bluuebunny/crossref_metadata_2025 huggingface dataset:
Incorporation of thio-pseudoisocytosine into triplex-forming peptide nucleic acids for enhanced recognition of RNA duplexes
Authors: Devi Gitali , Yuan Zhen , Lu Yunpeng , Zhao Yanli , Chen Gang
Published: January 2014

Peptide nucleic acids (PNAs) have been developed for applications in biotechnology and therapeutics. There is great potential in the development of chemically modified PNAs or other triplex-forming ligands that selectively bind to RNA duplexes, but not single-stranded regions, at near-physiological conditions. Here, we report on a convenient synthesis route to a modified PNA monomer, thio-pseudoisocytosine (L), and binding studies of PNAs incorporating the monomer L. Thermal melting and gel electrophoresis studies reveal that L-incorporated 8-mer PNAs have superior affinity and specificity in recognizing the duplex region of a model RNA hairpin to form a pyrimidine motif major-groove RNA2–PNA triplex, without appreciable binding to single-stranded regions to form an RNA–PNA duplex or, via strand invasion, forming an RNA–PNA2 triplex at near-physiological buffer condition. In addition, an L-incorporated 8-mer PNA shows essentially no binding to single-stranded or double-stranded DNA. Furthermore, an L-modified 6-mer PNA, but not pseudoisocytosine (J) modified or unmodified PNA, binds to the HIV-1 programmed −1 ribosomal frameshift stimulatory RNA hairpin at near-physiological buffer conditions. The stabilization of an RNA2–PNA triplex by L modification is facilitated by enhanced van der Waals contacts, base stacking, hydrogen bonding and reduced dehydration energy. The destabilization of RNA–PNA and DNA–PNA duplexes by L modification is due to the steric clash and loss of two hydrogen bonds in a Watson–Crick-like G–L pair. An RNA2–PNA triplex is significantly more stable than a DNA2–PNA triplex, probably because the RNA duplex major groove provides geometry compatibility and favorable backbone–backbone interactions with PNA. Thus, L-modified triplex-forming PNAs may be utilized for sequence-specifically targeting duplex regions in RNAs for biological and therapeutic applications.
Cure and Recovery
Authors: Davidson Larry
Published: January 2014

This chapter briefly discusses the history of the notion of "cure" in relation to serious mental illnesses from Pinel to the present day, including both theories on the nature of the illnesses and the nature of presumed therapeutic agents and mechanisms. The chapter then gives a brief overview of the notion of "recovery" in relation to serious mental illnesses, also from Pinel to the present day, and describes various definitions and forms of recovery as they have emerged over time. With this historical and conceptual background in place, the chapter then takes up the present state-of-the-art in psychiatry in relation to both concepts of cure and recovery, considers the empirical and neuroscientific evidence available relative to each concept, and then suggests several directions for research and philosophical reflection as the field continues to evolve. Two guiding principles that shape this discussion are that mental illnesses are not one-dimensional phenomena, but may be made up of several loosely related components which each have their own natural course, and that mental illnesses do not typically take over the entirety of a person's functioning, but also leave other aspects of functioning relatively intact. The combination of these principles suggests that cure and recovery are not likely to be binary functions in relation to serious mental illnesses (i.e., yes or no), but will more likely be more a matter of degree across multiple domains.
Interpersonal Relating
Authors: Hutto Daniel D.
Published: January 2014

Getting clear about the nature and basis of interpersonal relating is a central concern of many recent debates in the philosophy of mind. The first section of this chapter highlights some basic facts about the complexity and multifaceted character of interpersonal relating and briefly overviews some of its most prominent dysfunctions. Popular mind-minding hypotheses which claim that the dysfunctions in question are rooted in impaired capacities for attending to and attributing mental states to others are then introduced. Next, recent evidence from cognitive psychology and neuroscience with which these mind-minding hypotheses must be made compatible is summarized. The important differences between two main philosophical frameworks-frameworks that offer opposing ways of understanding the nature of mind minding capacities are then highlighted. Focusing on these differences, the final section highlights how adoption of these philosophical frameworks matters to thinking about the prognosis and strategies for the treatment of certain mental disorders.
Clinical Judgment, Tacit Knowledge, and Recognition in Psychiatric Diagnosis
Authors: Thornton Tim
Published: January 2014

This chapter contrasts the recent emphasis on operationalism as the route to reliability in psychiatry with arguments for an ineliminable role for tacit knowledge. Although Michael Polanyi popularized the idea of tacit dimension, the chapter argues that two clues he offers as to its nature-that we know more than we can tell and that knowledge is an active comprehension of things known-are better interpreted through regress arguments set out by Ryle and Wittgenstein. Those arguments, however, suggest that tacit knowledge is not inexpressible but merely inexpressible in context-free terms. The chapter suggests instead that tacit knowledge is best understood to be context-dependent practical knowledge. So understood, the regress arguments suggest that the operational approach to psychiatric diagnosis can never free itself from a tacit dimension. Given that claim, then Parnas' opposing view of diagnosis can be seen as a way to embrace, rather than deny, the importance of tacit knowledge and skilled clinical judgment for psychiatry.
Introduction
Authors: Fulford K.W.M. , Davies Martin , Gipps Richard G.T. , Graham George , Sadler John Z. , Stanghellini Giovanni , Thornton Tim
Published: January 2014

This Section examines several moral dilemmas and epistemological aporias in clinical practice and shows how clinicians can benefit from the introduction of philosophical methods and discourse. The authors develop these issues having in mind emblematic mental disorders (e.g. depression, personality disorders, schizophrenia) and typical clinical situations (e.g. how to establish an effective therapeutic relationship with borderline persons, dream interpretation, cognitive-behavioural therapy). One important claim shared by the Authors is that a great effort has been made to ground psychiatry on evidence-based science, and to tie it to our growing understanding of the human brain. This is obviously an exceedingly important project, but it would be a mistake to assume that the central questions of psychiatry can be completely resolved through scientific inquiry. Science offers guidance for clinical practice only in light of our concepts and normative judgments.
Depression, Decisional Capacity, and Personal Autonomy
Authors: Radoilska Lubomira
Published: January 2014

This chapter aims to address two related challenges the phenomenon of depression raises for theories which present autonomy as an agency concept and an independent source of justification. The first challenge is directed at an intuitive conception of intentional agency as implying a robust though not always direct link between evaluation and motivation, for in depression what appears to be choice-worthy does not get chosen. The second challenge targets the feasibility of a reliable distinction between autonomous and non-autonomous choices, for both value-neutral and value-laden accounts of depressive agency seem open to decisive objections. Drawing on Freud's interpretation of melancholia and Korsgaard's notion of practical identity, the chapter develops a conception of paradoxical identification which helps address the two challenges described and supports a revised value-neutral account of depressive agency as being non-autonomous.
Orthography and the Early History of Phonetics
Authors: MacMahon Michael K. C.
Published: January 2014

Phonetics has a long narrative history, stretching back through the Middle Ages and the Graeco-Roman period to the work of Sanskritic grammarians nearly 3,000 years ago. In the Middle and Far East, similar scholarly studies were undertaken, from the early Middle Ages onwards. The connection between the interpretation of aspects of Sanskritic literature and religious ritual and phonetics was paralleled in some medieval Arabic work on the interpretation of the Qur’an. The application of phonetic concepts in proposals for orthographic reforms in various languages, especially from the seventeenth century CE onwards, led to a varied series of proposals for change, some more practicable than others. Often however, at the same time it revealed the authors’ subjective awareness of the usefulness of the phonemic concept. Phonetics was to benefit, especially in the nineteenth century CE and afterwards, from the development of physiological and acoustic instrumentation in medicine and physics.
From Semitic to Afro-Asiatic
Authors: Lipiński Edward
Published: January 2014

The chapter sketches the development of Semitic linguistics. It opens with a presentation of Semitic languages and of the larger Afro-Asiatic phylum, to which Semitic belongs along with ancient Egyptian, Libyco-Berber, Cushitic, and Chadic. After recording the cuneiform lexicographic and grammatical work of the third and second millennia BC, the survey presents grammatical research on Syriac, Aramaic, Arabic, and Hebrew from the medieval period onwards. Ethiopian studies started in the sixteenth century, dealing first with Ge‘ez and Amharic, and in the nineteenth and twentieth centuries other Ethio-Semitic languages. The discovery and study of South Arabian started in the same period. The decipherment first of the Egyptian hieroglyphs and of the Akkadian cuneiform script, then of South Arabian and Ugaritic inscriptions was followed by grammatical studies which had a great impact on the linguistic analysis and perception of the Semitic languages. Ethio-Semitic relations with Cushitic languages extended the research field of Semitics to African languages. The formal similarity of verbal paradigms of Akkadian, Ethio-Semitic, and Libyco-Berber increased the attention paid to the Berber dialects of North Africa and to their affinity with Semitic idioms. There is a much weaker link with the Chadic languages. Polotsky’s studies on Egyptian grammar resulted in a deeper understanding of the difference between ancient Egyptian and Semitic, while Diakonov’s discovery of ergative characteristics in Libyco-Berber led to the perception of similar features in the other Afro-Asiatic languages. Recent Bohas’ studies of the Arabic and Hebrew roots provide a better understanding of the formation of the lexicon.
From Plato to Priscian
Authors: Atherton Catherine , Blank David
Published: January 2014

A literary canon remained the core of élite education in Classical Antiquity for centuries, while the discipline of grammar emerged to produce correct texts, explain, and evaluate it. But it was to philosophy that grammarians owed, not merely powerful theories of language’s origins, functions, constituents, and structures, all formulated in a rich meta-language, but the very conception of linguistic phenomena – as constituting a fundamentally rational system – that makes expert or scientific knowledge of them possible. Grammatical interests, whether accounting for (apparent) departures from formal or syntactic regularity, determining both the correct reading of a disputed Homeric verse and the correct rules for such a procedure, or defining the parts of speech in a school primer, of course ousted the original philosophical contexts and purposes: when the Stoic Chrysippus advised using nannies who spoke pure Greek, his aim, probably, was to improve their charges’ souls, not their economic or social prospects.
Functional and Cognitive Grammars
Authors: Siewierska Anna
Published: January 2014

This chapter presents an overview of the work that could be characterized as the functional-cognitive paradigm in linguistics. Separate sections are dedicated to functionally oriented theories on the one hand, and cognitively oriented theories on the other hand. The former type focuses on the use of language as the ultimate factor that defines its shape. The latter type starts out from the assumption that the human language should be understood from the perspective of human cognition in general. From both areas, three theories are discussed in somewhat more detail: SFG, FG, and RRG from the functional, and CC, CG, and RCG from the cognitive persuasion. A comparison is made between the respective theories in each of the two categories, in terms of their strengths and weaknesses. It is argued that, although there are apparent differences between the two approaches to grammar, there seems to be no fundamental reason why they could not be merged into one encompassing paradigm.
Lexical Semantics from Speculative Etymology to Structuralist Semantics
Authors: Geeraerts Dirk
Published: January 2014

This chapter contains an overview of the development of word meaning research up to and including the era of structuralist semantics: after a brief introduction to the pre-nineteenth-century traditions, the chapter has a closer look at historical–philological semantics, and at structuralist semantics. Within the latter, the chapter distinguishes between three main approaches: lexical field theory, componential analysis, and relational semantics.
Meaning in Texts and Contexts
Authors: Waugh Linda R. , Valencia José Aldemar Álvarez , Do Tom Hong , Michelson Kristen , Thomas M'Balia
Published: January 2014

This chapter traces twentieth-century interest within linguistics and other disciplines in the analysis of meaning in texts and contexts. Early approaches equated meaning with lexical meaning, although some differentiated sense and referent (Ogden and Richards) and analyzed the various senses of a word (Wittgenstein, prototype theory). Two groups differentiated themselves from the structuralist mainstream: Prague functional-structuralism (Mathesius, Jakobson, Troubetzkoy) and the London School (Firth) and Systemic Functional Linguistics (Halliday). This set the stage for the analysis of linguistic use and the development of the multidisciplinary area called discourse analysis. While there were earlier approaches in rhetoric and oratory, work on spoken language came from linguistics (information flow, deixis, spoken vs. written language), sociology (conversational analysis, variation studies, oral narrative, interactional sociolinguistics, Goffman), anthropology (ethnography of communication, focus on performance, language in verbal art and performance), and philosophy (pragmatics). For the written language, there was early interest in stylistics, and within linguistics work on text linguistics and critical discourse analysis, in addition to approaches influenced by literary studies (narratology/text semiotics, literary stylistics, genre analysis, and text pragmatics). The conclusion is that the turn to language in use has led to a dialogical, pluralistic, dynamic, and integrative view of how speakers, contexts, and meaning interplay.
Global Diversity Management
Authors: Özbilgin Mustafa , Jonsen Karsten , Tatli Ahu , Vassilopoulou Joana , Surgevil Olca
Published: January 2014

With increased globalization of the competitive business environment, companies must adjust their operating practices to accommodate the cultural styles, norms, and preferences of the regions of the world in which they operate. This chapter reviews theories and research related to global diversity management (GDM). In addition, a framework for studying the meaning, operation, and management of diversity across national borders is presented. In particular, the shift of emphasis from normative and process-based approaches to a contextual and multifaceted understanding of GDM is explored. The chapter also explores key challenges and contradictions facing GDM. Finally, future directions in research and practice are discussed.
Feminist Organizing: What’s Old, What’s New? History, Trends, and Issues
Authors: Ewig Christina , Ferree Myra Marx
Published: January 2014

This article introduces the concept of feminist organizing, which refers to the efforts of women to explicitly challenge their subordination to men. It differentiates feminist organizing from women’s movements and feminism and tries to understand the shifts where organizing occurs, the factors that influence these shifts, and the consequences for feminist objectives. The article studies the history of feminist organizing from the nineteenth century until the present and then emphasizes two critical issues in feminist organizing, namely, how solidarity is constructed and how the organizational form of feminist mobilization varies as political opportunities change. It also challenges the claims that feminism is declining and demobilized.
Introduction: Gender and Politics: A Gendered World, a Gendered Discipline
Authors: Celis Karen , Kantola Johanna , Waylen Georgina , Weldon S. Laurel
Published: January 2014

This article discusses the gendered nature of politics (as practice) and political science (as an academic discipline). It studies the sex-typing characteristic of most institutions in the modern world and describes how gender shapes the ways people organize, think, and know about the world. The article then identifies the changes that have occurred in politics and political science over the last hundred years and examines the politics and gender scholarship. Finally, it presents an understanding of the evolution of the gender and politics subfield as well as some of the challenges that remain.
Italy, Germany, Japan
Authors: Boltho Andrea
Published: January 2014

Over the last six decades, economic developments in the three countries that were defeated in World War II look strikingly similar. First came rapid reconstruction. Then followed the economic miracles of the Golden Age. The years that went from the first oil shock to the mid-1990s still saw fairly robust, and relatively similar, economic developments. Finally, during the last 15 years, the three countries held the dubious record of having the lowest output growth rates in the OECD area. The chapter looks primarily at Italy, using the examples of Germany and Japan to search for parallels and contrasts. Among the similarities, the main one lies in overall macroeconomic trends. The main differences are in economic policies (where Germany and Japan followed a much more orthodox stance than Italy), in labor market relations (with much greater conflict in Italy than in the other two countries), and in regional developments (where Italy was handicapped by the Mezzogiorno). Indeed, had Italy's government institutions, labor market relations and regional differentials been less problematic, Italy's growth performance might well have been superior to that of Germany and Japan.
Regional Convergence
Authors: Iuzzolino Giovanni , Pellegrini Guido , Viesti Gianfranco
Published: January 2014

In 150 years, the trends in regional disparities in economic development within Italy have differed depending on whether they are gauged by longitude or by latitude. The disparities between western and eastern regions first widened and then closed; the North-South gap, by contrast, remains the main open problem in the national history of Italy. This chapter focuses on the underlying causes of the turning points in regional disparities since national unification in 1861. The first came in the late nineteenth and early twentieth century, with the industrialization of the so-called "industrial triangle". This was followed by the "failed new turn" during the interwar years: not only were the beginnings of convergence blocked, but the North-South gap, until then still natural, inevitably, was transformed into a fracture of exceptional dimensions. The second turning point, in the twenty years after the World War, produced the first substantial, lasting convergence between southern and northern Italy, powered by rising productivity and structural change in the South. The last turning point was in the mid-1970s, when convergence was abruptly halted and a protracted period of immobility in the disparity began.
Writing with ring currents: selectively hydrogenated polycyclic aromatics as finite models of graphene and graphane
Authors: Fowler Patrick W. , Gibson Christopher M. , Bean David E.
Published: January 2014

Alternating partial hydrogenation of the interior region of a polycyclic aromatic hydrocarbon gives a finite model system representing systems on the pathway from graphene to the graphane modification of the graphene sheet. Calculations at the DFT and coupled Hartree–Fock levels confirm that sp2cycles of bare carbon centres isolated by selective hydrogenation retain the essentially planar geometry and electron delocalization of the annulene that they mimic. Delocalization is diagnosed by the presence of ring currents, as detected by ipsocentric calculation and visualization of the current density induced in theπsystem by a perpendicular external magnetic field. These induced ‘ring’ currents have essentially the same sense, strength and orbital origin as in the free hydrocarbon. Subjected to the important experimental proviso of the need for atomic-scale control of hydrogenation, this finding predicts the possibility of writing single, multiple and concentric diatropic and/or paratropic ring currents on the graphene/graphane sheet. The implication is that pathways for free flow of ballistic current can be modelled in the same way.
A continuum hyperelastic model for auxetic materials
Authors: Ciambella J. , Saccomandi G.
Published: January 2014

We propose a simple mathematical model to describe isotropic auxetic materials in the framework of the classical theory of nonlinear elasticity. The model is derived from the Blatz–Ko constitutive equation for compressible foams and makes use of a non-monotonic Poisson function. An application to the modelling of auxetic foams is considered and it is shown that the material behaviour is adequately described with only three constitutive parameters.
Statistical methods for temporal and space–time analysis of community composition data
Authors: Legendre Pierre , Gauthier Olivier
Published: January 2014

This review focuses on the analysis of temporal beta diversity, which is the variation in community composition along time in a study area. Temporal beta diversity is measured by the variance of the multivariate community composition time series and that variance can be partitioned using appropriate statistical methods. Some of these methods are classical, such as simple or canonical ordination, whereas others are recent, including the methods of temporal eigenfunction analysis developed for multiscale exploration (i.e. addressing several scales of variation) of univariate or multivariate response data, reviewed, to our knowledge for the first time in this review. These methods are illustrated with ecological data from 13 years of benthic surveys in Chesapeake Bay, USA. The following methods are applied to the Chesapeake data: distance-based Moran's eigenvector maps, asymmetric eigenvector maps, scalogram, variation partitioning, multivariate correlogram, multivariate regression tree, and two-way MANOVA to study temporal and space–time variability. Local (temporal) contributions to beta diversity (LCBD indices) are computed and analysed graphically and by regression against environmental variables, and the role of species in determining the LCBD values is analysed by correlation analysis. A tutorial detailing the analyses in the R language is provided in an appendix.
Habitat-mediated population limitation in a colonial central-place forager: the sky is not the limit for the black-browed albatross
Authors: Wakefield Ewan D. , Phillips Richard A. , Matthiopoulos Jason
Published: January 2014

Animal populations are frequently limited by the availability of food or of habitat. In central-place foragers, the cost of accessing these resources is distance-dependent rather than uniform in space. However, in seabirds, a widely studied exemplar of this paradigm, empirical population models have hitherto ignored this cost. In part, this is because non-independence among colonies makes it difficult to define population units. Here, we model the effects of both resource availability and accessibility on populations of a wide-ranging, pelagic seabird, the black-browed albatrossThalassarche melanophris. Adopting a multi-scale approach, we define regional populations objectively as spatial clusters of colonies. We consider two readily quantifiable proxies of resource availability: the extent of neritic waters (the preferred foraging habitat) and net primary production (NPP). We show that the size of regional albatross populations has a strong dependence, after weighting for accessibility, on habitat availability and to a lesser extent, NPP. Our results provide indirect support for the hypothesis that seabird populations are regulated from the bottom-up by food availability during the breeding season, and also suggest that the spatio-temporal predictability of food may be limiting. Moreover, we demonstrate a straightforward, widely applicable method for estimating resource limitation in populations of central-place foragers.
Paenibacillus doosanensis sp. nov., isolated from soil
Authors: Kim Jong-Hwa , Kang Hyeonji , Kim Wonyong
Published: January 2014

A Gram-stain-positive, aerobic, endospore-forming bacterium, designated CAU 1055T, was isolated from soil and its taxonomic position was investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence comparison revealed that the strain formed a distinct lineage within the genus

Paenibacillus

and was most closely related to

Paenibacillus contaminans

CKOBP-6T (similarity, 95.2 %) and

Paenibacillus terrigena

A35T (similarity, 95.2 %). The levels of 16S rRNA gene sequence similarity with other species of the genus

Paenibacillus

, including the type species of the genus,

Paenibacillus polymyxa

IAM 13419T (similarity, 91.7 %), were all <94.6 %. Strain CAU 1055T contained MK-7 as the only isoprenoid quinone and anteiso-C15 : 0 and iso-C16 : 0 as the major fatty acids. The cell-wall peptidoglycan of strain CAU 1055T contained meso-diaminopimelic acid. The polar lipids were composed of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, lysyl-phospatidylglycerol and three unidentified aminophospholipids. The DNA G+C content was 48.3 mol%. The results of physiological and biochemical tests allowed phenotypic differentiation of strain CAU 1055T from closely related recognized species. On the basis of phenotypic data and phylogenetic inference, strain CAU 1055T should be classified in the genus

Paenibacillus

, as a member of a novel species, for which the name Paenibacillus doosanensis sp. nov. is proposed. The type strain is CAU 1055T ( = KCTC 33036T = CCUG 63270T).
Environmental contamination by Aspergillus spp. in laying hen farms and associated health risks for farm workers
Authors: Cafarchia Claudia , Camarda Antonio , Iatta Roberta , Danesi Patrizia , Favuzzi Vincenza , Di Paola Giancarlo , Pugliese Nicola , Caroli Anna , Montagna Maria Teresa , Otranto Domenico
Published: January 2014

Data on the occurrence and epidemiology of Aspergillus spp. in laying hens farms are scant. With the aims of determining levels of airborne contamination in laying hen farms and evaluating the potential risk of infection for workers and animals, 57 air samples from 19 sheds (Group I), 69 from faeces (Group II), 19 from poultry feedstuffs (Group III) and 60 from three anatomical sites (i.e. nostrils, pharynx, ears) of 20 farm workers (Group IV) were cultured. The Aspergillus spp. prevalence in samples ranged from 31.6 % (Group III) to 55.5 % (Group IV), whereas the highest conidia concentration was retrieved in Group II (1.2×104 c.f.u. g−1) and in Group III (1.9×103 c.f.u. g−1). The mean concentration of airborne Aspergillus spp. conidia was 70 c.f.u. m−3 with Aspergillus fumigatus (27.3 %) being the most frequently detected species, followed by Aspergillus flavus (6.3 %). These Aspergillus spp. were also isolated from human nostrils (40 %) and ears (35 %) (P<0.05) (Group IV). No clinical aspergillosis was diagnosed in hens. The results demonstrate a relationship between the environmental contamination in hen farms and presence of Aspergillus spp. on animals and humans. Even if the concentration of airborne Aspergillus spp. conidia (i.e. 70 c.f.u. m−3) herein detected does not trigger clinical disease in hens, it causes human colonization. Correct management of hen farms is necessary to control environmental contamination by Aspergillus spp., and could lead to a significant reduction of animal and human colonization.
Immunization of pigs with an attenuated pseudorabies virus recombinant expressing the haemagglutinin of pandemic swine origin H1N1 influenza A virus
Authors: Klingbeil Katharina , Lange Elke , Teifke Jens P. , Mettenleiter Thomas C. , Fuchs Walter
Published: January 2014

Pigs can be severely harmed by influenza, and represent important reservoir hosts, in which new human pathogens such as the recent pandemic swine-origin H1N1 influenza A virus can arise by mutation and reassortment of genome segments. To obtain novel, safe influenza vaccines for pigs, and to investigate the antigen-specific immune response, we modified an established live-virus vaccine against Aujeszky’s disease of swine, pseudorabies virus (PrV) strain Bartha (PrV-Ba), to serve as vector for the expression of haemagglutinin (HA) of swine-origin H1N1 virus. To facilitate transgene insertion, the genome of PrV-Ba was cloned as a bacterial artificial chromosome. HA expression occurred under control of the human or murine cytomegalovirus immediate early promoters (P-HCMV, P-MCMV), but could be substantially enhanced by synthetic introns and adaptation of the codon usage to that of PrV. However, despite abundant expression, the heterologous glycoprotein was not detectably incorporated into mature PrV particles. Replication of HA-expressing PrV in cell culture was only slightly affected compared to that of the parental virus strain. A single immunization of pigs with the PrV vector expressing the codon-optimized HA gene under control of P-MCMV induced high levels of HA-specific antibodies. The vaccinated animals were protected from clinical signs after challenge with a related swine-origin H1N1 influenza A virus, and challenge virus shedding was significantly reduced.
A bout of voluntary running enhances context conditioned fear, its extinction, and its reconsolidation
Authors: Siette Joyce , Reichelt Amy C. , Westbrook R. Frederick
Published: January 2014

Three experiments used rats to examine the effect of a single bout of voluntary activity (wheel running) on the acquisition, extinction, and reconsolidation of context conditioned fear. In Experiment 1, rats provided with access to a wheel for 3 h immediately before or after a shocked exposure to a context froze more when tested in that context than rats provided with access to the wheels 6 h after the shocked exposure or rats not provided with access to the wheels. In Experiment 2, rats provided with access to the wheels immediately before or after a nonshocked exposure to the conditioned context froze less when tested in that context than rats provided with access to the wheels 6 h after the nonshocked exposure or rats not provided with access to the wheels. In Experiment 3, rats provided with access to wheels immediately after an extended nonshocked exposure to the conditioned context again froze less, whereas rats provided with access to the wheels after a brief nonshocked exposure froze more on the subsequent test than sedentary controls. These results show that a single bout of running can enhance acquisition, extinction, and reconsolidation of context conditioned fear.
Functional Convergence of Oxylipin and Abscisic Acid Pathways Controls Stomatal Closure in Response to Drought
Authors: Savchenko Tatyana , Kolla Venkat A. , Wang Chang-Quan , Nasafi Zainab , Hicks Derrick R. , Phadungchob Bpantamars , Chehab Wassim E. , Brandizzi Federica , Froehlich John , Dehesh Katayoon
Published: January 2014

Membranes are primary sites of perception of environmental stimuli. Polyunsaturated fatty acids are major structural constituents of membranes that also function as modulators of a multitude of signal transduction pathways evoked by environmental stimuli. Different stresses induce production of a distinct blend of oxygenated polyunsaturated fatty acids, “oxylipins.” We employed three Arabidopsis (Arabidopsis thaliana) ecotypes to examine the oxylipin signature in response to specific stresses and determined that wounding and drought differentially alter oxylipin profiles, particularly the allene oxide synthase branch of the oxylipin pathway, responsible for production of jasmonic acid (JA) and its precursor 12-oxo-phytodienoic acid (12-OPDA). Specifically, wounding induced both 12-OPDA and JA levels, whereas drought induced only the precursor 12-OPDA. Levels of the classical stress phytohormone abscisic acid (ABA) were also mainly enhanced by drought and little by wounding. To explore the role of 12-OPDA in plant drought responses, we generated a range of transgenic lines and exploited the existing mutant plants that differ in their levels of stress-inducible 12-OPDA but display similar ABA levels. The plants producing higher 12-OPDA levels exhibited enhanced drought tolerance and reduced stomatal aperture. Furthermore, exogenously applied ABA and 12-OPDA, individually or combined, promote stomatal closure of ABA and allene oxide synthase biosynthetic mutants, albeit most effectively when combined. Using tomato (Solanum lycopersicum) and Brassica napus verified the potency of this combination in inducing stomatal closure in plants other than Arabidopsis. These data have identified drought as a stress signal that uncouples the conversion of 12-OPDA to JA and have revealed 12-OPDA as a drought-responsive regulator of stomatal closure functioning most effectively together with ABA.
Risk of herpes zoster in psoriatic patients undergoing biologic treatment
Authors: Umezawa Yoshinori , Fukuchi Osamu , Ito Toshihiro , Saeki Hidehisa , Nakagawa Hidemi
Published: January 2014

The advent of biologic treatments for psoriasis has many benefits, such as considerably improved efficacy and lower frequency of organ toxicity. While the frequency of organ dysfunction during biologic treatment is considered to be low, the incidence of infection is slightly higher. Patients on biologic treatments are regularly monitored to be able to detect the onset of infection, because there is evidence of an increase in the risk of bacterial and fungal infections during treatment. A total of 144 patients who had received biologic treatment for a year were retrospectively examined. We encountered four cases, including one of 39 patients on infliximab treatment, two of 65 patients on adalimumab treatment and one of 40 patients on ustekinumab treatment, who developed herpes zoster (HZ) within 1 year of starting biologic treatment. Our experience shows that this incidence could be higher than that in the general population, although the data is retrospective. On consideration of previous studies and our own experiences, the risk of HZ occurrence during biologic treatments for psoriasis may increase.
Changing leaf nitrogen and canopy height quantify processes leading to plant and butterfly diversity loss in agricultural landscapes
Authors: Hodgson John G. , Tallowin Jerry , Dennis Roger L. H. , Thompson Ken , Poschlod Peter , Dhanoa Mewa S. , Charles Mike , Jones Glynis , Wilson Peter , Band Stuart R. , Bogaard Amy , Palmer Carol , Carter Gaylynne , Hynd Alison
Published: January 2014

We describe a novel method for quantifying ecosystem drivers that potentially compromise the effectiveness of agri‐environment schemes. We use three sources of data that for many countries are already in the public domain: governmental agricultural statistics, which provide a quantitative assessment of farming intensity in the ‘working landscape’, data on threat status and species distribution for plants and butterflies from conservation agencies and similar bodies and functional traits of plant species abstracted from published data bases.

Changes in land use alter ecosystem processes which in turn modify both biodiversity and representation of functional types at the landscape scale. We interpret functional shifts to quantify important ecological drivers of floristic and faunal change and their causal land use origins.

We illustrate the power of this approach by means of a worked example. We demonstrate that despite conservation policies to counteract them, eutrophication, identified by leaf nitrogen content, and abandonment, correlated with plant canopy height, are still causing biodiversity loss to native higher plants and butterflies in the English countryside.

We use our analyses to suggest how conservation policies can be made more effective and discuss how similar approaches could be applied elsewhere.
Accounting for individual behavioural variation in studies of habitat selection
Authors: Wirsing Aaron J. , Heithaus Michael R.
Published: January 2014

A caribou wearing an animal‐borne video camera (a) and animal‐borne video footage taken from systems deployed on mule deer (Odocoileus hemionus) in north‐central Washington state, USA (b‐d). When paired with tracking technology, animal‐borne video can reveal detailed information about behaviour and environmental features at each location: (b) feeding, (c) vigilant in the open, (d) vigilant in cover, (e) resting in the open. Accordingly, animal‐borne video systems should allow for analyses of habitat selection by individuals in particular behavioural states.

image

A caribou wearing an animal‐borne video camera (a) and animal‐borne video footage taken from systems deployed on mule deer (Odocoileus hemionus) in north‐central Washington state, USA (b‐d). When paired with tracking technology, animal‐borne video can reveal detailed information about behaviour and environmental features at each location: (b) feeding, (c) vigilant in the open, (d) vigilant in cover, (e) resting in the open. Accordingly, animal‐borne video systems should allow for analyses of habitat selection by individuals in particular behavioural states.

In Focus: DeCesare, N.J., Hebblewhite, M., Bradley, M., Hervieux, D., Neufeld, L. & Musiani, M. (2014) . Journal of Animal Ecology, 83, 343–352.

Resource selection is often assumed to confer enhanced fitness, but this assumption is rarely examined. In a study involving woodland caribou subject to grey wolf predation, DeCesare et al. (2014) show that while patterns of selection by caribou did correspond with a fitness proxy (survival probability), individuals did not avoid wolf predation risk to the extent that would minimize mortality. Here, we use the results of this paper as a springboard for discussing the choice of fitness proxies and the need to account for individual behavioural variation in studies of resource selection.
The LonB protease controls membrane lipids composition and is essential for viability in the extremophilic haloarchaeon Haloferax volcanii
Authors: Cerletti Micaela , Martínez María J. , Giménez María I. , Sastre Diego E. , Paggi Roberto A. , De Castro Rosana E.
Published: January 2014

Although homologs of the ATP‐dependent Lon protease exist in all domains of life, the relevance of this protease in archaeal physiology remains a mystery. In this study, we have constructed and phenotypically characterized deletion and conditional lon mutants in the model haloarchaeon Haloferax volcanii to elucidate the role of the unusual membrane‐bound LonB protease in archaea. Hvlon could be deleted from the chromosome only when a copy of the wild type gene was provided in trans suggesting that Lon is essential for survival in this archaeon. Successful complementation of the lethal phenotype of ΔHvlon was attained by expression of the heterologous protease gene Nmlon from the haloalkaliphilic archaeon Natrialba magadii, meaning that the biological function of Lon is conserved in these organisms. Suboptimal cellular levels of Lon protein affected growth rate, cell shape, cell pigmentation, lipid composition and sensitivity to various antibiotics. The contents of bacterioruberins and some polar lipids were increased in the lon mutants suggesting that Lon is linked to maintenance of membrane lipid balance which likely affects cell viability in this archaeon. The phenotypes associated to a membrane‐bound LonB protease mutant were examined for the first time providing insight on the relevance of this protease in archaeal physiology.
Contrasting genomic patterns and infection strategies of two co‐existing Bacteroidetes podovirus genera
Authors: Holmfeldt Karin , Howard‐Varona Cristina , Solonenko Natalie , Sullivan Matthew B.
Published: January 2014

Bacterial viruses (phages) are abundant, ecologically important biological entities. However, our understanding of their impact is limited by model systems that are primarily not well represented in nature, e.g. Enterophages and their hosts. Here, we investigate genomic characteristics and infection strategies among six aquatic Bacteroidetes phages that represent two genera of exceptionally large (∼70–75 kb genome) podoviruses, which were isolated from the same seawater sample using Cellulophaga baltica as host. Quantitative host range studies reveal that these genera have contrasting narrow (specialist) and broad (generalist) host ranges, with one‐step growth curves revealing reduced burst sizes for the generalist phages. Genomic comparisons suggest candidate genes in each genus that might explain this host range variation, as well as provide hypotheses about receptors in the hosts. One generalist phage, φ38:1, was more deeply characterized, as its infection strategy switched from lytic on its original host to either inefficient lytic or lysogenic on an alternative host. If lysogenic, this phage was maintained extrachromosomally in the alternative host and could not be induced by mitomycin C. This work provides fundamental knowledge regarding phage‐host ranges and their genomic drivers while also exploring the ‘host environment’ as a driver for switching phage replication mode.
Defence against antimicrobial peptides: different strategies in Firmicutes
Authors: Revilla‐Guarinos Ainhoa , Gebhard Susanne , Mascher Thorsten , Zúñiga Manuel
Published: January 2014

The Firmicutes constitute a phylum of bacteria that can be found in a wide variety of habitats, from soil to the gastrointestinal tract of animals, where they have to thrive in complex communities. Competition in these communities usually involves the production of compounds such as antimicrobial peptides (AMPs) to eliminate competitor organisms. Animals and plants also produce AMPs to control their associated microbiota. In turn, defence mechanisms have evolved to prevent the action of these compounds. The close association of some Firmicutes with humans as prominent pathogens or commensal organisms has driven a considerable research effort on defence mechanisms used by these bacteria against antimicrobial compounds. This review focuses on the most recent advances on two well‐characterized defence mechanisms against AMPs: the modification of the cell wall by D‐alanylation and the role of peptide antibiotic‐specific adenosine triphosphate‐binding cassette transporters.
Development and validation of the Emergency Department Assessment of Chest pain Score and 2 h accelerated diagnostic protocol
Authors: Than Martin , Flaws Dylan , Sanders Sharon , Doust Jenny , Glasziou Paul , Kline Jeffery , Aldous Sally , Troughton Richard , Reid Christopher , Parsonage William A , Frampton Christopher , Greenslade Jaimi H , Deely Joanne M , Hess Erik , Sadiq Amr Bin , Singleton Rose , Shopland Rosie , Vercoe Laura , Woolhouse‐Williams Morgana , Ardagh Michael , Bossuyt Patrick , Bannister Laura , Cullen Louise
Published: January 2014

Objective

Risk scores and accelerated diagnostic protocols can identify chest pain patients with low risk of major adverse cardiac event who could be discharged early from the ED, saving time and costs. We aimed to derive and validate a chest pain score and accelerated diagnostic protocol (ADP) that could safely increase the proportion of patients suitable for early discharge.

Methods

Logistic regression identified statistical predictors for major adverse cardiac events in a derivation cohort. Statistical coefficients were converted to whole numbers to create a score. Clinician feedback was used to improve the clinical plausibility and the usability of the final score (Emergency Department Assessment of Chest pain Score [EDACS]). EDACS was combined with electrocardiogram results and troponin results at 0 and 2 h to develop an ADP (EDACS‐ADP). The score and EDACS‐ADP were validated and tested for reproducibility in separate cohorts of patients.

Results

In the derivation (n = 1974) and validation (n = 608) cohorts, the EDACS‐ADP classified 42.2% (sensitivity 99.0%, specificity 49.9%) and 51.3% (sensitivity 100.0%, specificity 59.0%) as low risk of major adverse cardiac events, respectively. The intra‐class correlation coefficient for categorisation of patients as low risk was 0.87.

Conclusion

The EDACS‐ADP identified approximately half of the patients presenting to the ED with possible cardiac chest pain as having low risk of short‐term major adverse cardiac events, with high sensitivity. This is a significant improvement on similar, previously reported protocols. The EDACS‐ADP is reproducible and has the potential to make considerable cost reductions to health systems.
The relationship between plasma homocysteine level and HLA‐B51 in patients with Behcet's disease: a case‐control study
Authors: Shadmanfar Soraya , Shahram Farhad , Nadji Abdolhadi , Akhlaghi Maassoumeh , Faezi Seyedeh T. , Sadeghi‐Abdollahi Bahar , Faridar Alireza , Madanchi Nima , Davatchi Fereydoun
Published: January 2014

Background

Various coagulation disorders have been reported to explain hypercoagulability state in Behcet's disease (BD). A possible negative association between human leukocyte antigen (HLA)‐B51 and increased homocysteine level has been suggested in a previous report from Iranian patients with BD. The aim of this study was to find any possible relationship between plasma homocysteine levels and HLA‐B51.

Methods

In a case‐control study, BD patients (fulfilling the new International Criteria for BD) and controls (who had similar clinical symptoms but BD was clinically excluded in them) were included. Mean plasma homocysteine levels measured by enzyme‐linked immunosorbent assay in HLA‐B51 positive and negative individuals both in patients and controls were compared by t‐test, Mann–Whitney test and analysis of variance (F‐test).

Results

Ninety‐six BD patients and 152 controls were recruited. There was no significant difference between HLA‐B51 positive and negative individuals either in the mean plasma homocysteine levels (13.59 ± 9.03 vs. 12.95 ± 4.98 μmol/L, P = 0.514), or in the prevalence of hyperhomocysteinemia (17% vs. 21.4%, P = 0.504). This was true both for BD and control groups. In HLA‐B51 positive and negative BD patients, mean plasma homocysteine levels were 14.29 ± 12.02 and 12.62 ± 4.79 μmol/L, respectively (P = 0.33), and the prevalence of hyperhomocysteinemia was 20.8% versus 19.5% (P = 0.55). In the control group, the mean plasma homocysteine levels in HLA‐B51 positive and negative individuals were 12.85 ± 4.28 and 13.14 ± 5.10 μmol/L, respectively (P = 0.794), and the prevalence of hyperhomocysteinemia was 13% versus 22.1% (P = 0.23). The difference was non‐significant regarding sex (P > 0.71) and disease activity (P > 0.31).

Conclusion

In contrast to our previous report, we found no relationship between plasma homocysteine levels and HLA‐B51 in this study, either in BD or in the control group.