bluuebunny/crossref_metadata_2025 huggingface dataset:
Behavioral Political Science and Voter Turnout
Authors: Gerber Alan S. , Tucker Patrick D.
Published: November 2020

In recent decades, political scientists have placed greater emphasis on research designs that are able to measure causal effects credibly. The discipline has also participated in a social science–wide trend toward greater reliance on psychological and sociological theories to explain behavior. Both of these trends have been readily integrated into voter mobilization field experiments. This chapter reviews studies that employ field experimental designs that test the implications of psychological theories about political participation. It also reviews the use of field experiments to test psychological theories originally developed to explain behaviors outside of voting and applied and tested in the context of voting through mobilization messages. Finally, the chapter reflects on the limitations and future directions of behavioral political science as it relates to voter mobilization field experiments and political participation.
Private Law and Local Custom
Authors: Oman Nathan B.
Published: November 2020

This chapter explores the relationship between private law and common law. Both private law and the common law fit awkwardly into the dominant theoretical models of law, which emphasize regulation and social control by the state. Thus, the common law has long been criticized for failing to comply with the model of clearly articulated rules that are announced ex ante and applied ex post. The private law, for its part, contains numerous features that make it a poor candidate for a well-designed regulatory regime. The chapter then argues that developments in private law theory suggest a convergence between private law and the common law that responds to these issues, rendering the law both intelligible and providing an answer to the common objection that the common law involves ex post facto lawmaking. In addition, a recovery of this classical common law theory is both conceptually feasible and offers solutions to problems left currently unanswered by neoformalism.
Civil and Common Law
Authors: Smith Lionel
Published: November 2020

This chapter aims to answer the question, “what can the civil law tradition tell us about the New Private Law?” It seeks to do this by offering one civilian's perspective on private law, on U.S. private law, and on the New Private Law. In order to answer that question, it is necessary to say a little bit about what is a civilian perspective, or in other words, what makes a jurist a civilian. This is a question to which many different answers could be given. The chapter then looks at the different perspective that a civilian may have on what is the domain of private law. It also asks what insights the civilian's understanding of the discipline of law may offer to common lawyers. From a civilian perspective, the future of the New Private Law will be interesting indeed.
Property
Authors: Penner J. E.
Published: November 2020

This chapter discusses property law. It considers the idea that property had a “nominalist” ontology, and it was in danger of “disintegration” as a working legal category for that very reason. Nominalism about property has had a significant impact in U.S. case law. The concern here, however, is whether it is a helpful stance to take as a theorist of property. The chapter argues that it is not. There are indeed “high” level abstractions about property which one cannot plausibly do without if one is to understand property rights and property law doctrine. Moreover, the “bundle of rights” (BOR) challenge does not assist one in making sense of these abstractions. The chapter then looks at the conceptual failure of BOR and the New Private Law as it relates to property. BOR is generally regarded as being underpinned by what might be called the Hohfeld-Honoré synthesis. The synthesis rests upon a fairly serious mistake, which is that while the Hohfeldian examination of jural norms is analytic if it is anything, Honor’s elaboration of the incidents making up ownership is anything but—it is functional. This means that Honoré describes the situation of the owner not principally in terms of his Hohfeldian powers, duties, and rights vis-à-vis others, but in terms of the social or economic advantages that an owner has by virtue of his position, and the terms and limitations of those advantages.
Natural Rights and Natural Law
Authors: Klimchuk Dennis
Published: November 2020

This chapter argues for the continued relevance of the natural law tradition to inquiry into the philosophical foundations of private law. It focuses on the arc in the history of political philosophy that starts in Hugo Grotius and ends in Immanuel Kant. The original community of property on Grotius’s account and throughout the early modern tradition is a conceptual starting point, a representation of how people stand with respect to one another in the world abstracted from the institutions through which people administer the regime of private property. Grotius and others in the natural law tradition cast the moral aspect of that standing in terms of the natural laws that protected the natural rights of equals. The chapter then looks at two debates. Grotius’s and John Locke’s disagreements about the foundations of property rights and Grotius’s and Samuel von Pufendorf’s about the foundations of the right of necessity are, at their core, disagreements about how to render private ownership consistent with equality. The common ground against which these disagreements is framed is the view that, through its doctrines, the institution of private property inevitably expresses some view on this question, and in this way reveals its connection to the rest of people’s moral lives.
Insurance
Authors: Abraham Kenneth S.
Published: November 2020

This chapter highlights insurance law. One of the central principles of the New Private Law is that legal doctrine should be taken seriously. In insurance law, a corollary of that principle would seem to be that legal doctrine should take insurance policy language seriously. Insurance law and insurance law scholarship are largely—though not always—consistent with both the principle and its corollary. A contrasting view is that insurance law doctrine is, or should be, a vehicle for covert judicial regulation of insurance, for the purpose of policyholder protection or in order to promote more risk-spreading generally. This view can be called the “regulatory” conception of insurance law. Insurance law is not only a combination of common law doctrines and federal and state legislative and administrative directives. Insurance law also consists heavily of judicial interpretations of standard-form insurance policy language that has persisted unchanged for so long that the interpretations have the same practical effect as common law doctrines. These interpretations are so heavily anchored to the language of standard-form insurance policies that they are the locus of most insurance coverage disputes. The chapter then looks at the insurance application process; the insurance contract formation and interpretation; the general principles regarding the risks insured; the coordination of insurance coverage; and the remedies for breach of an insurance contract.
Sociological Research Ethics
Authors: Fozdar Farida , Israel Mark
Published: November 2020

Sociology has been at the forefront of scholarly debate about how to engage in social research ethically. This chapter considers sociology’s contribution to some of the key contemporary debates in this area. It begins with an outline of philosophical approaches to the ethics of undertaking social research, considering how these have been applied in sociological research. It also engages with the question of ethics governance models. The chapter then focuses on five established and emerging areas of ethical debate: the nature and formalization of consent; the use of new technologies and online data; the complexities of data sharing; the growing impact of insights from intercultural and indigenous research; and issues in autoethnography. It concludes with a question about the wider implications of sociological research as a social governance strategy.
Formats of Books
Authors: Gumbert J. P.
Published: November 2020

This chapter discusses the term “format” and the variety of ways it is applied to the description of manuscripts, including the size or proportion of the volume, the material composition of the quires, or the shape of the manuscript (codex, roll, concertina, bat books). The author also discusses copying on undivided sheets in a manner analogous to imposition in printed books.
New Roman Cursive
Authors: De Robertis Teresa
Published: November 2020

This chapter traces the graphic forms of New Roman Cursive script from its origins in the third and fourth centuries through the sixth and seventh centuries, illuminating its influence on the development of the various “national” scripts in the high Middle Ages.
Early Caroline
Authors: Ganz David
Published: November 2020

This chapter surveys Early Caroline (Carolingian) minuscule script in France and Germany, focusing on Tours as the source of the earliest examples of Caroline minuscule in the eighth century. The major writing centers of Western Francia, Eastern Francia, Mainz, Trier, Bavaria and Austria, Reims, Lorsch, Fulda, Würzburg, and Breton are discussed and illustrated, with particular attention to the distinctive features of these regional varieties.
The Palaeography of Numerals
Authors: Burnett Charles
Published: November 2020

This chapter examines the characters used to represent written numerals in Latin and European vernacular texts during the Middle Ages. Several numerical systems were in use simultaneously throughout the period, including Greek, Roman, and Arabic characters, and other methods of depicting numbers were also employed, such as representations of finger reckoning and of the counters on an abacus.
Participation in Continuing Education Programs
Authors: Feldman Daniel C. , Ng Thomas W. H.
Published: November 2020

This chapter focuses on continuing education opportunities offered to working adults. In the first section, the authors examine the antecedents to participation in continuing education programs; they consider both individual differences and situational factors. In the second section, the authors examine the outcomes of continuing education, including changes in employees’ attitudes, knowledge, skills, and behaviors on the job. In the third section, the authors explore the roles that organizations play in encouraging employee participation in continuing education and in facilitating the transfer of learning. Finally, the chapter concludes with a discussion of directions for future research on continuing education and implications for management practice.
Cultural Competency Interventions
Authors: Kerr Daniel Basil , Madden-Dent Tara , Shalabi Neivin
Published: November 2020

This chapter describes three theoretical frameworks used to increase cultural competency. Corresponding case studies follow each framework description to illustrate how the framework guided cultural interventions designed to help students and employees study and work in a culture different from their own. The three case study topics include mapping cultures in a Korean-owned Mexican automobile plant; pre-departure social, emotional, and academic development education with cultural intelligence training for Polish Fulbright scholars; and Schlossberg’s transition theory applied to Asian students during service learning in Canada. The frameworks and illustrative examples will contribute to the literature around cultural competency development and may specifically support the work of human resource professionals, higher education faculty and administrators, and researchers responsible for supporting cross-cultural communication, interactions, and transitions.
Transitions to Leadership as Foundation for Continuous Learning
Authors: London Manuel , Sherman Gary D.
Published: November 2020

The transition to leadership is a formative time during which the new leader’s motivation to lead and the organization’s culture and management influence the new leader’s evolving self-image and behavioral style that sets the foundation for future learning. This chapter reviews the literature on leader identity, motivation to lead, and variables that contribute to motivation and that underlie transformational and transactional leadership styles. Based on this review, we present a model of how a new leader’s motivation to lead may be influenced by characteristics such as achievement goals, sensitivity to others, and a keen desire to learn. The model indicates that new leaders’ motivation combined with the extent to which the organization and higher-level managers empower new leaders and support their development will influence the extent to which new leaders learn to lead by exerting dominance and/or garnering followers’ respect for their leadership competence and concern. Organizations that understand these processes can shape the extent to which new leaders learn transactional and transformational styles and identities that are the foundation for ongoing leadership development. Also, these processes can avoid negative power dynamics from a mismatch between individual characteristics and organizational culture.
Greek–Turkish Relations
Authors: Grigoriadis Ioannis N.
Published: November 2020

This chapter examines the development of Greek–Turkish relations under the influence of the European Union and the limits of the rapprochement between the two countries. The 1999 lifting of the Greek veto on the improvement of EU–Turkey relations triggered an improvement in bilateral relations which has remained unprecedented since the 1950s. Bilateral relations underwent a paradigmatic shift which allowed for zero-sum game-based approaches to be challenged. Economic and civil society ties grew stronger; minority problems were mitigated while longstanding bilateral diplomatic disputes remained unresolved and far from international adjudication. Turkey’s faltering EU membership ambitions weakened a crucial catalyst of Greek–Turkish rapprochement, yet there was no relapse to the pre-1999 problematic relations. Despite the severe economic and social crises that hit Greece and Turkey in the last decade, Greek–Turkish relations have not fallen victim to rampant populism. In both countries, the bilateral disputes and the Cyprus issue declined in importance compared to other foreign policy issues. This allowed both sides to focus on urgent questions but removed a strong incentive to take risks for conflict resolution. The costs of avoiding a bitter compromise appear low, and this provides a strong incentive to political leaders to refrain from necessary political risks. This poses substantial risks for the future and prevents the development of even closer economic and social relations.
The Maghreb al-Aqsa
Authors: Fili Abdallah
Published: November 2020

Islamic archaeology in Morocco has its roots in the colonial period and developed in concert with architectural and urban studies of the imperial cities of Fes, Marrakech, and Meknes. For many years, it remained the poor relation to classical archaeology, and it was only in the 1970s and 1980s that systematic excavations began at Islamic sites. Since then, there has been a significant rise in the number of projects and amount of evidence available for urban and rural sites, particularly between the 8th and 14th centuries, though many challenges remain in terms of funding, training, finds analysis, and the use of new scientific technologies. This chapter charts the development of Islamic archaeology and lays out the key developments in urban and rural archaeology and the study of material culture in Morocco.
Community Archaeology in the Islamic World
Authors: LaBianca Øystein S. , Ronza Maria Elena , Harris Noël
Published: November 2020

Community archaeology, or the notion that local officials, school teachers, community elders, workmen, and other community members might be recruited as partners in helping to preserve, protect, interpret, and present archaeological sites, is at best a nascent one in Islamic archaeology. This chapter provides a brief background to the concept and practice of community archaeology with special reference to its standing as an academic subspecialty within Islamic archaeology and its on-the-ground practice in countries with predominantly Muslim populations. The contribution of various international and professional organizations to the development of community archaeology in Islamic countries is assayed and specific projects are highlighted as examples of the kind of work that is being done in different countries. The chapter concludes by singling out the country of Jordan as being in the vanguard of a community archaeology revolution in the Islamic lands, including lessons learned in that country about best practices for implementing community archaeology projects.
Is There an “Islamic” Practice for the Preservation of Cultural Heritage?
Authors: Rico Trinidad
Published: November 2020

This discussion features an ongoing conversation that seeks to reveal the way that preservation practices arise from or react to uniquely “Islamic” articulations of material and immaterial cultural traditions. Although the aim of this debate is to further ethical cultural heritage preservation practices, it reveals a tension between two intellectual debates within critical heritage studies: on the one hand, a concern for the study, articulation, and stewardship of alternative heritage preservation approaches and, on the other hand, a concern with a tendency in heritage preservation to Orientalize “non-Western” heritage preservation practices as forcefully distinct from long-established “Western” practices.
Southern Syria
Authors: Walker Bethany J.
Published: November 2020

Traditionally associated with the “Holy Land” and the target of early scientific investigations, southern Syria is one of the most intensively studied regions by archaeologists. Islamic archaeology has very old roots here, and many of the debates that have driven development of the field arose first in this region. This chapter, focusing primarily on Palestine and the Transjordan, evaluates the contributions to the field by archaeologists working there and critiques recent fieldwork as it informs such highly debated topics as Islamization, the collapse of the Late Antique polis, the militarization of frontiers, and rural resilience in times of political chaos. A special emphasis is placed on environmental and landscape research that has been opening new windows on rural society and the later historical periods.
Arabia and the Gulf
Authors: Petersen Andrew
Published: November 2020

This chapter introduces the main ways in which archaeology has been used to investigate Arabia’s past during the Islamic era. While the potential for archaeology within the peninsula cannot be overstated, logistical obstacles and political difficulties have made field research difficult, with the result that it has lagged behind that of other areas in the Middle East. However, recent initiatives in most of the states within the Arabian Peninsula have meant that this is now one of the leading areas for archaeological research into Islamic society and culture. Although the chapter mentions some major recent archaeological projects, the aim is to highlight current trajectories of research rather than provide an exhaustive list of excavation and survey sites. Particular attention has been paid to settlement types, partly to counter ideas that the region was primarily inhabited by Bedouin nomads. The chapter emphasizes different regional traditions to reflect the geographical diversity of Arabia and its connections with other regions. The maritime cultures of the Gulf, the Red Sea, and the Indian Ocean are particularly important in this respect and have meant that Arabia is much less isolated than its often inhospitable interior would suggest.
Transcriptomics and metatranscriptomics in zooplankton: wave of the future?
Authors: Lenz Petra H , Lieberman Brandon , Cieslak Matthew C , Roncalli Vittoria , Hartline Daniel K
Published: November 2020

Molecular tools have changed the understanding of zooplankton biodiversity, speciation, adaptation, population genetics and global patterns of connectivity. However, the molecular resources needed to capitalize on these advances continue to be limited in comparison with those available for other eukaryotic plankton. This deficiency could be addressed through an Ocean Zooplankton Open ‘Omics Project (Ocean ZOOP) that would generate de novo assembled transcriptomes for hundreds of metazoan plankton species. A collection of comparable reference transcriptomes would generate a new framework for ecological and physiological studies. Defining species niches, identifying optimal habitats, assessing adaptive capacity and predicting changes in phenology are just a few examples of how such a resource could transform studies on zooplankton ecology.
Positive disease-specific autoantibodies have limited clinical significance in diagnosing IgG4-related disease in daily clinical practice
Authors: Mizushima Ichiro , Yamano Takahiro , Kawahara Hiroyuki , Hibino Shinya , Nishioka Ryo , Zoshima Takeshi , Hara Satoshi , Ito Kiyoaki , Fujii Hiroshi , Nomura Hideki , Kawano Mitsuhiro
Published: November 2020

Objectives

The 2019 ACR/EULAR classification criteria for IgG4-related disease (IgG4-RD) have exclusion criteria including positive disease-specific autoantibodies, and these have been documented to have a high specificity. This study aimed to further validate these criteria as well as identify characteristics of patients showing false-negative results.

Methods

We retrospectively analysed 162 IgG4-RD patients and 130 mimickers. The sensitivity, specificity and fulfilment rates for each criterion were calculated, and intergroup comparisons were performed to characterize the false-negative cases.

Results

Both the IgG4-RD patients and mimickers were aged ≥65 years with male predominance. The final diagnoses of mimickers were mainly malignancy, vasculitis, sarcoidosis and aneurysm. The classification criteria had a sensitivity of 72.8% and specificity of 100%. Of the 44 false-negative cases, one did not fulfil the entry criteria, 20 fulfilled one exclusion criterion and 27 did not achieve sufficient inclusion criteria scores. The false-negative cases had fewer affected organs, lower serum IgG4 levels, and were less likely to have received biopsies than the true-positive cases. Notably, positive disease-specific autoantibodies were the most common exclusion criterion fulfilled in 18 patients, only two of whom were diagnosed with a specific autoimmune disease complicated by IgG4-RD. In addition, compared with the true-positive cases, the 18 had comparable serum IgG4 levels, number of affected organs, and histopathology and immunostaining scores despite higher serum IgG and CRP levels.

Conclusions

The ACR/EULAR classification criteria for IgG4-RD have an excellent diagnostic specificity in daily clinical practice. Positive disease-specific autoantibodies may have limited clinical significance for the diagnosis of IgG4-RD.
Bleeding, Thromboembolism, and Clinical Outcomes in Venovenous Extracorporeal Membrane Oxygenation
Authors: Stokes John W. , Gannon Whitney D. , Sherrill Wren H. , Armistead Leslie B. , Bacchetta Matthew , Rice Todd W. , Semler Matthew W. , Casey Jonathan D.
Published: November 2020

Objectives:

Bleeding and thromboembolism are common during venovenous extracorporeal membrane oxygenation. The relative frequency of these complications and their impact on clinical outcomes have not been described, and no randomized trials exist to guide anticoagulation strategies in extracorporeal membrane oxygenation. Our objective was to examine the relative frequencies of bleeding and thromboembolic events and their associations with survival among a cohort of consecutive patients receiving venovenous extracorporeal membrane oxygenation.

Design:

Retrospective cohort study.

Setting:

A single academic medical center.

Patients:

Adult patients receiving venovenous extracorporeal membrane oxygenation and anticoagulation. Eligibility criteria for this analysis were selected to emulate the population that would be recruited for a randomized trial of anticoagulation strategies during venovenous extracorporeal membrane oxygenation. Patients were excluded if they had active bleeding or thromboembolism prior to extracorporeal membrane oxygenation initiation, a history of trauma or surgery in the 7 days prior to extracorporeal membrane oxygenation initiation, an arterial extracorporeal membrane oxygenation cannula, or if they received greater than 48 hours of extracorporeal membrane oxygenation support at another institution

Interventions:

None.

Measurements and Main Results:

Outcomes included bleeding and thromboembolic events, duration of extracorporeal membrane oxygenation support, hospital length of stay, and in-hospital survival among 55 patients receiving venovenous extracorporeal membrane oxygenation. Bleeding events occurred in 25 patients (45.5%), and thromboembolism occurred in eight patients (14.5%). Bleeding events were associated with longer duration of extracorporeal membrane oxygenation support (p = 0.007) and worse in-hospital survival (p = 0.02). Thromboembolic events did not appear to be associated with clinical outcomes.

Conclusions:

In this cohort of patients receiving venovenous extracorporeal membrane oxygenation and anticoagulation, bleeding occurred more frequently than thromboembolism and was associated with worse survival. These results highlight the need for randomized trials to evaluate the safety and efficacy of continuous IV anticoagulation among patients receiving venovenous extracorporeal membrane oxygenation.
Clinical and serological findings of Madariaga and Venezuelan equine encephalitis viral infections: A follow-up study five years after an outbreak in Panama
Authors: Carrera Jean-Paul , Pittí Yaneth , Molares-Matrínez Juan C. , Casal Eric , Pereyra-Elias Reneé , Saenz Lisseth , Guerrero Isela , Galué Josefrancisco , Rodriguez-Alvarez Fatima , Jackman Carmela , Pascale Juan Miguel , Armien Blas , Weaver Scott C. , Donnelly Christl A. , Vittor Amy Y.
Published: November 2020

Background

Human cases of Madariaga virus (MADV) infection were first detected during an outbreak in 2010 in eastern Panama, where Venezuelan equine encephalitis virus (VEEV) also circulates. Little is known about the long-term consequences of either alphavirus infection.

Methods

A follow-up study of the 2010 outbreak was undertaken in 2015. An additional survey was carried out two weeks after a separate 2017 alphavirus outbreak in a neighboring population in eastern Panama. Serological studies and statistical analysis were undertaken in both populations.

Results

Amongst the originally alphavirus-seronegative subjects (n=35 of 65), seroconversion was observed at a rate of 14.3% (95% CI: 4.8%-30.3%) for MADV and 8.6% (95% CI: 1.8%-23.1%) for VEEV over 5 years. Amongst the originally MADV seropositive subjects (n=14 of 65), VEEV seroconversion occurred in 35.7% (95% CI: 12.8%-64.9%). In the VEEV seropositive subjects (n=16 of 65), MADV seroconversion occurred in 6.3% (95% CI: 0.2%-30.2%). MADV seroreversion was observed in 14.3% (95% CI: 1.8%-42.8%) of those originally seropositive in 2010. VEEV seroconversion in the baseline MADV-seropositive subjects was significantly higher than in alphavirus-negative subjects. In the population sampled in 2017, MADV and VEEV seroprevalence was 13.2% and 16.8%, respectively. Memory loss, insomnia, irritability and seizures were reported significantly more frequently in alphavirus-seropositive subjects than in seronegative.

Conclusions

High rates of 5-year seroconversions to MADV and VEEV suggest continuous circulation of both viruses in Panama. Enhanced susceptibility may be conferred by MADV towards VEEV. We provide evidence of persistent neurologic symptoms up to 5 years following MADV and VEEV exposure.

summary

We estimate seroconversion rates over a 5-year period to Madariaga (MADV) and Venezuelan equine encephalitis (VEEV) alphaviruses in Panama. Individuals with MADV antibodies seroconverted to VEEV at a rate greater than individuals who were alphavirus-negative at baseline. This was not observed in individuals with VEEV antibodies, suggesting asymmetric cross-immunity. Neurological sequelae were reported more frequently by MADV and/or VEEV seropositive-versus seronegative subjects.
Mapping malaria by sharing spatial information between incidence and prevalence datasets
Authors: Lucas Tim C.D. , Nandi Anita K. , Chestnutt Elisabeth G. , Twohig Katherine A. , Keddie Suzanne H. , Collins Emma L. , Howes Rosalind E. , Nguyen Michele , Rumisha Susan F. , Python Andre , Arambepola Rohan , Bertozzi-Villa Amelia , Hancock Penelope , Amratia Punam , Battle Katherine E. , Cameron Ewan , Gething Peter W. , Weiss Daniel J.
Published: November 2020

As malaria incidence decreases and more countries move towards elimination, maps of malaria risk in low prevalence areas are increasingly needed. For low burden areas, disaggregation regression models have been developed to estimate risk at high spatial resolution from routine surveillance reports aggregated by administrative unit polygons. However, in areas with both routine surveillance data and prevalence surveys, models that make use of the spatial information from prevalence point-surveys have great potential. Using case studies in Indonesia, Senegal and Madagascar, we compare two methods for incorporating point-level, spatial information into disaggregation regression models. The first simply fits a Gaussian random field to prevalence point-surveys to create a new covariate. The second is a multi-likelihood model that is fitted jointly to prevalence point-surveys and polygon incidence data. We find that the simple model generally performs better than a baseline disaggregation model while the joint model performance was mixed. More generally, our results demonstrate that combining these types of data improves estimates of malaria incidence.
NERO: A Biomedical Named-entity (Recognition) Ontology with a Large, Annotated Corpus Reveals Meaningful Associations Through Text Embedding
Authors: Wang Kanix , Stevens Robert , Alachram Halima , Li Yu , Soldatova Larisa , King Ross , Ananiadou Sophia , Li Maolin , Christopoulou Fenia , Ambite Jose Luis , Garg Sahil , Hermjakob Ulf , Marcu Daniel , Sheng Emily , Beißbarth Tim , Wingender Edgar , Galstyan Aram , Gao Xin , Chambers Brendan , Khomtchouk Bohdan B. , Evans James A. , Rzhetsky Andrey
Published: November 2020

Machine reading is essential for unlocking valuable knowledge contained in the millions of existing biomedical documents. Over the last two decades1,2, the most dramatic advances in machine-reading have followed in the wake of critical corpus development3. Large, well-annotated corpora have been associated with punctuated advances in machine reading methodology and automated knowledge extraction systems in the same way that ImageNet4was fundamental for developing machine vision techniques. This study contributes six components to an advanced, named-entity analysis tool for biomedicine: (a) a new, Named-Entity Recognition Ontology (NERO) developed specifically for describing entities in biomedical texts, which accounts for diverse levels of ambiguity, bridging the scientific sublanguages of molecular biology, genetics, biochemistry, and medicine; (b) detailed guidelines for human experts annotating hundreds of named-entity classes; (c) pictographs for all named entities, to simplify the burden of annotation for curators; (d) an original, annotated corpus comprising 35,865 sentences, which encapsulate 190,679 named entities and 43,438 events connecting two or more entities; (e) validated, off-the-shelf, named-entity recognition automated extraction, and; (f) embedding models that demonstrate the promise of biomedical associations embedded within this corpus.
Modelling the neural code in large populations of correlated neurons
Authors: Sokoloski Sacha , Aschner Amir , Coen-Cagli Ruben
Published: November 2020

Neurons respond selectively to stimuli, and thereby define a code that associates stimuli with population response patterns. Certain correlations within population responses (noise correlations) significantly impact the information content of the code, especially in large populations. Understanding the neural code thus necessitates response models that quantify the coding properties of modelled populations, while fitting large-scale neural recordings and capturing noise correlations. In this paper we propose a class of response model based on mixture models and exponential families. We show how to fit our models with expectation-maximization, and that they capture diverse variability and covariability in recordings of macaque primary visual cortex. We also show how they facilitate accurate Bayesian decoding, provide a closed-form expression for the Fisher information, and are compatible with theories of probabilistic population coding. Our framework could allow researchers to quantitatively validate the predictions of neural coding theories against both large-scale neural recordings and cognitive performance.
ExTaxsI: an exploration tool of biodiversity molecular data
Authors: Agostinetto Giulia , Sandionigi Anna , Chahed Adam , Brusati Alberto , Parladori Elena , Balech Bachir , Bruno Antonia , Pescini Dario , Casiraghi Maurizio
Published: November 2020

Background

The increasing availability of multi omics data is leading to continually revise estimates of existing biodiversity data. In particular, the molecular data enable to characterize novel species yet unknown and to increase the information linked to those already observed with new genomic data. For this reason, the management and visualization of existing molecular data, and their related metadata, through the implementation of easy to use IT tools have become a key point for the development of future research. The more users are able to access biodiversity related information, the greater the ability of the scientific community to expand the knowledge in this area.

Results

In our research we have focused on the development of ExTaxsI (Exploring Taxonomies Information), an IT tool able to retrieve biodiversity data stored in NCBI databases and provide a simple and explorable visualization. Through the three case studies presented here, we have shown how an efficient organization of the data already present can lead to obtaining new information that is fundamental as a starting point for new research. Our approach was also able to highlight the limits in the distribution data availability, a key factor to consider in the experimental design phase of broad spectrum studies, such as metagenomics.

Conclusions

ExTaxI can easily produce explorable visualization of molecular data and its metadata, with the aim to help researchers to improve experimental designs and highlight the main gaps in the coverage of available data.
Selective co-activation of α7- and α4β2-nicotinic acetylcholine receptors reverses beta-amyloid-induced synaptic dysfunction
Authors: Roberts Jessica P. , Stokoe Sarah A. , Sathler Matheus F. , Nichols Robert A. , Kim Seonil
Published: November 2020

Beta-amyloid (Aβ) has been recognized as an early trigger in the pathogenesis of Alzheimer’s disease (AD) leading to synaptic and cognitive impairments. Aβ can alter neuronal signaling through interactions with nicotinic acetylcholine receptors (nAChRs), contributing to synaptic dysfunction in AD. The three major nAChR subtypes in the hippocampus are composed of α7-, α4β2-, and α3β4-nAChRs. Aβ selectively affects α7- and α4β2-nAChRs, but not α3β4-nAChRs in hippocampal neurons, resulting in neuronal hyperexcitation. However, how nAChR subtype selectivity for Aβ affects synaptic function in AD is not completely understood. Here, we showed that Aβ associated with α7- and α4-containing nAChRs but not α3-containing receptors. Computational modeling suggested two amino acids in α7-nAChRs, Arginine 208 and Glutamate 211, were important for the interaction between Aβ and α7-containing nAChRs. These residues were found to be conserved only in the α7 and α4 subunits. We therefore mutated these amino acids in α7-containing nAChRs to mimic the α3 subunit and found that mutant α7-containing receptors were unable to interact with Aβ, providing direct molecular evidence for how Aβ selectively interacted with α7- and α4-containing receptors, but not α3-containing nAChRs. Selective co-activation of α7- and α4β2-nAChRs was also sufficient to reverse Aβ-induced AMPA receptor (AMPAR) dysfunction, including Aβ-induced reduction of AMPAR phosphorylation and surface expression in hippocampal neurons. Moreover, the Aβ-induced disruption of long-term potentiation was reversed by co-stimulation of α7- and α4β2-nAChRs. These findings support a novel mechanism for Aβ’s impact on synaptic function in AD, namely the differential regulation of nAChR subtypes.
Cryptic prokaryotic promoters explain instability of recombinant neuronal sodium channels in bacteria
Authors: DeKeyser Jean-Marc , Thompson Christopher H. , George Alfred L.
Published: November 2020

Mutations in genes encoding the human brain-expressed voltage-gated sodium (NaV) channels NaV1.1, NaV1.2, and NaV1.6 are associated with a variety of human diseases including epilepsy, autism spectrum disorder, familial migraine, and other neurodevelopmental disorders. A major obstacle hindering investigations of the functional consequences of brain NaVchannel mutations is an unexplained instability of the corresponding recombinant complementary DNA (cDNA) when propagated in commonly used bacterial strains manifested by high spontaneous rates of mutation. Here we investigated the cause for instability of human NaV1.1 cDNA. We identified cryptic prokaryotic promoter-like elements that are presumed to drive transcription of translationally toxic mRNAs in bacteria as the cause of the instability, and demonstrated that mutations in these elements can mitigate the instability. Extending these observations, we generated full-length human NaV1.1, NaV1.2, and NaV1.6 plasmids using one or two introns that interrupt the cryptic reading frames along with a minimum number of silent nucleotide changes that achieved stable propagation in bacteria. Expression of the stabilized sequences in cultured mammalian cells resulted in functional NaVchannels with properties that matched their parental constructs. Our findings explain a widely observed instability of recombinant neuronal human NaVchannels, and we describe re-engineered plasmids that attenuate this problem.
Population receptive field shapes in early visual cortex are nearly circular
Authors: Lerma-Usabiaga Garikoitz , Winawer Jonathan , Wandell Brian A.
Published: November 2020

The visual field region where a stimulus evokes a neural response is called the receptive field (RF). Analytical tools combined with functional MRI can estimate the receptive field of the population of neurons within a voxel. Circular population RF (pRF) methods accurately specify the central position of the pRF and provide some information about the spatial extent (diameter) of the receptive field. A number of investigators developed methods to further estimate the shape of the pRF, for example whether the shape is more circular or elliptical. There is a report that there are many pRFs with highly elliptical pRFs in early visual cortex (V1-V3; Silson et al., 2018). Large aspect ratios (>2) are difficult to reconcile with the spatial scale of orientation columns or visual field map properties in early visual cortex. We started to replicate the experiments and found that the software used in the publication does not accurately estimate RF shape: it produces elliptical fits to circular ground-truth data. We analyzed an independent data set with a different software package that was validated over a specific range of measurement conditions, to show that in early visual cortex the aspect ratios are less than 2. Furthermore, current empirical and theoretical methods do not have enough precision to discriminate ellipses with aspect ratios of 1.5 from circles. Through simulation we identify methods for improving sensitivity that may estimate ellipses with smaller aspect ratios. The results we present are quantitatively consistent with prior assessments using other methodologies.

Significance Statement

We evaluated whether the shape of many population receptive fields in early visual cortex is elliptical and differs substantially from circular. We evaluated two tools for estimating elliptical models of the pRF; one tool was valid over the measured compliance range. Using the validated tool, we found no evidence that confidently rejects circular fits to the pRF in visual field maps V1, V2 and V3. The new measurements and analyses are consistent with prior theoretical and experimental assessments in the literature.
Dorsomedial prefrontal neural ensembles reflect changes in task utility that culminate in task quitting
Authors: Porter Blake S. , Hillman Kristin L.
Published: November 2020

When performing a physically demanding behavior, sometimes the optimal choice is to quit the behavior rather than persist in order to minimize energy expenditure for the benefits gained. The dorsomedial prefrontal cortex (dmPFC), consisting of the anterior cingulate cortex and secondary motor area, likely contributes towards such utility assessments. Here, we examined how male rat dmPFC single unit and ensemble level activity corresponded to changes in task utility and quitting in an effortful weight lifting task. Rats carried out two task paradigms: one that became progressively more physically demanding over time and a second fixed effort version. Rats could quit the task at any time. Dorsomedial PFC neurons were highly responsive to each behavioral stage of the task, consisting of rope pulling, reward retrieval, and reward area leaving. Activity was highest early in sessions, commensurate with the highest relative task utility, then decreased until the point of quitting. Neural ensembles consistently represented the sequential behavioral phases of the task. However, these representations were modified over time and became more distinct over the course of the session. These results suggest that dmPFC neurons represent behavioral states that are dynamically modified as behaviors lose their utility, culminating in task quitting.

New & Noteworthy

When carrying out a physically demanding task animals must continually assess whether to persist or quit. In this study we recorded neurons in the dorsomedial prefrontal cortex (dmPFC) of rats as they carried out a challenging weightlifting task, up to the point of quitting. We demonstrate that dmPFC neurons form a representation of the task that is modified, via a decrease in firing rate, by the decreasing utility of the task that may signal quitting.
In vivoproteomic mapping through GFP-directed proximity-dependent biotin labelling in zebrafish
Authors: Xiong Zherui , Lo Harriet P. , McMahon Kerrie-Ann , Martel Nick , Jones Alun , Hill Michelle M. , Parton Robert G. , Hall Thomas E.
Published: November 2020

Protein interaction networks are crucial for complex cellular processes. However, the elucidation of protein interactions occurring within highly specialised cells and tissues is challenging. Here we describe the development, and application, of a new method for proximity-dependent biotin labelling in whole zebrafish. Using a conditionally stabilised GFP-binding nanobody to target a biotin ligase to GFP-labelled proteins of interest, we show tissue-specific proteomic profiling using existing GFP-tagged transgenic zebrafish lines. We demonstrate the applicability of this approach, termed BLITZ (Biotin Labelling In Tagged Zebrafish), in diverse cell types such as neurons and vascular endothelial cells. We applied this methodology to identify interactors of caveolar coat protein, cavins, in skeletal muscle. Using this system, we defined specific interaction networks withinin vivomuscle cells for the closely related but functionally distinct Cavin4 and Cavin1 proteins.
The APETALA2 transcription factor LsAP2 regulates seed shape in lettuce
Authors: Luo Chen , Wang Shenglin , Ning Kang , Chen Zijing , Wang Yixin , Yang Jingjing , Qi Meixia , Wang Qian
Published: November 2020

Seeds are major vehicles of propagation and dispersal in plants. A number of transcription factors, including APETALA2 (AP2), play crucial roles during the seed development process in various plant species. However, genes essential for seed development and the regulatory networks during seed development remain unclear in lettuce. Here, we identified a lettuceAP2(LsAP2) gene that was highly expressed at the early stages of seed development.LsAP2knockout plants obtained by the CRISPR/Cas9 system were used to explore the biological function ofLsAP2. Compared with wild-type, the seeds of theLsap2mutant plants had increased length and decreased width, and developed an extended tip at the seed top. After further investigating the seed structural characteristics ofLsap2mutant plants, we proposed a new function ofLsAP2in seed dispersal. Moreover, we identified several interactors of LsAP2. Our results showed that LsAP2 directly interacted with the lettuce homolog of BREVIPEDICELLUS (LsBP) and promoted the expression ofLsBP. Transcriptome analysis revealed that LsAP2 might also be involved in brassinosteroid biosynthesis and signaling pathways. Taken together, our data indicate that LsAP2 has a significant function in regulating seed shape in lettuce.
Insula cortex gates the interplay of action observation and preparation for controlled imitation
Authors: Campbell Megan E. J. , Nguyen Vinh T. , Cunnington Ross , Breakspear Michael
Published: November 2020

Perceiving, anticipating and responding to the actions of another person are fundamentally entwined processes such that seeing another’s movement can prompt automatic imitation, as in social mimicry and contagious yawning. Yet the direct-matching of others’ movements is not always appropriate, so this tendency must be controlled. This necessitates the hierarchical integration of the systems for action mirroring with domain-general control networks. Here we use functional magnetic resonance imaging (fMRI) and computational modelling to examine the top-down and context-dependent modulation of mirror representations and their influence on motor planning. Participants performed actions that either intentionally or incidentally imitated, or counter-imitated, an observed action. Analyses of these fMRI data revealed a region in the mid-occipital gyrus (MOG) where activity differed between imitation versus counter-imitation in a manner that depended on whether this was intentional or incidental. To identify broader cortical network mechanisms underlying this interaction between intention and imitativeness, we used dynamic causal modelling to pose specific hypotheses which embody assumptions about inter-areal interactions and contextual modulations. These models each incorporated four regions - medial temporal V5 (early motion perception), MOG (action-observation), supplementary motor area (action planning), and anterior insula (executive control) – but differ in their interactions and hierarchical structure. The best model of our data afforded a crucial role for the anterior insula, gating the interaction of supplementary motor area and MOG activity. This provides a novel brain network-based account of task-dependent control over the integration of motor planning and mirror systems, with mirror responses suppressed for intentional counter-imitation.