults. However, few studies have investigated the epidemiology of uropathogens across diverse settings where older adults reside. METHODS: In this study, we whole-genome sequenced urinary isolates of Escherichia coli, Klebsiella species, and Enterobacter cloacae complex collected from individuals aged 70 and over living in the community and residential aged care facilities (RACFs) in Queensland, Australia. We investigated the prevalence of antimicrobial resistance (AMR), pathogen population structure, and transmission dynamics across the settings. RESULTS: E. coli was most frequently identified (82.2%, 447/544), followed by K. pneumoniae (10.8%, 59/544) and E. hormaechei (2.6%, 14/544). Intraspecies lineages were diverse, and a total of 177 sequence types were identified. The three predominant lineages were E. coli ST73 (10.7%, 54/504), ST95 (8.1%, 41/504), and ST131 (5.4%, 27/504). Transmission events were minimal, being identified in 13 patients (2.5%), mainly from the community. The resistance rate to antibiotics was low, with only a small proportion (9.7%) of multidrug-resistant (MDR) isolates. The predominant MDR lineage was E. coli ST131, which carried extended-spectrum beta-lactamase bla CTX-M genes. CONCLUSIONS: Community-acquired UTIs in older adults are predominantly caused by diverse E. coli lineages, with limited evidence of transmission within aged care facilities. The low rates of AMR in the community, along with the absence of strains adapted to a particular setting, suggest that current empiric therapy guidelines remain appropriate. Our prospective genomic surveillance offers valuable insights for monitoring UTIs in this population. It demonstrates the importance of an unbiased approach to accurately capture the prevalence and diversity of uropathogen lineages.

Enterobacteriaceae↗
PubMed2025

Proteomic snapshot of pattern triggered immunity in the Arabidopsis leaf apoplast.

The apoplast is a critical interface in plant-pathogen interactions, particularly in the context of pattern-triggered immunity (PTI), which is initiated by recognition of microbe-associated molecular patterns. Our study characterizes the proteomic profile of the Arabidopsis apoplast during PTI induced by flg22, a 22-amino-acid bacterial flagellin epitope, to elucidate the output of PTI. Apoplastic washing fluid was extracted with minimal cytoplasmic contamination for liquid chromatography-tandem mass spectrometry analysis. By comparing our data to publicly available transcriptome profiles of flg22 treatment from 1 to 18&#x2009;h, we observed that several highly abundant proteins exhibit relatively unchanged gene expression across all time points. We also observed topological bias in peptide recovery of 19 enriched receptor-like kinases with peptides predominantly recovered from their ectodomains. Notably, tetraspanin 8, an exosome marker, was enriched in PTI samples. We additionally confirmed increased concentrations of exosomes during PTI. This study enhances our understanding of the proteomic changes in the apoplast during plant immune responses and lays the groundwork for future investigations into the molecular mechanisms of plant defense under recognition of pathogen molecular patterns.

Arabidopsis↗
PubMed1975

Snapshot diagnosis: syndromes, facies and heart disease.

In some syndromes the facial appearance of the patients is so typical that a correct diagnosis can be made 'à vue'. The five cases presented here are examples of this statement and the additional clinical data make it possible to decide on the syndromes and the complicating cardiac anomalies.

Adolescent↗
PubMed2025

Trajectory inference from single-cell genomics data with a process time model.

Single-cell transcriptomics experiments provide gene expression snapshots of heterogeneous cell populations across cell states. These snapshots have been used to infer trajectories and dynamic information even without intensive, time-series data by ordering cells according to gene expression similarity. However, while single-cell snapshots sometimes offer valuable insights into dynamic processes, current methods for ordering cells are limited by descriptive notions of "pseudotime" that lack intrinsic physical meaning. Instead of pseudotime, we propose inference of "process time" via a principled modeling approach to formulating trajectories and inferring latent variables corresponding to timing of cells subject to a biophysical process. Our implementation of this approach, called Chronocell, provides a biophysical formulation of trajectories built on cell state transitions. The Chronocell model is identifiable, making parameter inference meaningful. Furthermore, Chronocell can interpolate between trajectory inference, when cell states lie on a continuum, and clustering, when cells cluster into discrete states. By using a variety of datasets ranging from cluster-like to continuous, we show that Chronocell enables us to assess the suitability of datasets and reveals distinct cellular distributions along process time that are consistent with biological process times. We also compare our parameter estimates of degradation rates to those derived from metabolic labeling datasets, thereby showcasing the biophysical utility of Chronocell. Nevertheless, based on performance characterization on simulations, we find that process time inference can be challenging, highlighting the importance of dataset quality and careful model assessment.

Single-Cell Analysis↗
PubMed2026

Long-read sequencing resolves complex CYP21A2 variants and identifies 2+0 carriers in 21-hydroxylase deficiency.

The complex CYP21A2 variants arising from high homology with its pseudogene CYP21A1P challenge the diagnosis of 21-hydroxylase deficiency (21-OHD). This study systematically evaluated long-read sequencing (LRS) for identifying complex structural variants of the CYP21A2 gene in 21-OHD in comparison with conventional molecular diagnostic methods, including multiplex ligation-dependent probe amplification (MLPA), CNVplex, and SNaPshot. Twenty patients with suspected 21-OHD and defined CYP21A2 structural variants identified via initial MLPA screening were enrolled. Variants were further analyzed using CNVplex and SNaPshot, then all samples underwent LRS for comprehensive variant detection, breakpoint mapping, and haplotype resolution. LRS overcame key limitations of conventional methods. It reliably identified a novel large-fragment deletion and defined its boundaries. Notably, LRS identified "2+0" carriers, where deletions masked by duplications cause false-negatives with standard techniques. Moreover, LRS accurately distinguished CYP21A1P/CYP21A2_CH-4 and CH-9 chimera subtypes which were indistinguishable by the combined conventional assays. Furthermore, LRS enabled the precise identification and characterization of TNXA/TNXB chimeric deletions. These are frequently misclassified as CYP21A1P/CYP21A2 chimeras by conventional methods but are critical for diagnosing associated conditions such as CAH-X syndrome. LRS provides a superior, integrated solution for the molecular diagnosis of 21-OHD, offering precise structural variant characterization, accurate carrier detection, and reliable breakpoint mapping. Its application enhances diagnostic accuracy, supports advanced genetic counseling, and paves the way for genotype-informed clinical management.

Journal Article↗
PubMed2025

Evaluation of sequencing reads at scale using rdeval.

MOTIVATION: Large sequencing datasets are being produced and deposited into public archives at unprecedented rates. The availability of tools that can reliably and efficiently generate and store sequencing read summary statistics has become critical. RESULTS: As part of the effort by the Vertebrate Genomes Project (VGP) to generate high-quality reference genomes at scale, we sought to address the community's need for efficient sequence data evaluation by developing rdeval, a standalone tool to quickly compute and interactively display sequencing read metrics. Rdeval can either run on the fly or store key sequence data metrics in tiny read 'snapshot' files. Statistics can then be efficiently recalled from snapshots for additional processing. Rdeval can convert fa*[.gz] files to and from other popular formats including BAM and CRAM for better compression. Overall, while CRAM achieves the best compression, the gain compared to BAM is marginal, and BAM achieves the best compromise between data compression and access speed. Rdeval also generates a detailed visual report with multiple data analytics that can be exported in various formats. We showcase rdeval's functionalities using long-read data from different sequencing platforms and species, including human. For PacBio long-read sequencing, our analysis shows dramatic improvements in both read length and quality over time, as well as the benefit of increased coverage for genome assembly, though the magnitude varies by taxa. AVAILABILITY AND IMPLEMENTATION: Rdeval is implemented in C++ for data processing and in R for data visualization. Precompiled releases (Linux, MacOS, Windows) and commented source code for rdeval are available under MIT license at https://github.com/vgl-hub/rdeval. Documentation is available on ReadTheDocs (https://rdeval-documentation.readthedocs.io). Rdeval is also available in Bioconda and in Galaxy (https://usegalaxy.org). An automated test workflow ensures the consistency of software updates.

Software↗
PubMed2026

Integrated Multi-Omics Analysis Reveals the Genetic Basis of Phenotypic Variation in Tibetan Sheep.

Body size is a key economic trait influencing the profitability of farmed animals. This study used genome-wide association studies (GWAS) to identify five single nucleotide polymorphisms (SNPs) significantly associated with body size in the Tibetan sheep population, advancing molecular breeding and providing a basis for genomic selection. These SNPs are located within five candidate genes. SNaPshot validated GWAS results, demonstrating significant correlations between candidate SNPs and body size traits in Tibetan sheep. Concurrently, hematoxylin and eosin staining, alongside muscle fiber analysis, confirmed pronounced morphological differences in muscle tissue between sheep of varying conformation. Therefore, transcriptome and proteomics were performed on the longest dorsi muscle from large and small Tibetan sheep of both sexes. The transcriptome, together with weighted gene co-expression network analysis (WGCNA), identified VEPH1 and PRKG1 as core genes regulating body characteristics in Tibetan sheep through their involvement in the PI3K-Akt signaling pathway and pathways related to fat deposition. The integrative analyses demonstrated significantly different expression of CARNS1 and CRYAB at both transcriptional and protein levels between the muscles of large- and small-sized Tibetan sheep of both sexes, suggesting their importance in body size traits by influencing muscle morphology. This study provides valuable genomic resources that advance sheep genetics research.

GWAS↗
PubMed2025

Mapping Active RNA Polymerases in Proliferating and Quiescent Fission Yeast Cells Using Precision Run-On Sequencing.

The development of next-generation sequencing (NGS) approaches to investigate the functioning of RNA polymerases has led to groundbreaking advances in the field of transcriptional regulation. One powerful method, Precision nuclear Run-On sequencing (PRO-seq), maps the locations of RNA polymerase active sites genome-wide at high resolution. PRO-seq provides a snapshot of strand-specific transcriptional activity and does not rely on immunoprecipitation of the polymerase of interest. Notably, this technique has been utilized to investigate the control of the RNA polymerase II transcription cycle in a variety of model systems. However, the initially published PRO-seq method required significant amounts of starting sample and was technically challenging, both of which were deterrents for its broader use. Recently, an improved and simplified version called qPRO-seq that reduced the length of the experiment and the quantity of necessary input sample was developed for human and Drosophila cell lines. Here we provide an updated, step-by-step protocol in which we have validated and optimized qPRO-seq for the fission yeast Schizosaccharomyces pombe. Importantly, we have implemented this method for assessing RNA polymerase activity in nutrient-limiting conditions, for both proliferating and nitrogen-depleted quiescent cells.

Schizosaccharomyces↗
PubMed2025

Application of Proteomic Methods in Oomycete Biology.

The biochemical makeup of any organism provides insight into key factors regarding its biological functions. These factors can be explored using proteomics, which allows us to obtain a snapshot of the protein content and abundance in an organism, cell type or sub-cellular compartment. Here, we describe proteomic methodologies that can be used to dissect the biochemical mechanism of phytopathogenicity in oomycetes. These methodologies include protein extraction, purification, subsequent processing, mass spectrometry analysis, and qualitative and quantitative data processing of oomycete proteomes for comparative studies. Additionally, the use of mass spectra to assist in gene validation and modelling in unfinished oomycete genomes is also described.

Oomycetes↗
PubMed1992

Causes of nonfatal injuries in the United States, 1986.

During the 1986 National Health Interview Survey (NHIS), data on injuries resulting in a doctor visit or restricted activity for at least a half day were collected and assigned E-codes. Based on 603 injuries, the estimated number of nonfatal injuries for civilian, noninstitutionalized U.S. residents in 1986 was 60,212,000. The most frequent cause of injury was a fall (11,547,000), followed by motor vehicle traffic crashes (4,361,000) and adverse effects of drugs and biologics (3,363,000). While cause-specific detail was limited by small numbers of injuries in the sample, the NHIS can provide a valuable snapshot of the causes of nonfatal injuries.

Humans↗