The Cancer Genomics Cloud: Collaborative, Reproducible, and Democratized—A New Paradigm in Large-Scale Computational Research

The aim of this paper is to discuss the major technological changes related to the implementation of large-scale cogeneration and biofuel production in the sugar and alcohol industry. The reduction of the process steam consumption, implementation of new alternatives in driving mills, the widespread practice of high steam parameters use in cogeneration facilities, the insertion of new technologies for biofuels production (hydrolysis and gasification), the energy conversion of sugarcane trash and vinasse, animal feed production, process integration and implementation of the biorefinery concept are considered. Another new paradigm consists in the wide spreading of sustainability studies of products and processes using the Life Cycle Assessment (LCA) and the implementation of sustainability indexes. Every approach to this issue has as an objective to increase the economic efficiency and the possibilities of the sugarcane as a main source of two basic raw materials: fibres and sugar. The paper briefly presents the concepts, indicators, state-of-the-art and perspectives of each of the referred issues.

Download Full-text

Findings from the Section on Bioinformatics and Translational Informatics

Yearbook of Medical Informatics ◽

10.15265/iy-2016-050 ◽

2017 ◽

Vol 26 (01) ◽

pp. 188-192 ◽

Cited By ~ 1

Author(s):

H. Dauchel ◽

T. Lecroq

Keyword(s):

Intelligent Systems ◽

Large Scale ◽

Cancer Genomics ◽

Clinical Care ◽

Evaluation Process ◽

Omics Data ◽

Health Domain ◽

Medical Genomics ◽

Research Activities ◽

Translational Informatics

Summary Objective: To summarize excellent current research and propose a selection of best papers published in 2016 in the field of Bioinformatics and Translational Informatics with applications in the health domain and clinical care. Methods: We provide a synopsis of the articles selected for the IMIA Yearbook 2017, from which we attempt to derive a synthetic overview of current and future activities in the field. As in 2016, a first step of selection was performed by querying MEDLINE with a list of MeSH descriptors completed by a list of terms adapted to the section coverage. Each section editor evaluated separately the set of 951 articles returned and evaluation results were merged for retaining 15 candidate best papers for peer-review. Results: The selection and evaluation process of papers published in the Bioinformatics and Translational Informatics field yielded four excellent articles focusing this year on the secondary use and massive integration of multi-omics data for cancer genomics and non-cancer complex diseases. Papers present methods to study the functional impact of genetic variations, either at the level of the transcription or at the levels of pathway and network. Conclusions: Current research activities in Bioinformatics and Translational Informatics with applications in the health domain continue to explore new algorithms and statistical models to manage, integrate, and interpret large-scale genomic datasets. As addressed by some of the selected papers, future trends would include the question of the international collaborative sharing of clinical and omics data, and the implementation of intelligent systems to enhance routine medical genomics.

Download Full-text

Cancer Genomics: Large-Scale Projects Translate into Therapeutic Advances

PLoS Medicine ◽

10.1371/journal.pmed.1002209 ◽

2016 ◽

Vol 13 (12) ◽

pp. e1002209 ◽

Cited By ~ 1

Author(s):

Elaine R. Mardis ◽

Marc Ladanyi

Keyword(s):

Large Scale ◽

Cancer Genomics

Download Full-text

OncoThreads: Visualization of Large Scale Longitudinal Cancer Molecular Data

10.31219/osf.io/b3n4u ◽

2021 ◽

Author(s):

Theresa A Harbig ◽

Sabrina Nusrat ◽

Tali Mazor ◽

Qianwen Wang ◽

Alexander Thomson ◽

...

Keyword(s):

Longitudinal Data ◽

Large Scale ◽

Cancer Genomics ◽

Temporal Patterns ◽

Molecular Data ◽

Liquid Biopsies ◽

Sequencing Technologies ◽

Molecular Features ◽

Wide Range ◽

The Impact

Molecular profiling of patient tumors and liquid biopsies over time with next-generation sequencing technologies and new immuno-profile assays are becoming part of standard research and clinical practice. With the wealth of new longitudinal data, there is a critical need for visualizations for cancer researchers to explore and interpret temporal patterns not just in a single patient but across cohorts. To address this need we developed OncoThreads, a tool for the visualization of longitudinal clinical and cancer genomics and other molecular data in patient cohorts. The tool visualizes patient cohorts as temporal heatmaps and Sankey diagrams that support the interactive exploration and ranking of a wide range of clinical and molecular features. This allows analysts to discover temporal patterns in longitudinal data, such as the impact of mutations on response to a treatment, e.g. emergence of resistant clones. We demonstrate the functionality of OncoThreads using a cohort of 23 glioma patients sampled at 2-4 timepoints. OncoThreads is freely available at http://oncothreads.gehlenborglab.org and implemented in Javascript using the cBioPortal web API as a backend.

Download Full-text

Impacts of Large-Scale NGSO Satellites: RFI and A New Paradigm for Satellite Communications and Radio Astronomy Systems

IEEE Transactions on Communications ◽

10.1109/tcomm.2019.2928537 ◽

2019 ◽

Vol 67 (11) ◽

pp. 7840-7855 ◽

Cited By ~ 1

Author(s):

Yucheng Dai ◽

Dong Han ◽

Hlaing Minn

Keyword(s):

Radio Astronomy ◽

Large Scale ◽

Satellite Communications ◽

New Paradigm

Download Full-text

Antifibrotic Potential of MiR-335-3p in Hereditary Gingival Fibromatosis

Journal of Dental Research ◽

10.1177/0022034519863300 ◽

2019 ◽

Vol 98 (10) ◽

pp. 1140-1149 ◽

Cited By ~ 1

Author(s):

Q. Gao ◽

K. Yang ◽

D. Chen ◽

Y. Song ◽

W. Qiao ◽

...

Keyword(s):

Large Scale ◽

Target Genes ◽

Transforming Growth Factor ◽

Target Prediction ◽

Transforming Growth Factor Β ◽

Human Gingival Fibroblasts ◽

High Recurrence Rate ◽

Gingival Fibroblasts ◽

New Paradigm ◽

Gingival Fibromatosis

Hereditary gingival fibromatosis (HGF) is a highly genetically heterogeneous disease, and current therapeutic method is limited to surgical resection with a high recurrence rate. MicroRNAs (miRNAs) are able to fine-tune large-scale target genes. Here we established a simple but effective computational strategy based on available miRNA target prediction algorithms to pinpoint the most potent miRNA that could negatively regulate a group of functional genes. Based on this rationale, miR-335-3p was top ranked by putatively targeting 85 verified profibrotic genes and 79 upregulated genes in HGF patients. Experimentally, downregulation of miR-355-3p was demonstrated in HGF-derived gingival fibroblasts as well as in transforming growth factor β–stimulated normal human gingival fibroblasts (NHGFs) compared to normal control. Ectopic miR-335-3p attenuated, whereas knockdown of miR-335-3p promoted, the fibrogenic activity of human gingival fibroblasts. Mechanically, miR-335-3p directly targeted SOS1, SMAD2/3, and CTNNB1 by canonical and noncanonical base paring. In particular, different portfolios of fibrotic markers were suppressed by silencing SOS1, SMAD2/3, or CTNNB1, respectively. Thus, our study first proposes a novel miRNA screening approach targeting a functionally related gene set and identifies miR-335-3p as a novel target for HGF treatment. Mechanically, miR-335-3p suppresses the fibrogenic activity of human gingival fibroblasts by repressing multiple core molecules in profibrotic networks. Our strategy provides a new paradigm in the treatment for HGF as well as other diseases.

Download Full-text

Towards learning line descriptors from patches: a new paradigm and large-scale dataset

International Journal of Machine Learning and Cybernetics ◽

10.1007/s13042-020-01207-2 ◽

2020 ◽

Author(s):

Hongmin Liu ◽

Yujie Liu ◽

Miaomiao Fu ◽

Yuhui Wei ◽

Zhanqiang Huo ◽

...

Keyword(s):

Large Scale ◽

New Paradigm ◽

Large Scale Dataset

Download Full-text

Maximum Closeness Centrality k-Clubs: A Study of Dock-Less Bike Sharing

Journal of Advanced Transportation ◽

10.1155/2020/1275851 ◽

2020 ◽

Vol 2020 ◽

pp. 1-16

Author(s):

Ali Rahim Taleqani ◽

Chrysafis Vogiatzis ◽

Jill Hough

Keyword(s):

Computational Complexity ◽

Large Scale ◽

Cost Benefit Analysis ◽

Cost Benefit ◽

Closeness Centrality ◽

Computational Time ◽

Greedy Heuristic ◽

New Paradigm ◽

Coordination Costs ◽

Bike Sharing

In this work, we investigate a new paradigm for dock-less bike sharing. Recently, it has become essential to accommodate connected and free-floating bicycles in modern bike-sharing operations. This change comes with an increase in the coordination cost, as bicycles are no longer checked in and out from bike-sharing stations that are fully equipped to handle the volume of requests; instead, bicycles can be checked in and out from virtually anywhere. In this paper, we propose a new framework for combining traditional bike stations with locations that can serve as free-floating bike-sharing stations. The framework we propose here focuses on identifying highly centralized k-clubs (i.e., connected subgraphs of restricted diameter). The restricted diameter reduces coordination costs as dock-less bicycles can only be found in specific locations. In addition, we use closeness centrality as this metric allows for quick access to dock-less bike sharing while, at the same time, optimizing the reach of service to bikers/customers. For the proposed problem, we first derive its computational complexity and show that it is NP-hard (by reduction from the 3-SATISFIABILITY problem), and then provide an integer programming formulation. Due to its computational complexity, the problem cannot be solved exactly in a large-scale setting, as is such of an urban area. Hence, we provide a greedy heuristic approach that is shown to run in reasonable computational time. We also provide the presentation and analysis of a case study in two cities of the state of North Dakota: Casselton and Fargo. Our work concludes with the cost-benefit analysis of both models (docked vs. dockless) to suggest the potential advantages of the proposed model.

Download Full-text

Stroke Care Services in Africa: A Systematic Review

Journal of Stroke Medicine ◽

10.1177/2516608518775233 ◽

2018 ◽

Vol 1 (1) ◽

pp. 55-64 ◽

Cited By ~ 4

Author(s):

Rufus O. Akinyemi ◽

Olaleye A. Adeniji

Keyword(s):

Large Scale ◽

Systems Of Care ◽

Care Delivery ◽

Stroke Care ◽

Developed Countries ◽

High Morbidity ◽

New Paradigm ◽

African Countries ◽

Care Services ◽

Stroke Services

Background: Stroke is the second leading cause of death and adult-onset disability globally. Although its incidence is reducing in developed countries, low- and middle-income countries, especially African countries, are witnessing an increase in cases of stroke, leading to high morbidity and mortality. Evidently, a new paradigm is needed on the continent to tackle this growing burden of stroke in its preventative and treatment aspects. Aims and Objectives: The aim of this study was to determine the scope of stroke care services, where they exist, and their relationship with currently existing health systems. Methods: A detailed literature search was undertaken referring to PubMed and Google Scholar for articles from January 1960 to March 2018, using a range of search terms. Of 93 publications, 45 papers were shortlisted, and 21 reviewed articles on existing stroke services were included. Results: The literature on models of stroke services in Africa is sparse. We identified focused systems of care delivery in the hyperacute, acute, and rehabilitative phases of stroke in a few African countries. There is a continent-wide paucity of data on the organization of prehospital stroke services. Only 3 African countries (South Africa, Egypt, and Morocco) reported experiences on thrombolysis. Also, the uptake of dedicated stroke units appears limited across the continent. Encouragingly, there are large-scale secondary prevention models on the continent, mostly within the context of experimental research projects, albeit with promising results. We found only 1 article on the interventional aspects of stroke care in our review, and this was a single-center report. Conclusions: The literature on the organization of stroke services is sparse in Africa. Dedicated action at policy, population, community, and hospital-based levels is urgently needed toward the organization of stroke services to tame the burgeoning burden of stroke on the African continent.

Download Full-text