bluuebunny/crossref_metadata_2025_split huggingface dataset:
MSMC and MSMC2: The Multiple Sequentially Markovian Coalescent
Authors: Schiffels Stephan , Wang Ke 
Published: January 2020

AbstractThe Multiple Sequentially Markovian Coalescent (MSMC) is a population genetic method and software for inferring demographic history and population structure through time from genome sequences. Here we describe the main program MSMC and its successor MSMC2. We go through all the necessary steps of processing genomic data from BAM files all the way to generating plots of inferred population size and separation histories. Some background on the methodology itself is provided, as well as bash scripts and python source code to run the necessary programs. The reader is also referred to community resources such as a mailing list and github repositories for further advice.
Coalescent Simulation with msprime
Authors: Kelleher Jerome , Lohse Konrad 
Published: January 2020

AbstractCoalescent simulation is a fundamental tool in modern population genetics. The library provides unprecedented scalability in terms of both the simulations that can be performed and the efficiency with which the results can be processed. We show how coalescent models for population structure and demography can be constructed using a simple Python API, as well as how we can process the results of such simulations to efficiently calculate statistics of interest. We illustrate ’s flexibility by implementing a simple (but functional) approximate Bayesian computation inference method in just a few tens of lines of code.
Fashioning Cosmology: Franco Burgersdijk as the Author of the Dutch Tractatus de sphaera
Authors: Buning Marius 
Published: January 2020

AbstractIn 1625, the highest authorities in the province of Holland prescribed the use ofDe sphaerain all the regional Latin schools. For the occasion, they decided that a new edition of the famous text by Johannes de Sacrobosco was needed, primarily to purify the textbook of its “barbaric” Latin. The task of editing the text was assigned to Leiden professor Franco Burgersdijk. In what follows, I situate Burgersdijk’s 1626 edition ofDe sphaerain the broader context of Leiden Aristotelianism, discussing the relationship between religion, educational practices, and astronomy in the first decades of Dutch independence. Teasing out some of the differences with the other contemporary manuals circulating on the market, I argue that Burgersdijk’s version of Sacrobosco’s textbook must be seen as an attempt to make the Dutch less dependent on Catholic literature and modes of knowledge production.
A Lathe and the Material Sphaera: Astronomical Technique at the Origins of the Cosmographical Handbook
Authors: Oosterhoff Richard J. 
Published: January 2020

AbstractEven though cosmographers loved to drape their discipline in the ancient dignity of Ptolemy, actual manuals of cosmography often depended on Johannes de Sacrobosco’s medieval introduction to spherical astronomy. In fact, certain strains of cosmography shared organization, principles, and even visual apparatus with Sacrobosco’sSphaeraand its growing commentary tradition, to the extent that these cosmographies can be seen as themselves commenting on theSphaera. This paper traces the origins of certain Renaissance cosmographical handbooks to the commentary on theSphaeraby Lefèvre d’Étaples and his colleagues at Paris around 1495. By focusing on the visual elements of this commentary, its instructions for calculating techniques, and the emergence of the “lathe” model of the “material sphere,” this chapter argues that one of the mixed mathematical genres now seen as most characteristic of the Renaissance—cosmography—in fact was based on a medieval textbook.
Francesco Capuano di Manfredonia
Authors: Nenci Elio 
Published: January 2020

AbstractOne of the most important commentaries on Sacrobosco’sTractatus de sphaerawas written by Francesco Capuano da Manfredonia and printed toward the end of the year 1499 in Venice. Capuano was professor of Astronomy at Padua and had already published a commentary on Peuerbach’sTheoricae planetarumin 1495. He subsequently entered into the ranks of the Lateran Canons Regular, taking the name Giovanni Battista. Later editions of his commentary on Sacrobosco’sTractatus(Venezia, 1518 and 1531) were published under the name Giovanni Battista Capuano and contain a revisited text of that work. The two different redactions of the commentary on theSphaeraallow us to illustrate the radical transformation the text underwent. The two redactions of the prologue that opens the commentary are compared.
Conrad Tockler’s Research Agenda
Authors: Valleriani Matteo , Citron Nana 
Published: January 2020

AbstractConrad Tockler, alias Noricus, was a university professor in Leipzig at the beginning of the sixteenth century andRector magnificusof the university from 1512 on. He was a physician adept at astrological medicine and was also a fairly skilled mathematician. His publication list begins in 1502 with aLibellus de sole, a commented reprint of Marsilius Ficinus’s homonimous work. Tockler also authored two different commented editions of Johannes de Sacrobosco’sTractatus de sphaera. In his view, cosmological knowledge was directly connected with his medical activities via astrology.The paper reconstructs the intellectual context in which Tockler was active with the aim to understand how much he can be considered innovative, or whether he was in truth a late expression of an already declining late Medieval knowledge system that unified astronomy, astrology, and medicine in form of a structure pivoted around cosmological knowledge.
John of Glogów
Authors: Barker Peter 
Published: January 2020

AbstractJohn of Glogów taught at Kraków from 1468 until his death. He wrote on grammar, logic, medicine and especially astronomy, including a commentary on Johannes de Sacrobosco’sSphaera(1506). An unusual feature of his Sacrobosco commentary is the extended use of the three-dimensional orb models popularized in Peuerbach’sTheoricae novae planetarum(Nuremberg 1474) and also used by Glogów’s colleague Albert of Brudzewo. To situate Glogów’s work, I describe the development of celestial orbs in astronomy by Islamicate followers of Ptolemy and their European reception. Early modern Europeans debated the physical reality of eccentrics, epicycles, and the corresponding orbs with the followers of Averroes. After reviewing Glogów’s criticisms of Sacrobosco, I conclude that he clearly sides with Ptolemy, Peuerbach and Brudzewo against Averroes. His work shows that astronomers after Peuerbach attributed physical reality to their theories, and claimed increasing autonomy for mathematical sciences against physics.
Sacrobosco’s Sphaera in Spain and Portugal
Authors: Crowther Kathleen M. 
Published: January 2020

AbstractThis paper analyzes sixteenth-century commentaries on Johannes de Sacrobosco’sSphaerain Portuguese and Spanish. Between the fifteenth and seventeenth centuries, there were more translations of theSphaerainto Castilian and Portuguese than into all other European vernaculars combined. A major reason for the interest inSphaeratranslations in Spain and Portugal was that the basic astronomical and geographical knowledge contained in this text could be used for navigation. Because of their enormous interests in overseas exploration and colonization, Iberian monarchs supported the development of cosmography, a subject that combined mathematics, astronomy, and geography. The astronomical information in theSphaerawas also valued on the Iberian Peninsula for its applications to astrology. Finally, theSphaerawas critical to a Christian education because it taught readers to appreciate the wonders of God’s creation. Spanish and Portuguese commentaries on Sacrobosco’sSphaerareflect this mix of practical, political, and spiritual concerns.
Solar Photochemistry in Flow
Authors: Cambié Dario , Noël Timothy 
Published: January 2020

AbstractIn recent years, photochemistry has been a highly active research field. This renaissance is linked to the upsurge of photoredox catalysis, a versatile platform for synthetic methodologies using visible light photons as a traceless reagent. In contrast with UV, visible light constitutes almost half of the ground solar irradiance, making the use of solar light in chemistry a sustainable and viable possibility. However, the direct use of sunlight to power chemical reactions is still little explored. This can be explained by both the hurdles associated with solar radiation (e.g., its variability, irreproducibility, high IR content, etc.) and the need for a specialized photoreactor. Most of these issues can be tackled with technological solutions, and especially with the recourse to flow chemistry. Flow chemistry goes hand in hand with photochemistry thanks to the uniform irradiation it provides to the reaction. Furthermore, a continuous-flow reactor can be easily integrated with different solar collectors (including compound parabolic concentrators and luminescent solar concentrators) and constitutes the most efficient approach to solar photochemistry. After a description of the characteristics of the solar radiation relevant to chemistry, this chapter critically describes the different type of solar photoreactors and their applications in synthetic organic chemistry. Finally, an outlook on the future of solar photochemistry in flow is included.
Affektregime der Primatologie
Authors: Shah Mira 
Published: January 2020

ZusammenfassungAffekte im Feld lassen sich in den Forschungsmemoiren der Primatologie, wie in den letzten beiden Teilen diskutiert, auf mindestens zweierlei Ebenen untersuchen: Es lässt sich erstens nach der Qualität von Affekten in der Forschung fragen und der epistemologische Wert von Emotionen in Forschungsprozessen aus dem Berichten über die daran beteiligten Prozesse herausarbeiten. Zweitens kann anhand der Darstellung von herausfordernden Erfahrungen aus dem Forschungskontext der affektpoetologische Zusammenhang von Form und Emotionalität beleuchtet werden. Die Thematisierbarkeit von Affektivität in der Forschung und die affektive Darstellung von Forschungserfahrungen sind jedoch beide drittens abhängig von dem, was zeitgenössisch denk- und darstellbar ist. Wie im Folgenden aufzuzeigen sein wird, sind die primatologischen Forschungsmemoiren nicht unabhängig von ihren jeweiligen gesellschaftlichen, kulturellen, politischen und/oder wissenschaftlichen Kontexten zu betrachten, denn diese geben in Form verschiedener Regime vor, ob, wie und wann von Emotionalität berichtet werden kann.
Digitale Epidemiologie
Authors: Brockmann Dirk 
Published: January 2020

ZusammenfassungDigitale Epidemiologie ist ein relativ neues, rapide wachsendes Forschungsgebiet. Die technologische Revolution des letzten Jahrzehnts, die globale Vernetzung, der Informationsaustausch über soziale Medien und insbesondere die nahezu gesamtgesellschaftliche Nutzung mobiler Endgeräte ermöglichen es, individuenspezifische Daten mit einer Auflösung zu erfassen, die noch vor einigen Jahren unmöglich erschien. Diese Daten werden in der digitalen Epidemiologie untersucht, um epidemiologische Fragen besser beantworten zu können.Dieser Artikel liefert einen Überblick. Es werden verschiedene Aspekte der digitalen Epidemiologie diskutiert. An Beispielen wird erläutert, wie epidemiologische und bioinformatische Daten auf interaktiven Internetplattformen zusammengeführt werden, wie durch Analyse der Inhalte und des Informationsaustauschs über soziale Medien und Netzwerke wichtige Erkenntnisse gewonnen werden und wie mithilfe mobiler Endgeräte in natürlichen Experimenten Kontakt- und Proximitätsnetzwerke rekonstruiert werden, um die Dynamik direkt übertragbarer Infektionskrankheiten besser verstehen, beschreiben und vorhersagen zu können.Es wird erklärt, wieso die moderne Netzwerktheorie, aber auch Methoden des maschinellen Lernens und künstliche Intelligenz bei der Analyse sehr großer Datensätze wichtige Werkzeuge sind und wie traditionelle, statistische Ansätze der Infektionsepidemiologie durch diese neuen Methoden ergänzt werden.Die ethischen Herausforderungen im Bereich Datenschutz, Datensicherheit und Persönlichkeitsrechte werden schließlich diskutiert. Konzepte und Wege, personenbezogene Verhaltensdaten einerseits nutzbar zu machen und andererseits die Datenhoheit jedes Einzelnen zu wahren, werden skizziert.
Whole body vibration training during allogeneic hematopoietic cell transplantation—the effects on patients’ physical capacity
Authors: Pahl Antonia , Wehrle Anja , Kneis Sarah , Gollhofer Albert , Bertz Hartmut 
Published: January 2020

AbstractPatients undergoing allogeneic hematopoietic cell transplantation (alloHCT) experience a considerable decline in physical and psycho-social capacity. Since whole body vibration (WBV) is known to efficiently stimulate the neuromuscular system and enhance cardiorespiratory fitness and muscle strength in frail individuals, we hypothesized that WBV would maintain various physical and psychological capacities in patients during alloHCT. Seventy-one patients were randomly allocated to either an intervention group (IG) doing WBV or an active control group (CG) doing mobilization exercises five times per week. We determined peak oxygen consumption (VO2peak) and maximum power, maximum strength, functional performance, body composition, quality of life (QoL), and fatigue. Tests were carried out before conditioning therapy, at hospital discharge and at day ± 180 (follow-up). As 18 patients did not participate in post-intervention assessment and follow-up data from 9 patients was not collectible, per-protocol (PP) analysis of 44 patients is presented. During hospitalization, WBV maintained maximum strength, height, and power output during jumping, as well as reported QoL, physical functioning, and fatigue level compared with mobilization. At follow-up, relative VO2peak(p = 0.035) and maximum power (p = 0.011), time and power performing chair-rising test (p = 0.022;p = 0.009), and reported physical functioning (p = 0.035) significantly increased in the IG, while fatigue decreased (p = 0.005). CG’s body cell mass and phase angle had significantly decreased at follow-up (p = 0.002;p = 0.004). Thus, WBV might maintain maximum strength, functional performance, QoL, and fatigue during alloHCT, while cardiorespiratory fitness might benefit from accelerated recovery afterwards.
A novel mutation in the mouse Pcsk1 gene showing obesity and diabetes
Authors: Muhsin Nor I. A. , Bentley Liz , Bai Ying , Goldsworthy Michelle , Cox Roger D. 
Published: January 2020

AbstractThe proprotein convertase subtilisin/Kexin type 1 (PCSK1/PC1) protein processes inactive pro-hormone precursors into biologically active hormones in a number of neuroendocrine and endocrine cell types. Patients with recessive mutations in PCSK1 exhibit a complex spectrum of traits including obesity, diarrhoea and endocrine disorders. We describe here a new mouse model with a point mutation in the Pcsk1 gene that exhibits obesity, hyperphagia, transient diarrhoea and hyperproinsulinaemia, phenotypes consistent with human patient traits. The mutation results in a pV96L amino acid substitution and changes the first nucleotide of mouse exon 3 leading to skipping of that exon and in homozygotes very little full-length transcript. Overexpression of the exon 3 deleted protein or the 96L protein results in ER retention in Neuro2a cells. This is the second Pcsk1 mouse model to display obesity phenotypes, contrasting knockout mouse alleles. This model will be useful in investigating the basis of endocrine disease resulting from prohormone processing defects.
Implementing a Clostridium difficile testing algorithm and its effect on isolation duration and treatment initiation: a pre- and post-implementation study
Authors: Vogelzang Erik Hans , Lankelma Jacqueline Marleen , van Mansfeld Rosa , van Prehn Joffrey , van Houdt Robin 
Published: January 2020

AbstractA proportion of patients suspected of Clostridium difficile infection are unnecessarily placed in contact isolation. By introducing a random-access glutamate dehydrogenase (GDH) test for C. difficile, we aimed to reduce isolation time. In addition, we investigated whether the result of the toxin A&B enzyme immunoassay (EIA) was associated with the decision to initiate antibiotic treatment against C. difficile. This retrospective pre- and post-implementation study was from June 3, 2016, to June 4, 2018. Pre-implementation, only a NAAT was performed. In the post-implementation period, a GDH test was performed; if positive, a toxin A&B EIA followed the same day and subsequently a NAAT. Contact isolation for CDI was discontinued when the GDH test was negative. Median time in isolation was 50.8 h pre-implementation (n = 189) versus 28.0 h post-implementation (n = 119), p < 0.001. The GDH test had a negative predictive value of 98.8% (95% CI 97.9–99.4). In 7/31 (22.6%) patients with a positive NAAT and GDH test and a negative toxin A&B EIA, no antibiotics against C. difficile were initiated versus 4/28 (14.3%) patients who were NAAT, GDH and toxin A&B EIA positive. Introducing a random-access screening test resulted in a significant decrease in patient isolation time. The GDH test had a high negative predictive value making it suitable to determine whether contact isolation can be discontinued. Furthermore, the result of a toxin A&B EIA had limited added value on the percentage of patients in whom antibiotic treatment against C. difficile was initiated.
Global citizenship education at the crossroads: Globalization, global commons, common good, and critical consciousness
Authors: Torres Carlos Alberto , Bosio Emiliano 
Published: January 2020

AbstractThis article-dialogue addresses current criticisms of global citizenship and challenges frequent misinterpretations of Global Citizenship Education (GCE), while discussing what it means to educate for critical global citizenry in an increasingly multicultural world. It starts by considering the phenomena of globalization and the UN Global Education First Initiative (GEFI), which aims at furthering global citizenship, to highlight the relationship between GCE, “global-peace”, global commons, and common good. Building on the assumption that GCE should be about learners’ emancipation toward critical consciousness, the dialogue concludes drawing a parallel between the “mission” of GCE in contemporary educational institutions and Paulo Freire’s notion of critical consciousness.
Characterization of a mine legacy site: an approach for environmental management and metals recovery
Authors: Dinis Maria de Lurdes , Fiúza António , Futuro Aurora , Leite Alexandre , Martins Diogo , Figueiredo Janine , Góis Joaquim , Vila Maria Cristina 
Published: January 2020

AbstractThe characterization of historical mine tailings provides important information for land-management decisions, in particular when considering potential reprocessing activities or the development of an environmental protection program. In addition, outcomes from such characterization may define the scope for a more detailed investigation. The present work describes the characterization of the waste material from the Cabeço do Pião tailings impoundment performed within the project ReMinE: Improve Resource Efficiency and Minimize Environmental Footprint. The purpose of the work was to investigate alternative mine waste management options such as the extraction of valuable resources from an environmental liability. The study involved the collection of 41 samples at different locations at two different depths, physical and chemical characterization of the wastes, natural leaching tests, and potential for acid generation. The results showed that, apart from the potential instability of the dyke (with an average slope of 35°), the drained solutions flowing by percolation contain very small particles with high arsenic contents that are being incorporated into the river sediments. In addition, these very fine-grained materials are available for the transport by the wind creating secondary sources of environmental contamination. This data is fundamental for economic and environmental assessment of the two main alternatives, reprocessing or removal.
Risks and benefits of pasture irrigation using treated municipal effluent : a lysimeter case study, Canterbury, New Zealand
Authors: Gutierrez-Gines Maria Jesus , Mishra Minakshi , McIntyre Cameron , Chau Henry Wai , Esperschuetz Juergen , McLenaghen Roger , Bourke Mike P. , Robinson Brett H. 
Published: January 2020

AbstractCompared to discharge into waterways, land application of treated municipal effluent (TME) can reduce the need for both inorganic fertilizers and irrigation. However, TME irrigation may result in the accumulation of phosphorus (P) or trace elements in soil, and increased salinity and sodicity, which could damage soil structure and reduce infiltration. TME irrigation can also result in groundwater contamination through nitrate leaching or surface water contamination through runoff. This study aimed to evaluate the effects of increasing TME irrigation rates on quantity and quality of leachate and pasture growth in a lysimeter experiment using a Fluvial Recent soil and a Fragic Pallic soil. Pasture growth in the lysimeters was up to 2.5-fold higher in the TME treatments compared to the non-irrigated treatments. There were no signs of toxicity or accumulation of B, Al, Cd, Cu, Fe, Mn, As, and Zn. TME significantly increased the concentration of P and Na in the pasture. Nitrogen leaching from the lysimeters was negligible (< 1 kg/ha−1 equiv.) in all treatments, but mineral N accumulated in the soil profile of the highest application rate (1672 mm/yr). Although more P was added than removed in pasture, the rate of accumulation indicated that over a 50-year period, P will still be within the current New Zealand thresholds for grazed pastures. Sodium accumulated in the soil columns in all the TME treatments. The rate of accumulation was not proportional to the TME application rate, indicating that Na was moving down through the soil profile and leaching. Results indicate a low to moderate risk of sodicity in soil or toxicity in plants caused by Na.
Against the Received Wisdom: Why the Criminal Justice System Should Give Kids a Break
Authors: Morse Stephen J. 
Published: January 2020

AbstractProfessor Gideon Yaffe’s recent, intricately argued book, The Age of Culpability: Children and the Nature of Criminal Responsibility, argues against the nearly uniform position in both law and scholarship that the criminal justice system should give juveniles a break because on average they have different capacities relevant to responsibility than adults. Professor Yaffe instead argues that kid should be given a break because juveniles have little say about the criminal law, primarily because they do not have a vote. For Professor Yaffe, age has political rather than behavioral significance. The book has many excellent general analyses about responsibility, but all are in aid of the central thesis about juveniles, which is the central focus of this essay review. After addressing a few preliminary issues, the essay discusses Professor Yaffe’s negative argument against the validity of the behavioral difference rationale for giving juveniles a break. If the negative case fails, which the essay argues it does, then the only issue is whether the book’s alternative is desirable. Again, the essay argues that it is not, and concludes by offering three positive arguments for the traditional rationale: (1) coherence and simplicity; (2) a benignly definitional argument that survives the negative argument and supports giving juveniles a break in the exceedingly unlikely event that the empirical assumptions of the traditional rationale are proven incorrect; and (3) a proposal for individualization of the culpability assessments of juveniles so that the criminal justice system blames and punishes them proportionately to their culpability.