bluuebunny/crossref_metadata_2025 huggingface dataset:
TTIP, CETA, and TiSA Behind Closed Doors
Authors: Delimatsis Panagiotis
Published: October 2017

Secrecy and informality rather than transparency traditionally reign trade negotiations at the bilateral, regional, and multilateral levels. Yet, transparency ranks among the most basic desiderata in the grammar of global governance and has been regarded as positively related to legitimacy. In the EU’s case, transparent trade diplomacy is quintessential for constitutional—but also for broader political—reasons. First, even if trade matters fall within the EU’s exclusive competence, the EU executive is bound by the Treaty on the Functioning of the European Union (TFEU) to inform the European Parliament, the EU co-legislator, in regular intervals. Second, transparency at an early stage is important to address public reluctance, suspicion, or even opposition regarding a particular trade deal. This chapter chronicles the quest for and turning moments relating to transparency during the EU trade negotiations with Canada (CETA); the US (TTIP), and various WTO members on services (TiSA).
Sartre on Sin
Authors: Kirkpatrick Kate
Published: October 2017

This book argues that Jean-Paul Sartre’s early, anti-humanist philosophy is indebted to the Christian doctrine of original sin. On the standard reading, Sartre’s most fundamental and attractive idea is freedom: he wished to demonstrate the existence of human freedom, and did so by connecting consciousness with nothingness. Taking Being and Nothingness as its primary exegetical focus, this book demonstrates that Sartre’s concept of nothingness (le néant) has a Christian genealogy which has been overlooked in philosophical and theological discussions of his work. Previous scholars have noted the resemblance between Sartre’s and Augustine’s ontologies: to name but one shared theme, both thinkers describe the human as the being through which nothingness enters the world. But no in-depth examination of this ‘resemblance’ has been made. Using historical, exegetical, and conceptual methods, Sartre on Sin demonstrates that Sartre’s intellectual formation prior to his discovery of phenomenology included theological elements—especially concerning the compatibility of freedom with sin and grace. After outlining the French Augustinianisms by which Sartre’s account of the human as ‘between being and nothingness’ was informed, the book offers a close reading of Being and Nothingness which shows (a) that the psychological, epistemological, and ethical consequences of Sartre’s le néant closely resemble the consequences of its theological predecessor and (b) that his account of freedom can be read as an anti-theodicy. Finally, it argues that Sartre’s insights are valuable resources for contemporary hamartiology.
The Irrationality of Action and Action Rationality: Decisions, Ideologies, and Organizational Actions
Authors: Brunsson Nils
Published: October 2017

This chapter addresses the effect of decisions on organizational action. It argues that decision-makers who choose to or must stick closely to the rule of rationality may be likely to make good choices; but they are also likely to face difficulties in realizing their decisions. Mobilizing organizational actions is easier when decision processes are systematically irrational — when decision-makers consider only one action option for instance, and when preferences and consequences that support this alternative are the only ones considered. This relationship between decision and action is dependent upon the tendency of decisions to produce both certainty and uncertainty. The institutionalized purpose of decisions is to achieve certainty, to determine and stabilize the future. But because decisions are interpreted as choices, they also produce uncertainty by highlighting the fact that the choice could have been different — or perhaps should have been different — and that the future is dependent upon the whims of human beings rather than on stable, reliable entities.
Phytoplankton Productivity
Authors: Raven John
Published: October 2017

This chapter describes the productivity of phytoplankton, from the initial energy and chemical requirements for photosynthesis to the rate of production of heterotrophic organisms. Phytoplankton are the planktonic organisms which account for most of the primary production in the ocean. Their characteristic trophic mode is the production of organic compounds using energy from light and chemical elements from inorganic compounds, known as phototrophy, or more strictly photolithotrophy. This process uses water as the electron donor and the reduction of inorganic carbon producing sugars, from which all other cell components are made using inorganic forms of nitrogen, phosphorus, and all the other chemical elements needed to produce cells.
Sampling, Preservation and Counting of Samples II: Zooplankton
Authors: Wiebe Peter H. , Bucklin Ann , Benfield Mark
Published: October 2017

This chapter reviews traditional and new zooplankton sampling techniques, sample preservation, and sample analysis, and provides the sources where in-depth discussion of these topics is addressed. The net systems that have been developed over the past 100+ years, many of which are still in use today, can be categorized into eight groups: non-opening/closing nets, simple opening/closing nets, high-speed samplers, neuston samplers, planktobenthos plankton nets, closing cod-end samplers, multiple net systems, and moored plankton collection systems. Methods of sample preservation include preservation for sample enumeration and taxonomic morphological analysis, and preservation of samples for genetic analysis. Methods of analysis of zooplankton samples include determination of biomass, taxonomic composition, and size by traditional methods; and genetic analysis of zooplankton samples.
Ctenophora
Authors: Licandro Priscilla , Lindsay Dhugal J.
Published: October 2017

This chapter describes the taxonomy of ctenophores. The ctenophores, or comb jellies, are gelatinous metazoans belonging to a small and entirely marine phylum of about 150 species. They are mostly planktonic, with the exception of the benthic order Platyctenida, where only the larvae are planktonic. The chapter covers their life cycle, ecology, and generalizmorphology. It includes a section that indicates the systematic placement of the taxon described within the tree of life, and lists the key marine representative illustrated in the chapter (usually to genus or family level). This section also provides information on the taxonomic authorities responsible for the classification adopted, recent changes which might have occurred, and lists relevant taxonomic sources.
Crustacea: Lophogastrida and Mysida
Authors: Castellani Claudia , Lehtiniemi Maiju , Meland Kenneth
Published: October 2017

This chapter describes the taxonomy of Lophogastrida and Mysida, small shrimp-like crustaceans commonly known as ‘opossum shrimps’ because of the ventral brood pouch in the female. Because of their highly adaptive nature, they have progressively invaded new areas via new connections of water systems and through ballast water. The chapter covers their life cycle, ecology, and general morphology. It includes a section that indicates the systematic placement of the taxon described within the tree of life, and lists the key marine representative illustrated in the chapter (usually to genus or family level). This section also provides information on the taxonomic authorities responsible for the classification adopted, recent changes which might have occurred, and lists relevant taxonomic sources.
Echinodermata
Authors: Conway David V.P. , Castellani Claudia , Southward Eve C.
Published: October 2017

This chapter describes the taxonomy of Echinodermata, a diverse group of organisms consisting systematically of five classes including sea stars (Asteroidea), brittle stars (Ophiuroidea), sea urchins (Echinoidea), sea cucumbers (Holothuroidea), and feather stars (Crinoidea). It covers their life cycle, ecology, and general morphology. It includes a section that indicates the systematic placement of the taxon described within the tree of life, and lists the key marine representative illustrated in the chapter (usually to genus or family level). This section also provides information on the taxonomic authorities responsible for the classification adopted, recent changes which might have occurred, and lists relevant taxonomic sources.
Rotifera
Authors: Conway David V.P. , Camp Robert , Castellani Claudia
Published: October 2017

This chapter describes the taxonomy of Rotifera, which includes some of the smallest multicellular marine zooplankton. They range between 50 μ‎ to 500 μ‎m in length although some species can reach up to 3 mm in length. Rotifers are characterized by having a crown or corona of fine cilia on two lobes surrounding the mouth area which gives them their common name ‘wheel animals’although the corona only appears to rotate. The chapter covers their life cycle, ecology, and general morphology. It includes a section that indicates the systematic placement of the taxon described within the tree of life, and lists the key marine representative illustrated in the chapter (usually to genus or family level). This section also provides information on the taxonomic authorities responsible for the classification adopted, recent changes which might have occurred, and lists relevant taxonomic sources.
Megadrought, Collapse, and Causality
Authors: Weiss Harvey
Published: October 2017

Recent discoveries of megadroughts, severe periods of drought lasting decades or centuries, during the course of the Holocene have revolutionized our understanding of modern climate history. Through advances in paleoclimatology, researchers have identified these periods of climate change by analyzing high-resolution proxy data derived from lake sediment cores, marine cores, glacial cores, speleothem cores, and tree rings. Evidence that megadroughts occurred with frequency and abruptly over the last 12,000 years, a timespan long assumed to be stable compared to earlier glacial periods, has also altered our understanding of societies’ trajectories. The fact that severe, multi-decadal or century-scale droughts coincided with societal collapses well known to archaeologists has challenged established multi-causal analyses of these events. Megadroughts, impossible to predict and impossible to withstand, may have caused political collapse, regional abandonment, and habitat tracking to still-productive regions. The nine megadrought and societal collapse events presented in this volume extend from the foraging-to-agriculture transition at the dawn of the Holocene in West Asia to the fifteenth-century AD collapse of the Khmer Empire in Angkor (Cambodia). Inevitably, this collection of essays also raises challenges to causal analyses of societal collapse and for future paleoclimatic and archaeological research.
Fourteenth to Sixteenth Centuries AD
Authors: Fletcher Roland , Buckley Brendan M. , Pottier Christophe , Simon Wang Shi-Yu
Published: October 2017

Angkor, the capital of the Khmer Empire in Southeast Asia, was the most extensive low-density agrarian-based urban complex in the world. The demise of this great city between the late 13th and the start of the 17th centuries AD has been a topic of ongoing debate, with explanations that range from the burden of excessive construction work to disease, geo-political change, and the development of new trade routes. In the 1970s Bernard-Phillipe Groslier argued for the adverse effects of land clearance and deteriorating rice yields. What can now be added to this ensemble of explanations is the role of the massive inertia of Angkor’s immense water management system, political dependence on a meticulously organized risk management system for ensuring rice production, and the impact of extreme climate anomalies from the 14th to the 16th centuries that brought intense, high-magnitude monsoons interspersed with decades-long drought. Evidence of this severe climatic instability is found in a seven-and-a-half century tree-ring record from tropical southern Vietnam. The climatic instability at the time of Angkor’s demise coincides with the abrupt transition from wetter, La Niña-like conditions over Indochina during the Medieval Warm Period to the more drought-dominated climate of the Little Ice Age, when El Niño appears to have dominated and the ITCZ migrated nearly five degrees southward. As this transition neared, Angkor was hit by the double impact of high-magnitude rains and crippling droughts, the former causing damage to water management infrastructure and the latter decreasing agricultural productivity. The Khmer state at Angkor was built on a human-engineered, artificial wetland fed by small rivers. The management of water was a massive undertaking, and the state potentially possessed the capacity to ride out drought, as it had done for the first half of the 13th century. Indeed, Angkor demonstrated just how powerful a water management system would be required and, conversely, how formidable a threat drought can be. The irony, then, is that extreme flooding destroyed Angkor’s water management capacity and removed a system that was designed to protect its population from climate anomalies.
Evaluating Qualitative Research
Authors: Cho Jeasik
Published: October 2017

This book provides the qualitative research community with some insight on how to evaluate the quality of qualitative research. This topic has gained little attention during the past few decades. We, qualitative researchers, read journal articles, serve on masters’ and doctoral committees, and also make decisions on whether conference proposals, manuscripts, or large-scale grant proposals should be accepted or rejected. It is assumed that various perspectives or criteria, depending on various paradigms, theories, or fields of discipline, have been used in assessing the quality of qualitative research. Nonetheless, until now, no textbook has been specifically devoted to exploring theories, practices, and reflections associated with the evaluation of qualitative research. This book constructs a typology of evaluating qualitative research, examines actual information from websites and qualitative journal editors, and reflects on some challenges that are currently encountered by the qualitative research community. Many different kinds of journals’ review guidelines and available assessment tools are collected and analyzed. Consequently, core criteria that stand out among these evaluation tools are presented. Readers are invited to join the author to confidently proclaim: “Fortunately, there are commonly agreed, bold standards for evaluating the goodness of qualitative research in the academic research community. These standards are a part of what is generally called ‘scientific research.’ ”
Getting Into the Field
Authors: Cho Jeasik
Published: October 2017

During the past few decades, the discourse on the evaluation of qualitative research has been scattered. Although a few seminal ideas and instruments have been available for assessing qualities of qualitative research, they have either remained the same or have made little progress. There are several ongoing issues regarding the evaluation of qualitative research, including (1) the fact that there is little agreement on the nature of evaluation in qualitative research, (2) the continuous impact of traditional positivist evaluation criteria on qualitative research, and (3) the broad political discourse on the politics of evidence. This chapter presents a series of definitions regarding evaluation, quality, standards, and excellence, and it discusses major evaluation concepts.
Change, Challenges, and Mixed Methods
Authors: Cho Jeasik
Published: October 2017

This chapter discusses three ongoing issues related to the evaluation of qualitative research. First, the chapter considers whether a set of evaluation criteria is either determinative or changeable. Due to the evolving nature of qualitative research, it is likely that the way in which qualitative research is evaluated can change—not all at once, but gradually. Second, qualitative research has been criticized by newly resurrected positivists whose definitions of scientific research and evaluation criteria are narrow. “Politics of evidence” and a recent big-tent evaluation strategy are examined. Last, this chapter analyzes how validity criteria of qualitative research are incorporated into the evaluation of mixed methods research. The elements of qualitative research seem to be fairly represented but are largely treated as trivial. A criterion, the fit of research questions to design, is identified as distinctive in the review guide of the Journal of Mixed Methods Research.
Lincoln Kirstein’s Social Modernism and the Cultural Front
Authors: Harris Andrea
Published: October 2017

This chapter takes a biographical approach to Lincoln Kirstein’s creation of a modernist theory of ballet to situate its development in the 1930s cultural wing of the Popular Front and explore its evolution through and after World War II. Fueled by the cultural front’s belief in the role of the arts in social revolution, Kirstein seized the opportunity to decouple ballet from existing biases about its elitism and triviality, and formulate new ideas about its social relevance in the Depression period. After exploring the development of Kirstein’s social modernism in the cultural front, chapter 2 then turns to the challenges posed to the 1930s belief that art could be productively combined with politics through two major turning points in Kirstein’s life. These are his experiences in World War II, and the erosion of his own artistic role in the ballet company after the formation of the New York City Ballet and the ascendance of George Balanchine’s dance-for-dance-sake aesthetic in the late 1940s. The chapter illustrates Kirstein’s attempts to negotiate the social modernist aesthetic he crafted under the wing of the cultural front within the volatile political, economic, and artistic circumstances of World War II, anticommunism, and the Cold War.
Making an American Ballet Institution in the Cultural Cold War in Europe
Authors: Harris Andrea
Published: October 2017

Chapter 4 examines the circumstances leading to the final success of Lincoln Kirstein’s American ballet in 1963, when Ford Foundation philanthropy made George Balanchine’s neoclassicism a national institution and a national style. Examining the New York City Ballet’s cultural diplomacy activities, it illustrates the advantageous position that Balanchine attained within the alliances between the government, private and corporate foundations, and the arts that developed in the cultural Cold War. Yet the chapter stresses the complexity of the collaboration between the ballet company and the government, insisting that the artists often had very different political motivations than the state. A main concern is how the belief in the social efficacy of art, nurtured in the 1930s, was affected by the transformational shift in arts funding, organization, and management that arose during the Cold War. This chapter concludes by raising questions about the consequences of the post-WWII institutionalization of the arts for the political agendas of the 1930s-era modernists.
“You Have the Consolation of Being Very Much in the Fight”
Authors: Kenney Padraic
Published: October 2017

Political prisoners leave behind a cause and a movement, and endeavor to represent them and to stay in contact while behind bars. They live in a world beyond the imagining of most of their fellow citizens. Whatever a movement loses when its leaders and enthusiasts go to jail, it faces the difficult challenge of keeping them relevant to the cause. This chapter explores the mechanics, limitations, and opportunities of letter writing, and examines the history of escapes from prison. Prisoner assistance movements in many cases—in particular Polish leftists fighting for independence, Irish Republicans, and the anti-apartheid movement in South Africa—were organized and led by women. Communists in Poland and around the world organized prisoner assistance as a way to inspire and mobilize support for the cause
“I Was Confusing the Prison”
Authors: Kenney Padraic
Published: October 2017

Political prisoners counter the regime’s effort to control them by endeavoring to deny information to their captors and to confuse them. They change their identities or insist on anonymity. They act individually, in ways the regime can neither predict nor understand, and refuse to act on the prison’s own terms—for example, by declining to make requests of prison guards or by playing mind games on those who are observing them. Collectively, they devise modes of action that are deliberately confusing, switching tactics often or engaging in counter-intuitive behavior, such as destroying their cells. The clothing strike, in which political prisoners refused to wear prison uniforms, culminated in the five-year battle over clothing by the IRA prisoners in Northern Ireland. While some prisoners may feign madness or attempt suicide with similar goals, madness may also be a genuine effect of the rigors of isolation.
Discontent and Early Experiments (1950–56)
Authors: Levy Benjamin R.
Published: October 2017

At the outset of the 1950s Ligeti began to compose secret musical experiments that would not get past the censors of the communist regime in Hungary. Musica ricercata can be seen as an initial attempt to move past the compositional model of Bartók, and in turn, this piano piece worked as a study for the String Quartet no. 1, Métamorphoses nocturnes. Alongside this, however, is a series of unpublished and unfinished projects including the Chromatische Phantasie, Variations concertantes, an unfinished Requiem movement that parallels the choral works Éjszaka and Reggel, and a setting of Sándor Weöres’s Istar pokoljárása. These all show the influence of Schoenberg’s twelve-tone composition at a time when Ligeti claimed to have had only a desultory knowledge of the concept.
Water
Authors: Clarke Andrew
Published: October 2017

Liquid water is essential for life, and a metabolically active cell is ~70% water. The physical properties of liquid water, and their temperature dependence, are dictated to a significant extent by the properties of hydrogen bonds. From an ecological perspective, the important properties of liquid water include its high latent heats of fusion and vapourisation, its high specific heat, the ionisation, low dynamic viscosity and high surface tension. The solubility in water of oxygen, carbon dioxide and the calcium carbonate used to build skeletons in many invertebrates groups all increase with decreasing temperature. The hydrophobic interaction is important in the formation of cellular membranes and the folding of proteins; its strength increases with temperature, which may be a factor in the cold-denaturation of cellular macromolecules. The cell is extremely crowded with macromolecules. Coupled with the highly structured water close to membranes or protein surfaces and the hydration shells around ions, this means that the behaviour of water in cells is different from that of bulk water. The thermal behaviour of isolated cellular components studied in dilute aqueous buffers many not reflect accurately their behaviour in the intact cell or tissue.
The Metabolic Theory of Ecology
Authors: Clarke Andrew
Published: October 2017

The model of West, Brown & Enquist (WBE) is built on the assumption that the metabolic rate of cells is determined by the architecture of the vascular network that supplies them with oxygen and nutrients. For a fractal-like network, and assuming that evolution has minimised cardiovascular costs, the WBE model predicts that s=metabolism should scale with mass with an exponent, b, of 0.75 at infinite size, and ~ 0.8 at realistic larger sizes. Scaling exponents ~ 0.75 for standard or resting metabolic rate are observed widely, but far from universally, including in some invertebrates with cardiovascular systems very different from that assumed in the WBE model. Data for field metabolic rate in vertebrates typically exhibit b ~ 0.8, which matches the WBE prediction. Addition of a simple Boltzmann factor to capture the effects of body temperature on metabolic rate yields the central equation of the Metabolic Theory of Ecology (MTE). The MTE has become an important strand in ecology, and the WBE model is the most widely accepted physical explanation for the scaling of metabolic rate with body mass. Capturing the effect of temperature through a Boltzmann factor is a useful statistical description but too simple to qualify as a complete physical theory of thermal ecology.
Temperature, growth and size
Authors: Clarke Andrew
Published: October 2017

Growth involves two flows of energy. The first is chemical potential energy in the monomers used to construct the proteins, lipids, polysaccharides and nucleic acids forming the new tissue. The second is the metabolic energy (ATP or GTP) used to construct the new tissue; this is the metabolic cost of growth and can be expressed as a dimensionless fraction of the energy retained in the new tissue. Its value is ~0.33. Typical temperature sensitivities for growth in the wild lie in the range Q10 1.5 – 3. Within species there may be evolutionary adjustments to growth rate to offset the effects of temperature, though these involve trade-offs with other physiological factors affecting fitness. Outside the tropics, many mammals and birds exhibit a cline in size, with larger species at higher latitudes (Bergmann’s rule). Carl Bergmann predicted such a cline from biophysical arguments based on endotherm thermoregulatory costs; Bergmann’s rule thus applies only to mammals and birds. Many ectotherms grow more slowly but attain a larger adult size when grown at lower temperatures (the temperature-size rule). The large size of some aquatic invertebrates at lower temperatures (notably in the polar regions and the deep sea) is associated with a higher oxygen content of the water.
Imposing Risk
Authors: Oberdiek John
Published: October 2017

Any normative framework of risk imposition must include at its foundation an account of the nature of risk imposition. If risk is understood as the probability of a bad event or harm, the menu of conceptions of risk would seem to be exhausted by the various accounts of probability that have been developed. The two main families of probability theory, objective and subjective, have opposite strengths and weaknesses as candidate conceptions of probability suitable for a normative framework of risk imposition. This chapter argues that objective accounts are suitably normative but insufficiently practical, while unreconstructed subjective accounts are suitably practical but insufficiently normative, and this casts doubt on the project of identifying a conception of risk that is suitable for a normative framework of risk imposition.
Experience and Compliance With Scanning Vaccines’ Two-Dimensional Barcodes to Record Data
Authors: Evanson Heather V. , Rodgers Loren , Reed Jenica , Daily Ashley , Gerlach Kenneth , Greene Michael , Koeppl Patrick , Cox Regina , Williams Warren
Published: October 2017

Automated population of data into health information system fields offers the potential to increase efficiencies and save time. Increasingly, as two-dimensional barcoded vaccine products and barcode scanning technology become more widely available, manual recording of vaccine data can be reduced. This evaluation explores how often two-dimensional barcodes on vaccine vials and syringes were scanned and the perceived benefits and challenges reported by vaccine providers. Eighty-two facilities that administer vaccines completed the evaluation. Twenty-seven of those facilities provided records from vaccines administered between July 2014 and January 2015. Among the 63 179 two-dimensional barcoded vaccine administrations recorded, 12 408 (19%) were scanned. We received 116 user surveys from 63 facilities; using content analysis, we identified perceived benefits of scanning, workflow challenges, scanning challenges, and other challenges. The findings of this evaluation can guide health information system developers, vaccine manufacturers, and vaccine providers on how to remove potential barriers to using two-dimensional barcode scanning.
Persistence and Adherence to Psychostimulants, and Psychological Well-Being Up to 3 Years After Specialized Treatment of Adult Attention-Deficit/Hyperactivity Disorder
Authors: Bijlenga Denise , Kulcu Semahat , van Gellecum Trevor , Eryigit Zeynep , Kooij J.J. Sandra
Published: October 2017

Background

Little is known about the long-term persistence and adherence of psychostimulant use in adults with attention-deficit/hyperactivity disorder (ADHD) and its relationship to their psychological well-being.

Methods

The persistence and adherence to psychostimulants and psychological well-being were examined in adults with ADHD in a naturalistic follow-up, starting directly after discharge from their specialized treatment of ADHD at an outpatient ADHD clinic. Ninety-six patients were included at the time of discharge, who were interviewed by telephone at 6 months, 1 year, and 3 years after discharge.

Results

At the time of discharge, 78% used a psychostimulant prescribed by a psychiatrist. Of those on psychostimulants at the time of discharge, approximately half still used any of these psychostimulants 3 years after discharge. However, adherence rates were good for those who persisted to use psychostimulants. The female sex and middle educational level (relative to a higher educational level) were near-significantly related to nonpersistence, and having a higher educational level and the combined ADHD subtype were related to nonadherence. In turn, nonadherence was related to worse general functioning, lower mood, and poorer sleep quality.

Conclusions

The importance of adherence should be discussed at the time of discharge, especially with female ADHD patients, those with a higher educational level, and those with a combined ADHD subtype, because nonadherence is associated with poorer outcomes.
Comparison of in-house IgM and IgG ELISAs for the serodiagnosis of melioidosis in Malaysia
Authors: Hii Shirley Yi Fen , Ali Noor Azila , Ahmad Norazah , Amran Fairuz
Published: October 2017

Melioidosis is an endemic infectious disease in Southeast Asia and northern Australia, caused by Burkholderia pseudomallei. However, the incidence rate in Malaysia is not well documented. The high mortality rate and broad range of clinical presentations require rapid and accurate diagnosis for appropriate treatment. This study compared the efficacy of in-house IgM and IgG ELISA methods using a local B. pseudomallei strain. The diagnostic accuracy of the in-house IgG ELISA was better than that of the IgM ELISA: sensitivity (IgG: 84.71 %, IgM: 76.14 %) and specificity (IgG: 93.64 %, IgM: 90.17 %); positive predictive value (IgG: 86.75 %, IgM: 79.76 %) and negative predictive value (IgG: 92.57 %, IgM: 89.66 %); likelihood ratio (LR) [IgG: 13.32, IgM: 7.75 (LR+); IgG: 0.16, IgM: 0.26 (LR–)], and was supported by the observation of the absorbance value in comparisons between culture and serology sampling. In-house IgG ELISA was shown to be useful as an early diagnostic tool for melioidosis.
Periodic variation of mutation rates in bacterial genomes associated with replication timing
Authors: Dillon Marcus M. , Sung Way , Lynch Michael , Cooper Vaughn S.
Published: October 2017

The causes and consequences of spatiotemporal variation in mutation rates remains to be explored in nearly all organisms. Here we examine relationships between local mutation rates and replication timing in three bacterial species whose genomes have multiple chromosomes:Vibrio fischeri, Vibrio cholerae, andBurkholderia cenocepacia. Following five evolution experiments with these bacteria conducted in the near-absence of natural selection, the genomes of clones from each lineage were sequenced and analyzed to identify variation in mutation rates and spectra. In lineages lacking mismatch repair, base-substitution mutation rates vary in a mirrored wave-like pattern on opposing replichores of the large chromosome ofV. fischeriandV. cholerae, where concurrently replicated regions experience similar base-substitution mutation rates. The base-substitution mutation rates on the small chromosome are less variable in both species but occur at similar rates as the concurrently replicated regions of the large chromosome. Neither nucleotide composition nor frequency of nucleotide motifs differed among regions experiencing high and low base-substitution rates, which along with the inferred ~800 Kb wave period suggests that the source of the periodicity is not sequence-specific but rather a systematic process related to the cell cycle. These results support the notion that base-substitution mutation rates are likely to vary systematically across many bacterial genomes, which exposes certain genes to elevated deleterious mutational load.
How we learn things we don’t know already: A theory of learning structured representations from experience
Authors: Doumas Leonidas A. A. , Puebla Guillermo , Martin Andrea E.
Published: October 2017

How a system represents information tightly constrains the kinds of problems it can solve. Humans routinely solve problems that appear to require structured representations of stimulus properties and relations. Answering the question of how we acquire these representations has central importance in an account of human cognition. We propose a theory of how a system can learn invariant responses to instances of similarity and relative magnitude, and how structured relational representations can be learned from initially unstructured inputs. We instantiate that theory in the DORA (Discovery of Relations by Analogy) computational framework. The result is a system that learns structured representations of relations from unstructured flat feature vector representations of objects with absolute properties. The resulting representations meet the requirements of human structured relational representations, and the model captures several specific phenomena from the literature on cognitive development. In doing so, we address a major limitation of current accounts of cognition, and provide an existence proof for how structured representations might be learned from experience.
Camelot – Intuitive Software for Camera Trap Data Management
Authors: Hendry Heidi , Mann Christopher
Published: October 2017

A variety of software tools for camera trap data management have been produced over the years, though the authors encountered numerous shortcomings with each. Camelot is a new open source cross-platform software application for managing camera trap survey data.

Camelot is designed to be both powerful and easy-to-use. It provides a number of innovative features, such as an extensible reporting system that serves as an integration point with specialised analysis tools. This combination of features and usability makes it a compelling alternative to existing camera trap data management software.
Speed tuning in the macaque posterior parietal cortex
Authors: Avila Eric , Lakshminarasimhan Kaushik J , DeAngelis Gregory C , Angelaki Dora E
Published: October 2017

Neurons in the macaque posterior parietal cortex are known to encode the direction of self-motion. But do they also encode one’s speed? To test this, we performed neural recordings from area 7a while monkeys were passively translated or rotated at various speeds. Visual stimuli were delivered as optic flow fields and vestibular stimuli were generated by a motion platform. Under both conditions, the responses of a fraction of neurons scaled linearly with self-motion speed, and speed-selective neurons were not localized to specific layers or columns. We analyzed ensembles of simultaneously recorded neurons and found that the precision of speed representation was sufficient to support path integration over modest distances. Our findings describe a multisensory neural code for linear and angular self-motion speed in the posterior parietal cortex of the macaque brain, and suggest a potential role for this representation.
Multi-band component analysis for EEG artifact removal and source reconstruction with application to gamma-band activity
Authors: Jonmohamadi Yaqub , Muthukumaraswamy Suresh D.
Published: October 2017

Independent component analysis (ICA) has been used extensively for artifact removal and reconstruction of neuronal time-courses in electroencephalography (EEG). Typically, ICA is applied on wide-band EEG (for example 1 to 100 Hz or similar ranges). Since EEG captures the activities of a large number of sources and the fact that number of the components separated by the ICA is limited by the number of the sensors, only the stronger sources (in terms of magnitude and duration) will be detected by the ICA, and the activity of weaker sources will be lost or scattered amongst the stronger components. Because of the 1/f nature of the EEG spectra this biases components to the lower frequency ranges. Here we used a versatile combination of a filter bank, PCA and ICA, calling it multi-band ICA, to both increase the number of the ICA components substantially and improve the SNR of the separated components. Using band-pass filtering we break the original signal mixture into several subbands, and using PCA we reduce the dimensionality of each subband, before applying ICA to a matrix containing all the principal components from each band. Using simulated sources and real EEG of participants, we demonstrate that multi-band ICA is able to outperform the traditional wide-band ICA in terms of both signal-noise ratio of the separated sources and the number of the identified independent components. We successfully separated the gamma-band neuronal components time-locked to a visual stimulus, as well as weak sources which are not detectable by wide-band ICA.
Oscillatory multiplexing indexes precision
Authors: Grabot Laetitia , Kononowicz Tadeusz W. , Dupré la Tour Tom , Gramfort Alexandre , Doyère Valérie , van Wassenhove Virginie
Published: October 2017

Oscillatory coupling has been implicated in the representation and in the processing of information in the brain. Specific hypotheses suggest that oscillatory coupling may be relevant for the temporal coding of information but to which extent this may translate to conscious timing is unknown. Here, we tested the hypothesis that the temporal precision of self-generated timed actions may be controlled by phase-amplitude coupling (PAC). Using a timing task, we show the existence of significant alpha-beta (α-β) PAC, robust at the individual level, and specific to temporal production. Second, an increase in the strength of α-β PAC was associated with a smaller variance in time production, i.e. an increased precision in timing, but there was no correlation with the duration of the produced interval. Our results suggest an active role for α-β coupling in maintaining the precision of the endogenous temporal goal during time production: specifically, α oscillations may maintain the content of current cognitive states, thus securing the endogenous temporal code for duration estimation instantiated in β band. Oscillatory multiplexing may thus index the variance of neuronal computations, which translates into the precision of behavioral performance.
Bipolar oscillations between positive and negative mood states in a computational model of Basal Ganglia
Authors: Balasubramani Pragathi Priyadharsini , Srinivasa Chakravarthy V.
Published: October 2017

Bipolar disorder is characterized by mood swings - oscillations between manic and depressive states. The swings (oscillations) mark the length of an episode in a patient’s mood cycle (period), and can vary from hours to years. The proposed modeling study uses decision making framework to investigate the role of basal ganglia network in generating bipolar oscillations. In this model, the basal ganglia system performs a two-arm bandit task in which one of the arms leads to a positive outcome, while the other leads to a negative outcome. In healthy conditions, the model chooses positive action and avoids negative one, whereas under bipolar conditions, the model exhibits slow oscillations in its choice of positive or negative outcomes, reminiscent of bipolar oscillations. The model is cast at three levels of abstraction: 1) a two-dimensional dynamical system model, 2) a phenomenological basal ganglia model, 3) a detailed network model of basal ganglia. Phase-plane analyses on the simple reduced dynamical system with two variables reveal the essential parameters that generate pathological ‘bipolar-like’ oscillations. Phenomenological and network models of the basal ganglia extend that logic, and interpret bipolar oscillations in terms of the activity of dopaminergic and serotonergic projections on the cortico-basal ganglia network dynamics. The network’s dysfunction, specifically in terms of reward and risk sensitivity, is shown to be responsible for the pathological bipolar oscillations. The study proposes a computational model that explores the effects of impaired serotonergic neuromodulation on the dynamics of the cortico basal ganglia network, and relates this impairment to abstract mood states (manic and depressive episodes) and oscillations of bipolar disorder.
Variable impact of Verticillium longisporum on oilseed rape yield in field trials in the United Kingdom
Authors: Depotter Jasper R. L. , Thomma Bart P.H.J. , Wood Thomas A.
Published: October 2017

The Verticillium genus comprises economically important plant pathogens that collectively affect a broad range of annual and perennial crops. Verticillium longisporum mainly infects brassicaceous hosts, including oilseed rape. The most conspicuous symptom of V. longisporum infection on oilseed rape is black stem striping that appears towards the end of the cropping season. Thus far, the impact of V. longisporum infection on oilseed yield remains unclear. Verticillium stem striping recently emerged as a new disease in UK and currently displays a widespread occurrence in England. In this study, we assessed the impact of Verticillium stem striping on British oilseed rape production. To this end, four cultivars (Incentive, Vision, Harper and Quartz) were grown in field plots with different levels of V. longisporum disease pressure at different locations over two consecutive years. Whereas Incentive and Vision developed relatively few stem striping symptoms, Harper and especially Quartz showed severe symptoms during these field experiments. Furthermore, higher inoculum levels induced more severe symptoms in these cultivars. Intriguingly, significant yield reductions upon V. longisporum infection only occurred in a single field trial on all tested oilseed rape cultivars. Thus we conclude that Verticillium stem striping does not consistently impact oilseed rape yield, despite the occurrence of abundant disease symptoms.
Distinguishing genetic correlation from causation across 52 diseases and complex traits
Authors: O’Connor Luke J. , Price Alkes L.
Published: October 2017

Mendelian randomization (MR) is widely used to identify causal relationships among heritable traits, but it can be confounded by genetic correlations reflecting shared etiology. We propose a model in which a latent causal variable mediates the genetic correlation between two traits. Under the latent causal variable (LCV) model, trait 1 isfully genetically causalfor trait 2 if it is perfectly genetically correlated with the latent causal variable, implying that the entire genetic component of trait 1 is causal for trait 2; it ispartially genetically causalfor trait 2 if it has a high genetic correlation with the latent variable, implying that part of the genetic component of trait 1 is causal for trait 2. To quantify the degree of partial genetic causality, we define thegenetic causality proportion(gcp). We fit this model using mixed fourth momentsE(α1α2) andE(α1α2) of marginal effect sizes for each trait, exploiting the fact that if trait 1 is causal for trait 2 then SNPs affecting trait 1 (large) will have correlated effects on trait 2 (largeα1α2), but not vice versa. We performed simulations under a wide range of genetic architectures and determined that LCV, unlike state-of-the-art MR methods, produced well-calibrated false positive rates and reliable gcp estimates in the presence of genetic correlations and asymmetric genetic architectures; we also determined that LCV is well-powered to detect a causal effect. We applied LCV to GWAS summary statistics for 52 traits (averageN=331k), identifying partially or fully genetically causal effects (1% FDR) for 59 pairs of traits, including 30 pairs of traits with high gcp estimates (gĉp > 0.6). Results consistent with the published literature included genetically causal effects on myocardial infarction (MI) for LDL, triglycerides and BMI. Novel findings included a genetically causal effect of LDL on bone mineral density, consistent with clinical trials of statins in osteoporosis. These results demonstrate that it is possible to distinguish between genetic correlation and causation using genetic data.
First draft genome assembly of an iconic clownfish species (Amphiprion frenatus)
Authors: Marcionetti Anna , Rossier Victor , Bertrand Joris A. M. , Litsios Glenn , Salamin Nicolas
Published: October 2017

Clownfishes (or anemonefishes) form an iconic group of coral reef fishes, particularly known for their mutualistic interaction with sea anemones. They are characterized by particular life history traits, such as a complex social structure and mating system involving sequential hermaphroditism, coupled with an exceptionally long lifespan. Additionally, clownfishes are considered to be one of the rare group to have experienced an adaptive radiation in the marine environment.

Here, we assembled and annotated the first genome of a clownfish species, the tomato clownfish (Amphiprion frenatus). We obtained a total of 17,801 assembled scaffolds, containing a total of 26,917 genes. The completeness of the assembly and annotation was satisfying, with 96.5% of the Actinopterygii BUSCOs (Benchmarking Universal Single-Copy Orthologs) being retrieved in A. frenatus assembly. The quality of the resulting assembly is comparable to other bony fish assemblies.

This resource is valuable for the advancing of studies of the particular life-history traits of clownfishes, as well as being useful for population genetic studies and the development of new phylogenetic markers. It will also open the way to comparative genomics. Indeed, future genomic comparison among closely related fishes may provide means to identify genes related to the unique adaptations to different sea anemone hosts, as well as better characterize the genomic signatures of an adaptive radiation.