bluuebunny/crossref_metadata_2025 huggingface dataset:
4. Neo-functionalism
Authors: Jensen Carsten Strøby
Published: January 2019

This chapter reviews a theoretical position, neo-functionalism, which was developed in the mid-1950s by scholars based in the United States. The fundamental argument of the theory is that states are not the only important actors on the international scene. As a consequence, neo-functionalists focus their attention on the role of supranational institutions and non-state actors, such as interest groups and political parties, who, they argue, are the real driving force behind integration efforts. The chapter that follows provides an introduction to the main features of neo-functionalist theory, its historical development since the 1950s and how neo-functionalism is used today. It focuses, more specifically, on three hypotheses advanced by neo-functionalists: the spillover hypothesis; the elite socialization hypothesis; and the supranational interest group hypothesis. The chapter also considers the main critiques of the theory and discusses the ups and downs in the intellectual use of neo-functionalism over the last 50 years. The final section scrutinizes the revival of interest in neo-functionalism and provides some examples of how today’s neo-functionalists differ from those of the 1950s. While neo-functionalism used to be conceptualized as a ‘grand theory’, it is now looked upon and used as a middle-range theory that explains only part of the European integration process.
8. Europeanization
Authors: Börzel Tanja A. , Panke Diana
Published: January 2019

The first section of the chapter explains what Europeanization means and outlines the main approaches to studying this phenomenon. The second section describes why this concept has become so prominent in research on the European Union (EU) and its member states. In the third section, the chapter reviews the state of the art with particular reference to how the EU affects states (‘top-down’ Europeanization). It illustrates the theoretical arguments with empirical examples. Similarly, the fourth section examines how states can influence the EU (‘bottom-up’ Europeanization) and provides some theoretical explanations for the empirical patterns observed. This is followed by a section that presents an overview of research that looks at linkages between bottom-up and top-down Europeanization, and considers the future of Europeanization research with regard to EU’s recent and current crises and challenges. The conclusion argues that Europeanization, despite the crises the EU has been facing, will remain an important field of EU research for the foreseeable future.
9. Democracy and Legitimacy in the European Union
Authors: Smismans Stijn
Published: January 2019

This chapter discusses the extent to which decision-making in the European Union can be considered democratic and legitimate. The chapter clarifies the concepts ‘democracy’ and ‘legitimacy’, and describes how, although initially the legitimacy of the European polity was not perceived as a problem, it became more problematic as the EU gained more competences. The European democratic deficit became an important issue of debate only during the 1990s after the Maastricht Treaty had transferred considerable powers to the EU. The main solution to the democratic deficit has been inspired by the parliamentary model of democracy and involves strengthening the European Parliament (EP), while also paying attention to the role of national parliaments and regional and local authorities. The chapter also shows how the governance debate at the start of the twenty-first century broadened the conceptual understanding of democracy in the EU by addressing the complexity of European governance (see also Chapter 7). By looking at different stages of policy-making and different modes of governance, while dealing with issues such as transparency and the role of civil society, the chapter discusses a wider range of issues associated with the democracy and legitimacy of the Union. It assesses the impact on EU democracy of the Constitutional Treaty and the Lisbon Treaty. The chapter concludes by warning that three main crises, namely the economic, migration, and security crises, have revived nationalist and populist movements exacerbating the challenges to the EU’s legitimacy.
13. The Court of Justice of the European Union
Authors: Kapsis Ilias
Published: January 2019

This chapter examines the Court of Justice of the European Union (CJEU), which consists of three courts: the Court of Justice (or ‘the Court’), the General Court, and the Civil Service Tribunal. It focuses on issues of structure and procedure, the extent of the Courts’ jurisdiction, and their role in the promotion of European integration. The chapter also discusses the criticism directed at the CJEU for the way it exercises its judicial powers, which allegedly involve political considerations normally unacceptable for a judicial body. Lastly, the chapter looks at role of the Courts in the current challenging environment facing the EU as a result inter alia of Brexit, the refugee crisis, the rise of populism, and the continuing impact of the economic crisis.
15. Citizens and Public Opinion in the European Union
Authors: Guerra Simona , Trenz Hans-Jörg
Published: January 2019

This chapter provides an overview of trends in public opinion toward the European Union. The chapter also discusses the key factors thought to explain differences in mass opinion regarding the EU. These include political economy and rationality; that is, opinions stemming from calculations about the costs and benefits of the EU; perceptions of the national government (domestic proxies); the influence of political elites; political psychology, including cognitive mobilization (attentiveness to politics) and concerns about the loss of national identity; and finally, the role of the mass media in driving opinions regarding the EU.
17. Trade and Development Policies
Authors: Smith Michael
Published: January 2019

This chapter focuses on the external economic relations of the European Union—the longest-established area of collective European international policy-making and action—and specifically on trade and development policy. The chapter begins by examining institutions and policy-making for trade, in which the Commission plays a central role in initiating and conducting policy and looks especially at the Common Commercial Policy (CCP). It goes on to examine development policy—an area of mixed competence, in which policy responsibility is shared between the EU institutions and national governments. The chapter then proceeds to explore the substance and impact of EU trade and development policies, and to assess the linkages between the two areas. The conclusions draw attention to a number of tensions and contradictions in EU trade and development policy.
19. The European Union’s Foreign, Security, and Defence Policies
Authors: Friis Anna Maria , Juncos Ana E.
Published: January 2019

EU cooperation in foreign, security, and defence policy has developed rapidly since the launch of the Common Foreign and Security Policy (CFSP) in the early 1990s. The first section of this chapter charts the first steps towards a common policy in this area, including the development of the Common Security and Defence Policy (CSDP) and the gradual militarization of the EU. The chapter then reviews the key theoretical debates on the EU’s role as a foreign and security actor. The subsequent section analyses the main actors involved in the CFSP, focusing in particular on the role of the member states and EU institutions in the development of the policy. The next section of the chapter evaluates the range of military and civilian CSDP operations and missions that the EU has undertaken to date, before examining the key challenges that the EU faces in this area.
20. The Single Market
Authors: Egan Michelle
Published: January 2019

This chapter charts the evolution of the Single Market project, from its original conception in the 1950s, beginning with the Treaty of Rome and ending with the Single Market Act I and II. It explores the role of the Court of Justice of the EU (CJEU) in promoting market access, the balance between different economic ideals, and regulatory strategies used to foster market integration. The chapter highlights the importance of the Single Market in seeking to promote competitiveness and growth as well as the diffusion of its regulations beyond its borders. It concludes by demonstrating how both traditional international relations theories of integration and newer approaches in comparative politics and international relations, can be used to shed light on the governance of the Single Market.
22. The Area of Freedom, Security, and Justice
Authors: Uçarer Emek M.
Published: January 2019

This chapter examines a European policy, Justice and Home Affairs (JHA), and its transformation into the Area of Freedom, Security, and Justice (AFSJ). The AFSJ, one of the newest additions to the European Union mandate, seeks to engage the EU in the areas of immigration and asylum policy as well as police and judicial cooperation. Cooperation in the AFSJ has evolved into a fully fledged and vibrant EU policy. The chapter first considers the early years of cooperation in the AFSJ and the Schengen Agreement before discussing the procedural steps taken by the Maastricht Treaty (1993), Amsterdam Treaty (1999), and Lisbon Treaty. It then turns to policy output, taking into account the Tampere European Council meeting, the Hague Programme, and the Stockholm Programme. It concludes with an overview of various challenges specific to AFSJ cooperation, with a particular focus on the EU’s post-2014 migration crisis. cooperation
23. Economic and Monetary Union
Authors: Verdun Amy
Published: January 2019

This chapter provides an introduction to economic and monetary union (EMU). It describes the key components of EMU and what happens when countries join. EMU was the result of decades of collaboration and learning, which have been subdivided here into three periods: 1969–91, taking us from the European Council’s first agreement to set up EMU to Maastricht, when the European Council included EMU in the Treaty on European Union (TEU); 1992–2002, from when plans for EMU were being developed to the irrevocable fixing of exchange rates; and 2002 onwards, once EMU had been established, and euro banknotes and coins were circulating in member states. Next, the chapter reviews various theoretical explanations, both economic and political, accounting for why EMU was created and looks at some criticisms of EMU. Finally, the chapter discusses how EMU has fared under the global financial crisis and the sovereign debt crisis. These crises brought to the fore various imperfections in the design of EMU. This section discusses what changes have been made since 2009 to address those flaws and at what we may expect in the years to come.
25. Environmental Policy
Authors: Benson David , Gravey Viviane , Jordan Andrew
Published: January 2019

Despite its very strong economic roots, the European Union has nonetheless become an international leader in environmental protection and sustainable development policy. Environmental concerns have consequently shifted from being a marginal aspect of the European integration process to one that routinely grabs news headlines and, unlike many other EU policy areas, generates relatively strong political support from EU citizens. These policies, which now impinge on most sectors and areas of the economy, have generally proven resilient to recent economic and deregulatory pressures. This chapter documents and explores the reasons behind the relatively rapid transformation in the EU’s governing capabilities in this policy area, explores the main dynamics of policy-making from different analytical perspectives, and identifies future challenges including Brexit.
The Reamer-Irrigator-Aspirator technique for manubriosternal non-union repair
Authors: Naruka Vinci , Nardini Marco , McVie James , Dunning Joel
Published: January 2019

Autologous bone graft is used in the treatment of fracture non-unions. A novel approach to treat painful manubriosternal non-unions is described with bone graft harvested from the femur and plating.
Numerical study on heat transfer performance of vacuum tube solar collector integrated with metal foams
Authors: Lu Yalin , Chen Zhenqian
Published: January 2019

Applying vacuum tube solar collector is one effective way to reduce heat loss in solar collection. However, low conductivity of pure water leads to poor heat transfer performance in vacuum tube. In order to enhance heat transfer in tube, a novel vacuum tube solar collector using water as medium and metal foams as filler is presented, which consists of outer glass tube, inner metal tube and metal foam filler. The heating process of vacuum tube with metal foam filler of different structural parameters (porosity in range of 0.8991–0.9546 and PPI of 5, 10 and 20) is numerically studied and local thermal equilibrium model is applied.The temperature distribution of vacuum tube collectors with and without metal foam filler are compared. The impact of porosity and PPI on heat transfer performance is obtained. The results show that metal foams plays a great role in heat transfer enhancement for vacuum tube solar collector. Thermal performance of the novel vacuum tube solar collector is influenced by porosity and PPI of metal foams. Compared with traditional vacuum tube solar collector, the proposed vacuum tube solar collector has better thermal performance and greater potential in solar building integration.
Use of Isokinetic Dynamometry To Assess Muscle Function In Burned Patients Is A Reliable Tool To Assist Progressive Resistance Exercise Prescription
Authors: Dean Julianna M , Murton Andrew J , Glover Shauna Q , Gutierrez Ileana , Andersen Clark R , Herndon David N , Lee Jong O , Suman Oscar E
Published: January 2019

Isokinetic dynamometry is used during exercise testing and rehabilitation to obtain a quantitative strength measurement on which progressive strength training programs can be based. This study assesses the test–retest reliability of isokinetic leg function in the knee flexors and extensors at 150°/s in children and young adults with severe burns to be used for rehabilitation exercise program prescription. In 39 severely burned patients (49 ± 14% total body surface area burn [TBSA], mean ± SD; 34 ± 21% TBSA 3rd degree; 14 ± 5 years, 153.3 ± 16.5 cm height; 53.8 ± 17.9 kg) knee flexion/extension isokinetic dynamometry at 150°/s was performed on each patient’s dominant leg in two sessions. The patient was acquainted with the test and performed 1 set of 10 repetitions at 150°/s. A second session of 1 set of 10 repetitions at 150°/ was performed within 24 h of the first. Muscle function outcomes were knee flexion/extension peak torque, average peak torque, and average power. One-sample paired t tests were performed for all muscle function outcomes; intraclass correlation coefficients and r2 values with session two as a function of session one were calculated. Sessions did not differ significantly in knee extension or flexion for any muscle function outcome or the hamstrings to quadriceps ratio. All intraclass correlation coefficients were >0.89 and r2 > 0.79. Test–retest isokinetic dynamometry functional measurements in the knee flexors and extensors at 150°/s are reliable in the burn population and may aid resistance rehabilitation program prescriptions.
Meta-analysis Comparing Platelet-Rich Plasma vs Hyaluronic Acid Injection in Patients with Knee Osteoarthritis
Authors: Han Yanhong , Huang Hetao , Pan Jianke , Lin Jiongtong , Zeng Lingfeng , Liang Guihong , Yang Weiyi , Liu Jun
Published: January 2019

Purpose

The purpose of this meta-analysis was to compare platelet-rich plasma (PRP) and hyaluronic acid (HA) in patients with knee osteoarthritis (KOA).

Methods

Randomized controlled trials (RCTs) comparing the use of PRP and HA in KOA patients were retrieved from each database from the establishment date to April 2018. Outcome measurements were the Western Ontario and McMaster Universities Arthritis Index (WOMAC), visual analog scale (VAS), International Knee Documentation Committee, and Lequesne Index scores and adverse events. The pooled data were evaluated with Review Manager 5.3.5.

Results

Fifteen RCTs (N = 1,314) were included in our meta-analysis. The present meta-analysis indicated that PRP injections reduced pain more effectively than HA injections in patients with KOA at six and 12 months of follow-up, as evaluated by the WOMAC pain score; the VAS pain score showed a significant difference at 12 months. Moreover, better functional improvement was observed in the PRP group, as demonstrated by the WOMAC function score at three, six, and 12 months. Additionally, PRP injections did not display different adverse event rates compared with HA injections.

Conclusion

In terms of long-term pain relief and functional improvement, PRP injections might be more effective than HA injections as a treatment for KOA. The optimal dosage, the timing interval and frequency of injections, and the ideal treatment for different stages of KOA remain areas of concern for future investigations.
Integration of Anatomy Ontologies and Evo-Devo Using Structured Markov Models Suggests a New Framework for Modeling Discrete Phenotypic Traits
Authors: Tarasov Sergei
Published: January 2019

Modeling discrete phenotypic traits for either ancestral character state reconstruction or morphology-based phylogenetic inference suffers from ambiguities of character coding, homology assessment, dependencies, and selection of adequate models. These drawbacks occur because trait evolution is driven by two key processes—hierarchical and hidden—which are not accommodated simultaneously by the available phylogenetic methods. The hierarchical process refers to the dependencies between anatomical body parts, while the hidden process refers to the evolution of gene regulatory networks (GRNs) underlying trait development. Herein, I demonstrate that these processes can be efficiently modeled using structured Markov models (SMM) equipped with hidden states, which resolves the majority of the problems associated with discrete traits. Integration of SMM with anatomy ontologies can adequately incorporate the hierarchical dependencies, while the use of the hidden states accommodates hidden evolution of GRNs and substitution rate heterogeneity. I assess the new models using simulations and theoretical synthesis. The new approach solves the long-standing “tail color problem,” in which the trait is scored for species with tails of different colors or no tails. It also presents a previously unknown issue called the “two-scientist paradox,” in which the nature of coding the trait and the hidden processes driving the trait’s evolution are confounded; failing to account for the hidden process may result in a bias, which can be avoided by using hidden state models. All this provides a clear guideline for coding traits into characters. This article gives practical examples of using the new framework for phylogenetic inference and comparative analysis.
Human extinction learning is accelerated by an angiotensin antagonist via ventromedial prefrontal cortex and its connections with basolateral amygdala
Authors: Zhou Feng , Geng Yayuan , Xin Fei , Li Jialin , Feng Pan , Liu Congcong , Zhao Weihua , Feng Tingyong , Guastella Adam J. , Kendrick Keith M. , Becker Benjamin
Published: January 2019

Recent translational research suggests a role of the renin-angiotensin (RA) system in threat extinction and underlying neuroplasticity; however, whether and how pharmacological modulation of the RA system influences physiological and neural manifestations of threat during extinction learning in humans is unclear. Here we report that pre-extinction administration of losartan, an angiotensin II type 1 receptor antagonist, accelerated attenuation of physiological threat expression. During early extinction, losartan enhanced threat-signal specific ventromedial prefrontal cortex (vmPFC) activation and its coupling with the basolateral amygdala. Multivoxel pattern analysis revealed that losartan reduced whole brain, particularly vmPFC, threat expression and voxel-wise mediation analyses further confirmed that losartan-accelerated extinction crucially involved vmPFC processing. Overall the results provide initial evidence for a critical role of the RA system in extinction learning in humans and suggest that adjunct losartan administration may facilitate the efficacy of extinction-based therapies.

ClinicalTrials.gov, Identifier: NCT03396523
Adaptive evolution among cytoplasmic piRNA proteins leads to decreased genomic auto-immunity
Authors: Wang Luyang , Barbash Daniel A. , Kelleher Erin S.
Published: January 2019

In metazoan germlines, the piRNA pathway acts as a genomic immune system, employing small RNA-mediated silencing to defend host DNA from the harmful effects of transposable elements (TEs). In response to dynamic changes in TE content, host genomes are proposed to alter the piRNAs that they produce in order to silence the most active TE families. Surprisingly, however, piRNA pathway proteins, which execute piRNA biogenesis and enforce silencing of targeted sequences, also evolve rapidly and adaptively in animals. If TE silencing evolves through changes in piRNAs, what necessitates changes in piRNA pathway proteins? Here we used interspecific complementation to test for functional differences betweenDrosophila melanogasterandD. simulansalleles of three adaptively evolving piRNA pathway proteins: Armitage, Aubergine and Spindle-E. Surprisingly, we observed interspecific divergence in the regulation of only a handful of TE families, which were more robustly silenced by the heterospecific piRNA pathway protein. This suggests that positive selection does not act on piRNA effector proteins to enhance their function in TE repression, but rather that TEs may evolve to “escape” silencing by homospecific alleles. We also discovered thatD. simulansalleles ofaubandarmiexhibit enhanced off-target effects on host transcripts in aD. melanogasterbackground, suggesting the avoidance of genomic auto-immunity as a critical target of selection. Our observations suggest that piRNA effector proteins are subject to an evolutionary trade-off between defending the host genome from the harmful effect of TEs while also minimizing friendly fire against host genes.

Author Summary

Transposable elements are mobile fragments of selfish DNA that burden host genomes with deleterious mutations and incite genome instability. Host cells employ a specialized small-RNA mediated silencing pathway, the piRNA pathway, to act as a genomic immune system suppressing the mobilization of TEs. Changes in genomic TE content are met with rapid changes in the piRNA pool, thereby maintain host control over transposition. However, piRNA pathway proteins—which enact piRNA biogenesis and silence target TEs—also evolve adaptively. To isolate forces that underlie this adaptive evolution, we examined functional divergence between twoDrosophilaspecies for three adaptively evolving piRNA pathway proteins. To our surprise, we found very few differences in TE regulation, suggesting that evolution has not generally acted to enhance control of TE parasites. Rather, we discovered interspecific differences in the regulation of host mRNAs for two proteins, which suggested that proteins evolve to avoid off-target silencing of host transcripts. We propose that the avoidance of such “genomic autoimmunity” is an important and underappreciated force driving the adaptive evolution of piRNA proteins.
SHARQnet - Sophisticated Harmonic Artifact Reduction in Quantitative Susceptibility Mapping using a Deep Convolutional Neural Network
Authors: Bollmann Steffen , Kristensen Matilde Holm , Larsen Morten Skaarup , Olsen Mathias Vassard , Pedersen Mads Jozwiak , Østergaard Lasse Riis , O’Brien Kieran , Langkammer Christian , Fazlollahi Amir , Barth Markus
Published: January 2019

Quantitative susceptibility mapping (QSM) reveals pathological changes in widespread diseases such as Parkinson’s disease, Multiple Sclerosis, or hepatic iron overload. QSM requires multiple processing steps after the acquisition of magnetic resonance imaging (MRI) phase measurements such as unwrapping, background field removal and the solution of an ill-posed field-to-source-inversion. Current techniques utilize iterative optimization procedures to solve the inversion and background field correction, which are computationally expensive and lead to suboptimal or over-regularized solutions requiring a careful choice of parameters that make a clinical application of QSM challenging. We have previously demonstrated that a deep convolutional neural network can invert the magnetic dipole kernel with a very efficient feed forward multiplication not requiring iterative optimization or the choice of regularization parameters. In this work, we extended this approach to remove background fields in QSM. The prototype method, called SHARQnet, was trained on simulated background fields and tested on 3T and 7T brain datasets. We show that SHARQnet outperforms current background field removal procedures and generalizes to a wide range of input data without requiring any parameter adjustments. In summary, we demonstrate that the solution of ill-posed problems in QSM can be achieved by learning the underlying physics causing the artifacts and removing them in an efficient and reliable manner and thereby will help to bring QSM towards clinical applications.
Hippocampal morphometry in sudden and unexpected death in epilepsy (SUDEP)
Authors: Somani Alyma , Zborovschi Anita-Beatrix , Liu Yan , Patodia Smriti , Michalak Zuzanna , Sisodiya Sanjay M , Thom Maria
Published: January 2019

Objective

To determine hippocampal morphometric parameters, including granule cell dispersion and features of malrotation, as potential biomarkers for SUDEP from an archival post-mortem series.

Methods

In a retrospective study of 187 archival post-mortems from three groups, SUDEP (68; 14 with hippocampal sclerosis (HS)), non-SUDEP epilepsy controls (EP-C =66; 25 with HS) and non-epilepsy controls (NEC= 53), Nissl/H&E stained sections from left and right hippocampus from five coronal levels were digitised. Image analysis was carried out for granule cell layer (GCL) thickness and measurements of hippocampal dimensions (HD) for shape [width (HD1), height (HD2)] and medial hippocampal positioning in relation to the parahippocampal gyrus (PHG) length (HD3). A qualitative evaluation of hippocampal malrotational (HMAL) features, dentate gyrus invaginations (DGI) and subicular/CA1 folds (SCF) was also made.

Results

GCL thickness was increased in HS more than those without (p<0.001). In non-HS cases increased GCL thickness was noted in EP-C compared to NEC (p<0.05) but not between SUDEP and NEC. There was no significant difference in the frequency of DGI, SCF, measurements of hippocampal shape (HD1, HD2 or ratio) or medial positioning between SUDEP, EP-C and NEC groups, when factoring in HS, coronal level and age at death. Comparison between left and right sides within cases showed significantly greater PHG lengths (HD3) on the right side in the SUDEP group only (p=0.018)

Conclusions

No hippocampal morphometric features were identified in support of either excessive granule cell dispersion or features of HMAL as biomarkers for SUDEP. Asymmetries in PHG measurements in SUDEP warrant further investigation as they may indicate abnormal central autonomic networks.
The time course of updating in running span
Authors: Kaur Shraddha , Norris Dennis , Gathercole Susan E
Published: January 2019

Running span can be performed by either passively listening to to-be-remembered items or actively updating the target set during presentation. This choice of strategy is influenced by the rate of presentation in the task. Previous research suggests that the active updating process is demanding and time-consuming. It is favored at relatively slow rates of presentation, while the passive strategy is more successful when applied at fast rates. In two experiments the time course of resource demand during task performance and its sensitivity to presentation rate was examined. We hypothesized that running span imposes a high cognitive load only when active updating is employed. Participants performed running span simultaneously with a spatial reaction time (RT) task, and RTs on the concurrent task were used to index the resource demands of the memory task. A slow-paced running span exhibited a large overall resource demand in comparison with the serial recall tasks (Experiment 1) and fast-paced running span (Experiment 2). This demand was observed from the position in the list from which participants are presumed to start updating, suggesting a cognitive shift to a demanding mode of updating. In addition, a demand burst was found approximately 1000ms following item onset at these later positions. These data establish that the process of active updating in running span task is slow and cognitively demanding and indicate that this limits its application during fast presentation rates.
Excessive deliberation in social anxiety
Authors: Hunter Lindsay E. , Meer Elana A. , Gillan Claire M. , Hsu Ming , Daw Nathaniel D.
Published: January 2019

A goal of computational psychiatry is to ground symptoms in more fundamental computational mechanisms. Theory suggests that rumination and other symptoms in mood disorders reflect dysregulated mental simulation, a process that normally serves to evaluate candidate actions. If so, these covert symptoms should have observable consequences: excessively deliberative choices, specifically about options related to the content of rumination. In two large general population samples, we examined how symptoms of social anxiety disorder (SAD) predict choices in a socially framed reinforcement learning task, the Patent Race game. Using a computational learning model to assess learning strategy, we found that self-reported social anxiety was indeed associated with an increase in deliberative evaluation. The effect was specific to learning from a particular (“upward counterfactual”) subset of feedback, broadly matching the biased content of rumination in SAD. It was also robust to controlling for other psychiatric symptoms. These results ground the symptoms of SAD, such as overthinking and paralysis in social interactions, in well characterized neuro-computational mechanisms and offer a rare example of enhanced function in disease
R-loops and regulatory changes in chronologically ageing fission yeast cells drive non-random patterns of genome rearrangements
Authors: Ellis David A. , Reyes-Martín Félix , Rodríguez-López María , Cotobal Cristina , Sun Xi-Ming , Jeffares Daniel C. , Marguerat Samuel , Tallada Víctor A. , Bähler Jürg
Published: January 2019

Aberrant repair of DNA double-strand breaks can recombine distant pairs of chromosomal breakpoints. Such chromosomal rearrangements are a hallmark of ageing and compromise the structure and function of genomes. Rearrangements are challenging to detect in non-dividing cell populations, because they reflect individually rare, heterogeneous events. The genomic distribution ofde novorearrangements in non-dividing cells, and their dynamics during ageing, remain therefore poorly characterized. Studies of genomic instability during ageing have focussed on mitochondrial DNA, small genetic variants, or proliferating cells. To gain a better understanding of genome rearrangements during cellular ageing, we focused on a single diagnostic measure – DNA breakpoint junctions – allowing us to interrogate the changing genomic landscape in non-dividing cells of fission yeast (Schizosaccharomyces pombe). Aberrant DNA junctions that accumulated with age were associated with microhomology sequences and R-loops. Global hotspots for age-associated breakpoint formation were evident near telomeric genes and linked to remote breakpoints on the same or different chromosomes, including the mitochondrial chromosome. An unexpected mechanism of genomic instability caused more local hotspots: age-associated reduction in an RNA-binding protein could trigger R-loop formation at target loci. This finding suggests that biological processes other than transcription or replication can drive genome rearrangements. Notably, we detected similar signatures of genome rearrangements that accumulated in old brain cells of humans. These findings provide insights into the unique patterns and potential mechanisms of genome rearrangements in non-dividing cells, which can be triggered by ageing-related changes in gene-regulatory proteins.
A Pipeline for Faecal Host DNA Analysis by Absolute Quantification of LINE-1 and Mitochondrial Genomic Elements Using ddPCR
Authors: He Kuang , Fujiwara Hideaki , Zajac Cynthia , Sandford Erin , Reddy Pavan , Choi Sung Won , Tewari Muneesh
Published: January 2019

Stool contains DNA shed from cells of the gastrointestinal (GI) tract and has great potential as a bio-specimen for non-invasive, nucleic acid-based detection of GI diseases. Whereas methods for studying faecal microbiome DNA are plentiful, there is a lack of well-characterised procedures for stabilisation, isolation, and quantitative analysis of faecal host DNA. We report an optimised pipeline for faecal host DNA analysis from the point-of-collection to droplet digital PCR (ddPCR) absolute quantification of host-specific gene targets. We evaluated multiple methods for preservation and isolation of host DNA from stool to identify the highest performing methods. To quantify host DNA even if present in partially degraded form, we developed sensitive, human-specific short-amplicon ddPCR assays targeting repetitive nuclear genomic elements (LINE-1) and mitochondrial genes. We validated the ability of these optimised methods to perform absolute quantification of host DNA in 200 stool DNA extracts from samples that were serially collected from three healthy individuals and three hospitalised patients. These specimens allowed assessment of host DNA day-to-day variability in stool specimens with widely varying physical characteristics (i.e., Bristol scores). We further extended this approach to mouse stool analysis, to enable faecal host DNA studies in animal disease models as well.
X-ray structures of two active secreted Bacteroides thetaiotaomicron C11 proteases in complex with peptide-based inhibitors
Authors: Roncase Emily J. , González-Páez Gonzalo E. , Wolan Dennis W.
Published: January 2019

Commensal bacteria secrete proteins and metabolites to influence host intestinal homeostasis and proteases represent a significant constituent of the components at the host:microbiome interface. Here, we determined the structures of the two secreted C11 cysteine proteases encoded by the established gut commensal Bacteroides thetaiotaomicron. We employed mutational analysis to demonstrate the two proteases, termed “thetapain” and “iotapain”, undergo in trans self-maturation after lysine and/or arginine residues, as observed for other C11 proteases. We determined the structures of the active forms of thetapain and iotapain in complex with irreversible peptide inhibitors, Ac-VLTK-AOMK and biotin-VLTK-AOMK, respectively. Structural comparisons revealed key active-site interactions important for peptide recognition are more extensive for thetapain; however, both proteases employ a glutamate residue to preferentially bind small polar residues at the P2 position. Our results will aid in the design of protease-specific probes to ultimately understand the biological role of C11 proteases in bacterial fitness, elucidate their host and/or microbial substrates, and interrogate their involvement in microbiome-related diseases.
High genetic diversity of Plasmodium falciparum in the low transmission setting of the Kingdom of Eswatini
Authors: Roh Michelle E. , Tessema Sofonias K. , Murphy Maxwell , Nhlabathi Nomcebo , Mkhonta Nomcebo , Vilakati Sibonakaliso , Ntshalintshali Nyasatu , Saini Manik , Maphalala Gugu , Chen Anna , Wilheim Jordan , Prach Lisa , Gosling Roly , Kunene Simon , Hsiang Michelle , Greenhouse Bryan
Published: January 2019

Background

To better understand transmission dynamics, we characterized Plasmodium falciparum (Pf) genetic diversity in Eswatini, where transmission is low and sustained by importation.

Methods

26 Pf microsatellites were genotyped in 66% of all confirmed cases from 2014-2016 (n=582). Population and within-host diversity were used to characterize differences between imported and locally-acquired infections, as determined by travel history. Logistic regression was used to assess the added value of diversity metrics to classify imported and local infections beyond epidemiology data alone.

Results

The parasite population in Eswatini was highly diverse (HE=0.75) and complex, with 67% polyclonal infections, a mean MOI of 2.2, and mean FWS of 0.84. Imported cases had comparable diversity to local cases, but exhibited higher MOI (2.4 versus 2.0; p=0.004) and lower mean FWS (0.82 vs. 0.85; p=0.03). Addition of MOI and FWS to multivariate analyses did not increase discrimination between imported and local infections.

Discussion

In contrast to the commonly held perception that Pf diversity declines with decreasing transmission intensity, isolates from Eswatini exhibited high parasite diversity consistent with high rates of malaria importation and limited local transmission. Estimates of malaria transmission intensity from genetic data need to consider the effect of importation, especially as countries near elimination.
Systemic signalling throughTCTP1controls lateral root formation in Arabidopsis
Authors: Branco Rémi , Masle Josette
Published: January 2019

As in animals, the plant body plan and primary organs are established during embryogenesis. However, plants have the ability to generate new organs and functional units throughout their whole life. These are produced through the specification, initiation and differentiation of secondary meristems, governed by the intrinsic genetic program and cues from the environment. They give plants an extraordinary developmental plasticity to modulate their size and architecture according to environmental constraints and opportunities. How this plasticity is regulated at the whole organism level is still largely elusive. In particular the mechanisms regulating the iterative formation of lateral roots along the primary root remain little known. A pivotal role of auxin is well established and recently the role of local mechanical signals and oscillations in transcriptional activity has emerged. Here we provide evidence for a role of Translationally Controlled Tumor Protein (TCTP), a vital ubiquitous protein in eukaryotes. We show that Arabidopsis AtTCTP1 controls root system architecture through a dual function: as a general constitutive growth promoter locally, and as a systemic signalling agent via mobility from the shoot. Our data indicate that this signalling function is specifically targeted to the pericycle and modulates the frequency of lateral root initiation and emergence sites along the primary root, and the compromise between branching and elongating, independent of shoot size. Plant TCTP genes show high similarity among species. TCTP messengers and proteins have been detected in the vasculature of diverse species. This suggests that the mobility and extracellular signalling function ofAtTCTP1to control root organogenesis might be widely conserved within the plant kingdom, and highly relevant to a better understanding of post-embryonic formation of lateral organs in plants, and the elusive coordination of shoot and root morphogenesis.
Comparative analysis of ionic strength tolerance between freshwater and marine Caulobacterales adhesins
Authors: Chepkwony Nelson K. , Berne Cécile , Brun Yves V.
Published: January 2019

Bacterial adhesion is affected by environmental factors, such as ionic strength, pH, temperature, and shear forces, and therefore marine bacteria must have developed holdfasts with different composition and structures than their freshwater counterparts to adapt to their natural environment. The dimorphicα-proteobacteriumHirschia balticais a marine budding bacterium in the Caulobacterales clade.H.balticauses a polar adhesin, the holdfast, located at the cell pole opposite the reproductive stalk for surface attachment and cell-cell adhesion. The holdfast adhesin has been best characterized inCaulobacter crescentus, a freshwater member of the Caulobacterales, and little is known about holdfast composition and properties in marine Caulobacterales. Here we useH. balticaas a model to characterize holdfast properties in marine Caulobacterales. We show that freshwater and marine Caulobacterales use similar genes in holdfast biogenesis and that these genes are highly conserved among the two genera. We also determine thatH. balticaproduces larger holdfast thanC. crescentusand that those holdfasts have a different chemical composition, as they contain N-acetylglucosamine and galactose monosaccharide residues and proteins, but lack DNA. Finally, we show thatH. balticaholdfasts tolerate higher ionic strength than those ofC. crescentus. We conclude that marine Caulobacterales holdfasts have physicochemical properties that maximize binding in high ionic strength environments.

IMPORTANCE

Most bacteria spend a large amount of their lifespan attached to surfaces, forming complex multicellular communities called biofilms. Bacteria can colonize virtually any surface, therefore they have adapted to bind efficiently in very different environments. In this study, we compare the adhesive holdfasts produced by the freshwater bacteriumC. crescentusand a relative, the marine bacteriumH. baltica. We show thatH. balticaholdfasts have a different morphology and chemical composition, and tolerate high ionic strength. Our results show thatH. balticaholdfast is an excellent model to study the effect of ionic strength on adhesion and providing insights on the physicochemical properties required for adhesion in the marine environment.
Identification of flavone and its derivatives as potential inhibitors of transcriptional regulator LasR of Pseudomonasaeruginosausing virtual screening
Authors: Abelyan Narek , Grabski Hovakim , Tiratsuyan Susanna
Published: January 2019

Antibiotic resistance is a global problem nowadays and in 2017 the World Health Organization published the list of bacteria for which treatment are urgently needed, wherePseudomonas aeruginosais of critical priority. Current therapies lack efficacy because this organism creates biofilms conferring increased resistance to antibiotics and host immune responses. The strategy is to “not kill, but disarm” the pathogen and resistance will be developed slowly. It has been shown that LasI/LasR system is the main component of the quorum sensing system inP. aeruginosa. LasR is activated by the interaction with its native autoinducer. A lot flavones and their derivatives are used as antibacterial drug compounds. The purpose is to search compounds that will inhibit LasR. This leads to the inhibition of the synthesis of virulence factors thus the bacteria will be vulnerable and not virulent. We performed virtual screening using multiple docking programs for obtaining consensus predictions. The results of virtual screening suggest benzamides which are synthetical derivatives of flavones as potential inhibitors of transcriptional regulator LasR. These are consistent with recently published experimental data, which demonstrate the high antibacterial activity of benzamides. The compounds interact with the ligand binding domain of LasR with higher binding affinity than with DNA binding domain. Among the selected compounds, by conformational analysis, it was found that there are compounds that bind to the same amino acids of ligand binding domain as the native autoinducer. This could indicate the possibility of competitive interaction of these compounds. A number of compounds that bind to other conservative amino acids ligand binding domain have also been discovered, which will be of interest for further study. Selected compounds meet the criteria necessary for their consideration as drugs and can serve as a basis for conducting furtherin vitro / in vivoexperiments. It could be used for the development of modern anti-infective therapy based on the quorum sensing system ofP. aeruginosa.

Highlights

Virtual screening using multiple docking programs for consensus predictions.

Virtual screening reveal benzamides as potential inhibitors of LasR.

Selected compounds bind to the same amino acids of LBD as the native autoinducer.

Selected compounds meet the criteria necessary for their consideration as drugs.

GRAPHICAL ABSTRACT

1: N- (1,3-benzodioxol-5-ylmethyl) -4- (6,8-dimethyl-4-oxochromen-2-yl) benzamide docking with LBD of LasR, A — ligand conformation predicted by AutoDock, B - by rDock and C - by LeDock,D - binding of CID 108754330 with LBD of LasR predicted by rDock.

2: Four types of P. aeruginosa quorum sensing signaling systems I. Las, II. Rhl, III. Pqs and IV. IQS.
Health workers’ perspectives on the outcomes, enablers, and barriers to the implementation of HIV “Treat All” guidelines in Abuja Nigeria
Authors: Odafe Solomon , Stafford Kristen A. , Gambo Aliyu , Onotu Dennis , Swaminathan Mahesh , Dalhatu Ibrahim , Ene Uzoma , Oladipo Ademola , Mukhtar Ahmed , Ibrahim Ramat , Ehoche Akipu , Debem Henry , Boyd Andrew T. , Aboje Sunday , Gobir Bola , Charurat Manhattan
Published: January 2019

Introduction

To improve access to lifesaving treatment for all people living with HIV (PLHIV), Nigeria implemented the Treat All guidelines in 2016. However, health workers’ perspectives on the implementation of the guidelines have not been evaluated.

Methods

We conducted in-depth interviews to explore health workers’ perspectives on the Treat All guidelines. Using purposive sampling, 20 health workers providing HIV patient care were recruited from six primary health care hospitals in Abuja to participate in semi-structured interviews. Data exploration was conducted using thematic content analysis.

Results

The five main themes that emerged were (1) the perceived benefits of guidelines use, (2) the perceived disadvantages of using the guidelines, (3) reported patients’ response to guideline change, (4) perceived barriers/enablers to guideline use and (5) health workers’ recommendations for improvement. Health workers perceived that the implementation of the Treat All guidelines has considerably improved patient care, particularly in increasing access to skilled health care, reducing stress on patients, and increasing hope for a better health outcome among patients. Other perceived benefits were reduced mortality, reduced pre-treatment attrition, reduction in delays between case detection and initiation on treatment. Perceived major disadvantages were increased workload and overcrowded clinics. Health workers reported that most patients were willing to start treatment early. Perceived key factors enabling guidelines use were health workers’ interest, patient benefits, training and availability of tools for implementation of guidelines, government supervisory visits and hospital management support. Perceived key barriers were poverty, inadequate human resources, lack of familiarity with guidelines, and lack of consistent supply of HIV test kits at some sites.

Conclusions

Implementation of the Treat All guidelines led to perceived improvement in patient care. Further improvements could be achieved by implementing an efficient supply chain system for HIV rapid test kits, and through guidelines distribution and training. Additionally, implementing differentiated approaches that decongest clinics, and programs that economically empower patients could improve access to treatment.