The production, attrition, and biologic life-time of surgeons in relation to the population of the United States: a look into the future through the clouded computer crystal.
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Adult↗
SEARCH · PubMed Health
Results for “cloud computing”
Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.
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Alignment of continuous video onto 3D point clouds.
We propose a general framework for aligning continuous (oblique) video onto 3D sensor data. We align a point cloud computed from the video onto the point cloud directly obtained from a 3D sensor. This is in contrast to existing techniques where the 2D images are aligned to a 3D model derived from the 3D sensor data. Using point clouds enables the alignment for scenes full of objects that are difficult to model; for example, trees. To compute 3D point clouds from video, motion stereo is used along with a state-of-the-art algorithm for camera pose estimation. Our experiments with real data demonstrate the advantages of the proposed registration algorithm for texturing models in large-scale semiurban environments. The capability to align video before a 3D model is built from the 3D sensor data offers new practical opportunities for 3D modeling. We introduce a novel modeling-through-registration approach that fuses 3D information from both the 3D sensor and the video. Initial experiments with real data illustrate the potential of the proposed approach.
Algorithms↗
Semiparametric efficient estimation of small genetic effects in large-scale population cohorts.
Population genetics seeks to quantify DNA variant associations with traits or diseases, as well as interactions among variants and with environmental factors. Computing millions of estimates in large cohorts in which small effect sizes and tight confidence intervals are expected, necessitates minimizing model-misspecification bias to increase power and control false discoveries. We present TarGene, a unified statistical workflow for the semi-parametric efficient and double robust estimation of genetic effects including $ k $-point interactions among categorical variables in the presence of confounding and weak population dependence. $ k $-point interactions, or Average Interaction Effects (AIEs), are a direct generalization of the usual average treatment effect (ATE). We estimate genetic effects with cross-validated and/or weighted versions of Targeted Minimum Loss-based Estimators (TMLE) and One-Step Estimators (OSE). The effect of dependence among data units on variance estimates is corrected by using sieve plateau variance estimators based on genetic relatedness across the units. We present extensive realistic simulations to demonstrate power, coverage, and control of type I error. Our motivating application is the targeted estimation of genetic effects on trait, including two-point and higher-order gene-gene and gene-environment interactions, in large-scale genomic databases such as UK Biobank and All of Us. All cross-validated and/or weighted TMLE and OSE for the AIE $ k $-point interaction, as well as ATEs, conditional ATEs and functions thereof, are implemented in the general purpose Julia package TMLE.jl. For high-throughput applications in population genomics, we provide the open-source Nextflow pipeline and software TarGene which integrates seamlessly with modern high-performance and cloud computing platforms.
Humans↗
Genomic Screening for Infants and Reproductive Adults.
Recent progress in genomic sequencing, bioinformatics, cloud computation, and artificial intelligence is advancing a more mature understanding of the architecture of childhood genetic diseases. This knowledge and these technologies are enabling expanded genomic screening of infant and reproductive adult populations. With many new disease-modifying and curative therapies in development and approval processes, there exists unparalleled opportunity to identify, treat, and decrease the population burden of genetic disease and transform medical genetics. Broad implementation of genomic population screening, however, requires investments for overcoming remaining evidence gaps and operational challenges, and for delivery in a sustainable manner that is acceptable to parents, prospective parents, and physicians.
Journal Article↗
Computer simulation of ion clouds in a Penning trap.
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Journal Article↗
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↗
[Computer simulation for infrared spectra of pollution clouds with FTIS remote detection].
A computer model of radiometric scene simulation for simulated spectra for pollution clouds in complicated environment is proposed. The model is used to introduce the effects of an actual hazardous pollution clouds, such as (CH3)2CHO(CH3)FPO or (CLCH2CH2)2S, into exiting measured background spectra by passive Fourier transform infrared spectrometer (FTIS). The simulated results agree well with the experimental results.
Air Pollutants↗
Streamlining large-scale genomic data management: Insights from the UK Biobank whole-genome sequencing data.
Biobank-scale whole-genome sequencing (WGS) studies are increasingly pivotal in unraveling the genetic bases of diverse health outcomes. However, managing and analyzing these datasets' sheer volume and complexity presents significant challenges. We highlight the annotated genomic data structure (aGDS) format, substantially reducing the WGS data file size while enabling seamless integration of genomic and functional information for comprehensive WGS analyses. The aGDS format yielded 23 chromosome-specific files for the UK Biobank 500k WGS dataset, occupying only 1.10 tebibytes of storage. We develop the vcf2agds toolkit that streamlines the conversion of WGS data from VCF to aGDS format. Additionally, the STAARpipeline equipped with the aGDS files enabled scalable, comprehensive, and functionally informed WGS analysis, facilitating the detection of common and rare coding and noncoding phenotype-genotype associations. Overall, the vcf2agds toolkit and STAARpipeline provide a streamlined solution that facilitates efficient data management and analysis of biobank-scale WGS data across hundreds of thousands of samples.
Humans↗
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↗
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↗
A work in progress. Centralized network monitoring and management get a boost from the right software suite.
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Computer Communication Networks↗
Wake-field and fast head-tail instability caused by an electron cloud.
In positron and proton storage rings, electrons produced by photoemission, ionization, and secondary emission accumulate in the vacuum chamber during multibunch operation with close spacing. A positron or proton bunch passing through this "electron cloud" experiences a force similar to a short-range wake field. This effective wake field can cause a transverse-mode-coupling instability, if the electron-cloud density exceeds a threshold value. In this report, we compute the electron-cloud induced wake in a region without external magnetic field both analytically and via computer simulation, for parameters representing the low-energy positron ring of KEKB and the LHC proton beam in the CERN SPS. We study the linearity and time dependence of the wake function and its variation with the size of the electron cloud. Using a broadband resonator model for the electron-cloud wake field, we then evaluate theoretical expressions for the transverse-mode-coupling instability based on the linearized Vlasov equation, and for the instability threshold of fast transverse blow up including its dependence on chromaticity.
Journal Article↗
[Mesenteric lipomatosis. A rare disease often misdiagnosed as ascites].
A 53-year-old man, a known alcoholic, was admitted to hospital, because of abdominal swelling, with the admission diagnosis of ascites. Treated with diuretics a severe hypokalaemia developed with subileus and moderate clouding of consciousness. Computed tomography revealed the correct diagnosis of intraabdominal extraperitoneal (mesenteric, pelvic, retroperitoneal) soft-tissue lipomatosis.
Alcoholism↗
Light-scattering properties of plate and column ice crystals generated in a laboratory cold chamber.
Angular scattering properties of ice crystal particles generated in a laboratory cloud chamber are measured with a lightweight polar nephelometer with a diode laser beam. This cloud chamber produces distinct plate and hollow column ice crystal types for light-scattering experiments and provides a controlled test bed for comparison with results computed from theory. Ice clouds composed predominantly of plates and hollow columns generated noticeable 22 degrees and 46 degrees halo patterns, which are predicted from geometric ray-tracing calculations. With the measured ice crystal shape and size distribution, the angular scattering patterns computed from geometrical optics with a significant contribution by rough surfaces closely match those observed from the nephelometer.
Journal Article↗
CLOUDS, a protocol for deriving a molecular proton density via NMR.
We demonstrate the feasibility of computing realistic spatial proton distributions for proteins in solution from experimental NMR nuclear Overhauser effect data only and with minimal assignments. The method, CLOUDS, relies on precise and abundant interproton distance restraints calculated via a relaxation matrix analysis of sets of experimental nuclear Overhauser effect spectroscopy crosspeaks. The MIDGE protocol was adapted for this purpose. A gas of unassigned, unconnected H atoms is condensed into a structured proton distribution (cloud) via a molecular dynamics simulated-annealing scheme in which the internuclear distances and van der Waals repulsive terms are the only active restraints. Proton densities are generated by combining a large number of such clouds, each computed from a different trajectory. After filtering by reference to the cloud closest to the mean, a minimal dispersion proton density (foc) is identified. The latter affords a quasi-continuous hydrogen-only probability distribution that conveys immediate information on the protein surface topology (grooves, protrusions, potential binding site cavities, etc.), directly related to the molecular structure. Feasibility of the method was tested on NMR data measured on two globular protein domains of low regular secondary structure content, the col 2 domain of human matrix metalloproteinase-2 and the kringle 2 domain of human plasminogen, of 60 and 83 amino acid residues, respectively.
Humans↗
Pithos - a scalable and secure data container for FAIR-compliant research data management in life sciences.
Modern research techniques have led to exponential growth in the volume and complexity of scientific data. Consequently, managing these volumes securely and efficiently has become a major challenge. While all research domains face these challenges, life science research is particularly affected because current approaches often rely on a large set of different file formats, with metadata stored in separated databases or spreadsheets. This leads to fragmented datasets, orphaned data, and compromised research reproducibility. Traditional solutions also force researchers to choose between security and accessibility, with encrypted files preventing selective access and indexed formats lacking adequate security for sensitive data. These limitations are particularly problematic in large-scale genomic studies where researchers must decompress multi-gigabyte files to access specific regions, creating computational bottlenecks and inefficient network usage when working with cloud-stored datasets. We introduce Pithos, a next-generation file format specifically designed for scientific data management in distributed cloud environments. The format uses content-defined chunking to enable efficient deduplication across distributed storage systems, thereby reducing storage costs and bandwidth requirements. The append-only structure ensures data immutability and allows for incremental updates without compromising content. Benchmark results show that Pithos outperforms existing solutions in read and write performance, with comparable or improved storage efficiency.
Biological Science Disciplines↗
Optical modeling of extraoral defects.
In order to reduce the stress caused to patients by conventional methods of modeling using computed tomography (CT) or magnetic resonance imaging (MRI), an optical modeling process has been developed for extraoral defects and body areas. The selected body part is digitized using optical 3-coordinate measuring technology, providing an extensive data record. This is adapted for further use by equalizing the point clouds to obtain a Computer Aided Design (CAD) model, which is converted to a physical model by means of a stereolithographic process. With this technology, the patient's physical and psychological stress may be reduced. This article describes a technique for optical modeling of an ocular prosthesis.
Computer-Aided Design↗
Efficient vector radiative transfer calculations in vertically inhomogeneous cloudy atmospheres.
Accurate radiative transfer calculations in cloudy atmospheres are generally time consuming, limiting their practical use in satellite remote sensing applications. We present a model to efficiently calculate the radiative transfer of polarized light in atmospheres that contain homogeneous cloud layers. This model combines the Gauss-Seidel method, which is efficient for inhomogeneous cloudless atmospheres, with the doubling method, which is efficient for homogeneous cloud layers. Additionally to reduce the computational effort for radiative transfer calculations in absorption bands, the cloud reflection and transmission matrices are interpolated over the absorption and scattering optical thicknesses within the cloud layer. We demonstrate that the proposed radiative transfer model in combination with this interpolation technique is efficient for the simulation of satellite measurements for inhomogeneous atmospheres containing one homogeneous cloud layer. For example, the Scanning Imaging Absorption Spectrometer for Atmospheric Cartography (SCIAMACHY) measurements in the oxygen A band (758-773 nm) and the Hartley-Huggins ozone band (295-335 nm) with a spectral resolution of 0.4 nm can be simulated for these atmospheres within 1 min on a 2.8 GHz PC with an accuracy better than 0.1%.
Journal Article↗