bluuebunny/crossref_metadata_2025 huggingface dataset:
Universal healthcare in our lifetime? All teach, all learn
Authors: Britnell Mark
Published: April 2019

The United Nation’s Sustainable Development Goals of achieving universal health coverage (UHC) by 2030 have energized many governments to devise bold strategies and make big investments in their health systems. The global movement around UHC has gathered momentum at blistering speed. Within a few years it has transformed the focus of healthcare in low- and middle-income countries from a few diseases to a comprehensive vision of affordable, accessible, and acceptable care for all. In this chapter, Mark Britnell looks at how Philippines, Vietnam, Kenya, India, Indonesia, Columbia, Costa Rica, Panama, Nigeria, South Africa, Cyprus, islands across the Caribbean, and many others have announced significant UHC reforms since the development goals were passed in 2014, and UHC has been a headline issue in a number of national elections. He analyses UHC across the world, and looks to at the future of healthcare globally.
The 2002–2004 Annan Plan in Cyprus
Authors: Loizides Neophytos , McGarry John
Published: April 2019

This chapter examines the 2002–04 Annan Plan for Cyprus, considered one of the most comprehensive peace plans in the history of the United Nations. The Annan Plan was conceived in an effort to secure agreement on a reunited federal Cyprus within the European Union. However, it was rejected during the two April 2004 referendums by the overwhelming majority (76 percent) of Greek Cypriots, although it was endorsed by 65 percent of Turkish Cypriots. The Annan Plan is significant for the wider empirical and conceptual issues it raises with regard to constitutional transitions and externally mediated peace agreements. The chapter first provides a background on the Cyprus conflict before discussing the constitutional negotiations around the Annan Plan and its unintended outcomes. It also highlights the broader lessons imparted by the process, pointing in particular to the Annan Plan’s provisions on power-sharing, sovereignty, security, and human rights.
States Reorganization and Accommodation of Ethno-Territorial Cleavages in India
Authors: Bhattacharyya Harihar
Published: April 2019

This chapter examines how the so-called “states reorganization” during the 1950s and 1960s and its accommodation of ethno-territorial cleavages has made ethnic peace and political stability possible in multi-ethnic India. It first sketches the political context that led to state reorganization before discussing the process of constitutional engagement and the constitutional changes associated with the various reorganizations. In particular, it analyzes the nature of the state’s institutional responses to ethno-linguistic cleavages, taking into account the role played by the States Reorganization Commission. It also describes the outcome of these exercises and shows how “subnational autonomy” emerged as major incentives for the regional political elites. Finally, it outlines the comparative lessons that can be learned from India’s approach to progressive staging of state creation, focusing on the effects of ongoing neo-liberal reforms (post-1991) in the country that have posed newer challenges for state autonomy and future territorial changes.
Dealing with Territorial Cleavages in Constitutional Transitions in Iraq
Authors: Al-Ali Zaid
Published: April 2019

This chapter examines why constitutional transition has failed to resolve Iraq’s territorial cleavages, especially the one between Arabs and Kurds. It first provides the context that led to the Constitution drafting process and the establishment of Iraq’s first federal arrangement that saw the merger of provinces to form larger regions. In particular, it considers a range of contentious issues that arose during the constitutional negotiations, not least of which was the ownership and management of oil and gas resources. Furthermore, the push for a more traditional form of federalism left minority views (generally those of the Kurdish negotiators) unrepresented. The chapter also analyzes the outcomes of Iraq’s constitutional transition, including the deterioration of the Kurdistan Region’s economic and political crises, before concluding with an overview of the key lessons that can be drawn from the process.
Nigeria’s Permanent Constitutional Transition
Authors: Suberu Rotimi
Published: April 2019

This chapter examines how Nigeria has made the transition under military rule from a relatively decentralized, parliamentary federation comprised of four ethnic regions to a centrist, presidential federalism with thirty-six states. It first provides a historical background on Nigeria’s constitutional evolution between 1914 and 1999 before discussing the period of constitutional engagement, focusing on the military’s Constitution-making procedures and especially its territorial restructuring initiatives, its centralization of constitutional functions and fiscal resources, its constitutional choice of a executive presidential system of government, and its establishment of the so-called agencies of restraint. The chapter also considers the outcomes of the military’s constitutional reforms and concludes with an analysis of lessons that can be drawn from the Nigerian case. In particular, it highlights the challenges that have developed since the return of civilian rule, giving rise to a relentless constitutional politics that underscores the permanent or continuous nature of Nigeria’s constitutional transition.
Yemen’s Failed Constitutional Transition
Authors: Anderson George
Published: April 2019

This chapter examines why Yemen’s constitutional transition during the period 2011–15 failed. In 2011 a popular uprising forced Yemeni President Ali Abdullah Saleh to resign. Neighboring Arab countries soon got involved in steering the constitutional process, which included a National Dialogue to address the design of a new constitution. The dialogue recommended a new federal regime, but failed to resolve the critical issue of the number and boundaries of states. The document presented in January 2015 by the Constitutional Drafting Committee tasked to draft a new constitution was deeply flawed and became the trigger for civil war. The chapter first considers the context leading up to the National Dialogue before discussing the outcomes of the constitutional process and three lessons that can be drawn from it: the role and design of sub-national governance arrangements; political legitimacy and process in a constitutional transition; and a more integrated approach to transitions.
Processes of Constitutional Transitions in the Face of Territorial Cleavages
Authors: Saunders Cheryl
Published: April 2019

This chapter discusses the implications of territorial cleavages for the process of constitutional transition by drawing on the experiences of various countries such as Bolivia, Bosnia-Herzegovina, Ethiopia, India, Iraq, Nepal, Philippines, Scotland, Spain, Sri Lanka, and Ukraine. It first considers four variables that are likely to affect the process for constitutional transition within a state in which there are significant cleavages along territorial lines: the nature of transition, the nature of territorial cleavage, the challenges confronting statehood, and the involvement of international actors. It then examines four dimensions of the processes of transition that may be influenced by territorial cleavages: phases of the transition process, agenda setting, deliberation and ratification, and implementation and other matters. Finally, it explains how constitutional transitions are shaped by the postponement of final decisions on key matters through deliberate ambiguity, incomplete prescription or reliance on the future operation of rules on constitutional amendments.
Constitutional Design and Territorial Cleavages
Authors: Ginsburg Tom
Published: April 2019

This chapter considers a variety of constitutional options for resolving and managing enduring territorial cleavages. Three categories of constitutional tools are discussed: those that involve allocation of decision-making to different levels of government, including federalism, autonomy, and various forms of devolution; those that concern central government institutions, including representation of territorial interests at the center, budget redistribution, and rights; and those that allow the territorial units to exit. The chapter also explores how Constitutions deal with secession and concludes with an analysis of the role of courts in establishing and guaranteeing constitutional bargains on territory as well as the role of international institutions in helping to resolve institutional problems of territorial cleavages. It shows that a combination of representation and decentralization may be sufficient to stabilize territorial cleavages, and that the traditional rationales for federalism do not seem to fit with the resolution of territorial cleavages.
Sources of Context-Dependence
Authors: Glanzberg Michael
Published: April 2019

This paper has two goals. The first is to defend a form of context-dependence for knowledge ascriptions. The second is to explore the different sources of context-dependence that natural language provides. Using knowledge ascriptions as an illustration, it argues that there are two very different sorts of sources of context-dependence in language. One is highly specific, typically lexical context-dependence. The other is general. Highly general features of extremely broad categories of expressions can create context-dependence that is only minimally associated with any one expression. The case of knowledge ascriptions provides an example of this kind of context-dependence. When it comes to philosophical concerns about contextualism, the difference points to something not always fully noted. Specific context-dependence can often reveal something important about the concept a given word expresses. General context-dependence does this in at best highly limited ways.
Semantic Explanations
Authors: Szabó Zoltán Gendler
Published: April 2019

This paper is a defense of substantive explanations in semantics. It begins by offering a diagnosis of why the view that semantic theories are merely descriptive has been widely accepted in philosophy and suggests that these grounds are not compelling. Then it argues that semantic explanations don’t have a uniform direction—upwards or downwards the syntactic tree. There is an explanatory division within the lexicon: the meanings of content words (nouns, verbs, adjectives, and adverbs) are semantically fundamental, while the meanings of function words (auxiliaries, connectives, copulas, derivational morphemes, determiners, expletives, prepositions, etc.) are derivative.
Copyright and the Court of Justice of the European Union
Authors: Rosati Eleonora
Published: April 2019

This title focuses specifically on the role, action, and legacy of the Court of Justice of the European Union (CJEU) in the field of copyright, providing an exclusive survey that covers two decades (1998–2018) of decisions in this area. The main objective is to give a sense of the direction of EU copyright, by attempting to ‘tidy up’ and rationalize existing rulings. The book consists of three parts. The first part explores the role of the CJEU in copyright cases. Besides outlining the history of EU harmonization and providing data concerning the Court’s activity, it extracts the key standards employed in copyright case law, explains their meaning and significance, and undertakes a novel statistical analysis aimed at mapping relations between said standards. Following a discussion of the impact of CJEU interpretation of certain provisions (notably their preemptive force on Member States’ freedom), the second part concerns CJEU action (and vision) in respect of three key areas: economic rights, exceptions and limitations, and enforcement. The final part focuses on CJEU legacy broadly intended. It tackles the effect on national copyright laws and the current policy discourse around EU copyright reform. As regards the former, the book discusses the default consequences of the departure of a Member State from the EU, with a special focus on Brexit. In relation to the latter, attention turns to a number of areas which need to be considered in light, not just of existing legislation, but also—and perhaps most importantly—existing case law.
God and Progress
Authors: Bennett Joshua
Published: April 2019

Exploring the rich relationship between historical thought and religious debate in Victorian culture, this book offers a unique and authoritative account of intellectual change in nineteenth-century Britain. The volume recovers a twofold process in which the growth of progressive ideas of history transformed British Protestant traditions, as religious debate, in turn, profoundly shaped Victorian ideas of history. It adopts a remarkably wide contextual perspective, embracing believers and unbelievers, Anglicans and nonconformists, and writers from different parts of the British Isles, fully situating British debates in relation to their European and especially German Idealist surroundings. The Victorian intellectual mainstream came to terms with religious diversity, changing ethical sensibilities, and new kinds of knowledge by encouraging providential, spiritualized, and developmental understandings of human time. A secular counter-culture simultaneously disturbed this complex consensus, grounding progress in appeals to scientific advances and the retreat of metaphysics. The book thus explores the ways in which divisions within British liberalism were fundamentally related to differences over the past, present, and future of religion. It also demonstrates that religious debate powered the process by which historicism acquired cultural authority in Victorian national life, and later began to lose it. The study reconstructs the ways in which theological dynamics, often relegated to the margins of nineteenth-century British intellectual history, effectively forged its leading patterns.
Contemplating Jesus Risen
Authors: Levering Matthew
Published: April 2019

This chapter argues that a contemplative attitude toward Scripture’s portraits of Jesus helps one appreciate the credibility of the proclamation that Jesus rose from the dead to glorified life. The alternative consists in taking a reductive approach that is inadequate to the testimony as a whole. The chapter first attends briefly to certain elements of what Aquinas has to say about contemplating Jesus Christ, by way of providing some background in the Christian tradition. Second, it examines the efforts of Joseph Ratzinger/Pope Benedict XVI to perceive the face of Christ through the biblical portraits of Christ. In his Jesus of Nazareth, his meditation upon the New Testament narratives about Jesus’ Resurrection provides him with grounds for judging the historicity of Jesus’ Resurrection. Third, the chapter surveys the case for the credibility of Christian claims that is offered by Hans Urs von Balthasar in his book Love Alone Is Credible.
Disjointedness in The Visiting Privilege
Authors: Mitchell Lee Clark
Published: April 2019

Joy Williams’s transition into a late style resembles Alice Munro’s, occurring gradually over her career as the achievement of a perspective envisioned long before, slowly acquired through narrative experimentation and honed possibilities. Her elliptical, disruptive strain is linked to a passion for liminal moments, when consciousness tilts awry, or plants begin to think while inanimate objects somehow magically communicate with us. Enigmas remain enigmatic, even as her descriptions rely heavily on biblical allusions and psychological commonplaces. The sly revelations of earlier stories become in later years deracinating revelations that do not quite add up, as revealed in two drastically different versions of “Another Season” (1966), which is extensively reconfigured in its later version in The Visiting Privilege.
Beyond Punishment?
Authors: Hoskins Zachary
Published: April 2019

People convicted of crimes are subject to a criminal sentence, but they are also subject to a host of other legal measures: Some are denied access to jobs, housing, welfare, the vote, or other goods. Some may be deported. Others are subject to continued detention. Many have their criminal records made publicly accessible. These measures are often more burdensome than an offender’s formal sentence. This is the first book-length philosophical examination of these burdensome legal measures, called collateral legal consequences (CLCs). The book draws on resources in moral, legal, and political philosophy to shed light on whether these measures are ever morally justified. It analyzes the various kinds of CLCs imposed in different legal systems and the important moral challenges they raise, and it makes the case that these challenges have been largely overlooked by philosophers. The book examines whether CLCs can ever be justified as forms of criminal punishment—whether they are consistent with the values and principles that we believe should govern punishment. Then it considers whether CLCs are ever justifiable as civil measures, and specifically what could justify the state in imposing additional burdensome measures on offenders in addition to their punishment. Whether CLCs function as forms of punishment or as civil measures, the book contends that they are justifiable in a far narrower range of cases than we find in current legal practice.
Language Politics and Public Sphere in North India
Authors: Jha Mithilesh Kumar
Published: April 2019

Moving beyond the existing scholarship on language politics in north India which implicitly or explicitly focuses on Hindi–Urdu debates, this book examines the formation of the Maithili movement in the context of expansion of Hindi as the ‘national’ language. For a long time, the Hindi–Urdu debate has provided an important source to critically asses various facets of the nationalist movement in north India. But much emphasis on this debate has undermined simultaneous developments taking place in ‘minor’ linguistic spheres within the ‘Hindi heartland’ like Maithili, Braj, Awadhi, and Bhojpuri. This work also revisits the dynamic hierarchy through which a distinction is produced between ‘major’ and ‘minor’ languages. Significance of these ‘minor’ linguistic movements lies in the ways through which they resist such domination and appropriations while asserting their own independence. Throughout the history of the Maithili movement, what one finds is not just an opposition to Hindi’s claim of Maithili being its ‘dialect’ or the ambivalent relationship between the two. But more appropriately, one can see a double movement. The authority of Hindi has strengthened within the Maithili-speaking region even when the movement for the recognition of Maithili as an independent language has become more assertive. Another paradox of the Maithili movement has been its increasing politicization—from Hindi–Maithili ambiguities and antagonisms to territorial consciousness and finally demands for a separate statehood of Mithila, along with the persistent indifferent attitude of the masses. This work examines these processes historically since the middle of the nineteenth century until the inclusion of Maithili into the eighth schedule of the Indian Constitution in 2004.
Power and Diplomacy
Authors: Singh Zorawar Daulet
Published: April 2019

The notion that a monolithic idea of ‘nonalignment’ shaped India’s foreign policy since its inception is a popular view. In Power and Diplomacy, Zorawar Daulet Singh challenges conventional wisdom by unveiling another layer of India’s strategic culture. In a richly detailed narrative using new archival material, the author not only reconstructs the worldviews and strategies that underlay geopolitics during the Jawaharlal Nehru and Indira Gandhi years, he also illuminates the significant transformation in Indian statecraft as policymakers redefined some of their fundamental precepts on India’s role in in the subcontinent and beyond. His contention is that those exertions of Indian policymakers are equally apposite and relevant today. Whether it is about crafting a sustainable set of equations with competing great powers, formulating an intelligent Pakistan policy, managing India’s ties with its smaller neighbours, dealing with China’s rise and Sino-American tensions, or developing a sustainable Indian role in Asia, Power and Diplomacy strikes at the heart of contemporary debates on India’s unfolding foreign policies.
The Indian Legal System
Authors: Singh Mahendra Pal , Kumar Niraj
Published: April 2019

The contemporary Indian legal system owes its origin predominantly to the English common law system. Although this system ushered modernity in India, it has failed to perform optimally on several counts owing to its significant incompatibility with existing Indian traditions. Taking into account indigenously created and evolved legal apparatuses, this volume examines all aspects of the Indian legal system in the context of historical, sociological, and anthropological realities of society. The establishment and growth of common law in India introduced a certain kind of dominant legal apparatus, significantly transforming the understanding of India’s legal plurality. The existence, however, of multiple non-state legal traditions challenges the singular identity of the Indian legal system. Postulating that legal systems cannot be seen or studied in isolation from the cultures of groups whose affairs they regulate, The Indian Legal System explores the preference for non-state legal practices among several communities in India, despite the existence of a formal state legal system.
Discharge against medical advice (DAMA) in paediatrics: An approach to promote safety and ethics
Authors: Kavanagh Aifric , Ostrow Olivia , Zlotnik Shaul Randi
Published: April 2019

Requests for discharge against medical advice are often challenging for clinicians to navigate, especially when the patient is a child. An informed, standardized approach to managing situations where children and their families are requesting to leave against medical advice is essential to maximizing safety and ethics for patients and staff, yet such situations are often not handled this way. Paediatric discharge against medical advice (DAMA) requests are best managed when clinicians ensure the patient’s best interests are met, understand and act upon their professional obligations, and engage in guided discussion with patients and families that involves both shared and informed decision-making strategies. A process map can capture these criteria and readily provide clinicians with a bedside reference tool when managing paediatric DAMA requests.
Comparison of comorbidities and treatment between ankylosing spondylitis and non-radiographic axial spondyloarthritis in the United States
Authors: Zhao Sizheng Steven , Ermann Joerg , Xu Chang , Lyu Houchen , Tedeschi Sara K , Liao Katherine P , Yoshida Kazuki , Moots Robert J , Goodson Nicola J , Solomon Daniel H
Published: April 2019

Objectives

This study aimed to compare comorbidities and biologic DMARD (bDMARD) use between AS and non-radiographic axial SpA (nr-axSpA) patients, using a large cohort of patients from routine clinical practice in the United States.

Methods

We performed a cross-sectional study using electronic medical records from two academic hospitals in the United States. Data were extracted using automated searches (⩾3 ICD codes combined with text searches) and supplemented with manual chart review. Patients were categorized into AS or nr-axSpA according to classification criteria. Disease features, comorbidities (from a list of 39 chronic conditions) and history of bDMARD prescription were compared using descriptive statistics.

Results

Among 965 patients identified, 775 (80%) were classified as having axSpA. The cohort was predominantly male (74%) with a mean age of 52.5 years (s.d. 16.8). AS patients were significantly older (54 vs 46 years), more frequently male (77% vs 64%) and had higher serum inflammatory markers than those with nr-axSpA (median CRP 3.4 vs 2.2 mg/dl). Half of all patients had at least one comorbidity. The mean number of comorbidities was 1.5 (s.d. 2.2) and similar between AS and nr-axSpA groups. A history of bDMARD-use was seen in 55% of patients with no difference between groups. The most commonly prescribed bDMARDs were adalimumab (31%) and etanercept (29%). Ever-prescriptions of individual bDMARDs were similar between AS and nr-axSpA.

Conclusion

Despite age differences, nr-axSpA patients had similar comorbidity burdens as those with AS. Both groups received comparable bDMARD treatment in this United States clinic-based cohort.
Phylogenetic systematics of the driftwood catfishes (Siluriformes: Auchenipteridae): a combined morphological and molecular analysis
Authors: Calegari Bárbara B , Vari Richard P , Reis Roberto E
Published: April 2019

A comprehensive phylogeny of species relationships of the Auchenipteridae is reconstructed here with a large-scale taxon sampling based on combined morphological and molecular datasets. The hypothesized phylogeny includes most species of Auchenipteridae (97 of 124 valid species) and multiple members of siluriform families as an outgroup (32 species) to embrace the diversity of forms among related catfishes. As the first large-scale phylogeny of the Auchenipteridae, comparison between taxa included information from both morphology (264 characters) and mitochondrial and nuclear molecular markers (3490 nucleotides) from five genes: coI, 16S, rag2, myh6 and SH3PX3. Trees were generated under two different optimality criteria (Maximum Parsimony and Bayesian Inference). A new classification for the family is presented herein to bring the taxonomy more in line with the new phylogenetic hypothesis. The strict consensus tree corroborates the monophyly of superfamily Doradoidea, family Auchenipteridae and its two subfamilies, Centromochlinae and Auchenipterinae. The new classification scheme proposes nine tribes in Auchenipteridae, based on the monophyly of major groups in both subfamilies. Centromochlus, Glanidium and Tatia are each recovered as paraphyletic. To maintain a monophyletic classification, some species treated as Tatia and Centromochlus are assigned to genera not previously recognized as valid.
Oncogenic PIK3CA mutations increase dependency on the mRNA cap methyltransferase, RNMT, in breast cancer cells
Authors: Dunn Sianadh , Lombardi Olivia , Lukoszek Radoslaw , Cowling Victoria H.
Published: April 2019

Basic mechanisms in gene expression are currently being investigated as targets in cancer therapeutics. One such fundamental process is the addition of the cap to pre-mRNA, which recruits mediators of mRNA processing and translation initiation. Maturation of the cap involves mRNA cap guanosine N-7 methylation, catalysed by RNMT (RNA guanine-7 methyltransferase). In a panel of breast cancer cell lines, we investigated whether all are equivalently dependent on RNMT for proliferation. When cellular RNMT activity was experimentally reduced by 50%, the proliferation rate of non-transformed mammary epithelial cells was unchanged, whereas a subset of breast cancer cell lines exhibited reduced proliferation and increased apoptosis. Most of the cell lines which exhibited enhanced dependency on RNMT harboured oncogenic mutations in PIK3CA, which encodes the p110α subunit of PI3Kα. Conversely, all cell lines insensitive to RNMT depletion expressed wild-type PIK3CA. Expression of oncogenic PIK3CA mutants, which increase PI3K p110α activity, was sufficient to increase dependency on RNMT. Conversely, inhibition of PI3Kα reversed dependency on RNMT, suggesting that PI3Kα signalling is required. Collectively, these findings provide evidence to support RNMT as a therapeutic target in breast cancer and suggest that therapies targeting RNMT would be most valuable in a PIK3CA mutant background.
Simultaneous evaluation of losartan and amlodipine besylate using second-derivative synchronous spectrofluorimetric technique and liquid chromatography with time-programmed fluorimetric detection
Authors: Shalan Shereen , Nasr Jenny Jeehan
Published: April 2019

This study is concerned with two sensitive, fast and reproducible approaches; namely, second-derivative synchronous fluorimetry (method I) and reversed phase high-performance liquid chromatography with fluorimetric detection (method II) for synchronized evaluation of losartan (LOS) and amlodipine besylate (AML). Method I is based on measuring second-derivative synchronous fluorescence spectra of LOS and AML at Δλ= 80 nm in water. The experimental factors influencing the synchronous fluorescence of the considered compounds were sensibly adjusted. The chromatographic analysis was executed on a Nucleodur MN-C18 column of dimensions; 250 × 4.6 mm i.d. and 5 µm particle size). The fluorimetric detection was time-programmed atλem = 440 nm for AML (0.0–7.5 min) and atλem = 400 nm for LOS (7.5–10 min) after excitation atλex = 245 nm. The mobile phase is a blend of acetonitrile with 0.02 M phosphate buffer in a proportion of 45 : 55, pH 4.0, pumped using a flow rate of 1 ml min−1. The calibration plots were established to be 0.1–4.0 µg ml−1for both drugs in method I and 0.05–4.0 µg ml−1for both drugs in method II. The study was extended to the evaluation of the two drugs in their co-formulated tablets.
Molecular convergence and positive selection associated with the evolution of symbiont transmission mode in stony corals
Authors: Dixon Groves B. , Kenkel Carly D.
Published: April 2019

Heritable symbioses have been critical for the evolution of life. The genetic consequences of evolving a heritable symbiosis from the perspective of the symbiont are well established, but concomitant changes in the host remain unresolved. In stony corals, heritable, vertical transmission has evolved repeatedly, providing a unique opportunity to investigate the genomic basis of this complex trait. We conducted a comparative analysis of 25 coral transcriptomes to identify orthologous genes exhibiting signatures of positive selection and convergent amino acid substitutions in vertically transmitting lineages. The frequency of convergence events tends to be higher among vertically transmitting lineages, consistent with the proposed role of selection in driving the evolution of convergent transmission mode phenotypes. Of 10 774 orthologous genes, 403 exhibited at least one molecular convergence event and evidence of positive selection in at least one vertically transmitting lineage. Functional enrichments among these top candidate genes include processes previously implicated in symbiosis including endocytosis, immune response, cytoskeletal protein binding and cytoplasmic membrane-bounded vesicles. Finally, several novel candidates were identified among 100 genes showing evidence of positive selection at the particular convergence event, highlighting the value of our approach for generating new insight into host mechanisms associated with the evolution of heritable symbioses.
The Structural Basis of the Genetic Code: Amino Acid Recognition by Aminoacyl-tRNA Synthetases
Authors: Kaiser Florian , Krautwurst Sarah , Salentin Sebastian , Haupt V. Joachim , Leberecht Christoph , Bittrich Sebastian , Labudde Dirk , Schroeder Michael
Published: April 2019

Storage and directed transfer of information is the key requirement for the development of life. Yet any information stored on our genes is useless without its correct interpretation. The genetic code defines the rule set to decode this information. Aminoacyl-tRNA synthetases are at the heart of this process. For the first time, we extensively characterize how these enzymes distinguish all natural amino acids based on the computational analysis of crystallographic structure data. The results of this meta-analysis show that the correct read-out of genetic information is a delicate interplay between the composition of the binding site, non-covalent interactions, error correction mechanisms, and steric effects.
Extension of thein vivohaploid induction system from maize to wheat
Authors: Liu Chenxu , Zhong Yu , Qi Xiaolong , Chen Ming , Liu Zongkai , Chen Chen , Tian Xiaolong , Li Jinlong , Jiao Yanyan , wang Dong , Wang Yuwen , Li Mengran , Xin Mingming , Liu Wenxin , Jin Weiwei , Chen Shaojiang
Published: April 2019

Doubled haploid breeding technology has been one of the most important techniques for accelerating crop breeding. In compare toin vivohaploid induction in maize, which is efficient and background independent, wheat haploid production by interspecific hybridization pollinated with maize is influenced by genetic background and requires rescue of young embryos. Here, we analyzed the homologues of maize haploid induction geneMTL/ZmPLA1/NLDin several crop species systematically, the homologues are highly conserved in sorghum, millet and wheat etc. Since wheat is a very important polyploidy crop, as a proof of concept, we demonstrated that thein vivohaploid induction method could be extended from diploid maize to hexaploid wheat by knocking out the wheat homologues (TaPLAs). Result showed that double knock-out mutation could trigger wheat haploid induction at ~ 2%-3%, accompanied by 30% - 60% seed setting rate. The performance of haploid wheat individual showed shorter plant, narrower leaves and male sterile. Our results also revealed that knockout ofTaPLA-A andTaPLA-D do not affect pollen viability. This study not only confirmed the function of the induction gene and explored a new approach for haploid production in wheat, but also provided an example that thein vivohaploid induction could be applied in more crop species with different ploidy levels. Furthermore, by combining with gene editing, it would be a fast and powerful platform for traits improvement in polyploidy crops breeding.
Ifit1 regulates norovirus infection and enhances the interferon response in murine macrophage-like cells
Authors: Mears Harriet V. , Emmott Edward , Chaudhry Yasmin , Hosmillo Myra , Goodfellow Ian G. , Sweeney Trevor R.
Published: April 2019

Background

Norovirus, also known as the winter vomiting bug, is the predominant cause of non-bacterial gastroenteritis worldwide. Disease control is predicated on a robust innate immune response during the early stages of infection. Double-stranded RNA intermediates generated during viral genome replication are recognised by host innate immune sensors in the cytoplasm, activating the strongly antiviral interferon gene programme. Ifit proteins, which are highly expressed during the interferon response, have been shown to directly inhibit viral protein synthesis as well as regulate innate immune signalling pathways. Ifit1 is well-characterised to inhibit viral translation by sequestration of eukaryotic initiation factors or by directly binding to the 5’ terminus of foreign RNA, particularly those with non-self cap structures. However, noroviruses have a viral protein, VPg, covalently linked to the 5’ end of the genomic RNA, which acts as a cap substitute to recruit the translation initiation machinery.

Methods

Ifit1 knockout RAW264.7 murine macrophage-like cells were generated using CRISPR-Cas9 gene editing. These cells were analysed for their ability to support murine norovirus infection, determined by virus yield, and respond to different immune stimuli, assayed by quantitative PCR. The effect of Ifit proteins on norovirus translation was also tested in vitro.

Results

Here, we show that VPg-dependent translation is completely refractory Ifit1-mediated translation inhibition in vitro and Ifit1 cannot bind the 5’ end of VPg-linked RNA. Nevertheless, knockout of Ifit1 promoted viral replication in murine norovirus infected cells. We then demonstrate that Ifit1 promoted interferon-beta expression following transfection of synthetic double-stranded RNA but had little effect on toll-like receptor 3 and 4 signalling.

Conclusions

Ifit1 is an antiviral factor during norovirus infection but cannot directly inhibit viral translation. Instead, Ifit1 stimulates the antiviral state following cytoplasmic RNA sensing, contributing to restriction of norovirus replication.
Induction of Chk2 signaling in the germarium is sufficient to cause oogenesis arrest inDrosophila
Authors: Durdevic Zeljko , Ephrussi Anne
Published: April 2019

The conserved RNA helicase Vasa is required for germ cell development in many organisms. It is established that inDrosophilaloss of piRNA pathway components, including Vasa, causes Chk2-dependent oogenesis arrest, however the stage at which Chk2-signaling is triggered was unknown. We found that absence of Vasa during the germarial stages arrests oogenesis due to Chk2 activation. Importantly, once induced in the germarium, Chk2-mediated arrest of oogenesis cannot be overcome by restoration of Vasa to the arrested egg-chambers. We conclude that Vasa activity specifically in the germarium is essential for germ cell lineage development.
A highly responsive pyruvate sensor reveals pathway-regulatory role of the mitochondrial pyruvate carrier MPC
Authors: Arce-Molina R , Cortés-Molina F , Sandoval PY , Galaz A , Alegría K , Schirmeier S , Barros LF , San Martín A
Published: April 2019

Mitochondria generate ATP and building blocks for cell growth and regeneration, using pyruvate as the main substrate. Here we introduce PyronicSF, a user-friendly GFP-based sensor of improved dynamic range that enables real-time subcellular quantitation of mitochondrial pyruvate transport, concentration and flux. We report that cultured mouse astrocytes maintain mitochondrial pyruvate in the low micromolar range, below cytosolic pyruvate, which means that the mitochondrial pyruvate carrier MPC controls the decision between respiration and anaplerosis/gluconeogenesis in an ultrasensitive fashion. The functionality of the sensor in living tissue is demonstrated in the brain ofDrosophila melanogasterlarvae. Mitochondrial subpopulations are known to coexist within a given cell, which differ in their morphology, mobility, membrane potential, and vicinity to other organelles. The present tool can be used to investigate how mitochondrial diversity relates to metabolism, to study the role of MPC in disease, and to screen for small-molecule MPC modulators.
Reference plasmid pHXB2_D is an HIV-1 molecular clone that exhibits identical LTRs and a single integration site indicative of an HIV provirus
Authors: Gener Alejandro R. , Zou Wei , Foley Brian T. , Hyink Deborah P. , Klotman Paul E.
Published: April 2019

Objective

To compare long-read nanopore DNA sequencing (DNA-seq) with short-read sequencing-by-synthesis for sequencing a full-length (e.g., non-deletion, nor reporter) HIV-1 model provirus in plasmid pHXB2_D.

Design

We sequenced pHXB2_D and a control plasmid pNL4-3_gag-pol(Δ1443-4553)_EGFP with long- and short-read DNA-seq, evaluating sample variability with resequencing (sequencing and mapping to reference HXB2) and de novo viral genome assembly.

Methods

We prepared pHXB2_D and pNL4-3_gag-pol(Δ1443-4553)_EGFP for long-read nanopore DNA-seq, varying DNA polymerases Taq (Sigma-Aldrich) and Long Amplicon (LA) Taq (Takara). Nanopore basecallers were compared. After aligning reads to the reference HXB2 to evaluate sample coverage, we looked for variants. We next assembled reads into contigs, followed by finishing and polishing. We hired an external core to sequence-verify pHXB2_D and pNL4-3_gag-pol(Δ1443-4553)_EGFP with single-end 150 base-long Illumina reads, after masking sample identity.

Results

We achieved full-coverage (100%) of HXB2 HIV-1 from 5’ to 3’ long terminal repeats (LTRs), with median per-base coverage of over 9000x in one experiment on a single MinION flow cell. The longest HIV-spanning read to-date was generated, at a length of 11,487 bases, which included full-length HIV-1 and plasmid backbone with flanking host sequences supporting a single HXB2 integration event. We discovered 20 single nucleotide variants in pHXB2_D compared to reference, verified by short-read DNA sequencing. There were no variants detected in the HIV-1 segments of pNL4-3_gag-pol(Δ1443-4553)_EGFP.

Conclusions

Nanopore sequencing performed as-expected, phasing LTRs, and even covering full-length HIV. The discovery of variants in a reference plasmid demonstrates the need for sequence verification moving forward, in line with calls from funding agencies for reagent verification. These results illustrate the utility of long-read DNA-seq to advance the study of HIV at single integration site resolution.
Osteocytes remodel bone by TGF-β-induced YAP/TAZ signaling
Authors: Kegelman Christopher D. , Coulombe Jennifer C. , Jordan Kelsey M. , Horan Daniel J. , Qin Ling , Robling Alexander G. , Ferguson Virginia. L , Bellido Teresita M. , Boerckel Joel D.
Published: April 2019

Osteocytes are bone matrix-entombed cells that form an interconnected network of processes called the lacunar/canalicular system, which enables osteocytes to coordinate bone formation and resorption. Osteocytes indirectly regulate osteoblast and osteoclast activity on bone surfaces but also directly resorb and deposit their surrounding bone matrix through perilacunar/canalicular remodeling. However, the molecular mechanisms by which osteocytes control bone remodeling remain unclear. We previously reported that the transcriptional regulators Yes-associated protein (YAP) and Transcriptional co-activator with PDZ-motif (TAZ) promote bone acquisition in osteoblast-lineage cells. Here, we tested the hypothesis that YAP and TAZ regulate osteocyte-mediated bone remodeling by conditional ablation of both YAP and TAZ from mouse osteocytes using 8kb-DMP1-Cre. Osteocyte conditional YAP/TAZ deletion reduced bone mass and dysregulated matrix collagen content and organization, which together impaired bone mechanical properties. YAP/TAZ deletion reduced osteoblast number and activity and increased osteoclast activity. In addition, YAP/TAZ deletion directly impaired osteocyte lacunar/canalicular network remodeling, reducing canalicular density, length, and branching, but did not alter lacunar size or shape. Further, consistent with recent studies identifying TGF-β signaling as a key inducer of perilacunar/canalicular remodeling through expression of matrix-remodeling enzymes, YAP/TAZ deletion in vivo decreased osteocyte expression of matrix proteases Mmp13, Mmp14, and Cathepsin K. In vitro, pharmacologic inhibition of YAP/TAZ transcriptional activity in osteocyte-like cells abrogated TGF-β-induced protease gene expression. Together, these data show that YAP and TAZ act downstream of TGF-β in osteocytes to control bone matrix accrual, organization, and mechanical properties indirectly by coordinating osteoblast/osteoclast activity and directly by regulating perilacunar/canalicular remodeling.
Molecular Diversity and Network Complexity in Growing Protocells
Authors: Kamimura Atsushi , Kaneko Kunihiko
Published: April 2019

A great variety of molecular components is encapsulated in cells. Each of these components is replicated for cell reproduction. To address an essential role of the huge diversity of cellular components, we study a model of protocells that convert resources into catalysts with the aid of a catalytic reaction network. As the resources are limited, it is shown that diversity in intracellular components is increased to allow the use of diverse resources for cellular growth. Scaling relation is demonstrated between resource abundances and molecular diversity. We then study how the molecule species diversify and complex catalytic reaction networks develop through the evolutionary course. It is shown that molecule species first appear, at some generations, as parasitic ones that do not contribute to replication of other molecules. Later, the species turn to be host species that support the replication of other species. With this successive increase of host species, a complex joint network evolves. The present study sheds new light on the origin of molecular diversity and complex reaction network at the primitive stage of a cell.
The feasibility of atrial and ventricular arrhythmias recognition using metrics of signal complexity for heartbeat intervals
Authors: Huang Ming , Kido Koshiro , Ono Naoaki , Altaf-UI-Amin  , Tamura Toshiyo , Kanaya Shigehiko
Published: April 2019

It is well known that the cardiac system is controlled by the complex nonlinear self-regulation and the heartbeat variability (HRV) is an independent indicator of the autonomic regulation. With the assumption that intrinsic differences of atrial fibrillation (A) and ventricular ectopic arrhythmias (V) can be unveiled by a proper approach based on of signal complexity, we examine the feasibility of detecting these arrhythmias of different pathological origins using metrics of complexity for heartbeat intervals (HRI). Specifically, the normal sinus rhythm (N), the A type and the V type are used as the targeted types of heartbeat. By extracting the entropy-based features from HRI of different lengths, i.e., from 300 heartbeats to 1000 heartbeats, we examined the distinguishability of these 3 types of heartbeat. By applying the features to the random forest model, the HRI signal of 600-heartbeat-length can be used to detect the A and V completely, i.e., with 100% of type-wise recall and precision. What is more, this approach is sensitive to the existence of the corresponding arrhythmias. The results substantiate our assumption about the intrinsic difference of the A and V type. A further investigation applying this approach to a wider spectrum and a finer stratification of arrhythmias/ cardiac diseases and may lead to the systematic understanding in the context of complexity and better insight for its practical use for wearable/unconstrained monitors.
deSALT: fast and accurate long transcriptomic read alignment with de Bruijn graph-based index
Authors: Liu Bo , Liu Yadong , Li Junyi , Guo Hongzhe , Zang Tianyi , Wang Yadong
Published: April 2019

Long-read RNA sequencing (RNA-seq) is promising to transcriptomics studies, however, the alignment of long RNA-seq reads is still non-trivial due to high sequencing errors and complicated gene structures. Herein, we propose deSALT, a tailored two-pass alignment approach, which constructs graph-based alignment skeletons to infer exons and uses them to generate spliced reference sequences to produce refined alignments. deSALT addresses several difficult technical issues, such as small exons and sequencing errors, which breakthroughs the bottlenecks of long RNA-seq read alignment. Benchmarks demonstrate that deSALT has a greater ability to produce accurate and homogeneous full-length alignments. deSALT is available at: https://github.com/hitbc/deSALT.
Cell type-specific genetic regulation of expression in the granule cell layer of the human dentate gyrus
Authors: Jaffe AE , Hoeppner DJ , Saito T , Blanpain L , Ukaigwe J , Burke EE , Tao R , Tajinda K , Deep-Soboslay A , Shin JH , Kleinman JE , Weinberger DR , Matsumoto M , Hyde TM
Published: April 2019

Laser capture microdissection followed by RNA-seq (LCM-seq) was used to profile the transcriptional landscape of the granule cell layer of the dentate gyrus (DG-GCL) in human hippocampus, and contrasted to homogenate tissue. We identified widespread cell type-specific aging and genetic effects in the DG-GCL that were either missing or directionally discordant in corresponding bulk hippocampus RNA-seq data from largely the same subjects. Of the ∼9 million eQTLs in the DG-GCL, 15% were not in bulk hippocampus, including 15 schizophrenia genome-wide association study (GWAS) risk variants. We then created custom transcriptome-wide association study (TWAS) genetic weights from the DG-GCL which identified many novel schizophrenia-associated genetic signals not found in TWAS from bulk hippocampus, including GRM3 and CACNA1C. These results highlight the biological resolution of cell type-specific expression profiling using targeted sampling strategies like LCM, and complement homogenate and single nuclei approaches in human brain.