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At least 19 recordsLinked to original sources
PubMed2025

Rehabilomics Strategies Enabled by Cloud-Based Rehabilitation: Scoping Review.

BACKGROUND: Rehabilomics, or the integration of rehabilitation with genomics, proteomics, metabolomics, and other "-omics" fields, aims to promote personalized approaches to rehabilitation care. Cloud-based rehabilitation offers streamlined patient data management and sharing and could potentially play a significant role in advancing rehabilomics research. This study explored the current status and potential benefits of implementing rehabilomics strategies through cloud-based rehabilitation. OBJECTIVE: This scoping review aimed to investigate the implementation of rehabilomics strategies through cloud-based rehabilitation and summarize the current state of knowledge within the research domain. This analysis aims to understand the impact of cloud platforms on the field of rehabilomics and provide insights into future research directions. METHODS: In this scoping review, we systematically searched major academic databases, including CINAHL, Embase, Google Scholar, PubMed, MEDLINE, ScienceDirect, Scopus, and Web of Science to identify relevant studies and apply predefined inclusion criteria to select appropriate studies. Subsequently, we analyzed 28 selected papers to identify trends and insights regarding cloud-based rehabilitation and rehabilomics within this study's landscape. RESULTS: This study reports the various applications and outcomes of implementing rehabilomics strategies through cloud-based rehabilitation. In particular, a comprehensive analysis was conducted on 28 studies, including 16 (57%) focused on personalized rehabilitation and 12 (43%) on data security and privacy. The distribution of articles among the 28 studies based on specific keywords included 3 (11%) on the cloud, 4 (14%) on platforms, 4 (14%) on hospitals and rehabilitation centers, 5 (18%) on telehealth, 5 (18%) on home and community, and 7 (25%) on disease and disability. Cloud platforms offer new possibilities for data sharing and collaboration in rehabilomics research, underpinning a patient-centered approach and enhancing the development of personalized therapeutic strategies. CONCLUSIONS: This scoping review highlights the potential significance of cloud-based rehabilomics strategies in the field of rehabilitation. The use of cloud platforms is expected to strengthen patient-centered data management and collaboration, contributing to the advancement of innovative strategies and therapeutic developments in rehabilomics.

Cloud Computing↗
PubMed2025

Fundamentals of FAIR biomedical data analyses in the cloud using custom pipelines.

As the biomedical data ecosystem increasingly embraces the findable, accessible, interoperable, and reusable (FAIR) data principles to publish multimodal datasets to the cloud, opportunities for cloud-based research continue to expand. Besides the potential for accelerated and diverse biomedical discovery that comes from a harmonized data ecosystem, the cloud also presents a shift away from the standard practice of duplicating data to computational clusters or local computers for analysis. However, despite these benefits, researcher migration to the cloud has lagged, in part due to insufficient educational resources to train biomedical scientists on cloud infrastructure. There exists a conceptual lack especially around the crafting of custom analytic pipelines that require software not pre-installed by cloud analysis platforms. We here present three fundamental concepts necessary for custom pipeline creation in the cloud. These overarching concepts are workflow and cloud provider agnostic, extending the utility of this education to serve as a foundation for any computational analysis running any dataset in any biomedical cloud platform. We illustrate these concepts using one of our own custom analyses, a study using the case-parent trio design to detect sex-specific genetic effects on orofacial cleft (OFC) risk, which we crafted in the biomedical cloud analysis platform CAVATICA.

Cloud Computing↗
PubMed1976

The structure of the mitochondrial cloud of Xenopus laevis oocytes.

The ultrastructure of the mitochondrial cloud (Balbiani body) of the pre-vitellogenic oocytes of Xenopus laevis has been examined using transmission and stereoscan electron microscopy. Examination of conventional thin sections confirm previous observations which suggest that the cloud consists essentially of many thousands mitochondria and numerous small vesicles; larger clouds, in oocytes greater than 200 mum in diameter, contain relatively more vesicles. Using a standard electron microscope at 100 kV very long and coursing arrays of mitochondrial profiles can be detected. The presence of very long mitochondrial elements has been confirmed using a high voltage microscope operating at 500-1000 kV. Stereoscan preparations, isolated from pre-vitellogenic oocytes, lend some support to the view that the mitochondrial cloud amy consist of a mass of long filamentous mitochondria and the possibility that there are large continuous regions of mitochondrial material cannot be ruled out.

Animals↗
PubMed2019

Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE): a cloud-based platform for curating and classifying germline variants.

Variant interpretation in the era of massively parallel sequencing is challenging. Although many resources and guidelines are available to assist with this task, few integrated end-to-end tools exist. Here, we present the Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE), a web- and cloud-based platform for annotation, identification, and classification of variations in known or putative disease genes. Starting from a set of variants in variant call format (VCF), variants are annotated, ranked by putative pathogenicity, and presented for formal classification using a decision-support interface based on published guidelines from the American College of Medical Genetics and Genomics (ACMG). The system can accept files containing millions of variants and handle single-nucleotide variants (SNVs), simple insertions/deletions (indels), multiple-nucleotide variants (MNVs), and complex substitutions. PeCanPIE has been applied to classify variant pathogenicity in cancer predisposition genes in two large-scale investigations involving >4000 pediatric cancer patients and serves as a repository for the expert-reviewed results. PeCanPIE was originally developed for pediatric cancer but can be easily extended for use for nonpediatric cancers and noncancer genetic diseases. Although PeCanPIE's web-based interface was designed to be accessible to non-bioinformaticians, its back-end pipelines may also be run independently on the cloud, facilitating direct integration and broader adoption. PeCanPIE is publicly available and free for research use.

Child↗
PubMed2021

RP-REP Ribosomal Profiling Reports: an open-source cloud-enabled framework for reproducible ribosomal profiling data processing, analysis, and result reporting.

Ribosomal profiling is an emerging experimental technology to measure protein synthesis by sequencing short mRNA fragments undergoing translation in ribosomes. Applied on the genome wide scale, this is a powerful tool to profile global protein synthesis within cell populations of interest. Such information can be utilized for biomarker discovery and detection of treatment-responsive genes. However, analysis of ribosomal profiling data requires careful preprocessing to reduce the impact of artifacts and dedicated statistical methods for visualizing and modeling the high-dimensional discrete read count data. Here we present Ribosomal Profiling Reports (RP-REP), a new open-source cloud-enabled software that allows users to execute start-to-end gene-level ribosomal profiling and RNA-Seq analysis on a pre-configured Amazon Virtual Machine Image (AMI) hosted on AWS or on the user's own Ubuntu Linux server. The software works with FASTQ files stored locally, on AWS S3, or at the Sequence Read Archive (SRA). RP-REP automatically executes a series of customizable steps including filtering of contaminant RNA, enrichment of true ribosomal footprints, reference alignment and gene translation quantification, gene body coverage, CRAM compression, reference alignment QC, data normalization, multivariate data visualization, identification of differentially translated genes, and generation of heatmaps, co-translated gene clusters, enriched pathways, and other custom visualizations. RP-REP provides functionality to contrast RNA-SEQ and ribosomal profiling results, and calculates translational efficiency per gene. The software outputs a PDF report and publication-ready table and figure files. As a use case, we provide RP-REP results for a dengue virus study that tested cytosol and endoplasmic reticulum cellular fractions of human Huh7 cells pre-infection and at 6 h, 12 h, 24 h, and 40 h post-infection. Case study results, Ubuntu installation scripts, and the most recent RP-REP source code are accessible at GitHub. The cloud-ready AMI is available at AWS (AMI ID: RPREP RSEQREP (Ribosome Profiling and RNA-Seq Reports) v2.1 (ami-00b92f52d763145d3)).

AMI↗
PubMed1975

Surface tension and cloud point changes of polyoxyethylenic non-ionic surfactants during autoxidation.

Changes in the surface tension-concentration curves of the non-ionic surfactant cetomacrogol, a polyoxyethylenic (POE) hexadecyl ether containing about 24 ethylene oxide (EO) groups, have been examined during autoxidation of aqueous solutions. The curves exhibit decreases in cmc values and changes in the slopes below and above the cmc which lead to the loss of the sharp break characteristic of micelle-formation. There is also a progressive decrease in the cloud point during autoxidation. Surface tensions and cloud points of a series of known POE hexadecyl ethers containing from 10 to 60 EO units have been measured and related to the number of EO units present. From these data, it is apparent that autoxidation of cetomacrogol is accompanied by degradation of POE chain rather than the hydrocarbon chain, the number of EO units lost up to the time at which the solution becomes turbid being about 14. The significance of such measurements is discussed in relation to the detection of decomposition and pending rapid decomposition in synthesized and commercial surfactants.

Catalysis↗
PubMed1975

Emulsion stabilization by non-ionic surfactants: the relevance of surfactant cloud point.

The effect of various additives, electrolytes and non-electrolytes, on the cloud point of non-ionic surfactants has been studied. Additives which salt-out the polyoxyethylene chains of the surfactants cause decreased stability of oil-in-water emulsions by decreasing the true hydrophile-lipophile balance (HLB) of the surfactant; additives such as sodium iodide and propanol salt-in the non-ionic surfactants and result in an increase in the effective or true HLB of the system. The latter additives do not increase the hydration of the polyoxyethylene chains but their effect must be on the structure of water so that the heat of hydration of the chains is altered. Experiments with free films of the aqueous surfactant (Brij 96) show that thinning rates are markedly affected by the additives, but there is little effect on the equilibrium thickness of the films (ca 11 nm). Nonetheless the thickness at the transition from thick film to equilibrium black film decreases with increasing cloud point of the solution indicating increased stability. The importance of structure formation in the liquid film separating the emulsion globules was demonstrated.

Chemical Phenomena↗
PubMed1975

A new mucolipidosis with psychomotor retardation, corneal clouding, and retinal degeneration.

A 23-year-old man had slow psychomotor development at 6 months of age and developed intermittent corneal clouding at about 18 months. He developed a truncal ataxia and hypotonia of the limbs combined with spasticity and active deep reflexes that did not progress. His skeleton and facies were normal. Between 1 and 13 years of age, he developed severe optic atrophy, absence of retinal blood vessels, and an extinguished electroretinogram. Biochemical analysis of cultured fibroblasts indicated no lysosomal hydrolase deficiency; cellular metachromasia was absent and there was no mucopolysaccharidoses. Ultrastructural studies indicated single-membrane-limited vacuoles containing lamellated membranes and a polymorphous substance in tissue-cultured cells and conjunctiva.

Adolescent↗
PubMed1975

Corneal clouding with increased acid mucopolysaccharide accumulation in Bowman's membrane.

Two infants had bilateral congenital corneal clouding and abnormal acid mucopolysaccharide accumulation in a thickened Bowman's membrane. This unusual entity was not associated with acid mucopolysaccharide deposits in the skin and visceral tissues or with increased levels of acid mucopolysaccharide in the urine. The similarity and differences have been compared to the systemic mucopolysaccharidosis and macular corneal dystrophy.

Basement Membrane↗
PubMed2026

Fedflow: cloud orchestration for federated learning with the FeatureCloud platform.

MOTIVATION: Federated learning (FL) enables collaborative model training on geographically distributed genomic and clinical datasets while complying with data privacy laws and regulatory constraints. FeatureCloud is an existing platform for FL that provides an accessible web-based interface and a large repository of implemented methods. However, due to its graphical interface, FeatureCloud requires manual interaction of all participants, limiting automation, iteration, and reproducibility. RESULTS: We introduce fedflow, a Python-based command-line tool for headless orchestration of FL tasks with FeatureCloud. This tool uses distributed computing resources such as virtual machines or cloud instances to automate such workflows. This allows for scalable federated computing either in local simulations or deployed in a trusted environment. Further, we demonstrate how fedflow can be used to integrate FeatureCloud in reproducible Snakemake workflows. For this, we reanalyse a metagenomic dataset with two federated algorithms and compare the results to the centralized approach with pooled data. Overall, fedflow enables automation of multi-client FL tasks, facilitates embedding of FeatureCloud in standard bioinformatics pipelines and thereby helps increase reproducibility. AVAILABILITY: Fedflow is open-source and available at https://github.com/W-L/fedflow.

Journal Article↗
PubMed1975

A new mucolipidosis with psychomotor retardation, corneal clouding, and retinal degeneration.

A man now 22 years of age had slow psychomotor development about 6 months after birth and developed intermittent corneal clouding at about 18 months. He developed truncal ataxia, hypotonia of the limbs combined with spasticity, and active deep reflexes. These have not progressed. His skeleton and facies are normal. Between his first and thriteenth year he developed sev ere optic atrophy, absence of retinal blood vessels, and an extinguished electroretinogram. Biochemical analysis of cultured fibroblasts indicated no lysosomal hydrolase deficiency; cellular metachromasia was absent and there was no mucopolysaccharidoses. Ultrastructural studies indicated single membrane vacuoles containing lamellated membranes and a polymorphous substance in tissue cultured cells and conjunctiva.

Adult↗
PubMedDate not supplied

The roles of corneal mucopolysaccharides and water contents in post-mortem corneal clouding.

The quantitative changes in mucopolysaccharides (MPS) and water contents in post-mortem rabbit corneas were studied. On the basis of the results, the post-mortem periods were classified into 4 stages. The first stage was during the first day after death when the MPS and the corneal water contents were observed to have maintained their initial values and the cornea was "clear". The second was 1 to 3 days after death when the MPS remained at approximately their initial value, whereas the water contents were very pronounced. In this second stage the cornea was "a little clear" or "cloudy". The third was 3 to 6 days after death when the MPS were found to have decreased gradually, but the water contents maintained their high level. The cornea in this third stage was "cloudy" or "very cloudy". The fourth was 6 or more days after death when the two parameters were found to have decreased significantly, and the cornea was "very cloudy".

Animals↗
PubMed1979

Dialysis/hemofiltration in schizophrenia: a journey by night and cloud.

Hypotheses for the etiology of schizophrenia are discussed and related to possible treatments utilizing artificial kidney systems. For hemofiltration particularly, a theoretical framework is presented for treatment planning. Emphasis is placed on the necessity of using rigid diagnostic criteria for patient selection. Results are reported on two "strict" schizophrenic patients after a series of hemofiltration treatments. One patient showed no clinical improvement after seventeen treatments and died subsequently in a mountaineering accident. Though clinical improvement was noted in the second patient (22 treatments in four months), it is unjustifiable to attribute this solely to hemofiltration. Increased family and medical staff attention towards the patient is sufficient explanation for all changes noted in the patient's symptomatology. Chemical analyses so far have failed to detect any endorphins, normal or abnormal, in the hemofiltrates of either the two patients or two normal controls (sensitivity 30 pmol/L).

Blood-Brain Barrier↗
PubMed1977

The white cloud. The changing pattern of hematologic research as exemplified by studies of oxygen transport.

Medical research has become an integral part of governmental health care systems. As a consequence of this subsidization, its resources are far greater, while its activities have become more directly responsible to the perceived needs of the people. Clinical investigation in particular has been affected by this adjustment, and its decreasing role in the total program needs scrutiny. Progress in our understanding of oxygen transport is reviewed as an example of the capacity of today's scientific community to explore and develop new areas of knowledge.

Altitude↗