bluuebunny/crossref_metadata_2025 huggingface dataset:
Maritime Business: A Paradigm of Global Business
Authors: Harlaftis Gelina , Theotokas Ioannis
Published: May 2020

Maritime business is a paradigm of a global business. Its importance cannot be underrated as 90% of the world’s trade is at the present day carried by sea. In fact, the vast majority of the goods that form our daily lives depend upon the shipping industry. As ships sail in the seas and oceans of the world, and as ports are nowadays hidden away and not part of the everyday life of people in port cities, much of the shipping business is invisible and remains so to the mainstream business and management literature. Maritime business since, at least, the early modern period has evolved as a main factor for the communication and formation of the international and eventually global markets.

Research in maritime business has evolved around the formation and transformation of shipping markets, the evolution of shipping firms and ship management, the effect of technology at sea transport and on its productivity and freight rates, on trends of the nationality of world fleet, and its denationalization or “flagging out,” on seafaring labor and risk at sea.

A shipping firm is the economic unit that uses the factors of production to produce and provide sea transport services. It serves the world trade system which was consolidated in the 19th century, and the formation and organization of shipping firms followed the type of cargoes that had to be carried: first, bulk commodities carried in huge quantities like raw materials and second manufactured and packaged goods. The first type of cargo has been served by the tramp/bulk shipping companies and the second type by the liner/container shipping companies. Technology has been a watershed in the formation and transformation of the shipping firm. Five periods can be distinguished in the last two centuries in the evolution of the shipping industry and the shipping firm according to transformation of shipping markets and the introduction of new technologies: (a) up to the 1820s, (b) from the 1830s to the 1870s, (c) from the 1880s to the 1930s, (d) from the 1940s to the 1970s, and (e) after the 1980s.

Until the last third of the 20th century Europe dominated the world fleet to be gradually replaced by the Asian fleets in the 21st century. Maritime business, is increasingly losing its “nationality” and is becoming global despite the fact that in sections of it there are powerful shipping families connected with certain nations. Shipping has always been a high-risk business, which, despite the evolution in many aspects of its operation, remains dependent on the acts of nature as well as on the acts of people, as the recent revitalization of piracy reveals.
Public Perceptions of Public Service in European Media
Authors: Just Natascha
Published: May 2020

In Western Europe, the notion of public service in the media was originally associated with traditional public-service broadcasters. However, since the 1990s, the general idea of public-service broadcasting and the continuing need for it in a digitized, content-abundant environment have been questioned. In particular, public-service broadcasters’ online activities have triggered controversial discussions and policy responses, not least because of direct competition with online services of the private media. At the same time, discussions have emerged about the meaning of public service and attendant concepts such as public value, challenging the hitherto commonly accepted attachment of the concept to a specific technology (broadcasting) and a specific—publicly procured and financed—organizational setting. In response to this and backed by politics, public-service broadcasters have reinvented themselves as public-service media. They have expanded their remit beyond television and radio into multimedia realms such as the Internet and, in addition to this, have started devoting new attention to the general public as their prime target of accountability—thus opposed to the original exclusive accountability to politics. Such accountability has been pursued, among other things, through direct cooperation with the public or other ways of connecting with it, for example, through personalization efforts and participatory formats. Although the public has rhetorically become the prime target of accountability, there is little discussion or acknowledgement of the actual perceptions that the public has about the general idea of public service and how public-service broadcasters accomplish this task. With few exceptions, studies continue the dominant paradigm of audience research, which construes the public almost exclusively as consumers.
Monitoring and Assessing Arctic Climate Change
Authors: Reiersen Lars-Otto , Corell Robert W.
Published: May 2020

This overview of climate observation, monitoring, and research for the Arctic region outlines the key elements essential to an enhanced understanding of the unprecedented climate change in the region and its global influences. The first recorded observation of sea ice extent around Svalbard date back to the whaling activities around 1600. Over the following 300 years there are periodic and inadequate observations of climate and sea ice from explorers seeking a northern sea route for sailing to Asia or reaching the North Pole. Around 1900 there were few fixed meteorological stations in the circumpolar North. During the Second World War and the following Cold War, the observation network increased significantly due to military interest. Since the 1970s the use of satellites has improved the climate and meteorological observations of Arctic areas, and advancements in marine observations (beneath the sea surface and within oceanic sediments) have contributed to a much improved network of climate and meteorological variables.

Climate change in the Arctic and its possible effects within the Arctic and on global climate such as extreme weather and sea level rise were first reported in the ACIA 2005 report. Since then there has been a lot of climate-related assessments based on data from the Arctic and ongoing processes within the Arctic that are linked to global systems.
The European Central Bank
Authors: Verdun Amy
Published: May 2020

The European Central Bank (ECB) has been in existence for almost 20 years and more if one considers its immediate predecessor the European Monetary Institute (1994–1997). During these two decades the ECB has become an established institution. It secures price stability and further increased its reputation as a lender of last resort during the financial crisis and its aftermath. In the 2010s, in response to the global financial crisis and the sovereign debt crisis, the ECB has also taken on the role of supervisor of the financial system and monitors developments in the Euro Area financial sector.

Political science literature on the ECB can be subdivided into different strands. One strand looks at the ECB as just another central bank and hence examines its role as a central bank with the usual instruments. Another strand of literature examines the role of the ECB as an institution that is insufficiently embedded into democratic checks and balances. This perennial criticism of the ECB was born when the European System of Central Banks (ESCB) was created to be independent from political influence. A third strand of the literature is newer and examines the unorthodox steps that the ECB (and other central banks) took, and have taken, to offset the financial crisis and the ensuing economic crisis. An analysis of European integration and the political economy of the Euro Area can contribute to a better understanding of why the ECB has taken a proactive role. The political science research of the ECB is discussed here as well as the various dimensions of research conducted on the ECB.
Nigeria: Regional Politics and Dynamics
Authors: Owen Oliver
Published: May 2020

The politics of Nigeria have often been considered a matter of managing social diversity in a political economy whose extremes have been exaggerated by oil money. But this story is incomplete without thinking instead more deeply about inequality, about political party origins and ideologies as well as identities, and about politics beyond parties and elections. Bureaucracy, mass mobilization, and everyday practice are equally important issues in Nigerian politics as the country moves through another economic transformation.

Nigeria’s political structures have been built around questions of managing diversity and allocating resources, and the country’s federal system embeds a tension between how much power is managed from the center and how much is devolved to the constituent states and local governments. As well as parties, legislatures, and executives, security institutions have been prominent in the country’s political formation, and public institutions are both formed around, and are vectors of forming, elite social networks.

Partly due to long-standing models of social legitimacy and partly as a result of the kind of identity politics Nigeria has chosen to manage diversity, models of citizenship based on localized belonging are pervasive drivers of political patterning. Political factions and parties, often characterized as election-winning aggregations of patron-client networks, also however embed distinct historical ideological traditions, which chart Nigeria’s movements between liberal capitalism and state-directed development and which have driven both domestic debates and a continental and regional leadership role.

Tensions around inequalities and the realm of the political more generally cannot be understood as a matter of governmental institutions alone but bring in religion, gender construction, labor movements, the media, civil society, and new social movements, as well as the “ineffable politics” of tactic, techniques, norms, and practices that fix the realm of the political as a key part of everyday social and economic life.
Aging and Olfaction
Authors: Doty Richard L.
Published: May 2020

Decreased ability to smell is common in older persons. Some demonstrable smell loss is present in more than 50% of those 65 to 80 years of age, with up to 10% having no smell at all (anosmia). Over the age of 80, 75% exhibit some loss with up to 20% being totally anosmic. The causes of these decrements appear multifactorial and likely include altered intranasal airflow patterns, cumulative damage to the olfactory receptor cells from viruses and other environmental insults, decrements in mucosal metabolizing enzymes, closure of the cribriform plate foramina through which olfactory receptor cells axons project to the brain, loss of selectivity of receptor cells to odorants, and altered neurotransmission, including that exacerbated in some age-related neurodegenerative diseases.
Cosmopolitanism and the Philosophy of Education
Authors: Papastephanou Marianna
Published: May 2020

In its most popular sense, cosmopolitanism is taken to be a way of life and a kind of selfhood. The cosmopolitan self learns from other cultures, embraces diversity, and considers her selfhood or lifestyle defined more by routes than by roots. Thus understood cosmopolitanism becomes a descriptive concept, that is, it says something about how the person lives and acts and about what the person is like. When this cosmopolitan existence is elevated to a political ideal or virtue, it strikes a normative note. For example, to say that a society or an individual is cosmopolitan is to attribute something good to such a society or individual, that is, to see in them a commendable feature or to summon them to acquire it. Philosophy has, from antiquity to the present, formulated, debated, contested, revisited, and negotiated the descriptive and normative aspects of cosmopolitan existence and citizenship. It has thus provided rich and diverse descriptions and prescriptions of cosmopolitanism. Political philosophy, in particular, investigates the relationship of cosmopolitanism with kindred or alternative descriptions and prescriptions of how we exist or should exist in the world.

In line with philosophy, the philosophy of education also considers what counts as cosmopolitan. Often transferring philosophical insights directly to educational frameworks, educational philosophy discusses whether cosmopolitanism (and which version of it) may be a desirable pedagogical aim. Questions such as “who embodies the cosmopolitan,” “what matters as cosmopolitan practice,” or “how to cultivate the cosmopolitan subject and the corresponding citizenship” are indicative of educational-philosophical concerns. At a deeper level, educational philosophy addresses challenges to identity, contestations of Western values, and contemporary, global changes that affect educational appreciations of cosmopolitanism. And it examines how critical approaches to cosmopolitanism and to related notions may shed new light on educational cosmopolitan sensibilities and reveal ambiguities in cosmopolitan political and pedagogical operations.
Feminist Frameworks for Educational Leadership in the United States
Authors: Marshall Catherine , Edwards Torrie
Published: May 2020

Feminist insights offer ways to rethink and restructure schooling to fit with realities faced by educators, students, and families. This article relies on its model of values affecting schooling policies and practices then presents the range of feminisms, It shows how feminisms would be seen as looking awry and would be assessed as inadequate and inappropriate for leaders. It then charts their implications for school leaders, who will be able to identify the values, structures, and power arrangements to be questioned and altered.
Land Education
Authors: Cruz Austin R.
Published: May 2020

Land education from an Indigenous perspective can be understood as the learning of deep social, political, ethical, and spiritual relationships on and with land. By extension, the approach of land-as-pedagogy applies the understanding that the primary and ultimate teacher is the very land itself. Land education offers scholars and students a nuanced, culturally responsive, and responsible critique of the notion of place and field of place-based education, particularly with regard to historically minoritized students and communities such as Indigenous peoples throughout the world. Building from Indigenous scholarship and drawing connections between global examples of Indigenous relationships to land, the educational implications of land education and land-as-pedagogy compel everyone involved in enacting curricula and pedagogy to center such ideas into all learning irrespective of academic “subject” or discipline. By acknowledging where events, relationships, experiences, and understanding happen, communities and learners are afforded the opportunity to reassess and reaffirm the ontological and epistemological basis that all knowledge is contextualized and that contextualization starts with/in land. Examples of the positive educational outcomes of such curricular, pedagogical, administrative, and educational policy change around land include the affirmation and strengthening of Indigenous peoples’ sovereignty, self-determination, and self-education, as well as the larger enculturation of non-Indigenous learners to more applied, reflexive, and explicit alliances and interdependencies with land and other communities. Repositioning land education and land-as-pedagogy from a marginal to central place within formal and informal education initiates the logical consequence and responsibility of such pedagogy: the complex, ethical, and historically informed process of Indigenous land repatriation.
Marketization and Educational Institutions
Authors: Teixeira Pedro Nuno
Published: May 2020

The way education is perceived socially and politically has changed significantly over the last half century. The growing pervasiveness of economic analysis in education has contributed significantly, among other societal and political factors, to a reformulation in the way educational organizations are conceived, particularly due to the economic and social effects of their activity. One of the major dimensions of that change has been the strengthening of a discourse that emphasized the advantages of market and competitive forces over public regulation and of privatization and quasi-private rationales over public ones. Despite significant social and political resistances, the education sector has been experiencing a growing influence of market and competitive forces, and this is particularly visible in the higher education sector. Hence, several policy developments have led to the strengthening of market forces and competition in higher education. This encompasses changes in the contextual conditions through which market forces have been strengthened and the subsequent impact of marketization, competition, and privatization policies at the institutional level. However, this faces resistance, not least due to the peculiarities of educational sectors and institutions, that begs reflection about the potential and limitations of approaching education institutions as economic organizations.
Fiscal Policy and Institutions in Imperial China
Authors: Zhang Taisu
Published: May 2020

Up until the final four decades of the Qing Dynasty, fiscal extraction in imperial China was primarily a matter of taxing agricultural production, generally in the form of an annual property tax assessed on the basis of landholding, and collected in either grain or cash. All major dynasties prior to the Qing wielded this fiscal instrument somewhat flexibly, with large-scale reforms, usually leading to significantly higher taxes, occurring around mid-dynasty, but the Qing broke this trend: the absolute volume of agricultural taxes remained locked in place for the great majority of its 278-year life span, despite a near tripling of both the population and the economy. This eventually rendered the Qing fiscal state an extreme outlier in both horizontal and vertical comparisons: relative to the economy it governed, not only was it much smaller than its major early modern competitors, ranging from Japan to Western European states to other central Asian empires, but it was also probably the smallest post-Qin dynastic state by far. Preexisting scholarship has largely failed to identify, let alone explain, this sudden and dramatic shift in fiscal policy towards the end of China’s imperial history. There are a number of possible explanations for it, some of which have appeared in the extant literature, but the most promising one—which has not appeared—seems to be that the extraordinary circumstances of the Ming–Qing transition served as the catalyst for a decisive conservative turn in Chinese fiscal thought, pushing the Qing state into a fundamentally different political and institutional equilibrium than its predecessors.
Njinga a Mbande: Power and War in 17th-Century Angola
Authors: Pantoja Selma
Published: May 2020

Njinga a Mbande (1582–1663) is the most famous and controversial historical figure in the history of the West-Central Africa region during the 17th century, the region of present-day Angola. Her political trajectory contributes to the understanding of the troubled context of the Portuguese expansion in the region and the establishment of the Atlantic slave trade. The Ndongo state was at the very core of this struggle, a state mainly comprised of the Mbundu peoples. It was also the Queen’s original birthplace and a major area in the dispute for ensuring control of the trade routes between the inland and coastal regions. The Portuguese arrived in the region in 1575, and settled on the coast. Luanda was the first area of the Portuguese occupation. From there the Portuguese waged wars of conquest, moving toward the sertão (hinterland). On the Portuguese side, the action unfolded in the constant attempt to control the sobas, the local authorities, the construction of fortresses in the Mbundu territory, and the wars that were initially meant to obtain captives and form an African Army (Guerra Preta). The army would later serve Portuguese interests in controlling the routes and fairs (i.e., the hubs, or centers, of slave trade). On the Mbundu authorities’ side, even before the queen’s reign, and later on at her command, the struggles took many forms: the deterrence of the fairs’ functioning; the disorganization of the “tax” system, in which the Portuguese charged the sobas; and the welcoming of hundreds of escaped slaves, as well as other central actions such as wars and diplomatic negotiations.

Njinga a Mbande took on the title Ngola (1624), the position of greatest authority and prestige in the Ndongo. In 1626, after a major campaign by Portuguese settlers, she was expelled from her territory. But by 1631 she re-emerged as a leader, now in another region, Matamba, an important base for her attacks on the areas controlled by the Portuguese. From this region, she made a peace agreement, governing until her natural death at the age of 82.

In the 21st century, historiographical questions abound: how was the leadership of this female figure viewed in terms of legitimacy and gender identity within the power structures of the Ndongo, how was her image publicly projected throughout the region, how did she rise in prominence in European reports, and what was her fundamental impact on the oral tradition of different peoples of West-Central Africa. The presence of Queen Njinga crossed the Atlantic and figures in the imagery of popular and mythical narratives in the Americas.
Capital Controls: A Survey of the New Literature
Authors: Rebucci Alessandro , Ma Chang
Published: May 2020

This paper reviews selected post–Global Financial Crisis theoretical and empirical contributions on capital controls and identifies three theoretical motives for the use of capital controls: pecuniary externalities in models of financial crises, aggregate demand externalities in New Keynesian models of the business cycle, and terms of trade manipulation in open-economy models with pricing power. Pecuniary and demand externalities offer the most compelling case for the adoption of capital controls, but macroprudential policy can also address the same distortions. So capital controls generally are not the only instrument that can do the job. If evaluated through the lenses of the new theories, the empirical evidence reviewed suggests that capital controls can have the intended effects, even though the extant literature is inconclusive as to whether the effects documented amount to a net gain or loss in welfare terms. Terms of trade manipulation also provides a clear-cut theoretical case for the use of capital controls, but this motive is less compelling because of the spillover and coordination issues inherent in the use of control on capital flows for this purpose. Perhaps not surprisingly, only a handful of countries have used capital controls in a countercyclical manner, while many adopted macroprudential policies. This suggests that capital control policy might entail additional costs other than increased financing costs, such as signaling the bad quality of future policies, leakages, and spillovers.
The Indeterminacy School in Macroeconomics
Authors: Farmer Roger E. A.
Published: May 2020

The indeterminacy school in macroeconomics exploits the fact that macroeconomic models often display multiple equilibria to understand real-world phenomena. There are two distinct phases in the evolution of its history. The first phase began as a research agenda at the University of Pennsylvania in the United States and at CEPREMAP in Paris in the early 1980s. This phase used models of dynamic indeterminacy to explain how shocks to beliefs can temporarily influence economic outcomes. The second phase was developed at the University of California Los Angeles in the 2000s. This phase used models of incomplete factor markets to explain how shocks to beliefs can permanently influence economic outcomes. The first phase of the indeterminacy school has been used to explain volatility in financial markets. The second phase of the indeterminacy school has been used to explain periods of high persistent unemployment. The two phases of the indeterminacy school provide a microeconomic foundation for Keynes’ general theory that does not rely on the assumption that prices and wages are sticky.
Adolescent Sexual and Reproductive Health
Authors: Prata Ndola , Weidert Karen
Published: May 2020

Adolescence, spanning 10 to 19 years of age, begins with biological changes while transitioning from a social status of a child to an adult. For millions of adolescents in low- and middle-income countries (LMICs), this is a period of exposure to vulnerabilities and risks related to sexual and reproductive health (SRH), compounded by challenges in having their SHR needs met. Globally, adolescent sexual and reproductive ill-health disease burden is concentrated in LMICs, with sexually transmitted infections and complications from pregnancy and childbirth accounting for the majority of the burden. Adolescents around the world are using their voices to champion access to high-quality, comprehensive SRH information and services. Thus, it is imperative that adolescents’ SRH and rights be reinforced and that investments in services be prioritized.
Interplanetary Dust Particles
Authors: Flynn George J.
Published: May 2020

Scattered sunlight from interplanetary dust particles, mostly produced by comets and asteroids, orbiting the Sun are visible at dusk or dawn as the Zodiacal Cloud. Impacts onto the space-exposed surfaces of Earth-orbiting satellites indicate that, in the current era, thousands of tons of interplanetary dust enters the Earth’s atmosphere every year. Some particles vaporize forming meteors while others survive atmospheric deceleration and settle to the surface of the Earth. NASA has collected interplanetary dust particles from the Earth’s stratosphere using high-altitude aircraft since the mid-1970s. Detailed characterization of these particles shows that some are unique samples of Solar System and presolar material, never affected by the aqueous and thermal processing that overprints the record of formation from the Solar Protoplanetary Disk in the meteorites. These particles preserve the record of grain and dust formation from the disk. This record suggests that many of the crystalline minerals, dominated by crystalline silicates (olivine and pyroxene) and Fe-sulfides, condensed from gas in the inner Solar System and were then transported outward to the colder outer Solar System where carbon-bearing ices condensed on the surfaces of the grains. Irradiation by solar ultraviolet light and cosmic rays produced thin organic coatings on the grain surfaces that likely aided in grain sticking, forming the first dust particles of the Solar System. This continuous, planet-wide rain of interplanetary dust particles can be monitored by the accumulation of 3He, implanted into the interplanetary dust particles by the Solar Wind while they were in space, in oceanic sediments. The interplanetary dust, which is rich in organic carbon, may have contributed important pre-biotic organic matter important to the development of life to the surface of the early Earth.
Economies of Advice
Authors: James Deborah , Koch Insa
Published: May 2020

Because of academic divisions of labor, anthropologists have come late to the study of the changing landscape of welfare and advice provisions in Euro-America (and beyond). However, this study is crucial to understanding contemporary economies. Attention to the increasing informalization, hybridization, plurality, and complexity of welfare-care-advice provisions in the context of 21st-century austerity in Europe challenges the widely held view of how state bureaucracies operate. The corollaries are the difficulties in accessing what help is available (hence the increasing need for advice) and an increase in grass-roots mutual aid and activism to supplement, and in some cases even supplant, state advice provisions.
Neurolinguistic Approaches in Morphology
Authors: Schiller Niels O.
Published: May 2020

Neurolinguistic approaches to morphology include the main theories of morphological representation and processing in the human mind, such as full-listing, full-parsing, and hybrid dual-route models, and how the experimental evidence that has been acquired to support these theories uses different neurolinguistic paradigms (visual and auditory priming, violation, long-lag priming, picture-word interference, etc.) and methods (electroencephalography [EEG]/event-related brain potential [ERP], functional magnetic resonance imaging [fMRI], neuropsychology, and so forth).
Critical Race Theory
Authors: Sulé V. Thandi
Published: May 2020

Critical race theory (CRT) is a framework that unapologetically asserts how and why race matters in the maintenance of U.S. policies and practices. In doing so, CRT counters discourse that situates discrimination and disparities within the realm of individual behaviors or psychological deficits. Therefore, racism is seen for what it is—a willful, institutionalized, and dehumanizing way of being. Though racism prevailed as the quintessential problem of the 20th century, the 21st century has revealed that the color line remains remarkably undisturbed. Whether one is focusing on housing, education, employment, wealth, health, safety, or justice, racial disparities and inequities exist to the disadvantage of racially minoritized people. Born out of discontent for legal remedies for inequality, CRT speaks to the universal way that racism immobilizes minoritized people—thereby providing an almost unwavering advantage to white people. This review provides an overview of the tenets of CRT and how those tenets connect with social work values and practice.
Poor oral hygiene, oral microorganisms and aspiration pneumonia risk in older people in residential aged care: a systematic review
Authors: Khadka Sangeeta , Khan Shahrukh , King Anna , Goldberg Lynette R , Crocombe Leonard , Bettiol Silvana
Published: May 2020

Background

aspiration pneumonia increases hospitalisation and mortality of older people in residential aged care.

Objectives

determine potentially pathogenic microorganisms in oral specimens of older people with aspiration pneumonia and the effect of professional oral care in reducing aspiration pneumonia risk.

Data Sources

PUBMED/MEDLINE, CINAHL, EMBASE, COCHRANE, PROQUEST, Google Scholar, Web of Science.

Study Eligibility Criteria

published between January 2001 and December 2019 addressing oral microorganisms, aspiration pneumonia, oral health and treatment.

Participants

people 60 years and older in residential aged care.

Study Appraisal and Synthesis Methods

the Newcastle–Ottawa Scale and the Standard Protocol Items: Recommendations for Intervention Trials checklist.

Results

twelve studies (four cross-sectional, five cohort and three intervention) reported colonisation of the oral cavity of older people by microorganisms commonly associated with respiratory infections. Aspiration pneumonia occurred less in people who received professional oral care compared with no such care. Isolation of Candida albicans, Staphylococcus aureus, methicillin-resistant S. aureus and Pseudomonas aeruginosa was related to mortality due to aspiration pneumonia. An interesting finding was isolation of Escherichia coli, a gut bacterium.

Limitations

more information may be present in publications about other co-morbidities that did not meet inclusion criteria. A high degree of heterogeneity prevented a meta-analysis. Issues included sampling size, no power and effect size calculations; different oral health assessments; how oral specimens were analysed and how aspiration pneumonia was diagnosed.

Conclusions and Implications of Key Findings

pathogenic microorganisms colonising the oral microbiome are associated with aspiration pneumonia in older people in residential care; professional oral hygiene care is useful in reducing aspiration pneumonia risk.
TandemTools: mapping long reads and assessing/improving assembly quality in extra-long tandem repeats
Authors: Mikheenko Alla , Bzikadze Andrey V , Gurevich Alexey , Miga Karen H , Pevzner Pavel A
Published: May 2020

Motivation

Extra-long tandem repeats (ETRs) are widespread in eukaryotic genomes and play an important role in fundamental cellular processes, such as chromosome segregation. Although emerging long-read technologies have enabled ETR assemblies, the accuracy of such assemblies is difficult to evaluate since there are no tools for their quality assessment. Moreover, since the mapping of error-prone reads to ETRs remains an open problem, it is not clear how to polish draft ETR assemblies.

Results

To address these problems, we developed the TandemTools software that includes the TandemMapper tool for mapping reads to ETRs and the TandemQUAST tool for polishing ETR assemblies and their quality assessment. We demonstrate that TandemTools not only reveals errors in ETR assemblies but also improves the recently generated assemblies of human centromeres.

Availability and implementation

https://github.com/ablab/TandemTools.

Supplementary information

Supplementary data are available at Bioinformatics online.
The string decomposition problem and its applications to centromere analysis and assembly
Authors: Dvorkina Tatiana , Bzikadze Andrey V , Pevzner Pavel A
Published: May 2020

Motivation

Recent attempts to assemble extra-long tandem repeats (such as centromeres) faced the challenge of translating long error-prone reads from the nucleotide alphabet into the alphabet of repeat units. Human centromeres represent a particularly complex type of high-order repeats (HORs) formed by chromosome-specific monomers. Given a set of all human monomers, translating a read from a centromere into the monomer alphabet is modeled as the String Decomposition Problem. The accurate translation of reads into the monomer alphabet turns the notoriously difficult problem of assembling centromeres from reads (in the nucleotide alphabet) into a more tractable problem of assembling centromeres from translated reads.

Results

We describe a StringDecomposer (SD) algorithm for solving this problem, benchmark it on the set of long error-prone Oxford Nanopore reads generated by the Telomere-to-Telomere consortium and identify a novel (rare) monomer that extends the set of known X-chromosome specific monomers. Our identification of a novel monomer emphasizes the importance of identification of all (even rare) monomers for future centromere assembly efforts and evolutionary studies. To further analyze novel monomers, we applied SD to the set of recently generated long accurate Pacific Biosciences HiFi reads. This analysis revealed that the set of known human monomers and HORs remains incomplete. SD opens a possibility to generate a complete set of human monomers and HORs for using in the ongoing efforts to generate the complete assembly of the human genome.

Availability and implementation

StringDecomposer is publicly available on https://github.com/ablab/stringdecomposer.

Supplementary information

Supplementary data are available at Bioinformatics online.
A Practical Guide for Faecal Calprotectin Measurement: Myths and Realities
Authors: D’Amico Ferdinando , Nancey Stéphane , Danese Silvio , Peyrin-Biroulet Laurent
Published: May 2020

Background and Aims

Faecal calprotectin [FC] is a valid and non-invasive marker of mucosal inflammation. It is widely used both in clinical trials and in daily clinical practice for patients with inflammatory bowel diseases, but currently no accepted standardization for FC testing is available. Our primary aim here was to provide a clinician’s guide containing all the practical information on FC measurement in order to avoid any confounding factors, to minimize intra- and inter-individual variability in dosage, and to ensure a better and adequate interpretation of the results.

Methods

We conducted a detailed search of the scientific literature in the PubMed/MEDLINE, EMBASE and Cochrane databases up to January 2020 to find all relevant and available articles on pre-analytical and analytical phases of FC measurement.

Results

FC testing is a multi-step procedure consisting of a pre-analytical phase aimed to collect and process the stool sample and a subsequent analytical phase of FC measurement. Several factors can influence test results determining false positives or false negatives. Importantly, this faecal marker is mostly used for patient follow-up and as a predictor of treatment response. For this reason, any altered data may affect the physicians’ decisions, negatively impacting on patient management.

Conclusions

This review provides for the first time practical advice to minimize dosage variability, although further dedicated studies are needed to compare commercially available tests and identify the best tools for the most precise and accurate FC measurement.
5-Year prognostic value of the right ventricular strain-area loop in patients with pulmonary hypertension
Authors: Hulshof Hugo G , van Dijk Arie P , Hopman Maria T E , Heesakkers Hidde , George Keith P , Oxborough David L , Thijssen Dick H J
Published: May 2020

Aims

Patients with pre-capillary pulmonary hypertension (PH) show poor survival, often related to right ventricular (RV) dysfunction. In this study, we assessed the 5-year prognostic value of a novel echocardiographic measure that examines RV function through the temporal relation between RV strain (ϵ) and area (i.e. RV ϵ-area loop) for all-cause mortality in PH patients.

Methods and results

Echocardiographic assessments were performed in 143 PH patients (confirmed by right heart catheterization). Transthoracic echocardiography was utilized to assess RV ϵ-area loop. Using receiver operating characteristic curve-derived cut-off values, we stratified patients in low- vs. high-risk groups for all-cause mortality. Kaplan–Meier survival curves and uni-/multivariable cox-regression models were used to assess RV ϵ-area loop’s prognostic value (independent of established predictors: age, sex, N-terminal pro B-type natriuretic peptide, 6-min walking distance). During follow-up 45 (31%) patients died, who demonstrated lower systolic slope, peak ϵ, and late diastolic slope (all P < 0.05) at baseline. Univariate cox-regression analyses identified early systolic slope, systolic slope, peak ϵ, early diastolic uncoupling, and early/late diastolic slope to predict all-cause mortality (all P < 0.05), whilst peak ϵ possessed independent prognostic value (P < 0.05). High RV loop-score (i.e. based on number of abnormal characteristics) showed poorer survival compared to low RV loop-score (Kaplan–Meier: P < 0.01). RV loop-score improved risk stratification in high-risk patients when added to established predictors.

Conclusion

Our data demonstrate the potential for RV ϵ-area loops to independently predict all-cause mortality in patients with pre-capillary PH. The non-invasive nature and simplicity of measuring the RV ϵ-area loop, support the potential clinical relevance of (repeated) echocardiography assessment of PH patients.
The SAFE-T upper endoscopy tool: a web-based application for the point-of-care evaluation of gastroenterology fellow performance in upper endoscopy
Authors: Kumar Navin L , Kugener Guillaume , Hathorn Kelly E , Perencevich Molly L , Jajoo Kunal , Saltzman John R
Published: May 2020

Background

Attending assessment is a critical part of endoscopic education for gastroenterology fellows. The aim of this study was to develop and validate a concise, web-based assessment tool to evaluate real-time fellow performance in upper endoscopy.

Methods

We developed the Skill Assessment in Fellow Endoscopy Training (SAFE-T) upper endoscopy tool to capture both summative and formative feedback in a concise, five-part questionnaire. The tool mirrors the previously validated SAFE-T colonoscopy tool and is administered electronically via a web-based application. We evaluated the tool in a prospective study of 15 gastroenterology fellows (5 fellows each from Years 1–3 of training) over the 2018–2019 academic year. An independent reviewer evaluated a subset of these procedures and completed both the SAFE-T and Assessment of Competency in Endoscopy (ACE) upper endoscopy forms for reliability testing.

Results

Twenty faculty completed 413 SAFE-T evaluations of the 15 fellows in the study. The mean SAFE-T overall score differentiated each sequential fellow year of training, with first-year cases having lower performance than second-year cases (3.31 vs 4.25, P < 0.001) and second-year cases having lower performance than third-year cases (4.25 vs 4.56, P < 0.001). The mean SAFE-T overall score decreased with increasing case-complexity score, with straightforward compared with average cases (3.98 vs 3.39, P < 0.001) and average compared with challenging cases (3.39 vs 2.84, P = 0.042). In dual-observed procedures, the SAFE-T tool showed excellent inter-rater reliability with a Kappa agreement statistic of 0.815 (P = 0.001). The SAFE-T overall score also highly correlated with the ACE upper endoscopy overall hands-on score (r = 0.76, P = 0.011).

Conclusions

We developed and validated the SAFE-T upper endoscopy tool—a concise and web-based means of assessing real-time gastroenterology fellow performance in upper endoscopy.
Citizenry and Nationality: the Participation of Immigrants in Urban Politics in Later Medieval England
Authors: Lambert Bart
Published: May 2020

This article explores the participation of immigrants, or people born outside the kingdom, in urban politics in later medieval England. It demonstrates that the nationality of these newcomers was of only secondary importance. What mattered most was whether immigrants’ economic and political interests aligned with those of the civic political elites. If they did not, aliens’ nationality could be mobilized to exclude them from urban politics. If, however, immigrants’ activities complemented those of the urban elites economically and politically, they had every chance to engage with all aspects of civic political life and be elected into the highest civic offices.
Factorization of Noncommutative Polynomials and Nullstellensätze for the Free Algebra
Authors: Helton J , Klep Igor , Volčič Jurij
Published: May 2020

This article gives a class of Nullstellensätze for noncommutative polynomials. The singularity set of a noncommutative polynomial $f=f(x_1,\dots ,x_g)$ is $\mathscr{Z}(\,f)=(\mathscr{Z}_n(\,f))_n$, where $\mathscr{Z}_n(\,f)=\{X \in{\operatorname{M}}_{n}({\mathbb{C}})^g \colon \det f(X) = 0\}.$ The 1st main theorem of this article shows that the irreducible factors of $f$ are in a natural bijective correspondence with irreducible components of $\mathscr{Z}_n(\,f)$ for every sufficiently large $n$. With each polynomial $h$ in $x$ and $x^*$ one also associates its real singularity set $\mathscr{Z}^{{\operatorname{re}}}(h)=\{X\colon \det h(X,X^*)=0\}$. A polynomial $f$ that depends on $x$ alone (no $x^*$ variables) will be called analytic. The main Nullstellensatz proved here is as follows: for analytic $f$ but for $h$ dependent on possibly both $x$ and $x^*$, the containment $\mathscr{Z}(\,f) \subseteq \mathscr{Z}^{{\operatorname{re}}} (h)$ is equivalent to each factor of $f$ being “stably associated” to a factor of $h$ or of $h^*$. For perspective, classical Hilbert-type Nullstellensätze typically apply only to analytic polynomials $f,h $, while real Nullstellensätze typically require adjusting the functions by sums of squares of polynomials (sos). Since the above “algebraic certificate” does not involve a sos, it seems justified to think of this as the natural determinantal Hilbert Nullstellensatz. An earlier paper of the authors (Adv. Math. 331 (2018): 589–626) obtained such a theorem for special classes of analytic polynomials $f$ and $h$. This paper requires few hypotheses and hopefully brings this type of Nullstellensatz to near final form. Finally, the paper gives a Nullstellensatz for zeros ${\mathcal{V}}(\,f)=\{X\colon f(X,X^*)=0\}$ of a hermitian polynomial $f$, leading to a strong Positivstellensatz for quadratic free semialgebraic sets by the use of a slack variable.
Neutrophils Are Required During Immunization With the Pneumococcal Conjugate Vaccine for Protective Antibody Responses and Host Defense Against Infection
Authors: Tchalla Essi Y I , Bhalla Manmeet , Wohlfert Elizabeth A , Bou Ghanem Elsa N
Published: May 2020

Neutrophils can shape adaptive immunity; however, their role in vaccine-induced protection against infections in vivo remains unclear. Here, we tested their role in the clinically relevant polysaccharide conjugate vaccine against Streptococcus pneumoniae (pneumococcus). We antibody depleted neutrophils during vaccination, allowed them to recover, and 4 weeks later challenged mice with pneumococci. We found that while isotype-treated vaccinated controls were protected against an otherwise lethal infection in naive mice, full protection was lost upon neutrophil depletion. Compared to vaccinated controls, neutrophil-depleted mice had higher lung bacterial burdens, increased incidence of bacteremia, and lower survival rates. Sera from neutrophil-depleted mice had less antipneumococcal IgG2c and IgG3, were less efficient at inducing opsonophagocytic killing of bacteria by neutrophils in vitro, and were worse at protecting naive mice against pneumococcal pneumonia. In summary, neutrophils are required during vaccination for optimal host protection, which has important implications for future vaccine design against pneumococci and other pathogens.
Breed- and trait-specific associations define the genetic architecture of calving performance traits in cattle
Authors: Purfield Deirdre C , Evans Ross D , Berry Donagh P
Published: May 2020

Reducing the incidence of both the degree of assistance required at calving, as well as the extent of perinatal mortality (PM) has both economic and societal benefits. The existence of heritable genetic variability in both traits signifies the presence of underlying genomic variability. The objective of the present study was to locate regions of the genome, and by extension putative genes and mutations, that are likely to be underpinning the genetic variability in direct calving difficulty (DCD), maternal calving difficulty (MCD), and PM. Imputed whole-genome single-nucleotide polymorphism (SNP) data on up to 8,304 Angus (AA), 17,175 Charolais (CH), 16,794 Limousin (LM), and 18,474 Holstein-Friesian (HF) sires representing 5,866,712 calving events from descendants were used. Several putative quantitative trait loci (QTL) regions associated with calving performance both within and across dairy and beef breeds were identified, although the majority were both breed- and trait-specific. QTL surrounding and encompassing the myostatin (MSTN) gene were associated (P < 5 × 10−8) with DCD and PM in both the CH and LM populations. The well-known Q204X mutation was the fifth strongest association with DCD in the CH population and accounted for 5.09% of the genetic variance in DCD. In contrast, none of the 259 segregating variants in MSTN were associated (P > × 10−6) with DCD in the LM population but a genomic region 617 kb downstream of MSTN was associated (P < 5 × 10−8). The genetic architecture for DCD differed in the HF population relative to the CH and LM, where two QTL encompassing ZNF613 on Bos taurus autosome (BTA)18 and PLAG1 on BTA14 were identified in the former. Pleiotropic SNP associated with all three calving performance traits were also identified in the three beef breeds; 5 SNP were pleiotropic in AA, 116 in LM, and 882 in CH but no SNP was associated with more than one trait within the HF population. The majority of these pleiotropic SNP were on BTA2 surrounding MSTN and were associated with both DCD and PM. Multiple previously reported, but also novel QTL, associated with calving performance were detected in this large study. These also included QTL regions harboring SNP with the same direction of allele substitution effect for both DCD and MCD thus contributing to a more effective simultaneous selection for both traits.