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"Fleet, David"
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Batman by Grant Morrison omnibus
\"One of the greatest storytellers of his generation, Grant Morrison's arrival onto the Dark Knight was one of the most hyped debuts in industry history. This collection includes time-spanning epic graphic novels featuring the cataclysmic events of FINAL CRISIS and the introduction of Batman's son, Damian Wayne! These blockbuster stories featured a deconstruction of super hero comics like never before, with challenging, thought-provoking takes on the modern, four-color icons.\"-- Provided by publisher.
Book
3DFlex: determining structure and motion of flexible proteins from cryo-EM
Modeling flexible macromolecules is one of the foremost challenges in single-particle cryogenic-electron microscopy (cryo-EM), with the potential to illuminate fundamental questions in structural biology. We introduce Three-Dimensional Flexible Refinement (3DFlex), a motion-based neural network model for continuous molecular heterogeneity for cryo-EM data. 3DFlex exploits knowledge that conformational variability of a protein is often the result of physical processes that transport density over space and tend to preserve local geometry. From two-dimensional image data, 3DFlex enables the determination of high-resolution 3D density, and provides an explicit model of a flexible protein’s motion over its conformational landscape. Experimentally, for large molecular machines (tri-snRNP spliceosome complex, translocating ribosome) and small flexible proteins (TRPV1 ion channel,
α
V
β
8 integrin, SARS-CoV-2 spike), 3DFlex learns nonrigid molecular motions while resolving details of moving secondary structure elements. 3DFlex can improve 3D density resolution beyond the limits of existing methods because particle images contribute coherent signal over the conformational landscape.
3D Flexible Refinement (3DFlex) is a generative neural network model for continuous molecular heterogeneity for cryo-EM data that can be used to determine the structure and motion of flexible biomolecules. It enables visualization of nonrigid motion and improves 3D structure resolution by aggregating information from particle images spanning the conformational landscape of the target molecule.
Journal Article
Non-uniform refinement: adaptive regularization improves single-particle cryo-EM reconstruction
Cryogenic electron microscopy (cryo-EM) is widely used to study biological macromolecules that comprise regions with disorder, flexibility or partial occupancy. For example, membrane proteins are often kept in solution with detergent micelles and lipid nanodiscs that are locally disordered. Such spatial variability negatively impacts computational three-dimensional (3D) reconstruction with existing iterative refinement algorithms that assume rigidity. We introduce non-uniform refinement, an algorithm based on cross-validation optimization, which automatically regularizes 3D density maps during refinement to account for spatial variability. Unlike common shift-invariant regularizers, non-uniform refinement systematically removes noise from disordered regions, while retaining signal useful for aligning particle images, yielding dramatically improved resolution and 3D map quality in many cases. We obtain high-resolution reconstructions for multiple membrane proteins as small as 100 kDa, demonstrating increased effectiveness of cryo-EM for this class of targets critical in structural biology and drug discovery. Non-uniform refinement is implemented in the cryoSPARC software package.
Membrane proteins exhibit spatial variation in rigidity and disorder, which poses a challenge for traditional cryo-EM reconstruction algorithms. Non-uniform refinement accounts for this spatial variability, yielding improved 3D reconstruction quality even for small membrane proteins.
Journal Article
cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination
A software tool, cryoSPARC, addresses the speed bottleneck in cryo-EM image processing, enabling automated macromolecular structure determination in hours on a desktop computer without requiring a starting model.
Single-particle electron cryomicroscopy (cryo-EM) is a powerful method for determining the structures of biological macromolecules. With automated microscopes, cryo-EM data can often be obtained in a few days. However, processing cryo-EM image data to reveal heterogeneity in the protein structure and to refine 3D maps to high resolution frequently becomes a severe bottleneck, requiring expert intervention, prior structural knowledge, and weeks of calculations on expensive computer clusters. Here we show that stochastic gradient descent (SGD) and branch-and-bound maximum likelihood optimization algorithms permit the major steps in cryo-EM structure determination to be performed in hours or minutes on an inexpensive desktop computer. Furthermore, SGD with Bayesian marginalization allows
ab initio
3D classification, enabling automated analysis and discovery of unexpected structures without bias from a reference map. These algorithms are combined in a user-friendly computer program named cryoSPARC (
http://www.cryosparc.com
).
Journal Article
Student Competition (Technology Innovation) ID 1970388
BackgroundThe evaluation of hand function after spinal cord injury (SCI) is conducted in clinical settings, which may not accurately reflect hand function in the real world, thereby limiting the efficacy assessment of new treatments. Wearable cameras, also known as egocentric video, are a novel method to evaluate hand function in non-clinical environments. Nonetheless, manual processing of vast quantities of complex video data is difficult, highlighting the need for automated data analysis. The objective of this study was to automatically identify distinct hand postures in egocentric video using unsupervised machine learning.MethodsSeventeen participants with cervical SCI recorded activities of daily living in a home simulation laboratory. A hand pose estimation algorithm was applied on detected hands to determine 2D joint locations, which were lifted to 3D coordinates. The resulting hand posture information was subjected to a number of clustering techniques. Hand grasps were manually labelled into four categories for evaluation purposes: power, precision, intermediate, and non-prehensile.ResultsK-Means clustering consistently exhibited the highest Silhouette score, which reflects the presence of discrete clusters in the data. When comparing with manual annotations, Spectral Clustering applied to a feature space consisting of 2D pose estimation with confidence scores yield the best performance as quantified by maximum match (0.48), Fowlkes-Mallows score (0.46), and normalized mutual information (0.22).ConclusionsThis is the first attempt to develop an unsupervised, data-driven hand taxonomy for individuals with SCI using wearable technology. The findings suggest that the method is capable of grouping similar hand grasps.
Journal Article
Replicate analyses of OSPAR beach litter data
Replicate surveys of beach litter have seldom been performed in the past. In this study, replicate surveys of beach litter were conducted on the beach north of Hörnum (Sylt, Germany), from 2015 to 2019, applying a slightly modified OSPAR protocol of beach litter monitoring. Descriptive statistics and power analyses were calculated on data resulting from these replicate surveys, to find out whether the scatter of replicate beach litter data decreases and the statistical power increases with increasing numbers of replicate surveys. From 2015 to 2019, mean total abundances, given as numbers of litter items, ranged from 19 to 185 litter items on a 50 m section of beach. With increasing numbers of replicate surveys, the scatter given by the coefficient of variation (CV) significantly increased up to 113%. Statistical power considerably increased with increasing numbers of replicate beach sections, e.g. from 82% (two beach sections) to nearly 100% (five beach sections) for a given reduction of beach litter of 50%. Based on these results from a morphologically straight coastline, the use of replicate surveys would be sensible for the future monitoring of beach litter. However, there is high need for studies, which consider coastlines with varying morphology.
Journal Article
Who’s talking to whom in agribusiness? And should anyone listen? The network of intellectual influence in agribusiness research
PurposeTo develop an understanding of communication among agribusiness journals and to examine patterns of citations that allow the measurement and description of the structure of communication flows among those journals in a network.Design/methodology/approachThe data for this study were gathered from the Journal Citation Reports (JCR) published by Thomson Scientific (Philadelphia). The authors conducted a bibliometric analysis, based on an international trade analogy to explain the network of agribusiness journals and how these journals communicate with business and economics journals.FindingsBusiness and economics journals and, particularly the traditionally major ones, surprisingly were scarcely every used. However, the British Food Journal stood out with 50 citations to marketing and strategic management journals.Research limitations/implicationsThere are predominantly four such limitations: only 33 journals were studied, only one 5-year time period was involved, that time period is a few years old and the journal characteristics were derived using data from the “Scopes” and “Information for Authors” text on the website of each journal.Practical implicationsExchanges of agribusiness knowledge and information among diverse stakeholders (consumers, suppliers and public agencies) in a complex environment require a better understanding of the network of agribusiness journals and their relation to traditional business and economics journals.Social implicationsNetworks of journals facilitate cooperation and interactions to improve developments in the field.Originality/valueExamining citations from and to the field of agribusiness is interesting and important because knowledge is transferred through networks comprise those who contribute to journals, read them and learn from them, i.e. by “talking” to each other as well as by practitioners who also read and learn from those journals.
Journal Article
Physics-Based Person Tracking Using the Anthropomorphic Walker
We introduce a physics-based model for 3D person tracking. Based on a biomechanical characterization of lower-body dynamics, the model captures important physical properties of bipedal locomotion such as balance and ground contact. The model generalizes naturally to variations in style due to changes in speed, step-length, and mass, and avoids common problems (such as footskate) that arise with existing trackers. The dynamics comprise a two degree-of-freedom representation of human locomotion with inelastic ground contact. A stochastic controller generates impulsive forces during the toe-off stage of walking, and spring-like forces between the legs. A higher-dimensional kinematic body model is conditioned on the underlying dynamics. The combined model is used to track walking people in video, including examples with turning, occlusion, and varying gait. We also report quantitative monocular and binocular tracking results with the HumanEva dataset.
Journal Article
Utility, Maximizing, and the Satisficing Concept: A Historical Approach at Reconciliation
Utility is used in both economic and business theories of decision-making. The tradition utility approach using maximizing concepts seems at odds with the concept of satisficing behavior. The relation between utility and the satisficing concept is suggested to be that satisficing refers to a process of adaptive behavior by which an economic unit strives to attain a satisfactory level of utility for higher ranking objectives before turning to lower-ranking objectives. There is no necessary inconsistency between utility and satisficing, although the assumption of maximization must be replaced, in positive analysis, by that of satisficing since the scope referred to by each of the concepts, positive and normative, is quite different. This paper uses historical material to develop a model, which is then used to analyze those relations.
Journal Article
Food integrity: a market-based solution
Purpose
The purpose of this paper is to proffer an alternative conceptualization of food integrity and a market-based food integrity intelligence system.
Design/methodology/approach
Food fraud is interpreted as a symptom of asymmetric knowledge. Consumer collaboration for knowledge exchange and diffusion of innovation (KEDI) safeguards food markets. The concept of communicative action is applied to conceptualize and analyze key elements for designing a collaborative food integrity intelligence system.
Findings
The model of market-based KEDI consists of three dimensions: intelligence flows, organization memory, and social sensitivities. Decentralized control is crucial to effect system innovation.
Originality/value
The paper integrates managerial, marketing, and economic approaches and develops a model for managing food integrity intelligence.
Journal Article