Simultaneous multiple-level magnification selective plane illumination microscopy (sMx-SPIM) imaging system

We report an optical-based (microscopy) imaging technology – Simultaneous Multiple-level Magnification Selective Plane Illumination Microscopy (sMx-SPIM) Imaging System – that addresses a longstanding (technological) challenge of obtaining images, specifically of the biological specimen non-destructively, at different fields of view (FOV) and spatial resolutions (or magnification powers) simultaneously in real-time. Thus, this imaging system provides not only 3D images but also time-resolved sequential images with temporal resolution msecs. Magnification powers (or FOVs) of the individual images can be controlled independently that can be achieved by housing two separate detection arms, in SPIM imaging system, fitted with objective lenses of different magnification powers. These unique features hold promises to observe and study of: (i) sub-microscopic details and entire structure of biological specimen side-by-side simultaneously and (ii) spatio-temporal dynamics of functional activities of biological specimen. For validation study of robustness of the proposed sMx-SPIM imaging system, experiments are conducted in various biological samples (zebrafish embryo, Drosophila melanogaster, and Allium cepa root). Experimental results demonstrate that the study is of significant impacts from two aspects (technological and biological applications).

The Importance of Reference Materials and Method Validation for Advancing Research on the Health Effects of Dietary Supplements and Other Natural Products

Insufficient assessment of the identity and chemical composition of complex natural products, including botanicals, herbal remedies, and dietary supplements, hinders reproducible research and limits understanding mechanism(s) of action and health outcomes, which in turn impede improvements in clinical practice and advances in public health. This review describes available analytical resources and good methodological practices that support natural product characterization and strengthen the knowledge gained for designing and interpreting safety and efficacy investigations. The practice of validating analytical methods demonstrates that measurements of constituents of interest are reproducible and appropriate for the sample (e.g., plant material, phytochemical extract, and biological specimen). In particular, the utilization of matrix-based reference materials enables researchers to assess the accuracy, precision, and sensitivity of analytical measurements of natural product constituents, including dietary ingredients and their metabolites. Select case studies are presented where the careful application of these resources and practices has enhanced experimental rigor and benefited research on dietary supplement health effects.

Towards non-blind optical tweezing by finding 3D refractive index changes through off-focus interferometric tracking

In modern 3D microscopy, holding and orienting arbitrary biological objects with optical forces instead of using coverslips and gel cylinders is still a vision. Although optical trapping forces are strong enough and related photodamage is acceptable, the precise (re-) orientation of large specimen with multiple optical traps is difficult, since they grab blindly at the object and often slip off. Here, we present an approach to localize and track regions with increased refractive index using several holographic optical traps with a single camera in an off-focus position. We estimate the 3D grabbing positions around several trapping foci in parallel through analysis of the beam deformations, which are continuously measured by defocused camera images of cellular structures inside cell clusters. Although non-blind optical trapping is still a vision, this is an important step towards fully computer-controlled orientation and feature-optimized laser scanning of sub-mm sized biological specimen for future 3D light microscopy.

Experimental Analysis of Fabricated Synthetic Midthoracic Paediatric Spine as Compared to the Porcine Spine Based on Range of Motion (ROM)

The present study is aimed at investigating the mechanical behaviour of fabricated synthetic midthoracic paediatric spine based on range of motion (ROM) as compared to porcine spine as the biological specimen. The main interest was to ensure that the fabricated synthetic model could mimic the biological specimen behaviour. The synthetic paediatric spine was designed as a 200% scaled-up model to fit into the Bionix Servohydraulic spine simulator. Biomechanical tests were conducted to measure the ROM and nonlinearity of sigmoidal curves at six degrees of freedom (DOF) with moments at ±4 Nm before the specimens failed. Results were compared with the porcine spine (biological specimen). The differences found between the lateral bending and axial rotation of synthetic paediatric spine as compared to the porcine spine were 18% and 3%, respectively, but was still within the range. Flexion extension of the synthetic spine is a bit stiff in comparison of porcine spine with 45% different. The ROM curves of the synthetic paediatric spine exhibited nonlinearities for all motions as the measurements of neutral zone (NZ) and elastic zone (EZ) stiffness were below “1.” Therefore, it showed that the proposed synthetic paediatric spine behaved similarly to the biological specimen, particularly on ROM.

Robust Integration of Biodiversity Data by Process- and State-based Representation of Object Histories and Modular Application Architecture

Biodiversity data is obtained by a variety of methodological approaches—including observation surveys, environmental sampling and biological object collection—employing diverse sample processing protocols and data transformations. While complete and accurate accounts of these data-generating processes are important to enable integration and informed reuse of data, the structure and content of published biodiversity data currently are often shaped by specific application goals. For example, data publishers that export specimen-based data from collection management systems for inclusion in aggregations like those in the Global Biodiversity Information Facility (GBIF) must frequently relax their internal models and produce unnatural joins to fit GBIF’s occurrences-based data structure. Third-party assertions over these aggregated data therefore assume the risk of irreproducibility or concept drift. Here we introduce process- and state-based representation of object histories as the main organizing principle for data about specimens and samples in Digital Information System for Natural History Data (DINA, Glöckler et al. 2020)-compliant collection management software (Fig. 1). Specimens, samples and objects in general are subjected to a variety of processes, including planned actions involving the object, e.g., collecting, preparing, subsampling, loaning. Object states are any particular mode of being of an object at a certain point in time. For example, any one intermediate step in preparing a collected specimen for long-term conservation in a collection would constitute an individual object state. An object’s history is the entire chain of these interrelated processes and states. We argue that using object histories as main conceptual modeling paradigm in DINA offers the generality required to accommodate a diverse, open set of use cases in biodiversity data representation, yet also offers the versatility to serve as basis for use-case specific data aggregation and presentation. Specifically, a representation based on object histories provides a coherent structure for documenting individual processes and states for any given object and for linking this documentation (e.g., textual descriptions or images pertaining to a given process or state), a natural representational structure of the real-world sequence of processes an object participates in and for the data generated in these processes (e.g., a DNA-extraction procedure and sequence information generated on its basis), a straightforward structure to link data about related objects (e.g., tissue samples, the biological specimen a bone is derived from) in a network of connected object histories. a coherent structure for documenting individual processes and states for any given object and for linking this documentation (e.g., textual descriptions or images pertaining to a given process or state), a natural representational structure of the real-world sequence of processes an object participates in and for the data generated in these processes (e.g., a DNA-extraction procedure and sequence information generated on its basis), a straightforward structure to link data about related objects (e.g., tissue samples, the biological specimen a bone is derived from) in a network of connected object histories. The approach is designed to be embedded in DINA’s modular application architecture, so that information on object histories can be accessed via corresponding APIs either through its own interfaces (Fig. 2) or by integration with external web services (Fig. 3). Viewing collection management tasks as part of object histories also informs delineation of modules to support these tasks with specialized functions and interfaces. It also admits the use of persistent, dereferencable identifiers for individual processes and states in object histories and for linking their representations to elements in ontologies and controlled vocabularies. In this contribution to the symposium, DINA's object histories as a main organizing principle for collection object data will be discussed and the utility of using it in the context of modular application architecture, data federation, and data integration in projects like BiCIKL will be illustrated.

Determination of Formaldehyde from Disposal of Formaldehyde Fixed Biological Specimen Buried in Soil

Biomedical waste specifically anatomical specimens and body parts will be incinerated by a local incineration facility. However, the incineration of formaldehyde fixed specimen from hospitals poses hazardous effect to human and environment due to an exposure of highly toxic gases such as dioxins and furans. In addition, this practise is considered as non-shariah compliance by Muslim community. Thus, a safer and shariah-compliance option to dispose anatomical specimens through deep burial has been introduced. The concern has been raised on the side effect of the formaldehyde treated specimen to the environment. Formaldehyde is used widely for preservation of surgical and anatomical specimens. The formaldehyde toxicity specifically on the soil, soil water, soil animals and plants should be considered after the burial of the anotamical specimens. Thus, the aim of this study was to investigate the side effect of formaldehyde on soil after the burial of formalin fixed specimen on the environment. In this study, the amount of soil elemental distribution and formaldehyde concentration of pre-burial and post-burial of biological specimen were evaluated by using Energy Dispersive X-Ray Fluorescence (EDXRF) and Ultraviolet-Visible Spectrophotometer instrument, respectively. For EDXRF analysis at Point C, soil elemental distribution after burial of dead biological specimens has higher concentration compared to before the burial. The concentration of formaldehyde at Point C was higher after the burial of dead biological specimen compared to before burial, which exceeds the tolerable concentration recommended by the World Health Organisation (WHO).

Characteristics of available studies and dissemination of research using major clinical data sharing platforms

Background/Aims: Over the past decade, numerous data sharing platforms have been launched, providing access to de-identified individual patient-level data and supporting documentation. We evaluated the characteristics of prominent clinical data sharing platforms, including types of studies listed as available for request, data requests received, and rates of dissemination of research findings from data requests. Methods: We reviewed publicly available information listed on the websites of six prominent clinical data sharing platforms: Biological Specimen and Data Repository Information Coordinating Center, ClinicalStudyDataRequest.com , Project Data Sphere, Supporting Open Access to Researchers–Bristol Myers Squibb, Vivli, and the Yale Open Data Access Project. We recorded key platform characteristics, including listed studies and available supporting documentation, information on the number and status of data requests, and rates of dissemination of research findings from data requests (i.e. publications in a peer-reviewed journals, preprints, conference abstracts, or results reported on the platform’s website). Results: The number of clinical studies listed as available for request varied among five data sharing platforms: Biological Specimen and Data Repository Information Coordinating Center (n = 219), ClinicalStudyDataRequest.com (n = 2,897), Project Data Sphere (n = 154), Vivli (n = 5426), and the Yale Open Data Access Project (n = 395); Supporting Open Access to Researchers did not provide a list of Bristol Myers Squibb studies available for request. Individual patient-level data were nearly always reported as being available for request, as opposed to only Clinical Study Reports (Biological Specimen and Data Repository Information Coordinating Center = 211/219 (96.3%); ClinicalStudyDataRequest.com = 2884/2897 (99.6%); Project Data Sphere = 154/154 (100.0%); and the Yale Open Data Access Project = 355/395 (89.9%)); Vivli did not provide downloadable study metadata. Of 1201 data requests listed on ClinicalStudyDataRequest.com , Supporting Open Access to Researchers–Bristol Myers Squibb, Vivli, and the Yale Open Data Access Project platforms, 586 requests (48.8%) were approved (i.e. data access granted). The majority were for secondary analyses and/or developing/validating methods ( ClinicalStudyDataRequest.com = 262/313 (83.7%); Supporting Open Access to Researchers–Bristol Myers Squibb = 22/30 (73.3%); Vivli = 63/84 (75.0%); the Yale Open Data Access Project = 111/159 (69.8%)); four were for re-analyses or corroborations of previous research findings ( ClinicalStudyDataRequest.com = 3/313 (1.0%) and the Yale Open Data Access Project = 1/159 (0.6%)). Ninety-five (16.1%) approved data requests had results disseminated via peer-reviewed publications ( ClinicalStudyDataRequest.com = 61/313 (19.5%); Supporting Open Access to Researchers–Bristol Myers Squibb = 3/30 (10.0%); Vivli = 4/84 (4.8%); the Yale Open Data Access Project = 27/159 (17.0%)). Forty-two (6.8%) additional requests reported results through preprints, conference abstracts, or on the platform’s website ( ClinicalStudyDataRequest.com = 12/313 (3.8%); Supporting Open Access to Researchers–Bristol Myers Squibb = 3/30 (10.0%); Vivli = 2/84 (2.4%); Yale Open Data Access Project = 25/159 (15.7%)). Conclusion: Across six prominent clinical data sharing platforms, information on studies and request metrics varied in availability and format. Most data requests focused on secondary analyses and approximately one-quarter of all approved requests publicly disseminated their results. To further promote the use of shared clinical data, platforms should increase transparency, consistently clarify the availability of the listed studies and supporting documentation, and ensure that research findings from data requests are disseminated.

Detection of Paratuberculosis in Dairy Herds by Analyzing the Scent of Feces, Alveolar Gas and Stable Air

Paratuberculosis is an important disease of ruminants caused by Mycobacterium avium ssp. paratuberculosis (MAP). Early detection is crucial for successful infection control, but available diagnostic tests are still dissatisfying. Methods allowing a rapid, economic, and reliable identification of animals or herds affected by MAP are urgently required. This explorative study evaluated the potential of volatile organic compounds (VOCs) to discriminate between cattle with and without MAP infections. Headspaces above fecal samples and alveolar fractions of exhaled breath of 77 cows from eight farms with defined MAP status were analyzed in addition to stable air samples. VOCs were identified by GC–MS and quantified against reference substances. To discriminate MAP-positive from MAP-negative samples, VOC feature selection and random forest classification were performed. Classification models, generated for each biological specimen, were evaluated using repeated cross-validation. The robustness of the results was tested by predicting samples of two different sampling days. For MAP classification, the different biological matrices emitted diagnostically relevant VOCs of a unique but partly overlapping pattern (fecal headspace: 19, alveolar gas: 11, stable air: 4–5). Chemically, relevant compounds belonged to hydrocarbons, ketones, alcohols, furans, and aldehydes. Comparing the different biological specimens, VOC analysis in fecal headspace proved to be most reproducible, discriminatory, and highly predictive.