De-risking transformative microscopy technologies for broad adoption.

This article focuses on measuring, describing, monitoring and publishing the quality and performance of grid resources. Life science communities can employ Service Level Agreements (SLAs) with their resource providers to ensure the delivery of services. For this, it is important for both the life science communities and their providers to understand and quantify the performance and service quality of different grid environments. However, measuring service quality in grid infrastructures utilizing different middle wares, as in the German Grid Initiative, is a complex problem. We describe the state of quality metrics which are currently used by the German life science communities MediGRID, Services@MediGRID and PneumoGrid. We also identify further quality metrics for defining and monitoring grid resource quality in D-Grid. It is important to publish and exchange the quality information by grid information systems, which are the entry points to grid services. Therefore, we also present how quality information can be handled by the GLUE v2.0 Schema, which is the upcoming standard data model used by grid information systems. For measuring and monitoring the quality metrics in multi-middleware environments two approaches are discussed. The first approach extracts quality information from an external benchmarking system and loads iit to the grid information systems. The second solution targets life science communities that do not utilize legacy benchmarking systems, but operate traditional monitoring systems, like Nagios.

Continually emerging biotechnologies and advancing techniques are increasing the world’s attention to the potential dual use of scientific research, and the possibility of significant risks to global health and security. It is imperative to establish a fundamental understanding in the life science community of the role scientists play in mitigating these risks and protecting national security. However, linking the life sciences and global security has not always been highly prioritized. Past surveys have shown a significant lack of biosecurity education and awareness in the life science community and has subsequently led to multiple plans, including policies, regulations, and awareness raising measures, to address this problem. Utilizing a review of the existing surveys and papers addressing the better integration of science and security, this paper proposes a way to create a true paradigm shift. By providing biosecurity education, as early as possible, to the next generation of scientists, it will be possible to change the way the life science community thinks about its active role in promoting and protecting security. Undergraduate life science course offerings at some of the top universities in the United States were surveyed. The results suggest there is a substantial void of biosecurity education offered to these young, future working scientists. It is vitally important that universities across the United States, and the rest of the world, develop programs and courses to fill this void, to build a foundational knowledge of biosecurity topics in undergraduate life scientists. This early education and awareness is essential to ensure the continued practice of responsible science that will help protect the global health security of the future.

Ensuring that cutting-edge science and technology are used solely for peaceful purposes is a challenge. One of the most urgent agendas facing current international society is how to address this challenge in the life sciences when there is a pervasive lack of awareness about dual-use issues in the life science community on a world-wide scale. To help mitigate this deficiency, we argue that education and awareness-raising among life scientists offer a strong foundation on which to build the responsible conduct in the life sciences. We therefore propose a comprehensive model to promote this education; starting with a background survey to highlight the current state of education about dualuse issues in life science degree courses in higher education, we follow with the development of education material and train-the-trainer programs, efforts are then recommended to influence the editors of science journals and the various funding bodies, with the final stage being the international sharing of emerging best practices in such education. We provide a rationale and current activities to illustrate each of the above agendas and show how nascent efforts have been made by individual institutions from the bottom-up and by governments and international organizations from the top-down.

abstractThis article links up with the debate in economic geography on “local buzz” and “global pipelines” as two distinct forms of interactive knowledge creation among firms and related actors and argues for a rethinking of the way social scientists should approach interactive knowledge creation. It highlights the importance of combining the insights from studies of clusters and innovation systems with an activity-oriented approach in which more attention is paid to the specific characteristics of the innovation processes and the conditions underpinning their organization. To illustrate the applicability and added value of such an alternative approach, the notion of embeddedness is linked with some basic ideas adopted from the literature on knowledge communities. The framework is then applied to a study of innovation activities conducted by firms and academic research groups working with biotechnology-related applications in the Swedish part of the Medicon Valley life science region. The findings reveal that local buzz is largely absent in these types of activities. Most interactive knowledge creation, which appears to be spontaneous and unregulated, is, on closer examination, found safely embedded in globally configured professional knowledge communities and attainable only by those who qualify.

The article aims to introduce an integrated web-based interactive data platform for molecular dynamic simulations using the datasets generated by different life science communities from Armenia. The suggested platform, consisting of data repository and workflow management services, is vital for current and future scientific discoveries in the life science domain. We focus on interactive data visualization workflow service as a key to perform more in-depth analyzes of research data outputs, helping to understand the problems efficiently and to consolidate the data into one collective illustration platform. The functionalities of the integrated data platform is presented as an advanced integrated environment to capture, analyze, process and visualize the scientific data.

Web services have gained a momentum as a means for packaging existing data and computational resources in a form that is amenable for use and composition by third party applications. They provide a well defined programming interface to integrate tools into applications over networks. Software applications written in various programming languages and running on various platforms can use web services to exchange data over the Internet. The life science community is certainly among the first adopters of web services.

International initiatives such as the Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) are collecting multiple datasets at different genome-scales with the aim of identifying novel cancer biomarkers and predicting survival of patients. To analyze such data, several statistical methods have been applied, among them Cox regression models. Although these models provide a good statistical framework to analyze omic data, there is still a lack of studies that illustrate advantages and drawbacks in integrating biological information and selecting groups of biomarkers. In fact, classical Cox regression algorithms focus on the selection of a single biomarker, without taking into account the strong correlation between genes. Even though network-based Cox regression algorithms overcome such drawbacks, such network-based approaches are less widely used within the life science community. In this article, we aim to provide a clear methodological framework on the use of such approaches in order to turn cancer research results into clinical applications. Therefore, we first discuss the rationale and the practical usage of three recently proposed network-based Cox regression algorithms (i.e., Net-Cox, AdaLnet, and fastcox). Then, we show how to combine existing biological knowledge and available data with such algorithms to identify networks of cancer biomarkers and to estimate survival of patients. Finally, we describe in detail a new permutation-based approach to better validate the significance of the selection in terms of cancer gene signatures and pathway/networks identification. We illustrate the proposed methodology by means of both simulations and real case studies. Overall, the aim of our work is two-fold. Firstly, to show how network-based Cox regression models can be used to integrate biological knowledge (e.g., multi-omics data) for the analysis of survival data. Secondly, to provide a clear methodological and computational approach for investigating cancers regulatory networks.

Data resources are essential for the long-term preservation of scientific data and the reproducibility of science. The SIB Swiss Institute of Bioinformatics provides the life science community with a portfolio of openly accessible, high-quality databases and software platforms, which vary from expert-curated knowledgebases, such as UniProtKB/Swiss-Prot (part of the UniProt consortium) and STRING, to online platforms such as SWISS-MODEL and SwissDrugDesign. SIB’s mission is to ensure that these resources are available in the long term, as long as their return on investment and their scientific impact are high. To this end, SIB provides its resources, in addition to stable financial support, with a range of high-quality, innovative services that are, to our knowledge, unique in the field. Through this first-class management framework with central services, such as user-centric consulting activities, legal support, open-science guidance, knowledge sharing and training efforts, SIB supports the promotion of excellence in resource development and operation. This review presents the ecosystem of data resources at SIB; the process used for the identification, evaluation and development of resources; and the support activities that SIB provides. A set of indicators has been put in place to select the resources and establish quality standards, reflecting their multifaceted nature and complexity. Through this paper, the reader will discover how SIB’s leading tools and databases are fostered by the institute, leading them to be best-in-class resources able to tackle the burning matters that society faces from disease outbreaks and cancer to biodiversity and open science.

We review the history, design principles, development, associated theoretical frameworks, and assessment of the group of curricula known as Introductory Physics for the Life Sciences (IPLS)—introductory physics courses designed for life science majors and pre-health students. IPLS courses were introduced in response to calls from the life science and medical community for improved physical sciences training for undergraduates in their fields, and the primary goal of such courses is to make meaningful connections between physics and the life sciences. Although much more assessment is needed, the work that has been done documents success toward the core goals of (1) helping students value physics as a meaningful component of understanding the life sciences, (2) developing students' abilities to use physics to analyze and model biological phenomena, and (3) developing students' interdisciplinary identity and sense of competence with physics. We also identify future work needed, ranging from further evaluation of student work and motivation to the development of appropriate assessments for topics not traditionally covered in the introductory course. We describe how this work contributes to the broader DBER enterprise, such as in the development of tools to evaluate interdisciplinary learning.

This paper raises the problematic of devising evidence-based public policy for high-tech, knowledge-based communities which are critical to national innovation and competitiveness. By applying an established framework of policy analysis to a specific life-science and biotechnology community, and by conducting an inclusive, systemic, and grounded analysis of the community, past and present policy support for the community are critically assessed and future avenues examined. Although community-level policy can, at times, be generic, an attitude embracing differentiation and contingency that reflects the specificities of community and subcommunity (population) organising may be more appropriate.

Increasing the industrial uptake of additive manufacturing processes: A training framework

Ultra-confined optical fields are of great importance in fundamental optics and optical technologies. The extreme field confinement in ultra-small nanostructures presents significant challenges in direct near-field characterization. Conventional scanning near-field optical microscopy encounters difficulties in characterizing sub-10-nm confined light fields due to significant disturbances of the optical field caused by the probe. Here, by employing a high spatial-resolved photoemission electron microscopy (PEEM), we succeeded in imaging the ultra-confined near fields of a nanoslit mode in a coupled nanowire pair (CNP) with weak disturbance for the first time and demonstrating a quasi-three-dimensional field distribution of the nanoslit mode. We also show that a PEEM image can identify fabrication defects that are influential to the confined field but are imperceptible to many other means. These results open an opportunity for weak-disturbance characterization of ultra-confined optical near fields, which is an essential step toward future optical devices or technology relying on ultra-confined light.

For over 100 years white-light cystoscopy has remained the gold-standard technique for the detection of bladder cancer (BCa). Some limitations in the detection of flat lesions (CIS), the differentiation between inflammation and malignancy, the inaccurate determination of the tumor margin status as well as the tumor depth, have led to a variety of technological improvements. The aim of this review is to evaluate the impact of these improvements in the diagnosis of BCa and their effectiveness in clinical practice. A systematic literature search was conducted according to the PRISMA statement to identify studies reporting on imaging modalities in the diagnosis of NMIBC between 2000 and 2017. A two-stage selection process was utilized to determine eligible studies. A total of 74 studies were considered for final analysis. Optical imaging technologies have emerged as an adjunct to white-light cystoscopy and can be classified according to their scope as macroscopic, microscopic and molecular. Macroscopic techniques including photodynamic diagnosis (PDD), narrow-band imaging (NBI) and the Storz Professional Image Enhancement System (IMAGE1 S, formerly known as SPIES) are similar to white-light cystoscopy, but are superior in the detection of bladder tumors by means of contrast enhancement. Especially the detection rate of very mute lesions in the bladder mucosa (CIS) could be significantly increased by the use of these methods. Microscopic imaging techniques like confocal laser endomicroscopy and optical coherence tomography permit a real-time high-resolution assessment of the bladder mucosa at a cellular and sub-cellular level with spatial resolutions similar to histology, enabling the surgeon to perform an 'optical biopsy'. Molecular techniques are based on the combination of optical imaging technologies with fluorescence labeling of cancer-specific molecular agents like antibodies. This labeling is intended to favor an optical distinction between benign and malignant tissue. Optical improvements of the standard white-light cystoscopy have proven their benefit in the detection of BCa and have found their way into clinical practice. Especially the combination of macroscopic and microscopic techniques may improve diagnostic accuracy. Nevertheless, HAL-PDD guided cystoscopy is the only approach approved for routine use in the diagnosis of BCa by most urological associations in the EU and USA to date.

A FAIRification roadmap for ELIXIR Software Management Plans

As a typical microscopic imaging technology, the emergence of the microscope has accelerated the pace of human exploration of the micro world. With the development of science and technology, microscopes have developed from the optical microscopes at the time of their invention to electron microscopes and even atomic force microscopes. The resolution has steadily improved, allowing humans to expand the field of research from the initial animal and plant tissues to microorganisms such as bacteria, and even down to the nanolevel. The microscope is now widely used in life science, material science, geological research, and other fields. It can be said that the development of microscopes also promotes the development of micro- and nanotechnology. It is foreseeable that microscopes will play a significant part in the exploration of the microworld for a long time to come. The development of microscope technology is the focus of this study, which summarized the properties of numerous microscopes and discussed their applications in micro and nanotechnology. At the same time, the application of microscopic imaging technology in micro- and nanofields was investigated based on the properties of various microscopes.