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"Roadmap"
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Machine Learning from Theory to Algorithms: An Overview
2018
The current SMAC (Social, Mobile, Analytic, Cloud) technology trend paves the way to a future in which intelligent machines, networked processes and big data are brought together. This virtual world has generated vast amount of data which is accelerating the adoption of machine learning solutions & practices. Machine Learning enables computers to imitate and adapt human-like behaviour. Using machine learning, each interaction, each action performed, becomes something the system can learn and use as experience for the next time. This work is an overview of this data analytics method which enables computers to learn and do what comes naturally to humans, i.e. learn from experience. It includes the preliminaries of machine learning, the definition, nomenclature and applications' describing it's what, how and why. The technology roadmap of machine learning is discussed to understand and verify its potential as a market & industry practice. The primary intent of this work is to give insight into why machine learning is the future.
Journal Article
Peripheral and central immune system crosstalk in Alzheimer disease — a research prospectus
2021
Dysregulation of the immune system is a cardinal feature of Alzheimer disease (AD), and a considerable body of evidence indicates pathological alterations in central and peripheral immune responses that change over time. Considering AD as a systemic immune process raises important questions about how communication between the peripheral and central compartments occurs and whether this crosstalk represents a therapeutic target. We established a whitepaper workgroup to delineate the current status of the field and to outline a research prospectus for advancing our understanding of peripheral–central immune crosstalk in AD. To guide the prospectus, we begin with an overview of seminal clinical observations that suggest a role for peripheral immune dysregulation and peripheral–central immune communication in AD, followed by formative animal data that provide insights into possible mechanisms for these clinical findings. We then present a roadmap that defines important next steps needed to overcome conceptual and methodological challenges, opportunities for future interdisciplinary research, and suggestions for translating promising mechanistic studies into therapeutic interventions.Evidence is accumulating that both central and peripheral immune responses are dysregulated in Alzheimer disease (AD). This roadmap reviews the current status of this research and provides a new research prospectus to advance our understanding of peripheral–central immune crosstalk in AD.
Journal Article
Beyond the physics and demonstration of ignition
by
Dean, Stephen O.
in
Discussion
2020
Fusion holds the promise of providing growing world energy demand with a carbon-free power source having a universally available fuel source and attractive safety and environmental characteristics. A significant global effort has been underway for over 50 years aimed at the achievement of fusion by inertial confinement. The effort to date has necessarily emphasized understanding the physics of compressing and heating a small amount of fusion fuel to the high densities and temperatures required for ignition and energy gain. Though steady progress has been and is still being made to achieve the required physics understanding and energy gain, those goals have not yet quite been met. It is timely to put progress toward fusion power by inertial confinement into perspective by developing an updated roadmap. Preparing a roadmap from present achievements to the ultimate goal of commercial fusion power requires formally identifying and implementing complementary efforts on a number of fronts. These include the choice, development and demonstration of high repetition rate compression drivers (e.g. lasers) to succeed present day single-pulse sources; design, fabrication and testing of high gain targets (gain of order 100); development of mass production, cost-effective, target fabrication and delivery systems capable of inserting targets into the reaction chamber several times per second, and demonstrating ability to accurately hit and efficiently compress those targets to reliably produce the required fusion yields; design and demonstration of reaction chambers capable of handling energy yields and target debris clearing at the levels required for achieving high power plant reliability with low induced radioactivity. A robust ongoing effort on competitive power plant conceptual design is necessary to guide the implementation of a roadmap, including the timing and level of effort on the ‘beyond ignition’ demonstrations.
This article is part of a discussion meeting issue ‘Prospects for high gain inertial fusion energy (part 1)’.
Journal Article
A framework for understanding the functions of biomolecular condensates across scales
by
Peeples, William B
,
Rosen, Michael K
,
Lyon, Andrew S
in
Binding sites
,
Biological activity
,
Biology
2021
Biomolecular condensates are found throughout eukaryotic cells, including in the nucleus, in the cytoplasm and on membranes. They are also implicated in a wide range of cellular functions, organizing molecules that act in processes ranging from RNA metabolism to signalling to gene regulation. Early work in the field focused on identifying condensates and understanding how their physical properties and regulation arise from molecular constituents. Recent years have brought a focus on understanding condensate functions. Studies have revealed functions that span different length scales: from molecular (modulating the rates of chemical reactions) to mesoscale (organizing large structures within cells) to cellular (facilitating localization of cellular materials and homeostatic responses). In this Roadmap, we discuss representative examples of biochemical and cellular functions of biomolecular condensates from the recent literature and organize these functions into a series of non-exclusive classes across the different length scales. We conclude with a discussion of areas of current interest and challenges in the field, and thoughts about how progress may be made to further our understanding of the widespread roles of condensates in cell biology.Biomolecular condensates are membraneless molecular assemblies formed via liquid–liquid phase separation. They have a plethora of roles, ranging from controlling biochemical reactions to regulating cell organization and cell function. This article provides a framework for the study of condensate functions across these cellular length scales, offering to bring new understanding of biological processes.
Journal Article
Towards the sustainable discovery and development of new antibiotics
by
Miethke, Marcus
,
Karlén, Anders
,
Winterhalter, Mathias
in
631/154/2426
,
692/700/565/1436
,
Analytical Chemistry
2021
An ever-increasing demand for novel antimicrobials to treat life-threatening infections caused by the global spread of multidrug-resistant bacterial pathogens stands in stark contrast to the current level of investment in their development, particularly in the fields of natural-product-derived and synthetic small molecules. New agents displaying innovative chemistry and modes of action are desperately needed worldwide to tackle the public health menace posed by antimicrobial resistance. Here, our consortium presents a strategic blueprint to substantially improve our ability to discover and develop new antibiotics. We propose both short-term and long-term solutions to overcome the most urgent limitations in the various sectors of research and funding, aiming to bridge the gap between academic, industrial and political stakeholders, and to unite interdisciplinary expertise in order to efficiently fuel the translational pipeline for the benefit of future generations.
Antimicrobial resistance is an increasing threat to public health and encouraging the development of new antimicrobials is one of the most important ways to address the problem. This Roadmap article aims to bring together industrial, academic and political partners, and proposes both short-term and long-term solutions to this challenge.
Journal Article
TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages version 2; peer review: 1 approved, 2 approved with reservations
by
D'Angelo, Fulvio
,
Colaprico, Antonio
,
Silva, Tiago C
in
Bioinformatics
,
Brain cancer
,
Genomics
2016
Biotechnological advances in sequencing have led to an explosion of publicly available data via large international consortia such as
The Cancer Genome Atlas (TCGA),
The Encyclopedia of DNA Elements (ENCODE), and
The NIH Roadmap Epigenomics Mapping Consortium (Roadmap). These projects have provided unprecedented opportunities to interrogate the epigenome of cultured cancer cell lines as well as normal and tumor tissues with high genomic resolution. The
Bioconductor project offers more than 1,000 open-source software and statistical packages to analyze high-throughput genomic data. However, most packages are designed for specific data types (e.g. expression, epigenetics, genomics) and there is no one comprehensive tool that provides a complete integrative analysis of the resources and data provided by all three public projects. A need to create an integration of these different analyses was recently proposed. In this workflow, we provide a series of biologically focused integrative analyses of different molecular data. We describe how to download, process and prepare TCGA data and by harnessing several key Bioconductor packages, we describe how to extract biologically meaningful genomic and epigenomic data. Using Roadmap and ENCODE data, we provide a work plan to identify biologically relevant functional epigenomic elements associated with cancer. To illustrate our workflow, we analyzed two types of brain tumors: low-grade glioma (LGG) versus high-grade glioma (glioblastoma multiform or GBM). This workflow introduces the following Bioconductor packages:
AnnotationHub,
ChIPSeeker,
ComplexHeatmap,
pathview,
ELMER,
GAIA,
MINET,
RTCGAToolbox,
TCGAbiolinks.
Journal Article
Plant Growth-Promoting Rhizobacteria: Context, Mechanisms of Action, and Roadmap to Commercialization of Biostimulants for Sustainable Agriculture
by
Ricci, Emily
,
Ilangumaran, Gayathri
,
Subramanian, Sowmyalakshmi
in
20th century
,
21st century
,
Agriculture
2018
Microbes of the phytomicrobiome are associated with every plant tissue and, in combination with the plant form the holobiont. Plants regulate the composition and activity of their associated bacterial community carefully. These microbes provide a wide range of services and benefits to the plant; in return, the plant provides the microbial community with reduced carbon and other metabolites. Soils are generally a moist environment, rich in reduced carbon which supports extensive soil microbial communities. The rhizomicrobiome is of great importance to agriculture owing to the rich diversity of root exudates and plant cell debris that attract diverse and unique patterns of microbial colonization. Microbes of the rhizomicrobiome play key roles in nutrient acquisition and assimilation, improved soil texture, secreting, and modulating extracellular molecules such as hormones, secondary metabolites, antibiotics, and various signal compounds, all leading to enhancement of plant growth. The microbes and compounds they secrete constitute valuable biostimulants and play pivotal roles in modulating plant stress responses. Research has demonstrated that inoculating plants with plant-growth promoting rhizobacteria (PGPR) or treating plants with microbe-to-plant signal compounds can be an effective strategy to stimulate crop growth. Furthermore, these strategies can improve crop tolerance for the abiotic stresses (e.g., drought, heat, and salinity) likely to become more frequent as climate change conditions continue to develop. This discovery has resulted in multifunctional PGPR-based formulations for commercial agriculture, to minimize the use of synthetic fertilizers and agrochemicals. This review is an update about the role of PGPR in agriculture, from their collection to commercialization as low-cost commercial agricultural inputs. First, we introduce the concept and role of the phytomicrobiome and the agricultural context underlying food security in the 21st century. Next, mechanisms of plant growth promotion by PGPR are discussed, including signal exchange between plant roots and PGPR and how these relationships modulate plant abiotic stress responses via induced systemic resistance. On the application side, strategies are discussed to improve rhizosphere colonization by PGPR inoculants. The final sections of the paper describe the applications of PGPR in 21st century agriculture and the roadmap to commercialization of a PGPR-based technology.
Journal Article
The potential and global outlook of integrated photonics for quantum technologies
by
Figueroa, Eden
,
Hannes, Hübel
,
Sciarrino, Fabio
in
Communication
,
Cryptography
,
Integrated circuits
2022
Integrated quantum photonics uses classical integrated photonic technologies and devices for quantum applications. As in classical photonics, chip-scale integration has become critical for scaling up and translating laboratory demonstrators to real-life technologies. Integrated quantum photonics efforts are centred around the development of quantum photonic integrated circuits, which can be monolithically, hybrid or heterogeneously integrated. In this Roadmap, we argue, through specific examples, for the value that integrated photonics brings to quantum technologies and discuss what applications may become possible in the future by overcoming the current roadblocks. We provide an overview of the research landscape and discuss the innovation and market potential. Our aim is to stimulate further research by outlining not only the scientific challenges of materials, devices and components associated with integrated photonics for quantum technologies but also those related to the development of the necessary manufacturing infrastructure and supply chains for delivering these technologies to the market.Photonics is one of the key platforms for emerging quantum technologies, but its full potential can only be harnessed by exploiting miniaturization via on-chip integration. This Roadmap charts new directions and discusses the challenges associated with the hybrid integration of a variety of materials, devices and components.
Journal Article
Cancer drug-tolerant persister cells: from biological questions to clinical opportunities
by
Sancho, Elena
,
Oren, Yaara
,
Mariella, Elisa
in
631/67/1059/2326
,
631/67/2329
,
Antibiotic resistance
2024
The emergence of drug resistance is the most substantial challenge to the effectiveness of anticancer therapies. Orthogonal approaches have revealed that a subset of cells, known as drug-tolerant ‘persister’ (DTP) cells, have a prominent role in drug resistance. Although long recognized in bacterial populations which have acquired resistance to antibiotics, the presence of DTPs in various cancer types has come to light only in the past two decades, yet several aspects of their biology remain enigmatic. Here, we delve into the biological characteristics of DTPs and explore potential strategies for tracking and targeting them. Recent findings suggest that DTPs exhibit remarkable plasticity, being capable of transitioning between different cellular states, resulting in distinct DTP phenotypes within a single tumour. However, defining the biological features of DTPs has been challenging, partly due to the complex interplay between clonal dynamics and tissue-specific factors influencing their phenotype. Moreover, the interactions between DTPs and the tumour microenvironment, including their potential to evade immune surveillance, remain to be discovered. Finally, the mechanisms underlying DTP-derived drug resistance and their correlation with clinical outcomes remain poorly understood. This Roadmap aims to provide a comprehensive overview of the field of DTPs, encompassing past achievements and current endeavours in elucidating their biology. We also discuss the prospect of future advancements in technologies in helping to unveil the features of DTPs and propose novel therapeutic strategies that could lead to their eradication.
Resistance to therapy remains the biggest challenge to achieving cures in patients with cancer. In this Roadmap, Russo et al. overview the field of cancer drug-tolerant persister cells providing paths to advance our understanding of their biology with innovative technologies and recommend strategies to therapeutically target them to ensure that more prolonged responses are achieved in patients with cancer.
Journal Article
Microbial Electrosynthesis: Where Do We Go from Here?
2021
The valorization of CO2 to valuable products via microbial electrosynthesis (MES) is a technology transcending the disciplines of microbiology, (electro)chemistry, and engineering, bringing opportunities and challenges. As the field looks to the future, further emphasis is expected to be placed on engineering efficient reactors for biocatalysts, to thrive and overcome factors which may be limiting performance. Meanwhile, ample opportunities exist to take the lessons learned in traditional and adjacent electrochemical fields to shortcut learning curves. As the technology transitions into the next decade, research into robust and adaptable biocatalysts will then be necessary as reactors shape into larger and more efficient configurations, as well as presenting more extreme temperature, salinity, and pressure conditions.
In the past decade, research in the field of microbial electrosynthesis (MES) has been driven forward by the development of cathode materials, electroactive bacteria or microbiome enrichment, and productivity improvements.As the close of three complete funding cycles for the field is reached, recent reviews have sought to refocus emphasis to the eventual application of MES; a means of measurably reducing CO2 waste via the formation of valuable products.Using present knowledge of bioelectrochemistry, and by learning lessons from adjacent fields, it becomes apparent that the simplest gains in performance are likely to come from advancements in the reactor rather than the biocatalysts. Varying the reactor and operating conditions of the system, however, require adapting these biocatalysts.
Journal Article