bluuebunny/crossref_metadata_2025 huggingface dataset:
Precision, accuracy and bias of walked line-transect distance sampling to estimate eastern grey kangaroo population size
Authors: Glass Ruth , Forsyth David M. , Coulson Graeme , Festa-Bianchet Marco
Published: December 2015

Context
Distance sampling is widely used to estimate the size of wildlife populations, including kangaroos. However, the performance of distance-sampling abundance estimates has seldom been evaluated for wild mammal populations of known size.

Aims
We evaluated the precision, accuracy, bias and interval coverage of abundance estimates from walked line-transect sampling, a commonly used distance-sampling method, for a marked free-ranging population of eastern grey kangaroos (Macropus giganteus) at Yanakie Isthmus, Wilsons Promontory National Park, south-eastern Australia.

Methods
In each of two study periods (November 2012 and May 2013) we first determined the true size of the uniquely marked kangaroo population by conducting 10 intensive searches of the study area. We then conducted distance sampling along six systematically spaced line transects. We walked each transect four times in November 2012 and seven times in May 2013. Data were analysed using Program DISTANCE.

Key results
Our intensive searches revealed that 141 and 124 collared kangaroos were present in the study area in November 2012 and May 2013, respectively. When transects were walked four or more times (i.e. ≥400 observations), maximum precision (coefficient of variation; CV of ~13%) was achieved in both survey periods. Walking transects twice (i.e. ~200 observations) produced abundance estimates with CVs of <20% in each study period. The accuracy (root mean square error) of abundance estimates varied from 1 to 13 (November 2012) and from 3 to 28 (May 2013). Bias ranged from −9% to +23%, but stabilised at between −1% and −9% when transects were walked four or more times in each study period. The 95% confidence intervals for the abundance estimates always included the true population size.

Conclusions
Our results indicated that walked line-transect distance sampling is a precise and accurate method for estimating eastern grey kangaroo abundance. The small negative biases that occurred when sample sizes were large were likely to be due to some animals moving outside the study area.

Implications
Provided that the key design elements and assumptions are met, estimates of kangaroo abundance from walked line-transect distance sampling should have good precision (CV < 20%) and minimal (<10%) bias.
Oxidization without substrate unfolding triggers proteolysis of the peroxide-sensor, PerR
Authors: Ahn Bo-Eun , Baker Tania A.
Published: December 2015

Significance

Life in aerobic environments inevitably generates reactive oxygen species (ROS), which damage proteins and other cellular components, often irreversibly. Cells must degrade these potentially harmful, damaged macromolecules. A bacterial ROS sensor, the transcriptional repressor PerR, is itself controlled by irreversible oxidation of its metal-binding site. We found that active PerR is stable, but that this oxidation marks PerR for degradation by the protease LonA. We identified a LonA-binding site in PerR, which is exposed in structures of unliganded or oxidized PerR, but buried in the liganded active form. Therefore, we propose that an oxidation-induced and activity-coupled conformational change in PerR triggers its degradation. Similar allostery may explain how site-specific and mild oxidation can commit proteins to degradation.
Laser resurfacing of Al–Zn–Mg–Si coatings
Authors: Peng C. T. , Chen Z. , Liu Q. , Nolan D. , Li H.
Published: December 2015

The feasibility of refinement of Al–Zn–Mg–Si hot dip coatings by diode laser resurfacing has been demonstrated. The microstructure of the laser resurfaced coatings was characterised mainly by transmission electron microscopy and also by scanning electron microscopy. The variance of heat input results in different cooling rates and varying degrees of refinement; that is, the higher the power density, the lower the cooling rate and the larger the secondary dendrite arm spacing of α-Al dendrites. In addition, the inherent variation of chemical composition in coatings also affects the microstructure as well as phase distribution. This laser resurfacing technique has not only reduced the secondary dendrite arm spacing/α-Al dendrites but also changed the solidification path and produce different phases and microstructure in the interdendritic areas.
Risk and return in social finance
Authors: Nicholls Alex , Tomkinson Emma
Published: December 2015

The chapter explores how far existing tools and framework for calculating risk and return parameters in mainstream finance can be applied to modelling the likely social returns to a given allocation of capital. After considering risk and return in mainstream finance the chapter reviews the limited work to date on social risk and return. The categories of probability risk, variance risk, and uncertainty risk drawn from the established risk literature are applied to social outcomes. The correlations between particular types of social risk and expected social returns are considered—the patterns of correlation are found to be complex. The chapter makes some observations concerning how to measure and manage social risk in social finance. Conclusions suggest some of the opportunities offered to social investors by developing more rigorous conceptualizations of social risk and return.
The roles of government and policy in social finance
Authors: Addis Rosemary
Published: December 2015

This chapter sets out new thinking and research on how various public policy tools have been building the social finance market around the world as a catalytic force. The chapter considers the rationale for policy interventions, looking firstly at a market-based analysis and then at arguments for a broader role for the state in encouraging innovation. It sets out a new ‘toolbox’ for policy, drawing upon examples from around the globe. The chapter concludes with consideration of how social finance can provide a focal point for new collaborations across sector boundaries to shape a more productive generation of public private partnerships.
Islamic finance as social finance
Authors: Schoon Natalie
Published: December 2015

This chapter explores the linkages between Islamic finance and social finance. The chapter opens with a brief overview of the history of finance to provide a context for some of the subsequent precepts of Islamic finance. Next, the most well-known prohibition in Islamic finance—the prohibition on charging interest—is reviewed. This is followed by an overview of the different product types available in this market. The next section considers other, lesser-known prohibitions specifically focused on social responsibility within Islamic finance. Finally, conclusions summarize the main issues and arguments in the chapter and draw the key themes together.
Environmental impact investing
Authors: Harold Jacob , Spitzer Joshua , Emerson Jed , Spence Marieke
Published: December 2015

This chapter explores the area of environmental finance. Specifically, it sets out the intersection of households, the economics of environmental management, and the environmental consequences of economic investment. The analysis is organized into four main elements: the first section begins by exploring the main themes in environmental economics. Next, it goes on to investigate the link between environmental investing and financial return and then proposes a framework for understanding the different forums in which environmentally oriented investment occurs. The second part proposes ten key propositions on how environmental concerns are connected to financial investment. Section three focuses on one particularly tangible domain—real estate—and includes three case studies to illustrate existing strategies for incorporating environmental value into real estate investment. The final section presents conclusions and recommendations for further research.
Postscript
Authors: Gregory Dan
Published: December 2015

This chapter starts with an uncompromising appraisal of the prevailing political economy—where both the public and the private sectors are discredited and in disarray. It then explores the promise of cooperation both at the level of the firm—as a source of beneficial competition within particular markets—and as a basis for more constructive forms of industrial regulation and public service governance, through increased cooperation across and between the sectors. The central proposition is the need to better align incentives between taxpayers, producers/service providers, and consumers/service users. Unless this is tackled, negative externalities, mutual distrust, and contractual complexity all spiral. The paradox, as the chapter shows, is that although the cooperative alternative regularly attracts cross-party support, its basic precepts challenge many practices that are now taken for granted and underpinned by statute.
Aims and structures
Authors: Bauer Laurie , Lieber Rochelle , Plag Ingo
Published: December 2015

This chapter sets out the basic goals of the volume. The volume is intended to be a comprehensive description of all aspects of English word-formation and inflection based on extensive exemplification from contemporary corpora. The descriptive chapters give equal attention to form and meaning. Although the focus of this volume is primarily descriptive, it also considers the implications of English morphology for various issues of morphological theory. The book is divided into five parts. After the introductory part there are parts devoted to inflection, derivation, compounding, interactions and theoretical themes, respectively.
Verb inflection
Authors: Bauer Laurie , Lieber Rochelle , Plag Ingo
Published: December 2015

This chapter describes the morphosyntactic categories of the verb in English, drawing on evidence from different subdisciplines of linguistics. It starts out with the morphological differences between lexical and auxiliary verbs. Then the distinction between regular and irregular verbs is examined, paying special attention to the various ways in which irregular verbs may be classified. This is followed by a discussion of the inflection of the modal auxiliary verbs. Additional topics dealt with include auxiliary clitics and weak forms, the encoding of negation, and the incorporation of infinitival to into certain verbs.
Noun inflection
Authors: Bauer Laurie , Lieber Rochelle , Plag Ingo
Published: December 2015

This chapter discusses two morphological processes: plural and genitive marking. Plural marking shows a great deal of variation and irregularity, which contrasts with the relative regularity of the genitive. With respect to plurals, phonological and orthographic matters are examined, the status of foreign plurals, and cases in which plural is unmarked. For the genitive again phonological and orthographic matters are considered, but also the factors that condition the appearance of the s-genitive as opposed to the of-genitive.
Derivation
Authors: Bauer Laurie , Lieber Rochelle , Plag Ingo
Published: December 2015

This chapter gives an overview of phenomena in derivation where morphology and phonology interact. It provides a general introduction to the role of phonology in English derivation and the principles that govern the morpho-phonological behaviour of many of the morphological categories to be described in the subsequent chapters. Semi-regularity or lexical government prevails and variation is all-pervasive. The chapter also considers types of base and affixalallomorphy, the status of extenders, the role of stress and prosodic morphology, as well as haplology effects. Very generally speaking, there are conflicting demands that have to be met by derived words in the mental lexicon. On the one hand, derivatives, being new or different words, must be different in shape and in meaning from their base, but not too different, so that the relationship between base and derivative is still recoverable.
Derived nouns: personal and participant
Authors: Bauer Laurie , Lieber Rochelle , Plag Ingo
Published: December 2015

This chapter discusses morphological processes which derive personal or participant nouns, that is, nouns denoting agents, patients, themes, instruments, inhabitants, locations, and gendered forms. These are formed primarily by affixation in contemporary English, specifically by the suffixes -an, -ant, -arian, -ee, -eer, -er, -ese, -ess, -ette,-i, -ish, -ist, -ite, -meister, -nik, -ster and-trix, as well as by the prefixes grand-, great-,step-, and vice-. Some of the nominalizing processes discussed in Chapter 10 are revisited, looking at the ways in which they overlap with the function of the primary personal and participant affixes discussed here. Similarly, this chapter touches on a few of the affixes that will be given a more detailed treatment in Chapter12 as forming collective or abstract nouns, but which double to some extent in creating participant nouns.
Derived adverbs
Authors: Bauer Laurie , Lieber Rochelle , Plag Ingo
Published: December 2015

This chapter looks at the ways in which adverbs are formed in English. Two possibly controversial theoretical assumptions are discussed, namely that adverbs are a separate category from adjectives, and that the affixation involved in creating adverbs is a matter of derivation rather than inflection. The categorial issue is taken up first, and then the specifics of adverb-forming processes in English. Although the formation of adverbs is far less central to English word-formation than the other major types considered, there are nevertheless some interesting questions. These include the phonological conditioning of the -ly affix, the analysis of forms like -ways, and the status and semantics of ‑wise.
Size, quantity, and attitude
Authors: Bauer Laurie , Lieber Rochelle , Plag Ingo
Published: December 2015

This chapter considers morphological ways of marking size, frequency, and quantity. The pertinent expressions are also often used to show attitude or evaluation and therefore they are all treated in one chapter. The chapter looks at evaluatives such as affixal diminutives, affixal hypocoristics and clippings, augmentatives, reduplication, and expletive insertion. It also treats affixes that convey non-evaluative attitude and affixes concerned with quantity and measure. The chapter concludes with a description of the morphology of English numbers.
The analysis and limits of conversion
Authors: Bauer Laurie , Lieber Rochelle , Plag Ingo
Published: December 2015

This chapter considers the three interlinked topics of competition, blocking, and productivity. It focuses on the theoretical constructs that are the foundations of dealing with these aspects of the morphology of English. It is shown that competition, blocking, and productivity are interlocking concepts in the study of morphology. It is concluded that the data show so much competition in domains of productivity that there is little empirical support for any strong notion of blocking. The notion of productivity is important in morphological description, but its theoretical importance is open to interpretation and remains controversial.
Blocking, competition, and productivity
Authors: Bauer Laurie , Lieber Rochelle , Plag Ingo
Published: December 2015

This chapter is devoted to the role of lexical strata in English Morphology, those aspects of morphology that are native to the language and those aspects that come into English as a result of wholesale borrowing from French and the classical languages Latin and Greek. It is shown shows that a study of contemporary corpora sheds considerable light on theoretical issues that arise with regard to the interaction of different strata in English morphology. The theoretical issues have hinged primarily on the extent to which and the specific ways in which these strata can interact with each other. Thus, it is often claimed that that there are stratum-specific restrictions on the combinability of affixes. This chapter suggests that these claims have largely been based on an incomplete picture, and that there is less in the way of stratification in English derivation than has been assumed.
English morphology in a typological perspective
Authors: Bauer Laurie , Lieber Rochelle , Plag Ingo
Published: December 2015

The chapter then looks at a variety of theoretical principles that are relatively independent of broader frameworks. Here it is argued that the corpus data provide strong arguments against many of the specific claims or principles that have been proposedin the literature such as the righthandhead rule, the unitary base, hypothesis, theunitary output hypotheses, blocking, lexical phonology and morphology, the monosuffixconstraint, the first sister principle, and the lexical integrity hypothesis. Finally, the chapter turns to what we do know, and how that knowledge should help us to frame new theoretical models.
Back to the Schrödinger equation on a lattice
Authors: Manousakis Efstratios
Published: December 2015

This chapter goes back to the discrete lattice in order to transform the basis to momentum eigenstates. In addition, the chapter takes the continuum limit of space and we recover known relations and the delta function.
Time evolution and wavepackets
Authors: Manousakis Efstratios
Published: December 2015

Here, the chapter discusses time evolution in quantum mechanics and in particular of a free-particle state which is initially prepared as a wavepacket.
Simultaneous observables
Authors: Manousakis Efstratios
Published: December 2015

This chapter discusses when two observables, which are represented by operators, –can be simultaneously observable. The chapter discusses the uncertainty principle in the general case and when two operators can share eigenstates. It also discuss the consequences of symmetry.
Scattering in one dimension
Authors: Manousakis Efstratios
Published: December 2015

This chapter discusses scattering in one dimension. It considers simple examples, it discusses tunneling and it analyzes the analytic structure of the scattering amplitude. It also discusses resonances.
Periodic potentials
Authors: Manousakis Efstratios
Published: December 2015

This chapter explores the consequences of the translational symmetry of a periodic Potential. It discusses Bloch’s theorem and its consequencies. It also analyzes the so-called Kronig–Penney model.
Quantum mechanics and path integrals
Authors: Manousakis Efstratios
Published: December 2015

This chapter discusses the Feymann path-integral approach to quantum mechanics. First, it derives a path integral expression for the evolution operator. Next, it shows that the classical equations of motion, that is, those obtained from the principle of least action, are obtained from this path integral formulation in the limit where the variation in the action of the problem at hand is small as compared to the Planck’s constant h. Last, it discusses how the WKB approximation is derived from the path integral formulation.
Applications of path integrals
Authors: Manousakis Efstratios
Published: December 2015

This chapter discusses some applications of path integrals. First, it illustrates how their qualitative use can yield insights. As an example, it applies it to the so-called Bohm–Aharonov effect. Then, it discusses the generalization of the path-integral formalism for the so-called many-body problem. It only treats distinguishable particles (what we call Boltzmannons) in this chapter. The book will discuss indistinguishable particles in a future chapter. This chapter will also discuss the formulation of quantum statistical mechanics of Boltzmannons.
Bound states in spherically symmetric potentials
Authors: Manousakis Efstratios
Published: December 2015

This chapter deals with bound states in the case where the potential is spherically symmetric. As a result, it discusses the spherical Bessel equation, the spherical Bessel and Newmann functions and their relation to the Legendre polynomials, and the ordinary Bessel functions.
The hydrogen-like atom
Authors: Manousakis Efstratios
Published: December 2015

This chapter solves the problem of two particles interacting via a 1/r type of interaction, as in the case of the hydrogen atom. It finds the eigenstates and the energy eigenvalues of this system. As a result, it discusses the Laguerre polynomials.
Time-dependent Hamiltonian
Authors: Manousakis Efstratios
Published: December 2015

This chapter discusses how to treat the case of a perturbation which depends on time. It also discusses the case of the so-called real-time evolution and the adiabatic process which has received more recent attention because of experiments on quantum dynamics in trapped cold atoms.
Spin angular momentum
Authors: Manousakis Efstratios
Published: December 2015

This chapter discusses the case of spin as an internal angular momentum-like degree of freedom. It considers and analyzes the case of spin-1/2 explicitly. It also discusses the coupling of spin to an externally applied magnetic field. Furthermore, it discusses rotations in the spin space.
Interaction of radiation with charged particles
Authors: Manousakis Efstratios
Published: December 2015

This chapter treats fully quantum mechanically the interaction of charged particles with a fluctuating electromagnetic field using time-dependent perturbation theory. It discusses absorption, spontaneous emission, and stimulated emission in atomic physics.
Verb frames
Authors: Pinkster Harm
Published: December 2015

This chapter deals with the valency of verbs and adjectives in Latin, making a distinction between one-, two-, and three-place verbs and one- and two-place adjectives. Contexts are discussed in which arguments can be omitted (so-called absolute use). By contrast, other verbs are discussed that are used in more or less fixed combinations, so-called support verb constructions. After an introductory section on the concept of valency, the valency frames of verbs and adjectives are discussed in a systematic way using both formal parameters (the use of cases and prepositions) and semantic ones. Special attention is devoted to auxiliary verbs and copular verbs and the ways to distinguish them from other verbs.
The semantic values of the Latin tenses and moods
Authors: Pinkster Harm
Published: December 2015

This chapter starts with a theoretical introduction to the notions of tense, aspect, and mood. It is assumed that the Latin verbal system is essentially a temporal system based on a combination of reference point and relative position (anteriority, simultaneity, and posteriority). Finite forms have a reference time, which, by contrast, non-finite forms are lacking. Latin has three moods: indicative, subjunctive, and imperative. For the interpretation of the subjunctive (which indicates non-factivity or counterfactivity) the type of sentence in which it is used is decisive. The discussion of the moods and tenses is presented separately for main clauses and subordinate clauses. In subordinate clauses the subjunctive functions both as a semantic mood and as a grammatical mood. A relatively large amount of space is devoted to the semantic value of the perfect and to the so-called sequence of tenses.
Cases and prepositions
Authors: Pinkster Harm
Published: December 2015

This chapter deals with the function of cases and prepositions and their contribution to a correct interpretation of the context in which they are used. Frequency data are provided, which show the use of cases and prepositions to mark constituents at the clause and noun phrase levels, that is, for arguments, adjuncts, disjuncts, and attributes. Special attention is paid to the question how it is possible that the same case or preposition is used at different levels. It is difficult to find one ‘core’ meaning for each case or preposition that covers these various uses. The meaning of the nouns and verbs and the context in which they are used contributes much to a correct interpretation. In the course of the history of Latin the function of cases and prepositions changed, but the final break down of the case system occurred much later than the period covered by the Syntax.
Introduction
Authors: Payne Richard K.
Published: December 2015

This chapter introduces the homa and the theoretical issue of studying ritual change over long periods of time and across the boundaries of ritual cultures. The cross-cultural transmission of the ritual out of the Indian subcontinent throughout the entire tantric world poses methodological issues, such as the balancing of textual and ethnographic studies. It considers the idea of ritual invariance which has long been characteristic of scholarly and popular understandings of ritual. The conception of ritual as invariant, however, has impeded the historical study of ritual change. The chapter closes by introducing each subsequent chapter.
The Structure of Japanese Buddhist Homa
Authors: Tachikawa Musashi
Published: December 2015

This chapter is based on the dualism of sacred and profane as explicated by Mircea Eliade. The ritual sequence of homa in Japan moves from the profane to the sacred, a transition made more complex by the continuing dynamic mediation between the two states, rather than a simple transition from one to the other. Additional nuance is added to this dualism by the way in which the chapter introduces the categories of pure and impure. These do not simply matching the oppositional categories of sacred and profane, but rather operate across those two categories. It also discusses the relation between individual, subjective experience and collective experience in the context of ritual performance.
The VedicHomaand the Standardization of HinduPūjā
Authors: Lubin Timothy
Published: December 2015

This chapter examines the way in which the traditional solemn rites (śrauta), requiring three fires, are simplified. This change results in the creation of the domestic, or “homely” rituals as the chapter calls them. The systematic integration of ritual practices in the Purāṇas and Āgamas—the penumbra of the Vedic tradition—involved assimilating food offerings to well-known Vedic forms. Thus, pūjā was provided with a Vedic framework and warrant. The domestic rites (gṛhya) thus initiated were much simpler than the solemn rites, as they only require a single fire for their performance. Similarly, there is an accompanying reduction in the number of officiants required for the performance of the domestic rites.
Homa Rituals in the Indian Kālacakra-tantra Tradition
Authors: Wallace Vesna A.
Published: December 2015

The Kālacakra-tantra is considered one of the most authoritative tantric traditions, and the chapter examines the homa as found in that tradition. Instructions for the construction of a ritual site include color symbolism, revealing another layer of symbolic associations between the type of ritual and the requirements for its effective performance. Also discussed are the directions and locations where a ritual hearth is best constructed, along with its size and shape. In contrast to other texts discussed in this collection, the texts discuss five kinds of ritual performance. According to this tradition, while external homa can accomplish mundane goals, it is only the internal homa in which the awakened consciousness acts as the ritual fire that can accomplish the ultimate goal of awakening.
Demographic Anxiety
Authors: Orgad Liav
Published: December 2015

New waves of immigrants have normally been accompanied by exaggerated feelings of threat to national identity and unity. Quite often, they have prompted an extreme and disproportionate response. By analyzing three cases—Hispanics in America, Muslims in Europe, and Palestinians in Israel—this chapter demonstrates a modern disproportionate reaction to immigration. The cases are radically different one from the other, but they nevertheless have a common denominator—“demographobia.” The purpose of this chapter is to present a typology of demographic concerns—civic, cultural, and ethnic; show how these concerns are frequently accompanied by exaggerated facts, false conclusions, and public hysteria; and demonstrate how they initiate anti—immigration laws. Generally, the chapter illustrates how liberal democracies want to have it both ways—enjoying the economic benefits of immigration, while not being willing to fully accommodate the cultural changes which it brings about.
National Constitutionalism
Authors: Orgad Liav
Published: December 2015

This chapter suggests a two—stage process for regulating immigration and access to citizenship. In the first stage, immigrants would have to accept basic liberal—democratic principles as a prerequisite for admission; these principles are not culture—oriented, but constitute a system of structural rules governing human behavior. In the second stage, as part of the naturalization process required to obtain citizenship of a specific state, immigrants would be asked to accept fundamental constitutional principles—which include linguistic and fundamental cultural elements. However, these principles must be essential to citizenship and as just as one could reasonably expect, given the state’s overall circumstances. I call this concept “national constitutionalism.” In general, the chapter provides a normative framework for immigration regulation that protects a thin version of the majority cultural identity within the liberal discourse.
Immigration Policy and Constitutional Identity
Authors: Orgad Liav
Published: December 2015

The book conducts a systematic analysis of immigration requirements in liberal states. But don’t be mistaken: the book is more about “us” than about immigrants. We are those who define the type and number of people we permit to join our community, and what rules apply to the naturalization process. Immigration law, hence, is a unique platform to examine our choices. It shapes who we are as a people and, at the same time, functions as a mirror reflecting those qualities that we value in others. By putting immigrants to test, we put our own values to test. The concluding chapter traces what immigration policy can teach us about constitutional identity. In an attempt to define what the process of becoming a citizen means—how to become British, French, and German—states are exploring their own ethos—what Britishness, Frenchness, and Germanness means. Regulating immigration is a journey into ourselves.
OMPPM: online multiple palindrome pattern matching
Authors: Kim Hwee , Han Yo-Sub
Published: December 2015

Motivation: A palindrome is a string that reads the same forward and backward. Finding palindromic substructures is important in DNA, RNA or protein sequence analysis. We say that two strings of the same length are pal-equivalent if, for each possible centre, they have the same length of the maximal palindrome. Given a text T of length n and a pattern P of length m, we study the palindrome pattern matching problem that finds all indices i such that P and T[i−m+1:i] are pal-equivalent.

Results: We first solve the online palindrome pattern matching problem in O(m2) preprocessing time and O(mn) query time using O(m2) space. We then extend the problem for multiple patterns and solve the online multiple palindrome pattern matching problem in O(mkM) preprocessing time and O(mkn+c) query time using O(mkM) space, where M is the sum of all pattern lengths, mk is the longest pattern length and c is the number of pattern occurrences.

Availability and implementation: The source code for all algorithms is freely available at http://toc.yonsei.ac.kr/OMPPM

Contact:  kimhwee@cs.yonsei.ac.kr

Supplementary information:  Supplementary data are available at Bioinformatics online.
Spatial and temporal activity patterns of ocelots Leopardus pardalis in lowland forest of eastern Ecuador
Authors: Blake John G. , Mosquera Diego , Loiselle Bette A. , Swing Kelly , Guerra Jaime , Romo David
Published: December 2015

Ocelots ( Leopardus pardalis ) are common in lowland forests of Amazonia. We used camera traps to document the occurrence and activity of ocelots at a site in eastern Ecuador during 2005–2012 (15,058 trap-days). We accumulated 384 independent images of 16 males (147 images), 19 females (234 images), and 3 not assigned to individual or sex. Individuals varied in number of images (1 to > 50), number of camera locations (1–8), and number of months from first to last image (1–85). Photographic rate varied across years, from 15.3 to 29.9/1,000 trap-days in 2006 and 2010, respectively. Males and females were primarily active at night and showed similar hourly patterns of activity. Up to 3 individual males and 4 individual females were recorded at different camera locations each year. Resident males typically were photographed at more locations (mean of 4.1) than females (mean of 3.2). Results indicate that multiple ocelots, of both sexes, may be found within a relatively small (~650 ha) area of lowland forest in eastern Ecuador and emphasize the importance of the region for conservation of ocelots and other species.

Los ocelotes ( Leopardus pardalis ) son felinos comunes en los bosques de tierras bajas de la Amazonía. Utilizamos cámaras trampa para documentar la ocurrencia y actividad de ocelotes en un sitio en el Este de Ecuador durante 2005–2012 (15.058 días-trampa). Acumulamos 384 imágenes independientes de 16 machos (147 fotografías), 19 hembras (234 fotografías), y tres a los que no se les asignó individuo o sexo. Los individuos variaron en número de imágenes (1 a > 50), número de locaciones de las cámaras (1 a 8) y en el número de meses desde la primera hasta la última imagen (1 a 85). La tasa de captura fotográfica varió a través de los años, de 15,3 a 29,9 / 1.000 días-trampa en 2006 y 2010, respectivamente. Machos y hembras fueron activos principalmente durante la noche y mostraron patrones similares de actividad por hora. Hasta tres individuos machos y cuatro individuos hembras fueron registrados en diferentes locaciones cada año. Machos residentes fueron fotografiados en más lugares (media de 4,1) que hembras (media de 3,2). Los resultados indican que varios ocelotes, de ambos sexos, pueden encontrarse dentro de un área relativamente pequeña (~ 650 ha) de bosques de tierras bajas en el Este de Ecuador y enfatizan en la importancia de la región para la conservación de ocelotes y otras especies.
NuSTAR catches the unveiling nucleus of NGC 1068
Authors: Marinucci A. , Bianchi S. , Matt G. , Alexander D. M. , Baloković M. , Bauer F. E. , Brandt W. N. , Gandhi P. , Guainazzi M. , Harrison F. A. , Iwasawa K. , Koss M. , Madsen K. K. , Nicastro F. , Puccetti S. , Ricci C. , Stern D. , Walton D. J.
Published: December 2015

We present a NuSTAR and XMM–Newton monitoring campaign in 2014/2015 of the Compton-thick Seyfert 2 galaxy, NGC 1068. During the 2014 August observation, we detect with NuSTAR a flux excess above 20 keV (32 ± 6 per cent) with respect to the 2012 December observation and to a later observation performed in 2015 February. We do not detect any spectral variation below 10 keV in the XMM–Newton data. The transient excess can be explained by a temporary decrease of the column density of the obscuring material along the line of sight (from NH ≃ 1025 cm−2 to NH = 6.7 ± 1.0 × 1024 cm−2), which allows us for the first time to unveil the direct nuclear radiation of the buried active galactic nucleus in NGC 1068 and to infer an intrinsic 2–10 keV luminosity L$_{\rm X}=7^{+7}_{-4} \times 10^{43}$ erg s−1.
Far East Scarlet-Like Fever: A Review of the Epidemiology, Symptomatology, and Role of Superantigenic Toxin: Yersinia pseudotuberculosis-Derived Mitogen A
Authors: Amphlett A.
Published: December 2015

Far East scarlet-like fever (FESLF) is a severe inflammatory disease that occurs sporadically and in outbreaks in Russia and Japan. Far East scarlet-like fever is caused by Yersinia pseudotubuclosis infection, an organism that typically causes self-limiting gastroenteritis in Europe. Studies suggest the ability of Far Eastern strains to produce superantigen toxin Y pseudotuberculosis-derived mitogen A is integral to FESLF pathogenesis.

In Europe, human Y pseudotuberculosis infection typically occurs sporadically, in the form of a self-limiting gastroenteritis. In Russia and Japan, outbreaks of Y pseudotuberculosis infection cause severe systemic inflammatory symptoms. This disease variant is called FESLF. Geographical heterogeneity exists between virulence factors produced by European and Far Eastern Y pseudotuberculosis strains, implicating superantigen Y pseudotuberculosis-derived mitogen A (YPMa) in the pathogenesis of FESLF. This article describes the epidemiology and clinical features of FESLF, and it presents the evidence for the role of YPMa in FESLF pathogenesis.
Oral Polio Vaccination and Hospital Admissions With Non-Polio Infections in Denmark: Nationwide Retrospective Cohort Study
Authors: Sørup Signe , Stensballe Lone G. , Krause Tyra G. , Aaby Peter , Benn Christine S. , Ravn Henrik
Published: December 2015

Background.  Live vaccines may have nonspecific beneficial effects on morbidity and mortality. This study examines whether children who had the live-attenuated oral polio vaccine (OPV) as the most recent vaccine had a different rate of admissions for infectious diseases than children with inactivated diphtheria-tetanus-pertussis-polio-Haemophilus influenzae type b vaccine (DTaP-IPV-Hib) or live measles-mumps-rubella vaccine (MMR) as their most recent vaccine.

Methods.  A nationwide, register-based, retrospective cohort study of 137 403 Danish children born 1997–1999, who had received 3 doses of DTaP-IPV-Hib, were observed from 24 months (first OPV dose) to 36 months of age.

Results.  Oral polio vaccine was associated with a lower rate of admissions with any type of non-polio infection compared with DTaP-IPV-Hib as most recent vaccine (adjusted incidence rate ratio [IRR], 0.85; 95% confidence interval [CI], .77–.95). The association was separately significant for admissions with lower respiratory infections (adjusted IRR, 0.73; 95% CI, .61–.87). The admission rates did not differ for OPV versus MMR.

Conclusions.  Like MMR, OPV was associated with fewer admissions for lower respiratory infections than having DTaP-IPV-Hib as the most recent vaccination. Because OPV is now being phased-out globally, further studies of the potential beneficial nonspecific effects of OPV are warranted.
Upper Cervical Fusion in Children With Spondyloepiphyseal Dysplasia Congenita
Authors: Serhan Er Mehmet , Abousamra Oussama , Rogers Kenneth , Akyol Yakup , Palocaren Thomas , Takemitsu Masakazu , Campbell Jeffrey W. , Mackenzie William G.
Published: December 2015

Background:

Paraplegia or death secondary to upper cervical spine instability and spinal cord compression are known consequences of spondyloepiphyseal dysplasia congenita (SEDC). Stabilization and occasionally decompression of the upper cervical spine are indicated to treat upper cervical instability and stenosis. The purpose of this study was to report the results of upper cervical spine fusion in children with SEDC who had upper cervical instability.

Methods:

Twenty children (17 females and 3 males) with SEDC who underwent upper cervical spine fusion at a mean age of 72 months were retrospectively analyzed. Three of these children were under the age of 2. Fifteen children had posterior instrumentation and fusion whereas 5 children had posterior in situ fusion without use of any implant. Thirteen of 20 children had iliac crest autograft. Radiographic and clinical results were reported.

Results:

The average follow-up period was 8 years and 8 months. All children with instrumentation achieved fusion. Three of 5 children who had no instrumentation had nonunion (1 child had a stable nonunion and did not need revision; 1 had a single noninstrumented revision and ended up with a stable nonunion without further intervention; and the third one had a noninstrumented revision and had to have a second, instrumented, revision to achieve fusion). Six children had thoracolumbar scoliosis or kyphoscoliosis which required surgical management.

No postoperative neurological deficits were observed. Two of the 3 children with a preoperative neurological deficit showed full recovery and the third one remained unchanged. Pseudarthrosis is the main complication for the noninstrumented group. Distal junctional instability after successful fusion is seen at long-term follow-up (average=6 y) for 13% of patients in instrumented group.

Conclusions:

Instrumentation and iliac bone grafting results in 100% upper cervical fusion for SEDC children who demonstrated instability before surgery.

Level of Evidence:

Level IV—therapeutic.
Collagen V-heterozygous and -null supraspinatus tendons exhibit altered dynamic mechanical behaviour at multiple hierarchical scales
Authors: Connizzo Brianne K. , Han Lin , Birk David E. , Soslowsky Louis J.
Published: December 2015

Tendons function using a unique set of mechanical properties governed by the extracellular matrix and its ability to respond to varied multi-axial loads. Reduction of collagen V expression, such as in classic Ehlers–Danlos syndrome, results in altered fibril morphology and altered macroscale mechanical function in both clinical and animal studies, yet the mechanism by which changes at the fibril level lead to macroscale functional changes has not yet been investigated. This study addresses this by defining the multiscale mechanical response of wild-type, collagen V-heterozygous and -null supraspinatus tendons. Tendons were subjected to mechanical testing and analysed for macroscale properties, as well as microscale (fibre re-alignment) and nanoscale (fibril deformation and sliding) responses. In many macroscale parameters, results showed a dose-dependent response with severely decreased properties in the null group. In addition, both heterozygous and null groups responded to load faster than in wild-type tendons via earlier fibre re-alignment and fibril stretch. However, the heterozygous group exhibited increased fibril sliding, while the null group exhibited no fibril sliding. These studies demonstrate that dynamic responses play an important role in determining overall function and that collagen V is a critical regulator in the development of these relationships.
Tunability of collagen matrix mechanical properties via multiple modes of mineralization
Authors: Smith Lester J. , Deymier Alix C. , Boyle John J. , Li Zhen , Linderman Stephen W. , Pasteris Jill D. , Xia Younan , Genin Guy M. , Thomopoulos Stavros
Published: December 2015

Functionally graded, mineralized collagen tissues exist at soft-to-hard material attachments throughout the body. However, the details of how collagen and hydroxyapatite mineral (HA) interact are not fully understood, hampering efforts to develop tissue-engineered constructs that can assist with repair of injuries at the attachments of soft tissues to bone. In this study, spatial control of mineralization was achieved in collagen matrices using simulated body fluids (SBFs). Based upon previous observations of poor bonding between reconstituted collagen and HA deposited using SBF, we hypothesized that mineralizing collagen in the presence of fetuin (which inhibits surface mineralization) would lead to more mineral deposition within the scaffold and therefore a greater increase in stiffness and toughness compared with collagen mineralized without fetuin. We tested this hypothesis through integrated synthesis, mechanical testing and modelling of graded, mineralized reconstituted collagen constructs. Results supported the hypothesis, and further suggested that mineralization on the interior of reconstituted collagen constructs, as promoted by fetuin, led to superior bonding between HA and collagen. The results provide us guidance for the development of mineralized collagen scaffolds, with implications for bone and tendon-to-bone tissue engineering.
The Arabidopsis Auxin Receptor F-box proteins AFB4 and AFB5 are Required for Response to the Synthetic Auxin Picloram
Authors: Prigge Michael J. , Greenham Kathleen , Zhang Yi , Santner Aaron , Castillejo Cristina , O’Malley Ronan C. , Ecker Joseph R. , Estelle Mark
Published: December 2015

The plant hormone auxin is perceived by a family of F-box proteins called the TIR1/AFBs. Phylogenetic studies reveal that these proteins fall into four clades in flowering plants called TIR1, AFB2, AFB4, and AFB6 (Parryet al. 2009). Genetic studies indicate that members of the TIR1 and AFB2 groups act as positive regulators of auxin signaling by promoting the degradation of the Aux/IAA transcriptional repressors (Dharmasiriet al. 2005; Parryet al. 2009). In this report, we demonstrate that both AFB4 and AFB5 also function as auxin receptors based onin vitroassays. We also provide genetic evidence that both AFB4 and AFB5 are targets of the picloram family of auxinic herbicides. In contrast to previous studies we find that nullafb4alleles do not exhibit obvious defects in seedling morphology or auxin hypersensitivity. We conclude that AFB4 and AFB5 act in a similar fashion to other members of the family but exhibit a distinct auxin specificity.
The KIAA0319 Gene Polymorphisms are Associated with Developmental Dyslexia in Chinese Uyghur Children
Authors: Zhao Hua , Chen Yun , Zhang Bao-ping , Zuo Peng-xiang
Published: December 2015

To investigate the association of KIAA0319 gene polymorphisms and developmental dyslexia in individuals of Uyghurian descent. Eighteen single nucleotide polymorphisms (SNP) of gene KIAA0319 were screened in a group of 196 patients with dyslexia and 196 controls of Uyghur descent by determined the genotypes using a custom-by-design 48-Plex SNPscan™ Kit. SAS 9.1.3 software were used for data analysis. Seven SNPs(Pmm=0.001) of KIAA0319 have significant differences between the cases and controls under specific genotype models. Especially for rs6935076(Padjusted=0.020 under dominant model;Padjusted=0.028 under additive model) and rs3756821(Padjusted=0.021 under additive model), which still associated with dyslexia after Bonferroni correction. The linkage disequilibrium analysis showed four block within gene KIAA0319 and only the ten-maker haplotype(P=0.013) in block 4 was significantly more common in dyslexia children than in controls. The results indicated that genetic polymorphisms of KIAA0319 are associated with increased risk of developmental dyslexia in Uyghur population.
MicroScope: ChIP-seq and RNA-seq software analysis suite for gene expression heatmaps
Authors: Khomtchouk Bohdan B. , Hennessy James R. , Wahlestedt Claes
Published: December 2015

We propose a user-friendly ChIP-seq and RNA-seq software suite for the interactive visualization and analysis of genomic data, including integrated features to support differential expression analysis, interactive heatmap production, principal component analysis, gene ontology analysis, and dynamic network analysis.

MicroScope is hosted online as an R Shiny web application based on the D3 JavaScript library:http://microscopebioinformatics.org/. The methods are implemented in R, and are available as part of the MicroScope project at:https://github.com/Bohdan-Khomtchouk/Microscope.