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Orion by Walt Simonson
\"Walt Simonson's stunning, unmistakable art and storytelling are on full display here in his groundbreaking work ORION. Expanding the beloved universe originally created by Jack Kirby, Simonson's sprawling storylines and dynamic artwork elevate his titular hero, as well as the rest of the Fourth World's indispensible characters, to incredible new heights. Collected here for the first time are all twenty-five issues of Walter Simonson's ORION, as well as never-before reprinted short stories, pinups and sketch material.\"-- Provided by publisher.
BOOK
Quality filtering of Illumina index reads mitigates sample cross-talk
Background
Multiplexing multiple samples during Illumina sequencing is a common practice and is rapidly growing in importance as the throughput of the platform increases. Misassignments during de-multiplexing, where sequences are associated with the wrong sample, are an overlooked error mode on the Illumina sequencing platform. This results in a low rate of cross-talk among multiplexed samples and can cause detrimental effects in studies requiring the detection of rare variants or when multiplexing a large number of samples.
Results
We observed rates of cross-talk averaging 0.24 % when multiplexing 14 different samples with unique i5 and i7 index sequences. This cross-talk rate corresponded to 254,632 misassigned reads on a single lane of the Illumina HiSeq 2500. Notably, all types of misassignment occur at similar rates: incorrect i5, incorrect i7, and incorrect sequence reads. We demonstrate that misassignments can be nearly eliminated by quality filtering of index reads while preserving about 90 % of the original sequences.
Conclusions
Cross-talk among multiplexed samples is a significant error mode on the Illumina platform, especially if samples are only separated by a single unique index. Quality filtering of index sequences offers an effective solution to minimizing cross-talk among samples. Furthermore, we propose a straightforward method for verifying the extent of cross-talk between samples and optimizing quality score thresholds that does not require additional control samples and can even be performed
post hoc
on previous runs.
Journal Article
Leveraging the past to prepare for the future of Air Force intelligence analysis
\"This report describes steps the U.S. Air Force can take to help ensure that it has the capability needed to provide intelligence analysis support to a broad range of service and combatant commander needs, including support to ongoing irregular warfare operations, and to conventional warfare with a near-peer competitor. It describes lessons from past operations that have direct implications for Air Force intelligence analysis or that Air Force intelligence analysis could help to address. It also describes future challenges for Air Force intelligence analysis. It makes recommendations related to doctrine, training and career field development, analysis tools, and processes that can help to address the lessons from the past and prepare Air Force intelligence analysts for the challenges of the future\"--Publisher's description.
Book
Ten simple rules for hitting a home run with your elevator pitch
A bit longer than the half second a baseball travels from mound to mitt, pitching yourself effectively can spread the word about your work and open doors for your future academic success in only a few minutes. Pitches fall into 1 of 3 categories, depending on your goal: (i) creating connection with your audience in order to establish shared values or build communion, (ii) encouraging collaboration by getting the audience to take action or bring them to your side, or (iii) generating awareness through education and being informative [1]. Remember that you are a natural pitcher and have been making pitches through your emails and conversations for years [4]. [...]your audience is secretly cheering for you to succeed, as it may benefit them too [5]. Just like a baseball pitcher might use a changeup to keep the batter on their toes, using a dynamic voice (tone, pace, and volume) will energize your pitch.
Journal Article
Sample-efficient identification of high-dimensional antibiotic synergy with a normalized diagonal sampling design
Antibiotic resistance is an important public health problem. One potential solution is the development of synergistic antibiotic combinations, in which the combination is more effective than the component drugs. However, experimental progress in this direction is severely limited by the number of samples required to exhaustively test for synergy, which grows exponentially with the number of drugs combined. We introduce a new metric for antibiotic synergy, motivated by the popular Fractional Inhibitory Concentration Index and the Highest Single Agent model. We also propose a new experimental design that samples along all appropriately normalized diagonals in concentration space, and prove that this design identifies all synergies among a set of drugs while only sampling a small fraction of the possible combinations. We applied our method to screen two- through eight-way combinations of eight antibiotics at 10 concentrations each, which requires sampling only 2,560 unique combinations of antibiotic concentrations.
Journal Article
THE HIJACKING OF AEROFLOT FLIGHT 244
Focusing on the first successful hijacking of a Soviet aircraft and its complicated aftermath, this article explores the rise and fall of ‘air piracy’ in the final decades of the Cold War, when hijackings became a common occurrence. Although the motivations of hijackers spanned the political spectrum, hijacking seemed to offer marginal individuals the opportunity to mount a challenge to Cold War borders and forge global connections. The hijacking of Aeroflot Flight 244, which garnered widespread attention because it tested Cold War claims about the freedom of movement, was debated in a series of court cases in Turkey, the Soviet Union, and the United States that helped define the boundaries of nationality and legality in a globalizing world. While hijacking’s proliferation confirms the importance of non-state actors in this period, its decline demonstrates how governments devised new ways to patrol their borders and regulate the global mobility of people on airplanes. In the process, hijacking was redefined as terrorism, and hijackers were rendered stateless. The hijacking of Aeroflot Flight 244 reveals a more uneven history of globalization, one in which global flows of information and transnational advocacy coincided with the extension of state jurisdiction in the skies.
Journal Article
Quality filtering of Illumina index reads mitigates sample cross-talk
Multiplexing multiple samples during Illumina sequencing is a common practice and is rapidly growing in importance as the throughput of the platform increases. Misassignments during de-multiplexing, where sequences are associated with the wrong sample, are an overlooked error mode on the Illumina sequencing platform. This results in a low rate of cross-talk among multiplexed samples and can cause detrimental effects in studies requiring the detection of rare variants or when multiplexing a large number of samples. We observed rates of cross-talk averaging 0.24 % when multiplexing 14 different samples with unique i5 and i7 index sequences. This cross-talk rate corresponded to 254,632 misassigned reads on a single lane of the Illumina HiSeq 2500. Notably, all types of misassignment occur at similar rates: incorrect i5, incorrect i7, and incorrect sequence reads. We demonstrate that misassignments can be nearly eliminated by quality filtering of index reads while preserving about 90 % of the original sequences. Cross-talk among multiplexed samples is a significant error mode on the Illumina platform, especially if samples are only separated by a single unique index. Quality filtering of index sequences offers an effective solution to minimizing cross-talk among samples. Furthermore, we propose a straightforward method for verifying the extent of cross-talk between samples and optimizing quality score thresholds that does not require additional control samples and can even be performed post hoc on previous runs.
Journal Article
Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science
Within clinical, biomedical, and translational science, an increasing number of projects are adopting graphs for knowledge representation. Graph‐based data models elucidate the interconnectedness among core biomedical concepts, enable data structures to be easily updated, and support intuitive queries, visualizations, and inference algorithms. However, knowledge discovery across these “knowledge graphs” (KGs) has remained difficult. Data set heterogeneity and complexity; the proliferation of ad hoc data formats; poor compliance with guidelines on findability, accessibility, interoperability, and reusability; and, in particular, the lack of a universally accepted, open‐access model for standardization across biomedical KGs has left the task of reconciling data sources to downstream consumers. Biolink Model is an open‐source data model that can be used to formalize the relationships between data structures in translational science. It incorporates object‐oriented classification and graph‐oriented features. The core of the model is a set of hierarchical, interconnected classes (or categories) and relationships between them (or predicates) representing biomedical entities such as gene, disease, chemical, anatomic structure, and phenotype. The model provides class and edge attributes and associations that guide how entities should relate to one another. Here, we highlight the need for a standardized data model for KGs, describe Biolink Model, and compare it with other models. We demonstrate the utility of Biolink Model in various initiatives, including the Biomedical Data Translator Consortium and the Monarch Initiative, and show how it has supported easier integration and interoperability of biomedical KGs, bringing together knowledge from multiple sources and helping to realize the goals of translational science.
Journal Article