Posted on August 26, 2019
By Shawn Douglas
Journal articles
In this brief article by Greene
et al. of the National Institute of Standards and Technology (NIST), details of the organization's attempt to open access to it scientific data infrastructure are provided. After introducing the details of the type of data held at NIST, as well as the U.S. governments "open access to research" (OAR) initiative, the authors describe the technological architecture that went towards making NIST's data more open. They describe the OAR application workflow all the way to the end, where efforts to "enable data interoperability as much as possible in order to maximize the usability of NIST data" were put in place. The authors conclude that their system not only meets OAR requirements, making basic data access a breeze, but it also "will facilitate the use of AI and machine learning applications and help solve many complexities in mining data-rich resources."
Posted on August 19, 2019
By Shawn Douglas
Journal articles
In this 2019 paper by Baratta
et al., published in
Frontiers in Pharmacology, the authors examine a variety of different procedures for preparing decoctions and oil-based extracts using the
Cannabis plant. Using the different formulations as a base, they wanted to determine the efficacy of the various "standard operating procedures for the preparation and optimization of
Cannabis-based galenic formulations." After discussing the materials and methods, and reviewing the results, the authors discussed the ramifications of their research, in particular in contrast to what the Italian government recommends procedure-wise. They concluded that their "β-4" method of oil preparation yielded "significantly higher [recovered THC and CBD] compared to those with water-based extraction (decoctions) or other current oil-based extraction techniques."
Posted on August 12, 2019
By Shawn Douglas
Journal articles
Where do technology, security, and the DNA synthesis market intersect? Most notably is the need for minimizing biological risks and maximizing the safety and security of DNA synthesis practices around the world. Diggans and Leproust of Twist Bioscience highlight this major intersection and discuss what they and the International Gene Synthesis Consortium (IGSC) view as the most important aspects of DNA synthesis to address in order to mitigate risks and improve global safety and security. Using the IGSC's
Harmonized Screening Protocol as a base, the authors provide background on the subject and address current industry best practices and how they could be improved using cybersecurity and strong software testing methodologies. They also address how research funding priorities should be addressed to build and maintain databases, reduce risks, and "democratize access to sequence screening." The authors conclude that a multi-faceted approach of practices such as "red teaming," stronger investments in screening—particularly with oligonucleotide pools—and stronger efforts to "teach and promote the evaluation of the security implications of new synthetic biology techniques or materials" to practicing synthetic biologists will yield positive results for the future of DNA synthesis.
Posted on August 6, 2019
By Shawn Douglas
Journal articles
In this 2019 paper published in
Geospatial Health, Oyashi
et al. present details on the Japan Aerospace Exploration Agency’s (JAXA) Public-health Monitoring and Analysis Platform (PMAP). The web-based system was designed to take a wide variety of environmental data and present it in such a way so as to allow epidemiologists to make local, regional, national, or even global insights. Using more than 30 years of archived Earth-observed satellite data from multiple sources, the authors demonstrate the system and explain its underlying technology. While recognizing some of the inherent limitations of optical-sensor-based data towards user goals, the team concludes that its JPMAP system successfully takes "various satellite-derived environmental information related to epidemiological data and pre-processes the data to improve its accessibility for epidemiological research."
Posted on July 29, 2019
By Shawn Douglas
Journal articles
Where do government regulations, privacy, big data, and the management of the energy grid infrastructure collide? The implementation and management of modern smart grids, that's where. In this 2019 paper by Hatzakis
et al., a major distribution system operator (DSO) in the Netherlands is at the heart of discovering how Europe's General Data Protection Regulation (GDPR) are affecting modern implementations of smart energy grids. From cybersecurity risks to public concerns about the privacy of their energy data, this article reviews various ethical issues, concluding with "the need for clarification in practice of privacy policies (particularly of GDPR) to lift concerns about the capability of organizations to remain within its boundaries without holding back progress."
Posted on July 23, 2019
By Shawn Douglas
Journal articles
This brief perspective article by Anwar
et al. of the BHF Centre for Cardiovascular Science at University of Edinburgh examines the potential for using health informatics to improve heart failure outcomes in clinical settings. Noting "decompensated heart failure accounts for up to five percent of all acute unscheduled hospital admissions and has the longest length of stay of any cardiac condition," the authors remind readers that despite significant evidence-based practices backed by science, there continues to be a disconnect between those practices and actual clinical practice. They then turn to a 2019 cohort study of nearly 100,000 U.K patients to provide hints at how collecting, managing, and effectively using heart failure data in contemporary clinical practice can be beneficial to many. The authors conclude that "we need to collate healthcare data from across both primary and secondary care settings in real time and use robust methodology to evaluate major changes in clinical practice or policy decisions" and attempt to show a visual of what such a platform would look like.
Posted on July 16, 2019
By Shawn Douglas
Journal articles
Cybersecurity for biopharmaceutical manufacturing? The "rapid pace of innovation dictates that it is not too early to consider the cyberbiosecurity implications" of the potential dangers that can arise in the industry, argue Mantle
et al. in this 2019 paper published in
Frontiers in Bioengineering and Biotechnology. From compromised master cell banks to intentional corruption of " the design, reading, and writing of DNA sequences to produce pathogenic, self-replicating entities," the authors demonstrate worst case scenarios and practical considerations that scientists should be considering when incorporating various forms of automation into biopharmaceutical manufacturing. After presenting their scenarios and considerations, they conclude that "current best practices from industrial manufacturing and state-of-the-art cybersecurity could serve as a starting point to safeguard and mitigate against cyberbiosecurity threats to biomanufacturing."
Posted on July 9, 2019
By Shawn Douglas
Journal articles
What are the trends and glaring holes in scientific publications regarding the
Cannabis plant? We know some parts of the world have been more proactive in said research, often thanks to slightly more lax regulations than other countries. But where is the research coming from, and what still must be addressed? Matielo
et al. tested this concept in a bibliometric analysis of roughly six decades of publications. They found an increase in the relational study of cannabis and its affects on human genetics but a significant dearth of publications on the genetics of the plant itself. Only since about 2005 has genetics studies of the plant picked up. The authors found several other patterns in their analysis, included in the paper's "Discussion" section.
Posted on July 2, 2019
By Shawn Douglas
Journal articles
This 2017 paper by Mudge
et al. proposes a means for analyzing the
Cannabis plant and its flowers in such a way so as to reduce the use of chlorinated solvents and provide a safer work environment for laboratorians. The authors test methanol as a greener alternative and present the results of their tests, concluding the method as "a significant improvement over previous methods that can be used in a variety of settings and has the potential to be expanded for inclusion of new cannabinoids as required." Along with being greener and improving lab safety, the authors also suggest a reduction in material cost as a benefit of the method.
Posted on June 24, 2019
By Shawn Douglas
Journal articles
Many laboratorians and researchers who have investigated open-source laboratory information management systems (LIMS) have run across LabKey Server. LabKey has been especially useful to those working with high-throughput assays, flow cytometry, genotyping/sequencing, proteomics, specimen tracking, and observational study data management. It's also an extensible LIMS, and as can be seen in this 2019 journal article by Brusniak
et al., where they describe the process of updating LabKey to handle "generalized engineered protein compounds workflow that tracks entities and assays from creation to preclinical experiments." Noting rapid advances in protein therapeutics, the authors developed LabKey into Optide-Hunter to handle optimized peptides (thus, optides) and their production. After discussing its inner workings, the authors conclude that their open-source Optide-Hunter solution fits the bill for a "cost-effective and flexible LIMS for early-stage experimental pipeline development for engineered protein therapeutics development."
Posted on June 18, 2019
By Shawn Douglas
Journal articles
In this brief perspective article by Caswell
et al,, of various U.S. Department of Energy Laboratories, the topic of mitigating the risks—expected and unexpected—associated with public biological databases is briefly presented, pointing out "several existing research areas that can be leveraged to protect against accidental and intentional modifications and misuse." The authors provide background on the data integrity and vulnerability concerns of these databases, including sources of errors and exploitation of weaknesses in the systems inadvertently or by bad-faith actors. Then they suggest a wide variety of tools, methodologies, and other approaches that are available to gatekeepers of this type of data. They close by comparing these databases to the creation of the internet and its "wide penetration of open functionality" but initial lack of having "integrity and security in mind," stating that now is the time to focus on mitigating risks to the integrity of public biological databases.
Posted on June 11, 2019
By Shawn Douglas
Journal articles
Hospital information systems (HIS) represent an important information and function management system for hospitals, providing assistance with diagnosis, management, and education functions for improved service and practice. But how effective are they at what they're designed to do? This work by Ebnehoseini
et al. offers a mechanism for gauging HIS effectiveness through statistics and the information systems success model (ISSM). The authors applied their methodology to the Ibn-e Sina and Dr. Hejazi Psychiatry Hospital in Mashhad, Iran and determined a 65% success rate for the hospital's HIS. They conclude that their methodology "can be adopted for HIS evaluation in future studies" by others and that their results provide a clearer picture into "the viewpoints of HIS users in a developing country."
Posted on June 4, 2019
By Shawn Douglas
Journal articles
With a growing number of big data and artificial intelligence (AI) implementations (referred to as "smart information systems" or SIS) in enterprises, important ethical questions related to cybersecurity must be asked. Has proper informed consent been given? Have discovered vulnerabilities been handled in such a way as to limit potential harm to users? How is trust and transparency handled? These and other questions are asked by Macnish
et al. in this 2019 research report published in
ORBIT Journal. Noting that technical and ethical issues both underpin the tenants of cybersecurity, the authors discuss the ethical issues of using SIS in cybersecurity and provide their own case study of a major U.K. business using SIS in their cybersecurity practices. After providing their ethical implications of the case study, they conclude "that ethical concerns regarding SIS in cybersecurity go further than mere privacy issues" and "claim that there is a need to improve the ethics of research in SIS."
Posted on May 28, 2019
By Shawn Douglas
Journal articles
In this 2018 paper published in
Scientific Reports, Mudge
et al. of the University of British Columbia attempt to demonstrate how a growing loss of biodiversity is occurring across strains of
Cannabis due to cultivation practices. The authors introduce current research on the "understanding of metabolite commonality and diversity within plant species" and hypothesize that simply measuring cannabinoid potency (Δ9-tetrahydrocannabinol or THC) and cannabidiol (CBD) content is not sufficient in painting a proper picture of cannabinoid composition and the resulting impact of breeding programs. The authors then get into the results of their analytical research, discuss their findings, and conclude that, at least in Canada, " evaluating single metabolite classes [of available
Cannabis strains] does not provide sufficient information to understand the phytochemical diversity available."
Posted on May 21, 2019
By Shawn Douglas
Journal articles
We take another look at the security of biological data, this time through the eyes of Berger and Schneck, and the discussion of major players such as China. The authors first introduce advances in biotechnology and benefits and challenges that arise from it today, including exploitation of the resulting data "by state actors, malicious nonstate actors, and hackers." They then discuss common approaches used to protect this soft of data, as well as the various vulnerabilities that come from (or from the lack of) those approaches. The authors close their paper by offering four specific strategies "toward protecting biological data from unauthorized acquisition and use, enhancing efforts to preserve data integrity and provenance, and enabling future benefit of biotechnological advances."
Posted on May 14, 2019
By Shawn Douglas
Journal articles
In this 2019 paper published in
Frontiers in Public Health, Wholey
et al. propose a curriculum for an effective and modern public health informatics (PHI) higher education program. Drawing competencies from computer, information, and organizational sciences, the researchers provide program design objectives, competencies, and challenges involved in implementing such a curriculum focused on the professional role of the informatician. Based on the information systems program of Carnegie Mellon, the authors report that their proposed curriculum has already seen success with its implementation at the School of Public Health at the University of Minnesota. They conclude that the proposed curriculum "is a starting point," keeping in mind that practices, knowledge, and technology change often, requiring program vigilance for improvement to best ensure "an effective and relevant workforce that can navigate the changing trends of public health to improve population health."
Posted on May 7, 2019
By Shawn Douglas
Journal articles
Here is one more journal article on the topic of cyberbiosecurity, this time discussing related vulnerabilities and the need for a resilient infrastructure to limit them. Schabacker
et al. of the Argonne National Laboratory present a base "assessment framework for cyberbiosecurity, accounting for both security and resilience factors in the physical and cyber domains." They first discuss the differences between "emerging" and "converging" technologies and how they contribute to vulnerabilities, and then they lead into risk mitigation strategies. The authors also provide clear definitions of associated terminology for common understanding, including the topics of dependency and interdependency. Then they discuss the basic framework, keeping vulnerabilities in mind. They close with a roadmap for a common vulnerability assessment framework, encouraging the application of "lessons learned from parallel efforts in related fields," and reflection on "the complex multidisciplinary cyberbiosecurity environment."
Posted on April 29, 2019
By Shawn Douglas
Journal articles
From software development companies to pharmaceutical manufacturers, businesses, governments, and non-profit entities alike are beginning to adopt tools meant to improve communication, information sharing, and productivity. In some cases, this takes the form of an enterprise social media platform (ESMP) with chat rooms, discussion boards, and file repositories. But while this can be beneficial, adding a focused attempt at sharing to work culture can create its own share of problems, argues Norwegian University of Science and Technology's Halvdan Haugsbakken, particularly due to varying definitions and expectations of what information "sharing" actually is. Using a case study of regional government in Norway, Haugsbakken found "when the end-users attempted to translate sharing into a manageable practice—as the basis for participation in a knowledge formation process—they interpreted sharing as a complicated work practice, with the larger consequence of producing disengaged users." This result "suggests a continued need for the application of theoretical lenses that emphasize interpretation and practice in the implementation of new digital technologies in organizations."
Posted on April 22, 2019
By Shawn Douglas
Journal articles
Following up on the cyberbiosecurity article posted a few weeks ago, this one by Murch
et al. steps away from the strong agriculture focus of the prior and examines cyberbiosecurity from a more broad perspective. Not only do the authors provide background into the convergence of cybersecurity, cyber-physical security, and biosecurity, but they also provide a look at how it extends to biomanufacturing facilities. They conclude that cyberbiosecurity could be applied to various domains—from personalized genomics and medical device manufacturing to food production and environmental monitoring— though continued "[d]irect and ordered engagements of the pertinent sectors of the life sciences, biosecurity, and cyber-cybersecurity communities," as well as tangentially within academia and government, must continue to occur in order "to harmonize the emerging enterprise and foster measurable value, success, and sustainability."
Posted on April 15, 2019
By Shawn Douglas
Journal articles
In 2017, Washington State's cannabis testing laboratories were going through a mini-crisis, with questions of credibility being raised about certain laboratories' testing methodologies and practices. How much were differences in tested samples based on differences in methodologies? What more can be done by laboratories in the industry? This 2018 paper by Jikomes and Zoorob answer these questions and more, using "a large dataset from Washington State’s seed-to-sale traceability system." Their analyses of this dataset showed "systematic differences in the results obtained by different testing facilities in Washington," leading to "cannabinoid inflation" in certain labs. The authors conclude that despite the difficulties of having cannabis illegal at the federal level, efforts to standardize testing protocols etc. must continue to be made in order to protect consumers and increase confidence in the testing system.