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PubMed2025

Designing smart spatial omics experiments with S2Omics.

Spatial omics technologies have transformed biomedical research by enabling high-resolution molecular profiling while preserving the native tissue architecture. These advances provide unprecedented insights into tissue structure and function. However, the high cost and time-intensive nature of spatial omics experiments necessitate careful experimental design, particularly in selecting regions of interest (ROIs) from large tissue sections. Currently, ROI selection is performed manually, which introduces subjectivity, inconsistency, and a lack of reproducibility. Previous studies have shown strong correlations between spatial molecular patterns and histological features, suggesting that readily available and cost-effective histology images can be leveraged to guide spatial omics experiments. Here, we present S2Omics, an end-to-end workflow that automatically selects ROIs from histology images with the goal of maximizing molecular information content in the ROIs. Through comprehensive evaluations across multiple spatial omics platforms and tissue types, we demonstrate that S2Omics enables systematic and reproducible ROI selection and enhances the robustness and impact of downstream biological discovery.

digital pathology↗

PubMed2026

Emerging Trends in Mass Spectrometry-Based Quantitative Proteome and Phosphoproteome Profiling in Maize.

Maize (Zea mays) is both an agronomically important crop and a reference model organism that has enabled the dissection of the molecular basis of plant development and environmental responses. Mass spectrometry-based proteomics provides a powerful approach to identify and quantify proteins and their post-translational modifications, facilitating the discovery of molecular mechanisms underlying complex biological processes. Unlike the study of gene expression using transcriptomics, analysis of the proteome and phosphoproteome provides direct measurement of proteins, which are responsible for driving or regulating nearly all cellular processes, thus offering a more complete picture of the cell's functional state. Over the past two decades, advancements in mass spectrometry have enabled large-scale profiling of protein abundance and phosphorylation sites in maize, improving our understanding of various biological phenomena. Here, we briefly summarize some of the major biological insights gained from maize proteome and phosphoproteome studies, and provide an overview of mass spectrometry sample preparation and acquisition/analysis workflows for the quantitative and reproducible analysis of protein abundance and phosphorylation dynamics in maize.

Zea mays↗

PubMed2005

Multimodal imaging and computer assisted diagnosis for functional tumour characterisation.

Radiological modalities, especially CT, mainly provide morphological and structural information with high spatial resolution covering large volumes. Novel developments, which are predominantly MR-based, also deliver 'functional' information, which can be used for individual characterisation of tumour biology. Both aspects and modalities, additionally complemented by ultrasound, have to be combined in the radiological workflow of cancer patients including volumetric visualisation, information extraction from multimodal imaging, quantitative surrogates, intelligent interpretation assistance and image-guided procedures. Based on volumetric visualisation and the generation of 3D+t maps, CAD tools have to address registration of different image series from different modalities, and extraction of quantitative surrogates. The latter will then serve tumour characterisation, therapeutic decision-making, image-guided procedures and efficacy evaluation.

Diagnosis, Computer-Assisted↗

PubMed2026

Towards time-resolved MicroED grid preparation using mix-and-inject gas dynamic virtual nozzles.

Recent progress in gas dynamic virtual nozzle (GDVN) technologies in combination with high-brilliance synchrotron and X-ray free-electron lasers (XFELs) has allowed the visualization of protein dynamics in crystallo by mixing macromolecular protein crystals with a substrate using tunable mixing times on the order of milliseconds to seconds prior to serial X-ray diffraction data collection. This has become the method of choice for high-resolution structure determination of intermediate states. However, such experiments require large counts of crystals of proper sizes for high-resolution data collection, and premium beam times for screening efforts. Cryogenic microcrystal electron diffraction (MicroED) represents a complementary technique that may be a more accessible avenue for time-resolved nanocrystallography compared with serial X-ray diffraction experiments. MicroED can produce full diffraction datasets from just a few submicrometre-thick crystals, and the approach is more readily accessible, requiring standard cryogenic transmission electron microscopy (TEM) equipment available at many universities and institutes. Cryogenic MicroED, like other forms of cryo-EM, begins with rapidly freezing biological material on electron microscopy grids. In the case of MicroED, micro- to nano-crystals (<500 nm thick) are deposited onto electron microscopy grids and plunge-frozen for subsequent electron diffraction data collection. Here, we have incorporated GDVN technology developed originally for XFEL experiments into the freezing process as a first step towards time-resolved studies. We describe the limited deposition efficiency of the model MicroED protein proteinase K on TEM grids using GDVNs, preceding sample vitrification and successful MicroED data collection. We discuss both the initial results from such experiments and the methodological challenges in developing this approach into a reliable workflow for millisecond-to-second time-resolved structural studies of macromolecules. Our results promise a strategy to deposit crystals on grids using GDVNs and determine high-resolution structures by MicroED, constituting a first step towards development of time-resolved MicroED experiments.

MicroED↗

PubMed2004

Personal health information management system and its application in referral management.

We developed a web-based personal health record (PHR) that can be used by patients to collect and manage their health information (e.g., medical history, past surgeries, medications, and allergies), to request self-referrals, and to store a record of their consultations. The PHR also includes a messaging system that can be structured into the workflow of referral management as well as allowing more general communications. A preliminary study was conducted with 61 patients. Thirty-two patients completed a survey in which 85% of respondents were satisfied with the usability and 94% were satisfied with the overall online referral process. The consulting physicians were satisfied with the content of subjects' personal health information and referral problem descriptions and found the information detailed enough to triage all requested referrals. Patients, physicians, and patient care coordinators reported that their communications were enhanced by the system and found the messaging component convenient to use.

Adult↗

PubMed2006

Automatic image hanging protocol for chest radiographs in PACS.

Chest radiography is one of the most widely used techniques in diagnostic imaging. It comprises at least one-third of all diagnostic radiographic procedures in hospitals. However, in the picture archive and communication system, images are often stored with the projection and orientation unknown or mislabeled, which causes inefficiency for radiologists' interpretation. To address this problem, an automatic hanging protocol for chest radiographs is presented. The method targets the most effective region in a chest radiograph, and extracts a set of size-, rotation-, and translation-invariant features from it. Then, a well-trained classifier is used to recognize the projection. The orientation of the radiograph is later identified by locating the neck, heart, and abdomen positions in the radiographs. Initial experiments are performed on the radiographs collected from daily routine chest exams in hospitals and show promising results. Using the presented protocol, 98.2% of all cases could be hung correctly on projection view (without protocol, 62%), and 96.1% had correct orientation (without protocol, 75%). A workflow study on the protocol also demonstrates a significant improvement in efficiency for image display.

Algorithms↗

PubMed2006

Robust online orientation correction for radiographs in PACS environments.

In picture archiving and communications systems (PACS), images need to be displayed in standardized ways for radiologists' interpretations. However, for most radiographs acquired via computed radiography (CR), digital radiography (DR), or digitized films, the image orientation is undetermined because of the variations in examination conditions and patients' situations. To address this problem, an automatic orientation correction method is developed. It first detects the most indicative region in a radiograph for image orientation, and then extracts a set of low-level visual features from the region. Based on these features, a well-trained classifier, using support vector machines, is employed to recognize the correct orientation of the radiograph and reorient it to the desired position. A large-scale experiment was conducted on more than 12 000 radiographs, which covered a wide variety of exam types, to validate the method. The overall success rate of orientation correction was 96.1%. A workflow study on the method also demonstrated a significant improvement in efficiency for image display. To our knowledge, this work represents the first robust system designed to handle all radiographic exam types using a unified framework instead of using dedicated strategies for different exam types.

Algorithms↗

PubMed2004

A real-time architecture for time-aware agents.

This paper describes the specification and implementation of a new three-layer time-aware agent architecture. This architecture is designed for applications and environments where societies of humans and agents play equally active roles, but interact and operate in completely different time frames. The architecture consists of three layers: the April real-time run-time (ART) layer, the time aware layer (TAL), and the application agents layer (AAL). The ART layer forms the underlying real-time agent platform. An original online, real-time, dynamic priority-based scheduling algorithm is described for scheduling the computation time of agent processes, and it is shown that the algorithm's O(n) complexity and scalable performance are sufficient for application in real-time domains. The TAL layer forms an abstraction layer through which human and agent interactions are temporally unified, that is, handled in a common way irrespective of their temporal representation and scale. A novel O(n2) interaction scheduling algorithm is described for predicting and guaranteeing interactions' initiation and completion times. The time-aware predicting component of a workflow management system is also presented as an instance of the AAL layer. The described time-aware architecture addresses two key challenges in enabling agents to be effectively configured and applied in environments where humans and agents play equally active roles. It provides flexibility and adaptability in its real-time mechanisms while placing them under direct agent control, and it temporally unifies human and agent interactions.

Algorithms↗

PubMed2006

Identifying protein construct variants with increased crystallization propensity--a case study.

This study describes an efficient multiparallel automated workflow of cloning, expression, purification, and crystallization of a large set of construct variants for isolated protein domains aimed at structure determination by X-ray crystallography. This methodology is applied to MAPKAP kinase 2, a key enzyme in the inflammation pathway and thus an attractive drug target. The study reveals a distinct subset of truncation variants with improved crystallization properties. These constructs distinguish themselves by increased solubility and stability during a parallel automated multistep purification process including removal of the recombinant tag. High-throughput protein melting point analysis characterizes this subset of constructs as particularly thermostable. Both parallel purification screening and melting point determination clearly identify residue 364 as the optimal C terminus for the kinase domain. Moreover, all three constructs that ultimately crystallized feature this C terminus. At the N terminus, only three amino acids differentiate a noncrystallizing from a crystallizing construct. This study addresses the very common issues associated with difficult to crystallize proteins, those of solubility and stability, and the crucial importance of particular residues in the formation of crystal contacts. A methodology is suggested that includes biophysical measurements to efficiently identify and produce construct variants of isolated protein domains which exhibit higher crystallization propensity.

Cloning, Molecular↗

PubMed2026

Evaluation of bone preparation approaches using length-based analysis and targeted sequencing for forensic human identification of historic skeletal remains.

Advances in DNA technology have significantly enhanced the forensic community's ability to develop genetic profiles from unidentified human skeletal remains. However, sampling requires mechanical grinding of hard tissues before DNA isolation. This processing can compromise genetic profiles, particularly in aged bones. We compared the industry-standard pulverization method with an alternative powder-free preparation involving prolonged demineralization and subsequent slicing of 19th-century cortical bone. Data from DNA quantification, STR genotyping, and targeted SNP sequencing were used to evaluate powdered samples versus demineralized slices from paired human bones. Average human DNA yields for pulverized samples and demineralized slices were 0.032 ng and 0.692 ng, respectively. Demineralized slices recovered more amplifiable DNA than traditional homogenization methods (p < 0.05). No pulverized samples produced STR profiles, whereas demineralized slices from the same bone samples yielded partial profiles. Samples underwent DNA repair, library preparation, and hybridization capture using the FORensic Capture Enrichment (FORCE) panel. Applying low-coverage (1X) analysis of high-throughput sequencing (HTS) data, demineralized slices outperformed those prepared by traditional pulverization methods (p < 0.05) and substantially increased the information recovered compared with conventional STR analysis methods. Based on HTS data from pulverized samples, DNA fragment length ranged from 27 to 95 bp, and FORCE SNP recovery was 33.23%. In contrast, for demineralized slices, DNA fragment length ranged from 85 to 114 bp, and FORCE SNP recovery was 83.24%. The required reagents and equipment are typically available in forensic labs, and the workflow outlined herein significantly increases the success of DNA recovery from challenging skeletal samples.

Humans↗

PubMed2026

A novel relationship between time offsets in capillary electrophoresis and DNA sequence variations in short tandem repeats.

Next-generation sequencing (NGS) provides increased discriminatory power in forensic DNA analysis due to the detection of isoalleles. Differences in sequences between alleles allow for a second layer of differentiation between DNA contributors beyond the number of short tandem repeat (STR) repeat units. However, because NGS is a more time and resource-intensive analysis than conventional capillary electrophoresis (CE), laboratories may benefit from indicators that suggest NGS is likely to provide added value. This study examined whether CE migration offsets, measured as residuals in the OSIRIS analysis software, can differ significantly among STR isoalleles. Residuals represent the time offset between a sample allele peak and its corresponding allelic ladder peak. Paired CE and NGS data from 95 single source samples were analyzed for CE-based residual differences, as the NGS data provided the sequence information of the corresponding isoalleles. Residual values differed significantly among isoalleles at several STR loci. Statistically significant differences were identified at D16S539 and D3S1358, as well as at specific allele lengths within D12S391, D13S317, and D8S1179. These findings demonstrate that CE residual variation can reflect underlying STR sequence differences between contributors. In practice, residual-based metrics could help laboratories to identify casework reference samples where NGS is likely to provide additional discrimination, without the need for processing outside of a routine CE workflow. Due to the potentially large number of isoalleles, community wide efforts to aggregate CE residual differences versus isoallele sequences may be useful in the validation and implementation of this approach to add value to forensic DNA analyses.

Electrophoresis, Capillary↗

PubMed2026

Combining Annotation Software to Identify Orthologous Genes (CASIO) Provides a New Dataset of Orthologous Genes for Swallowtail Butterflies.

With the massive increase in genomic resources, it is becoming increasingly popular to analyse thousands of loci across many species. However, many of the available genomes are not annotated, which hinders an efficient search for orthologous protein-coding genes. Here, we aim to develop a semi-automated pipeline and compare four genomic annotation methods (BRAKER2, BUSCO, Miniprot and Scipio). Our results highlight the importance of integrating multiple annotation tools to optimise ortholog detection and improve genomic studies. Each annotation method showed different strengths. BRAKER2 annotated a substantial number of genes. BUSCO, despite limitations inherent to its reference database, identified a higher number of orthologs. Miniprot exhibited notable flexibility in accommodating diverse protein datasets, whereas Scipio successfully recovered a considerable set of genes that were not detected by the other tools. The combination of these tools allowed for more comprehensive ortholog detection. Taking advantage of this pipeline, we developed a comprehensive dataset of orthologous genes for swallowtail butterflies (Lepidoptera: Papilionidae), called Papilionidae_odb, which will facilitate future studies, especially for a non-model group with abundant genomic data and few transcriptomic resources. We tested Papilionidae_odb by inferring a robust phylogenetic framework for Leptocircini using 142 complete genomes, which improved branch support for some phylogenetic relationships, although challenges remained in resolving relationships within certain species groups, likely due to rapid radiations. Our results highlight the complementary nature of the annotation methods and suggest that combining these tools can yield more accurate results in genomic research. This approach was implemented in a Snakemake workflow called CASIO (Combining Annotation Software to Identify Orthologous genes) and can easily be applied to other non-model groups to improve genomic datasets in diverse taxa where transcriptomic resources are still limited.

Animals↗

PubMed2026

AI In Leukemia Diagnostics: Complementing the Pathologist's Role.

Artificial intelligence (AI) is reshaping every stage of leukemia diagnostics, from digital morphology and multiparameter flow cytometry to next-generation sequencing, multi-omics analysis, and emerging computational frontiers such as quantum-inspired feature selection. This review outlines how contemporary AI tools can automate labor-intensive quantitation, flag diagnostically salient patterns, and standardize interpretation, while the pathologist or hematologist retains authority over validation, context-specific integration, and clinical decision-making. We present an illustrative "human-in-the-loop" workflow that embeds AI modules within current laboratory information systems, emphasizing points where expert oversight mitigates algorithmic bias and resolves discordant findings. We further map the validator-integrator role across morphology, flow cytometry, and genomic/multi-omic interpretation and provide practical training competencies and use cases for AI-assisted hematopathology. Beyond technical deployment, the article addresses the educational transformation required for sustainable adoption. Drawing on international competency frameworks, including the Digital Health Competencies in Medical Education Framework and recently proposed AI-specific Entrustable Professional Activities, we map core skills that future hematopathologists must master: data-science literacy, critical appraisal of AI outputs, and ethical governance. We highlight evaluated training models such as the Pathology Informatics Essentials for Residents curriculum, Stanford Artificial Intelligence in Machine and Imaging workshops, and College of American Pathologists bootcamps and propose integration strategies adaptable across resource settings. By pairing rigorous validation with targeted education, AI can elevate rather than eclipse the diagnostic role of the leukemia specialist, enabling more timely, reproducible, and personalized patient care.

Humans↗

PubMed2005

Practical color calibration for dermoscopy, applied to a digital epiluminescence microscope.

BACKGROUND/PURPOSE: The assessment of colors is essential for melanoma (MM) diagnosis, both for pattern analysis on dermoscopic images, and when using semiquantitative methods. Our aim was to provide a simple, precise characterization and reproducible calibration of the color response for dermoscopic instruments. METHODS: Three processes were used to correct the non-uniform illumination pattern of the instrument, to easily estimate the camera gamma settings and to describe the color space conversion matrices required to produce standard images, in any color space. A specific color space was also developed to optimize the representation of dermatoscopic colors. The calibration technique was tested both on synthetic reference surfaces and on real images by comparing the difference between the images colors obtained with two different equipments. RESULTS: The differences between the images acquired by means of the two instruments, calculated on the reference patterns after calibration, were up to 10 times lower then before, while comparison of histograms referring to real images provided an improvement of about seven times on average. CONCLUSIONS: A complete workflow for dermatologic image calibration, which allows the user to continue using his own software and algorithms, but with a much higher informative content, is presented. The technique is simple and may improve cooperation between different research centers, in teleconsulting contexts or for result comparisons.

Algorithms↗

PubMed2006

An evaluation of nursing practice models in the context of the severe acute respiratory syndrome epidemic in Hong Kong: a preliminary study.

AIM AND OBJECTIVE: Like other health-care workers, Hong Kong nurses had their professional knowledge and skills seriously challenged during the SARS outbreak. Could current nursing practices support the care of SARS or SARS-like patients in the future? If not, alternative practices would be needed. Providing a preliminary understanding, this paper compares the conventional with different nursing delivery models in a simulated SARS ward and focuses on nurses' efficiency, infection control practices and views of the two models. DESIGN AND METHODS: This study was conducted in three phases. First, a baseline understanding of nursing practices was achieved through four workflow observations. In an eight-hour day, four research assistants observed nursing activities in the medical and fever wards. These data were used in the second phase to construct two sets of clinical vignettes, pertaining to SARS patient care in both conventional and alternative practice models. These scripts were discussed with nine nurses of various ranks from the hospital under study for their expert validation and input. In the third phase, nurse participants and patient actors enacted the vignettes in a simulated setting. Video-taped observations and four nurse participant interviews were employed. Observational data were analysed through descriptive statistics and independent t-tests. Textual data were coded and categorized for common meanings. RESULTS: Conventional practice from the findings consisted of cubicle and named nurse nursing. While the former reflected modified team and functional nursing, it did not confine patient care within a cubicle as suggested by its name. The latter depicted a modified primary nursing approach in a team, with delegation of care. Preliminary findings concerning infection control and nurse satisfaction revealed that the alternative model had an advantage over the conventional. RELEVANCE TO CLINICAL PRACTICE: This study findings lay the foundation for clinical trials, which would evaluate the significance of patient-care quality, cost-effectiveness and better human resource management by restructuring current nursing practices.

Clinical Competence↗

PubMed2006

Governing time in operating rooms.

AIM: This paper examines how time is controlled and governed in operating rooms through interpersonal communication between nurses and doctors. BACKGROUND: Time is a valuable commodity in organizations with improvements often directed towards maximizing efficiencies. As a consequence, time can be a source of tension and interpersonal conflict as individuals compete for control of its use. METHODS: The data in this paper emanate from an ethnographic study that explored a range of communication practices in operating room nursing. Participants comprised 11 operating room nurses. Data were collected over two years in three different institutional settings and involved participant observation, interviews and the keeping of a personal diary. A deconstructive analysis of the data was undertaken. RESULTS: Results are discussed in terms of the practices, in which clinicians are engaged in, to govern and control their use of time. The four practices presented in this paper include; questioning judgment and timing, controlling speed, estimating surgeons' use of time and coping with different perceptions of time. CONCLUSIONS: Time and speed were hotly contested by nurses. They used their personal knowledge of individual surgeon's habits of time to govern and control practice. Nurses thought about surgeons in terms of time and developed commonly accepted understandings about the length of surgical procedures. They used this knowledge to manage the scheduling of operations in the departments and to control the workflow in individual operating rooms. Knowledge of individual surgeons was a source of power for operating room nurses. RELEVANCE TO CLINICAL PRACTICE: Nurses have more power in the operating room than might be imagined but they exercise this power in subtle ways. If operating rooms are to work effectively, the operating room team must understand each others' work better.

Adaptation, Psychological↗

PubMed2005

Estimating resource use and cost of prophylactic management of neutropenia with filgrastim.

The study objective is to develop a methodology for the measurement of time, resource use and cost of the prophylactic management of neutropenia with filgrastim in different settings where the drug is routinely used: in-hospital care, outpatient care and home care. The activity-based costing method is used to analyse the cost of managing prophylactically neutropenia and comprises four steps. First, department heads in each of the chosen settings were selected and interviewed to obtain key elements in the workflow that involves the management of neutropenia, followed by the second step involving in-depth, structured interviews of key personnel. The third step was the measurement of the time required for frequently occurring activities in monitoring neutropenia and the administration of filgrastim by a study nurse. Finally, information on resource unit costs and personnel salaries were collected from the administration units to calculate an average cost. Sensitivity analyses were undertaken on estimated variables in the study. A list of eight to 14 consecutive activities linked to the prophylactic management of neutropenia was observed. The number and type of activities do not differ between an in-hospital oncology ward and an outpatient setting except for blood samplings. The difference is more pronounced between hospital and home care settings, as in the latter the patient performs many of the activities him/herself. The cost estimate per setting for prophylactic drug use is 6.30 Euros for in-hospital care, 3.67 Euros for outpatient care and 5.49 Euros for home care. Taking the two most frequently occurring scenarios per chemotherapy cycle (i.e. with or without febrile neutropenia), the following cost estimates are obtained: 60.41 Euros for a patient with febrile neutropenia and 56.77 Euros for a patient without febrile neutropenia, excluding drug costs. With the activity-based costing method it is possible to accurately demonstrate cost savings in the management of neutropenia using the newer drug therapies.

Ambulatory Care↗

PubMed2006

A bioinformatics pipeline for high-throughput microbial multilocus sequence typing (MLST) analyses.

Multilocus sequence typing (MLST) analysis for semi-routine applications is hindered by the downstream, manually intensive steps of processing the raw sequence data files. This report describes the development of an MLST pipeline that automates DNA sequence editing and analysis in order to significantly reduce the time required for processing data. Validation using a pneumococcal dataset revealed complete agreement between the results generated by manual and automated workflows. The MLST pipeline was developed for both double-strand and single-strand sequencing.

Bacteria↗