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At least 19 recordsLinked to original sources
PubMed2026

Computational metabolomics at scale: from open data to insight.

Metabolomics data are currently generated at scale thanks to the evolution of technologies that have led to marked improvements in the number of metabolites detected, spanning all chemical classes. These data are increasingly submitted to public repositories for data reuse, integration, and interpretation. Despite the availability of public resources and associated computational tools, the field still lacks a widely adopted, consistent data and analytics infrastructure capable of transforming this wealth of information into scientific insight. Indeed, the metabolomics field is just now scratching the surface of being able to harness the power of new computational technologies. In this review, we summarize discussions from the "Dagstuhl-Seminar 24181 Computational Metabolomics: Towards Molecules, Models, and their Meaning" with a focus on public data availability, open data standards, data and knowledge integration, and education. Our goal is to raise awareness and adoption of the latest open science resources while highlighting key areas needing further development.

Metabolomics↗
PubMed2026

Ethical Governance of Open Data Across Biomedical Research, Healthcare, and Public Health: Privacy, Equity, Trust, and Controlled Access.

Open data has become central to biomedical research and public health, but health information is uniquely sensitive and difficult to share responsibly. In this narrative review, open data is considered as a spectrum of health-data sharing arrangements, ranging from public aggregate datasets to controlled-access repositories, federated analysis, and synthetic data. This narrative review synthesizes the scientific and societal rationale for greater openness with the ethical, legal, and governance constraints that shape what "open" can realistically mean in healthcare. We examine how data sharing supports reproducibility, machine learning, and more efficient research, while also enabling public health surveillance and learning health systems. Against these benefits, we analyze privacy and re-identification risks, consent challenges in large-scale secondary use, inequities including data colonialism, and tensions introduced by commercialization. We integrate lessons from prominent case examples spanning pandemic data sharing, genomic initiatives, population registries, patient-led rare disease infrastructures, and regional data spaces. Across these domains, experience suggests that durable progress depends less on unrestricted openness than on calibrated access, privacy-preserving architectures, clear accountability, and sustained public engagement. We conclude by proposing a pragmatic ethical orientation for healthcare open data: treat openness as a spectrum of controlled sharing arrangements, embed equity and reciprocity into governance, and institutionalize trust-building measures that can persist beyond emergencies and political cycles.

Data colonialism↗
PubMed1978

Variations in depth-dose data between open and wedge fields for 4-MV X-rays.

Central-axis depth-dose data for 4-MV x rays, including tissue-maximum ratios, were measured for wedge fields. Comparison with corresponding open-field data revealed differences in magnitude which increased with depth, field size, and wedge thickness. However, phantom scatter correction factors for the wedge fields differed less than 1% from corresponding open-field factors. The differences in central-axis per cent depth doses between the two types of fields indicate beam hardening by the wedge filter. This study also implies that the derivation of tissue-maximum ratios from central-axis per cent depth is as valid for wedge as for open fields.

Humans↗
PubMed2026

The need for standardization and improved open (meta)data practices in metaproteomics.

Metaproteomics enables functional insight into microbial communities by identifying and quantifying proteins in complex samples. Yet, heterogeneous analytical workflows and the lack of standardization across experimental and bioinformatics stages hinder reproducibility and comparability, limiting integration with other omics data. We here present a community-developed reporting checklist tailored to the specific needs of metaproteomics. We also outline current efforts to enable structured and interoperable metadata capture, drawing on standards from proteomics and microbiome research wherever possible. By promoting transparent reporting and advancing metadata practices, our recommendations aim to align metaproteomics more closely with FAIR principles and support reproducible and interoperable research practices. Video Abstract.

Proteomics↗
PubMed2005

The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging.

The Open Microscopy Environment (OME) defines a data model and a software implementation to serve as an informatics framework for imaging in biological microscopy experiments, including representation of acquisition parameters, annotations and image analysis results. OME is designed to support high-content cell-based screening as well as traditional image analysis applications. The OME Data Model, expressed in Extensible Markup Language (XML) and realized in a traditional database, is both extensible and self-describing, allowing it to meet emerging imaging and analysis needs.

Computational Biology↗
PubMedDate not supplied

Progress in multidimensional NMR investigations of peptide and protein 3-D structures in solution. From structure to functional aspects.

2-D and 3-D NMR techniques were used to investigate the conformations in solution of several peptides and proteins for which crystalline structures are not available yet. Insect defensin A is a small (40 aa) antibiotic protein exhibiting a characteristic 'loop-helix-beta-sheet' structure. A striking analogy was found with charybdotoxin, a scorpion toxin in which a CSH (cysteine stabilized alpha-helix) motif is also present. Wheat phospholipid transfer protein (PLTP) (90 aa) has a 3-D structure resulting from the packing of four helices and of a C-terminal less well-defined fragment. Preliminary results show that PLTP forms a complex with lyso-PC and that such an interaction results in a conformational change affecting principally the C-terminal half of the protein. A last example is given with surfactin, a lipopeptide biosurfactant from bacterial origin. Its protonated form shows a very compact structure in which the two acidic residues located on the top of a 'horse saddle' topology face each other, whereas the ionized form could adopt a more extended conformation. A common property of these compounds is their capacity to interact with lipids. The present structural data open the way for a further establishment of structure-activity relationships.

Amino Acid Sequence↗
PubMed1976

Interchromosomal asynchrony of DNA replication in polytene chromosomes of Drosophila pseudoobscura.

Analysis of 3H-thymidine autoradiograms of late third instar larval salivary glands of Drosophila pseudoobscura revealed a unique example of asynchrony of replication in the autosome complement. The two autosomal arms, 2 and 3, show similar labeling pattern during the initial phases, DD to 3C, and thereafter, the chromosome 3 has fewer labeled sites than chromosome 2 until the most terminal pattern, 1D. Detailed sitewise analysis of 3H-thymidine labeling shows that while nearly 54% of the sites examined in chromosome 2 have a labeling frequency greater than 50%, only 13% of all sites in chromosome 3 have labeling frequency at that range. The number of labeled sites on chromosome 3 plotted against that on chromosome 2 shows a hyperbolic profile rather than a linear relationship. The silver grain ratio of the 2nd to 3rd increases from 1.5 to 3.1 through different stages of the cycle. These results suggest that both chromosomes start replication simultaneously but the third chromosome appears to complete the replication earlier than the second. These data open up the possibility of separate control mechanisms for the initiation and termination of DNA replication in polytene chromosomes.

Animals↗
PubMed1991

Taurine receptors in membranes from retinal pigment epithelium cells in culture.

[3H]Taurine-specific binding to membranes from retinal pigment epithelium was demonstrated. A single saturable system was found, with KB = 237 nM and Bmax = 2.8 pmol/mg protein. Binding to freshly prepared membranes showed partial Na(+)-dependence while in frozen/thawed membranes, binding remained unchanged in the absence or presence of this ion. A 30-40% increase in binding was observed at physiological temperature (37 degrees C) compared to 4 degrees C in fresh but not in frozen membranes. Accumulation of taurine was followed during differentiation in vitro; results showed that changes in uptake and receptor binding to frozen membranes are not parallel, discarding the possibility of an interaction with uptake sites. Pharmacology of these binding sites suggests that they could be common to other amino acids, since displacement experiments showed that glycine, beta-alanine and strychnine were as potent as taurine itself in displacing [3H]taurine. Our data open the possibility of taurine being involved in the communication between the retina and the retinal pigment epithelium through an interaction with specific receptors.

Amino Acids↗
PubMed1992

Morphological and biochemical evidence for partial nuclear localization of annexin 1 in endothelial cells.

Using immunofluorescence, an affinity-purified anti-annexin-1 polyclonal antibody showed both cytoplasmic and nuclear staining, whereas antibodies against annexins 2, 5 and 6 labelled almost exclusively the cytoplasm of cultured endothelial cells. This was further confirmed by immunogold labelling and electron microscopy using a monoclonal antibody, annexin 1 being detected close to the plasma membrane, in the cytoplasm, as well as inside the nucleus. Finally, using immunoblotting, purified nuclei were shown to contain annexin 1, which was not removed by EDTA treatment. These data open some new perspectives in the understanding of annexin function, including possible involvement in nucleoskeleton dynamics and regulation of proliferation through cell signalling.

Animals↗
PubMed1992

Partial remission of hemiplegia and somatoparaphrenia through vestibular stimulation in a case of unilateral neglect.

In a case of long lasting severe neglect resulting from a large right parieto-temporo-occipital infarct, vestibular stimulation produced a temporary reduction of the motor deficit and disappearance of the somatoparaphrenic delusion, in addition to the already reported improvement of extrapersonal and personal neglect and anosognosia. These data open new perspectives in the understanding of the neglect syndrome and of functional involvement of the parietal lobe in space representation.

Aged↗
PubMed1975

Integration of viral genomes.

DNA transcripts of infectious RNA viruses were found to be integrated in the DNA of chronically-infected tissue cultures. DNA sequences homologous to RNA of measles virus were found in tissues affected with systemic lupus erythemotosus. These data open up a new class of virus-cell interaction that may be a result of cooperation between infectious and oncogenic viruses.

Animals↗
PubMed1992

Cardiostimulatory and antiarrhythmic activity of tubulin-binding agents.

Rhythmic, spontaneously pulsating cardiac cells cultured from newborn rats are immediately stimulated to beat faster by addition of a number of tubulin-binding agents but not by their non-tubulin-binding analogues. The tubulin-binding agents tested include vinblastine, vincristine, navelbine, two analogs of vinblastine (S12362 and S12363), nocodazole, colchicine, and podophylotoxin. In addition to binding tubulin, all of the above agents also depolymerize microtubules. In contrast, taxol, a tubulin-binding agent that stabilizes microtubules, does not stimulate cardiac cells. Moreover, the immediate and ensuing cardiac stimulation by vinblastine at 0.05 microgram/ml is completely blocked by pre- and cotreatment with taxol at 1.0 microgram/ml. The time necessary to reverse the cardiostimulatory effect of vinblastine is significantly longer than that required for nocodazole, further implicating depolymerization of microtubules in the cardiac activity of these agents. All of the tubulin-binding agents tested (including taxol) also immediately reverse adriamycin-induced arrhythmias. By using a monoclonal antibody to alpha-tubulin, typical filamentous microtubules are visualized in cardiac muscle and cocultured non-muscle cells by immunofluorescence. When cells are treated for 2 hr with vinblastine at 0.05 microgram/ml, fluorescence is detected in cross-striated patterns in cardiac muscle cells. Overall, these data open the possibility of uncovering an additional relationship between cytoskeletal elements (other than actin and myosin) and the contractility of cardiac muscle. They also suggest an alternative mechanism for affecting cardiac cell function in vitro (namely, by tubulin-binding agents). If these agents are shown to be cardioactive in vivo, they may provide another approach to the treatment and management of cardiac arrhythmias.

Alkaloids↗
PubMed1992

Inert gas single-breath washout and structural alteration of respiratory bronchioles.

With the perspective of establishing a link between a respiratory function test and alterations of membranous bronchioles, respiratory bronchioles, and alveolar ducts, we performed forced expirations and four kinds of single-breath washout maneuvers on 27 men due to undergo a lobectomy for peripheral bronchial carcinoma. For the single-breath washouts, the inhaled gas mixture consisted of 90% O2, 5% He, 5% SF6. The four maneuvers were the standard vital capacity test and three successive inhalations of 0.5, 1, and 1.5 L from functional residual capacity. The slopes of N2, He, and SF6 for each maneuver were computed, as well as a new index (I2) describing the relative decrease of the difference between the SF6 and the He slopes induced by a larger inspiratory volume. The histologic analysis focused on pigmentation, inflammation, and fibrosis of membranous bronchioles, respiratory bronchioles, and alveolar ducts. There was a linear relationship with a highly significant correlation coefficient between the new index I2 and the degree of inflammatory (r = 0.73) and fibrotic (r = 0.63) changes of the respiratory bronchioles; this correlation persisted in patients with a normal FEV1/VC ratio. These preliminary data open the way to finding a test for early peripheral (intraacinar) airway dysfunction.

Adult↗
PubMed1975

Evaluation of the significance of scintillation angiocardiography for determination of the left ventricular volume.

A method for the determination of the left ventricular volume by scintillation angiocardiography following a peripheral venous injection of a radioactive isotope was described. Salient points in its methodology were as follows: 1. This volume study was composed of non-gated scintillation angiocardiography and cumulative gated scintiphotography. 2. The non-gated scintillation data were stored into video recording system. 3. The gated scintiphotography was performed during a play-back of non-gated scintillation data, opening the gate at desired points of time during a cardiac cycle. 4. The left ventricular scintillation image was photographied in life-size on x-ray film by superimposing, 10-20 times, the gated image of the several consecutive heart beats during the "left ventricular phase" of the dilution of intravenously injected radionuclide. For validation of this method, the stroke volume obtained with this method was compared with that obtained by precordial radionuclide dilution curve recordable during the non-gated scintillation angiocardiography, and also with that obtained by non-simultaneous radiocardiography. It was concluded that the present method may be sufficiently accurate for clinical use.

Adolescent↗
PubMed1992

[Tubulo-interstitial nephritis (TIN) with no glomerular lesions, distal renal tubular acidosis and asteatosis cutis in a patient with systemic lupus erythematosus (SLE): a case report].

We report a 28-year-old woman with systemic lupus erythematosus (SLE) who showed tubulo-interstitial nephritis (TIN) without any glomerular changes. In 1990, she was admitted to our hospital, complaining of anorexia, vomiting and persistent high fever. Laboratory findings showed proteinuria, pancytopenia, hypocomplementemia and positive for antinuclear antibody, anti-DNA antibody, anti-Sm antibody, anti-SSA antibody and anti-SSB antibody. We made a diagnosis of SLE. Furthermore, distal renal tubular acidosis and asteatosis cutis were revealed. The diagnosis of Sjögren's syndrome was not made. We treated with high-dose prednisolone (60mg/day) and achieved improvement of symptoms and laboratory data. Open renal biopsy showed TIN without any glomerular changes. Predominant TIN is very rare in SLE. We discussed its pathogenesis and relation to the renal lesions of Sjögren's syndrome.

Acidosis, Renal Tubular↗
PubMed1976

[The neuroendocrinology of sleep].

It is now well established that some pituitary hormones have a pattern of secretion closely linked to the sleep-waking cycle. These data open a new approach to the problem of sleep disturbances and suppose a completely new evaluation of their meaning.

Adrenocorticotropic Hormone↗