bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Classic Expertise Approach and Its Evolution
Authors: Gobet Fernand 
Published: February 2019

AbstractThis chapter reviews the “classic expertise approach,” which is defined as the research line starting with Simon and Chase’s (1973) chunking theory, culminating in the early 1980s, and dominating expertise research until the 1990s. After briefly reviewing early research (e.g., Binet, 1894b; De Groot, 1946), an overview of the key experimental and theoretical results obtained with this approach is provided. The chapter also discusses influential theories stemming from the classic approach, such as long-term working memory (Ericsson & Kintsch, 1995), EPAM-IV (Richman, Staszewski, & Simon, 1995) and template theory (Gobet & Simon, 1996). The discussion highlights the defining research methods and theoretical assumptions of this approach. Directions of research for the future are discussed, based on the characteristics that made the classic approach highly successful.
Expertise in Intelligence Analysis
Authors: Jenkins Michael P. , Pfautz Jonathan D. 
Published: February 2019

AbstractTo conduct an intelligence analysis (IA), analysts perform multiple perceptual and cognitive tasks to understand the past, present, and/or future states of some real-world environment or situation, often employing abductive reasoning due to the significant degree of uncertainty characterizing the domains analysts operate in and the substantive problems they operate on. Although the tasks and cognitive processes that analysts carry out have remained relatively unchanged over the past half-century, research on the challenges, complexities, and constraints that make analyst sensemaking performance difficult has evolved, providing a better understanding of the key characteristics that define expertise in this field. This chapter highlights the unique characteristics of expert IA practitioners, compared to other domains. It highlights a range of past research characterizing the domain, from both a workflow perspective and an information processing perspective. Applying these characterizations, the chapter then highlights elements of expert behaviors that emerge throughout the IA process, and the implications of these elements on emerging research directions and the design of new assistive technologies to augment intelligence analysts executing modern and next generation IA.
Teamwork in Spaceflight Operations
Authors: Fischer Ute , Mosier Kathleen 
Published: February 2019

AbstractHuman spaceflight is a multiteam effort requiring the coordination and collaboration not only of individuals within a team (mission control or space crew) but importantly also between teams. In this chapter, the strategies and procedures these expert teams have established to ensure common task and team models, and to facilitate their communication and joint performance, will be discussed. The chapter also includes a discussion of the component teams of the mission control/space crew multiteam system, highlighting important features of their (intra)teamwork. The teamwork challenges of future long-duration space exploration are discussed, as are ongoing efforts and research needs to address them.
Macrocognitive Models of Expertise
Authors: Hutton Robert J. B. 
Published: February 2019

Abstract
The purpose of this chapter is to provide a brief understanding of macrocognition, some of its theoretical and methodological underpinnings, and three examples of macrocognitive models: the recognition-primed decision model, the data–frame model of sensemaking, and the flexecution model of replanning and adaptation. These models are presented to provide the reader with a sense of the character of macrocognitive models, their purpose, and the current evidence which underpins each model. Macrocognitive models are models of experienced, often expert performers, and have been developed primarily from the study of decision making and cognitive work in naturalistic settings, as opposed to well-controlled laboratory experiments. They describe how people manage uncertainty and complexity in the world of work. The limitations and applications of these models are also illustrated in order to provide a future-oriented perspective on how the models might be improved and how they might be applied to support more effective cognitive work and more resilient work systems.
The Value of Offshore Secrets: Evidence from the Panama Papers
Authors: O’Donovan James , Wagner Hannes F , Zeume Stefan 
Published: February 2019

AbstractWe exploit one of the largest data leaks, to date, to study whether and how firms use secret offshore vehicles. From the leaked data, we identify 338 listed firms as users of secret offshore vehicles and document that these vehicles are used to finance corruption, avoid taxes, and expropriate shareholders. Overall, the leak erased $\$$174 billion in market capitalization among implicated firms. Following the increased transparency brought about by the leak, implicated firms experience lower sales from perceptively corrupt countries and avoid less tax. We conservatively estimate that 1 in 7 firms have offshore secrets.Received May 29, 2017; editorial decision December 2, 2018 by Editor Itay Goldstein. Authors have furnished an Internet Appendix, which is available on the Oxford University Press Web site next to the link to the final published paper online.
The coevolutionary biology of brood parasitism: a call for integration
Authors: Thorogood Rose , Spottiswoode Claire N. , Portugal Steven J. , Gloag Ros 
Published: February 2019

Obligate brood-parasitic cheats have fascinated natural historians since ancient times. Passing on the costs of parental care to others occurs widely in birds, insects and fish, and often exerts selection pressure on hosts that in turn evolve defences. Brood parasites have therefore provided an illuminating system for researching coevolution. Nevertheless, much remains unknown about how ecology and evolutionary history constrain or facilitate brood parasitism, or the mechanisms that shape or respond to selection. In this special issue, we bring together examples from across the animal kingdom to illustrate the diverse ways in which recent research is addressing these gaps. This special issue also considers how research on brood parasitism may benefit from, and in turn inform, related fields such as social evolution and immunity. Here, we argue that progress in our understanding of coevolution would benefit from the increased integration of ideas across taxonomic boundaries and across Tinbergen’s Four Questions: mechanism, ontogeny, function and phylogeny of brood parasitism. We also encourage renewed vigour in uncovering the natural history of the majority of the world's brood parasites that remain little-known. Indeed, it seems very likely that some of nature’s brood parasites remain entirely unknown, because otherwise we are left with a puzzle: if parental care is so costly, why is brood parasitism not more common?
This article is part of the theme issue ‘The coevolutionary biology of brood parasitism: from mechanism to pattern’.
Under the radar: detection avoidance in brood parasitic bees
Authors: Litman Jessica R. 
Published: February 2019

Brood parasitism is a specialized form of parasitism in which the offspring of a parasite develops on the food provisions gathered by a host species for its own young. Obligate brood parasitic lineages have lost the ability to acquire provisions for their young and thus rely entirely on the location of an appropriate host to serve as a food-provider. Solitary bees provide some of the most fascinating examples of brood parasitism in animals. Most solitary bees build and provision their own nests. Some, however, usurp the nests of other species of bees. These brood parasites, or ‘cuckoo’ bees, deposit their eggs on the pollen provisions collected by a host bee for her own offspring. The provisions stored by the host bee are not sufficient to sustain the development of both the host's larva and that of the brood parasite and the parasite must kill the offspring of its host in order to obtain enough nourishment to complete its development. As a consequence, there is fierce competition between the host bee seeking to protect her nest from attack and the brood parasite seeking to avoid detection by the host in order to successfully deposit her eggs in an appropriate nest. In this paper, I review the behaviours that allow brood parasitic bees to escape detection by their hosts. Identifying these behaviours, and placing them within the general context of strategies employed by brood parasitic bees to parasitize the nests of their hosts, is key to understanding how brood parasitic lineages may have evolved from nest-building ancestors, decrypting the selective pressures that drive evolutionary transitions from one strategy to another and, more broadly, revealing how similar selective pressures in widely divergent lineages of animals have given rise to remarkably convergent behaviours.This article is part of the theme issue ‘The coevolutionary biology of brood parasitism: from mechanism to pattern’.
The brood parasite's guide to inclusive fitness theory
Authors: Gloag Ros , Beekman Madeleine 
Published: February 2019

Hamilton's theory of inclusive fitness provides a framework for understanding the evolution of social behaviour between kin, including parental and alloparental care. Brood parasitism is a reproductive tactic in which parasites exploit the care of other individuals of the same species (conspecific parasitism) or different species (interspecific parasitism) to rear their brood. Here, drawing from examples in birds and social insects, we identify two insights into brood parasitism that stem from inclusive fitness theory. First, the kin structure within nests, or between neighbouring nests, can create a niche space favouring the evolution of conspecific parasitism. For example, low average relatedness within social insect nests can increase selection for reproductive cheats. Likewise, high average relatedness between adjacent nests of some birds can increase a female's tolerance of parasitism by her neighbour. Second, intrabrood conflict will be high in parasitized broods, from the perspective of both parasite and host young, relative to unparasitized broods. We also discuss offspring recognition by hosts as an example of discrimination in a kin-selected social behaviour. We conclude that the inclusive fitness framework is instructive for understanding aspects of brood parasite and host evolution. In turn, brood parasites present some unique opportunities to test the predictions of inclusive fitness theory.
This article is part of the theme issue ‘The coevolutionary biology of brood parasitism: from mechanism to pattern’.
Monogamy without parental care? Social and genetic mating systems of avian brood parasites
Authors: Feeney William E. , Riehl Christina 
Published: February 2019

Classic evolutionary theory predicts that monogamy should be intimately linked with parental care. It has long been assumed, therefore, that avian brood parasites—which lay their eggs in the nests of ‘host’ species and provide little, if any, parental care—should be overwhelmingly promiscuous. However, recent studies have revealed that the social mating systems of brood parasites are surprisingly diverse, encompassing lek polygyny, monogamy, polygamy and promiscuity. What ecological or phylogenetic factors explain this variation, and why are some brood parasites apparently monogamous? Here we review the social and genetic mating systems of all 75 brood parasitic species for which data are available and evaluate several hypotheses that may help explain these patterns. We find that social monogamy is widespread, often co-occurring with territoriality and cooperative behaviour by the mated pair. Comparative studies, though preliminary, suggest that in some species, monogamy is associated with low host density and polygamy with higher host density. Interestingly, molecular data show that genetic and social mating systems can be entirely decoupled: genetic monogamy can occur in parasitic species that lack behavioural pair-bonds, possibly as a by-product of territoriality; conversely, social monogamy has been reported in parasites that are genetically polygamous. This synthesis suggests that social and genetic monogamy may result from very different selective pressures, and that male–female cooperative behaviours, population density and territoriality may all interact to favour the evolution of monogamous mating in brood parasites. Given that detailed descriptive data of social, and especially genetic, mating systems are still lacking for the majority of brood parasitic species, definitive tests of these hypotheses await future work.
This article is part of the theme issue ‘The coevolutionary biology of brood parasitism: from mechanism to pattern’.
Early life-history features associated with brood parasitism in the cuckoo catfish,Synodontis multipunctatus(Siluriformes: Mochokidae)
Authors: Cohen Marcus S. , Hawkins M. Brent , Stock David W. , Cruz Alexander 
Published: February 2019

The cuckoo catfish,Synodontis multipunctatus, is the only known obligate brood parasite among fishes, exploiting the parental care of mouthbrooding cichlids endemic to Lake Tanganyika. Comparisons of this system to brood parasitism in birds may reveal broader principles that underlie the evolution of this life-history strategy in vertebrates. However, little is known about the features of the cuckoo catfish that enable this species to successfully parasitize cichlids. Here, we examine early ontogeny of the cuckoo catfish and compare it to that of its cichlid hosts as well as a non-parasitic congener. We found that cuckoo catfish embryos develop and hatch in advance of host embryos, and begin feeding on cichlid young just as they start to hatch. Overall timing of ontogeny in the cuckoo catfish was found to be similar to that of the substrate-spawning congenerSynodontis lucipinnis, suggesting that more rapid development of the cuckoo catfish relative to cichlids is not a unique adaptation to brood parasitism. However, we found that cuckoo catfish progeny exhibit extensive morphological differences fromS.lucipinnis, which may represent adaptations to brood parasitism. These life-history observations reveal both similarities and differences between the cuckoo catfish system and brood parasitism in other lineages.This article is part of the theme issue ‘The coevolutionary biology of brood parasitism: from mechanism to pattern’.
Vive la difference! Self/non-self recognition and the evolution of signatures of identity in arms races with parasites
Authors: Spottiswoode Claire N. , Busch Robert 
Published: February 2019

In arms races with parasites, hosts can evolve defences exhibiting extensive variability within populations, which signals individual identity (‘signatures’). However, few such systems have evolved, suggesting that the conditions for their evolution are uncommon. We review (a) polymorphic egg markings that allow hosts of brood-parasitic birds to recognize and reject parasitic eggs, and (b) polymorphic tissue antigens encoded in the major histocompatibility complex (MHC), which present self- and pathogen-derived peptides to T cells of the immune system. Despite the profound differences between these systems, they share analogous features: (i) self/non-self discrimination by a highly specific recognition system (bird eyes and T-cell antigen receptor, respectively), which antagonists may escape by evolving evasion or mimicry; (ii) a self substrate upon which diversifying selection can act (eggs, and MHC molecules); (iii) acquired knowledge of self (resulting in acceptance of own eggs, and immune tolerance); and (iv) fitness costs associated with attack on self or lack of parasite detection. We suggest that these features comprise a set of requirements for parasites to drive the evolution of identity signatures in hosts, which diminish the likelihood of recognition errors. This may help to explain the variety of trajectories arising from arms races in different antagonistic contexts.
This article is part of the theme issue ‘The coevolutionary biology of brood parasitism: from mechanism to pattern’.
VAMPr: VAriant Mapping and Prediction of antibiotic resistance via explainable features and machine learning
Authors: Kim Jiwoong , Greenberg David E , Pifer Reed , Jiang Shuang , Xiao Guanghua , Shelburne Samuel A , Koh Andrew , Xie Yang , Zhan Xiaowei 
Published: February 2019

ABSTRACTAntimicrobial resistance (AMR) is an increasing threat to public health. Current methods of determining AMR rely on inefficient phenotypic approaches, and there remains incomplete understanding of AMR mechanisms for many pathogen-antimicrobial combinations. Given the rapid, ongoing increase in availability of high density genomic data for a diverse array of bacteria, development of algorithms that could utilize genomic information to predict phenotype could both be useful clinically and assist with discovery of heretofore unrecognized AMR pathways. To facilitate understanding of the connections between DNA variation and phenotypic AMR, we developed a new bioinformatics tool, variant mapping and prediction of antibiotic resistance (VAMPr), to (1) derive gene ortholog-based sequence features for variants; (2) interrogate these explainable gene-level variants for their known or novel associations with AMR; and (3) build accurate models to predict AMR based on whole genome sequencing data. Following the Clinical & Laboratory Standards Institute (CLSI) guidelines, we curated the publicly available sequencing data for 3,393 bacterial isolates from 9 species along with AMR phenotypes for 29 antibiotics. We detected 14,615 variant genotypes and built 93 association and prediction models. The association models confirmed known genetic antibiotic resistance mechanisms, such as blaKPC and carbapenem resistance consistent with the accurate nature of our approach. The prediction models achieved high accuracies (mean accuracy of 91.1% for all antibiotic-pathogen combinations) internally through nested cross validation and were also validated using external clinical datasets. The VAMPr variant detection method, association and prediction models will be valuable tools for AMR research for basic scientists with potential for clinical applicability.
Optical measurement of voltage sensing by endogenous ion channels
Authors: Thapa Parashar , Stewart Robert , Sepela Rebecka J. , Vivas Oscar , Parajuli Laxmi K. , Lillya Mark , Fletcher-Taylor Sebastian , Cohen Bruce E. , Zito Karen , Sack Jon T. 
Published: February 2019

ABSTRACTA primary goal of molecular physiology is to understand how conformational changes of proteins affect the function of cells, tissues, and organisms. Here, we describe an imaging method for measuring the conformational changes of the voltage sensors of endogenous ion channel proteins within live tissue, without genetic modification. We synthesized GxTX-594, a variant of the peptidyl tarantula toxin guangxitoxin-1E, conjugated to a fluorophore optimal for two-photon excitation imaging through light-scattering tissue. GxTX-594 targets the voltage sensors of Kv2 proteins, which form potassium channels and plasma membrane–endoplasmic reticulum junctions. GxTX-594 dynamically labels Kv2 proteins on cell surfaces in response to voltage stimulation. To interpret dynamic changes in labeling intensity, we developed a statistical thermodynamic model that relates the conformational changes of Kv2 voltage sensors to labeling intensity. We used two-photon excitation imaging of rat brain slices to image Kv2 proteins in neurons. This imaging method enabled identification of conformational changes of endogenous Kv2 voltage sensors in tissue.
InterLig: a fast and accurate software for ligand-based virtual screening
Authors: Mirabello Claudio , Wallner Björn 
Published: February 2019

AbstractIn the past few years, drug discovery processes have been relying more and more on computational methods to sift out the most promising molecules before time and resources are spent to test them in experimental settings. Whenever the protein target of a given disease is not known, it becomes fundamental to have accurate methods for ligand-based Virtual Screening, which compare known active molecules against vast libraries of candidate compounds. Recently, 3D-based similarity methods have been developed that are capable of scaffold-hopping and to superimpose matching molecules. Here, we present InterLig, a new method for the comparison and superposition of small molecules based on 3D, topologically-independent alignments of atoms. We test InterLig on a standard benchmark and show that it compares favorably to the best currently available 3D methods.InterLig is open source and is available to everyone at: http://wallnerlab.org/interlig.
SIMON, an automated machine learning system reveals immune signatures of influenza vaccine responses
Authors: Tomic Adriana , Tomic Ivan , Rosenberg-Hasson Yael , Dekker Cornelia L. , Maecker Holden T. , Davis Mark M. 
Published: February 2019

AbstractMachine learning holds considerable promise for understanding complex biological processes such as vaccine responses. Capturing interindividual variability is essential to increase the statistical power necessary for building more accurate predictive models. However, available approaches have difficulty coping with incomplete datasets which is often the case when combining studies. Additionally, there are hundreds of algorithms available and no simple way to find the optimal one. Here, we developed Sequential Iterative Modelling “OverNight” or SIMON, an automated machine learning system that compares results from 128 different algorithms and is particularly suitable for datasets containing many missing values. We applied SIMON to data from five clinical studies of seasonal influenza vaccination. The results reveal previously unrecognized CD4+and CD8+T cell subsets strongly associated with a robust antibody response to influenza antigens. These results demonstrate that SIMON can greatly speed up the choice of analysis modalities. Hence, it is a highly useful approach for data-driven hypothesis generation from disparate clinical datasets. Our strategy could be used to gain biological insight from ever-expanding heterogeneous datasets that are publicly available.
Design and evaluation of novel 4-anilinoquinolines and quinazolines EGFR inhibitors in lung cancer and chordoma
Authors: Asquith Christopher R. M. , Maffuid Kaitlyn A. , Laitinen Tuomo , Torrice Chad D. , Tizzard Graham J. , Alamillo-Ferrer Carla , Koshlap Karl M. , Crona Daniel J. , Zuercher William J. 
Published: February 2019

ABSTRACTEpidermal growth factor receptor (EGFR) inhibitors have been used to target non-small cell lung cancer (NSCLC) and chordomas with varying amounts of success. We have probed several key structural features including an interaction with Asp855 within the EGFR DGF motif and interactions with the active site water network. The EGFR target engagement was then evaluated in an in-cell assay. Additionally, inhibitors were profiled in representative cellular models of NSCLC and chordomas. In addition to a structure activity relationship insights for EGFR inhibtior design, we also identified a compound (18) that is the most potent inhibitor (IC50 = 310 nM) on the UCH-2 chordoma cell line to date.