bluuebunny/crossref_metadata_2025 huggingface dataset:
Dual-modality gene reporter for in vivo imaging
Authors: Patrick P. Stephen , Hammersley Jayne , Loizou Louiza , Kettunen Mikko I. , Rodrigues Tiago B. , Hu De-En , Tee Sui-Seng , Hesketh Robin , Lyons Scott K. , Soloviev Dmitry , Lewis David Y. , Aime Silvio , Fulton Sandra M. , Brindle Kevin M.
Published: December 2013

Significance

Gene reporters can be used to track viable cells in vivo and their patterns of gene expression. There have been numerous attempts to develop gene reporters for magnetic resonance imaging (MRI), however these give only modest image contrast and often this is negative, which can be difficult to detect. We describe here a dual-imaging modality reporter that gives intense and positive contrast in magnetic resonance images (up to ∼8× increase in signal), which can also be used with radionuclide imaging, thus combining the sensitivity of radionuclide imaging with the spatial resolution of MRI. The contrast obtained is directly related to the degree of gene expression and is readily reversible, thus allowing longitudinal studies of changes in expression.
Do the Static-99 and Static-99R Perform Similarly for White, Black, and Latino Sexual Offenders?
Authors: Varela JorgeG. , Boccaccini MarcusT. , Murrie DanielC. , Caperton JenniferD. , Gonzalez Ernie
Published: December 2013

The Static-99 is the most widely used sex offender risk assessment measure in the world, but predictive effects for the Static-99 have been relatively low in several U.S. samples, particularly in states with high levels of racial or ethnic diversity. The current study uses data from one of the largest predictive validity studies of Static-99 in the U.S. to examine whether Static-99 and Static-99R scores predict recidivism similarly for White ( n = 912), Black ( n = 411), and Latino ( n = 588) offenders. Although predictive effects with both measures were, at times, large enough to reach statistical significance for White and Black offenders, they were never large enough to reach significance for Latino offenders. On the Static-99R, the measure recommended for use in practice, AUC values ranged from .62 to .69 ( d = .43 to .71) for Black offenders, .59 to .65 ( d = .33 to .56) for White offenders, but only .56 to .58 ( d = .17 to .33) for Latino offenders. Findings have implications for fairness in testing and highlight the need for continued research regarding the potentially moderating role of offender race/ethnicity in risk research.
The Multifaceted Construct of Psychopathy: Association with APD, Clinical, and Criminal Characteristics among Male and Female Inmates
Authors: Warren JanetI. , Burnette Mandi
Published: December 2013

Our study examined the multiple facets of psychopathy and their relationship with personality, mental health and criminal behavior in male and female inmates. At an item level, many Antisocial Personality Disorder (APD) symptoms were not significantly associated with the Affective facet of the PCL-R, yet all were significantly associated with the other three facets of psychopathy. At a diagnostic level, the associations between APD and PCL-R facets were consistent and pervasive, but varied in strength by psychopathy facet. Despite a great deal of overlap between psychopathy and APD, we found some differences in the direction and magnitude of association between APD, psychopathy facets, and criminal and clinical characteristics. Notably, among a forensic sample, psychopathy facets conferred additional risk for antisocial behavior, violence, and other forms of personality pathology, even after adjusting for levels of APD. Future directions for psychopathy research are discussed.
Expert Evidence About Violence Risk Assessment: A Study of Canadian Legal Decisions
Authors: Storey JenniferE. , Campbell ValerieJ. , Hart StephenD.
Published: December 2013

In recent decades the practice of violence risk assessment and use of violence risk assessment instruments has become widespread in the criminal justice system. How are courts reacting to these developments? Herein the findings of a survey of Canadian case law are reported. Using Quick Law 35 cases were systematically identified in which judges commented on expert evidence regarding violence risk. Judicial comments were summarized with respect to evaluator qualifications, assessment procedures used, and presentation of findings and opinions. Findings indicate a wide variety of judicial preferences including the skill and knowledge of the evaluator, the type of information used, the description of findings and procedures, and the applicability of legal rules. Although potentially useful to evaluators caution is urged regarding the incorporation of some judicial preferences.
Analytical Mechanics for Relativity and Quantum Mechanics
Authors: Johns Oliver
Published: December 2013

This book provides an innovative and mathematically sound treatment of the foundations of analytical mechanics, and of the relation of classical mechanics to relativity and quantum theory. A distinguishing feature is its integration of special relativity into the teaching of classical mechanics. After a thorough review of the traditional theory, Part II of the book introduces extended Lagrangian and Hamiltonian methods that treat time as a transformable coordinate rather than the fixed parameter of Newtonian physics. Advanced topics such as covariant Langrangians and Hamiltonians, canonical transformations, and Hamilton-Jacobi methods are simplified by the use of this extended theory. The definition of canonical transformation no longer excludes the Lorentz transformation of special relativity. This is also a book for those who study analytical mechanics to prepare for a critical exploration of quantum mechanics since comparisons to quantum mechanics appear throughout the text. The extended Hamiltonian theory with time as a coordinate is compared to Dirac's formalism of primary phase space constraints. The chapter on relativistic mechanics shows how to use covariant Hamiltonian theory to write the Klein-Gordon and Dirac equations. The chapter on Hamilton-Jacobi theory includes a discussion of the closely related Bohm hidden variable model of quantum mechanics. Classical mechanics itself is presented with an emphasis on methods such as linear vector operators and dyadics that will familiarise the student with similar techniques in quantum theory. Several of the current fundamental problems in theoretical physics require a rethinking of the quantum–classical connection.
Maps between Riemann surfaces
Authors: Donaldson Simon
Published: December 2013

This chapter first presents two simple lemmas from complex analysis which serve as the foundation for the chapter. It then examines monodromy and the Riemann Existence Theorem covering the monodromy of covering maps; compactifying algebraic curves; the Riemann surface of a holomorphic function; and quotients.
Calculus on surfaces
Authors: Donaldson Simon
Published: December 2013

This chapter develops the theory of differential forms on smooth surfaces and Riemann surfaces. The analysis begins with smooth surfaces, covering cotangent spaces and 1-forms; 2-forms and integration. It then turns to de Rham cohomology, which includes cohomology with compact support, and Poincaré duality. The final section discusses calculus on Riemann surfaces, covering decomposition of the 1-forms; the Laplace operator and harmonic functions; and the Dirichlet norm.
Moduli and deformations
Authors: Donaldson Simon
Published: December 2013

This chapter first examines almost-complex structures, Beltrami differentials, and the integrability theorem. It then discusses deformations and cohomology.
Characterization of primate environments through assessment of plant phenology
Authors: Marshall Andrew J. , Wich Serge
Published: December 2013

Plant allocation to reproduction and growth is not evenly spread over time. This variability creates substantial temporal and spatial variation in the availability of plant foods and consequently primate diets, with important implications for primate reproduction, grouping, ranging, and sociality. Accurate characterization of plant phenology is therefore important to many facets of field primatology. This chapter provides an overview of the methods primatologists employ to assess plant phenology. It focuses on practical issues most relevant to field primatologists seeking to characterize the environments inhabited by their study subjects. It discusses the benefits and limitations of various sampling methods, the selection of a sample to monitor, and the scale and scope of sampling. It also considers ways in which phenological data can be described, analyzed, and presented.
Methods in ethnoprimatology: exploring the human–non-human primate interface
Authors: Riley Erin P. , Ellwanger Amanda L.
Published: December 2013

This chapter provides a comprehensive synthesis and evaluation of the appropriate methods to use for a number of ethnoprimatology’s research foci, including the impact of anthropogenic disturbance on a primate’s ecology and behaviour; overlapping resource use between humans and nonhuman primates; and cultural perceptions of primates. It begins with a discussion of logistical issues associated with ethnoprimatological research, including how to navigate different cultural landscapes and deal with multifaceted ethical considerations. It then describes the key research foci of ethnoprimatology and the methods used to accomplish such research. It concludes with a discussion on the future trajectory of ethnoprimatological research.
Social and spatial relationships between primate groups
Authors: Brown Michelle , Crofoot Margaret
Published: December 2013

Studying relationships among primate social groups poses a number of logistical challenges: encounters between groups occur relatively infrequently, interactions are often fast-paced and hectic and, unless all the social groups in a study area are habituated, the presence of human observers may have a significant impact on the outcome of intergroup conflicts. This chapter encourages a more focused approach to the study of intergroup interactions by detailing methods that researchers can use to facilitate inter-specific and inter-site comparisons. It begins by clarifying some of the terms commonly used to describe intergroup relationships, followed by a discussion of observational and experimental methods used to study interactions between primate social groups, and a review of methods for analyzing the impact of intergroup interactions on ranging patterns and space use. It concludes with a brief outline of some important avenues for future research.
ISCB: past–present perspective for the International Society for Computational Biology
Authors: Rost Burkhard
Published: December 2013

Since its establishment in 1997, International Society for Computational Biology (ISCB) has contributed importantly toward advancing the understanding of living systems through computation. The ISCB represents nearly 3000 members working in >70 countries. It has doubled the number of members since 2007. At the same time, the number of meetings organized by the ISCB has increased from two in 2007 to eight in 2013, and the society has cemented many lasting alliances with regional societies and specialist groups. ISCB is ready to grow into a challenging and promising future. The progress over the past 7 years has resulted from the vision, and possibly more importantly, the passion and hard working dedication of many individuals.
Tyk2 is a therapeutic target for psoriasis-like skin inflammation
Authors: Ishizaki Masayuki , Muromoto Ryuta , Akimoto Toshihiko , Sekine Yuichi , Kon Shigeyuki , Diwan Manish , Maeda Hiroaki , Togi Sumihito , Shimoda Kazuya , Oritani Kenji , Matsuda Tadashi
Published: December 2013

Tyrosine kinase 2 (Tyk2), a member of the Jak kinase family, mediates signals triggered by various cytokines, which are related to the pathogenesis of psoriasis. In this study, we investigated the role of Tyk2 in IL-23-induced psoriasis-like skin inflammation. Tyk2−/− mice when injected with IL-23 showed significantly reduced ear skin swelling with epidermal hyperplasia and inflammatory cell infiltration compared with wild-type mice. In addition, Tyk2 deficiency reduced production of pro-inflammatory cytokines and psoriasis-relevant anti-microbial peptides. More noteworthy is that Tyk2 directly regulated IL-22-dependent inflammation and epidermal hyperplasia. Taken together with the inhibition of IL-23-induced inflammation by treatment with neutralizing antibodies against IL-17 or IL-22, Tyk2 participates in both IL-23 and IL-22 signal transduction to mediate psoriasis-like skin inflammation. On the basis of these findings, we demonstrated for the first time that a small-molecule Tyk2 inhibitor significantly inhibited IL-23-induced inflammation and cytokine production in the skin. These observations demonstrate the important role of Tyk2 in experimental skin inflammation and indicate the therapeutic potential of Tyk2 inhibition in human psoriasis.
Characterization of a Tryptophan 2-Monooxygenase Gene from Puccinia graminis f. sp. tritici Involved in Auxin Biosynthesis and Rust Pathogenicity
Authors: Yin Chuntao , Park Jeong-Jin , Gang David R. , Hulbert Scot H.
Published: December 2013

The plant hormone indole-3-acetic acid (IAA) is best known as a regulator of plant growth and development but its production can also affect plant–microbe interactions. Microorganisms, including numerous plant-associated bacteria and several fungi, are also capable of producing IAA. The stem rust fungus Puccinia graminis f. sp. tritici induced wheat plants to accumulate auxin in infected leaf tissue. A gene (Pgt-IaaM) encoding a putative tryptophan 2-monooxygenase, which makes the auxin precursor indole-3-acetamide (IAM), was identified in the P. graminis f. sp. tritici genome and found to be expressed in haustoria cells in infected plant tissue. Transient silencing of the gene in infected wheat plants indicated that it was required for full pathogenicity. Expression of Pgt-IaaM in Arabidopsis caused a typical auxin expression phenotype and promoted susceptibility to the bacterial pathogen Pseudomonas syringae pv. tomato DC3000.
First Report of Rust Caused by Pucciniastrum boehmeriae on Māmaki (Pipturus albidus) in Hawaii
Authors: Demers J. E. , McKemy J. M. , Bushe B. , Conant P. , Kumashira B. , Ko M. , Castlebury L. A.
Published: December 2013

Pipturus albidus (Hook. & Arn.) A. Gray or māmaki is a flowering plant species in the Urticaceae (nettles) endemic to the Hawaiian Islands. Māmaki is a forest and agricultural commodity, as well as a traditional medicinal and fiber crop. In August 2013, leaf rust was observed in Kuristown, Hawaii, on 15 māmaki plants. Infected leaves had vein-delimited chlorotic spots on the adaxial surface and yellow to orange uredinia on the abaxial surface. Uredinia were scattered, minute, pulverulent, subepidermal, and dome-shaped with a central pore, consistent with Pucciniastrum. Urediniospores were 16 to 23 × 10 to 14 μm, echinulate, ellipsoid to pyriform, walls hyaline, 0.5 μm thick, contents pale yellow to bright yellow. No teliospores were observed. A voucher specimen was deposited in the U.S. National Fungus Collections (BPI 892695). The only species of Pucciniastrum previously known on Pipturus, Pucciniastrum pipturi Syd. [syn. Uredo pipturi (Syd.) Hirats. f.], has larger urediniospores, 26.5 to 40.0 × 19.5 to 27.5 μm, and is currently reported from Japan and the Philippines (3). The pathogen was identified as Pucciniastrum boehmeriae (Dietel) Syd. & P. Syd., which infects Boehmeria Jacq., also in the Urticaceae, and has urediniospores that are 18 to 27 × 13 to 18 μm and similar in shape (2). DNA was extracted from uredinial lesions and the nuclear ribosomal internal transcribed spacer (ITS2) region and the 5′ end of large subunit (28S) rDNA were amplified and sequenced following the protocol of Aime (1). The resulting fragment (GenBank Accession No. KF711854) was 100% identical to authenticated and vouchered P. boehmeriae ITS2/28S rDNA sequences (AB221449 to AB221451 and AB221391 to AB221393) (4). Sequences from P. pipturi are not available for comparison, but host family, molecular, and morphological data support the identification of the rust as P. boehmeriae, which is found throughout eastern Asia. To our knowledge, this is the first report of P. boehmeriae on māmaki and the first report in Hawaii on any host. Plant health professionals and regulatory officials can utilize this information to establish survey methods and implement appropriate management practices for this rust disease.

References: (1) M. C. Aime. Mycoscience 47:112, 2006. (2) N. Hiratsuka. Revision of Taxonomy of the Pucciniastreae. Kasai Publishing and Printing, Tokyo, 1958. (3) M. Kakishima and T. Kobayashi. Mycoscience 35:125, 1994. (4) Y.-M. Liang et al. Mycoscience 47:137, 2006.
Hamilton Acute Pain Service Safety Study
Authors: Paul James E. , Buckley Norman , McLean Richard F. , Antoni Karen , Musson David , Kampf Marianne , Buckley Diane , Marcoux Michelle , Frketich Rosemary , Thabane Lehana , Cheng Ji
Published: December 2013

Background:

Although intravenous patient-controlled analgesia opioids and epidural analgesia offer improved analgesia for postoperative patients treated on an acute pain service, these modalities also expose patients to some risk of serious morbidity and even mortality. Root cause analysis, a process for identifying the causal factor(s) that underlie an adverse event, has the potential to identify and address system issues and thereby decrease the chance of recurrence of these complications.

Methods:

This study was designed to compare the incidence of adverse events on an acute pain service in three hospitals, before and after the introduction of a formal root cause analysis process. The “before” cohort included all patients with pain from February 2002 to July 2007. The “after” cohort included all patients with pain from January 2009 to December 2009.

Results:

A total of 35,384 patients were tracked over the 7 yr of this study. The after cohort showed significant reductions in the overall event rate (1.47 vs. 2.35% or 1 in 68 vs. 1 in 42, the rate of respiratory depression (0.41 vs. 0.71%), the rate of severe hypotension (0.78 vs. 1.34%), and the rate of patient-controlled analgesia pump programming errors (0.0 vs. 0.08%). Associated with these results, the incidence of severe pain increased from 6.5 to 10.5%. To achieve these results, 26 unique recommendations were made of which 23 being completed, 1 in progress, and 2 not completed.

Conclusions:

Formal root cause analysis was associated with an improvement in the safety of patients on a pain service. The process was effective in giving credibility to recommendations, but addressing all the action plans proved difficult with available resources.
Maternal antibodies contribute to sex-based difference in hantavirus transmission dynamics
Authors: Kallio Eva R. , Henttonen Heikki , Koskela Esa , Lundkvist Åke , Mappes Tapio , Vapalahti Olli
Published: December 2013

Individuals often differ in their ability to transmit disease and identifying key individuals for transmission is a major issue in epidemiology. Male hosts are often thought to be more important than females for parasite transmission and persistence. However, the role of infectious females, particularly the transient immunity provided to offspring through maternal antibodies (MatAbs), has been neglected in discussions about sex-biased infection transmission. We examined the effect of host sex upon infection dynamics of zoonotic Puumala hantavirus (PUUV) in semi-natural, experimental populations of bank vole (
Myodes glareolus
). Populations were founded with either females or males that were infected with PUUV, whereas the other sex was immunized against PUUV infection. The likelihood of the next generation being infected was lower when the infected founders were females, underlying the putative importance of adult males in PUUV transmission and persistence in host populations. However, we show that this effect probably results from transient immunity that infected females provide to their offspring, rather than any sex-biased transmission efficiency
per se
. Our study proposes a potential contrasting nature of female and male hosts in the transmission dynamics of hantaviruses.
Current concepts: tissue engineering and regenerative medicine applications in the ankle joint
Authors: Correia S. I. , Pereira H. , Silva-Correia J. , Van Dijk C. N. , Espregueira-Mendes J. , Oliveira J. M. , Reis R. L.
Published: December 2013

Tissue engineering and regenerative medicine (TERM) has caused a revolution in present and future trends of medicine and surgery. In different tissues, advanced TERM approaches bring new therapeutic possibilities in general population as well as in young patients and high-level athletes, improving restoration of biological functions and rehabilitation. The mainstream components required to obtain a functional regeneration of tissues may include biodegradable scaffolds, drugs or growth factors and different cell types (either autologous or heterologous) that can be cultured in bioreactor systems (in vitro) prior to implantation into the patient. Particularly in the ankle, which is subject to many different injuries (e.g. acute, chronic, traumatic and degenerative), there is still no definitive and feasible answer to ‘conventional’ methods. This review aims to provide current concepts of TERM applications to ankle injuries under preclinical and/or clinical research applied to skin, tendon, bone and cartilage problems. A particular attention has been given to biomaterial design and scaffold processing with potential use in osteochondral ankle lesions.
Photosynthetic light harvesting: excitons and coherence
Authors: Fassioli Francesca , Dinshaw Rayomond , Arpin Paul C. , Scholes Gregory D.
Published: December 2013

Photosynthesis begins with light harvesting, where specialized pigment–protein complexes transform sunlight into electronic excitations delivered to reaction centres to initiate charge separation. There is evidence that quantum coherence between electronic excited states plays a role in energy transfer. In this review, we discuss how quantum coherence manifests in photosynthetic light harvesting and its implications. We begin by examining the concept of an exciton, an excited electronic state delocalized over several spatially separated molecules, which is the most widely available signature of quantum coherence in light harvesting. We then discuss recent results concerning the possibility that quantum coherence between electronically excited states of donors and acceptors may give rise to a quantum coherent evolution of excitations, modifying the traditional incoherent picture of energy transfer. Key to this (partially) coherent energy transfer appears to be the structure of the environment, in particular the participation of non-equilibrium vibrational modes. We discuss the open questions and controversies regarding quantum coherent energy transfer and how these can be addressed using new experimental techniques.
More than just slippery: the impact of biofilm on the attachment of non-sessile freshwater mayfly larvae
Authors: Ditsche Petra , Michels Jan , Kovalev Alexander , Koop Jochen , Gorb Stanislav
Published: December 2013

While terrestrial insects can usually attach directly to a substrate, for aquatic insects the situation is more complicated owing to the presence of a biofilm on the primary substrates. This important fact has been neither the subject of investigation nor commonly taken into account in the interpretation of functional aspects of attachment in mobile freshwater animals. In this study, we investigate the impact of a biofilm on the attachment of living mayfly larvae. We performedin vivoattachment experiments in a flow channel using different substrates with defined surface roughness. Additionally, we measured friction forces directly generated by dissected tarsal claws on the same substrates. On substrates with smooth or slightly rough surfaces, which have little or no surface irregularities large enough for the claws to grasp, the presence of a biofilm significantly increases the friction force of claws. Consequently, larvae can endure higher flow velocities on these smooth substrates. The opposite effect takes place on rough substrates, where the friction force of claws decreases in the presence of a biofilm. Consequently, a biofilm is a critical ecological structure for these larvae, and other aquatic organisms, not only as a food source but also as a factor influencing attachment ability.
Circadian clocks optimally adapt to sunlight for reliable synchronization
Authors: Hasegawa Yoshihiko , Arita Masanori
Published: December 2013

Circadian oscillation provides selection advantages through synchronization to the daylight cycle. However, a reliable clock must be designed through two conflicting properties: entrainability to synchronize internal time with periodic stimuli such as sunlight, and regularity to oscillate with a precise period. These two aspects do not easily coexist, because better entrainability favours higher sensitivity which may sacrifice regularity. To investigate conditions for satisfying the two properties, we analytically calculated the optimal phase–response curve with a variational method. Our results indicate an existence of a dead zone, i.e. a time period during which input stimuli neither advance nor delay the clock. A dead zone appears only when input stimuli obey the time course of actual solar radiation, but a simple sine curve cannot yield a dead zone. Our calculation demonstrates that every circadian clock with a dead zone is optimally adapted to the daylight cycle.
Lord Justice of Appeal John Fletcher Moulton and explosives production in World War I: ‘the mathematical mind triumphant’
Authors: Van der Kloot William
Published: December 2013

At the end of November 1914 Lord Moulton (1844–1921) became the director of explosives production in the War Office. A 70-year-old jurist may seem an extraordinary choice, but he was an extraordinary man. He was Senior Wrangler at Cambridge, was elected to the Royal Society for research on electricity, and learned about chemistry as a barrister for dye and explosives manufacturers. He assembled an able team of administrators and chemists who designed and managed mammoth new national explosives factories. They could not make enough TNT and picric acid from obtainable precursors, so Moulton persuaded the reluctant armed services to adopt mixtures of TNT and ammonium nitrate, which enabled them to make even more than was needed. In mid-1915 they moved to the new Ministry of Munitions, where they also became responsible for fertilizers and poison gases. In 1917 they produced explosives at a higher rate than was attained in World War II.
Does climate limit species richness by limiting individual species’ ranges?
Authors: Boucher-Lalonde Véronique , Kerr Jeremy T. , Currie David J.
Published: December 2013

Broad-scale geographical variation in species richness is strongly correlated with climate, yet the mechanisms underlying this correlation are still unclear. We test two broad classes of hypotheses to explain this pattern. Bottom-up hypotheses propose that the environment determines individual species’ ranges. Ranges then sum up to yield species richness patterns. Top-down hypotheses propose that the environment limits the number of species that occur in a region, but not which ones. We test these two classes of hypotheses using a natural experiment: seasonal changes in environmental variables and seasonal range shifts of 625 migratory birds in the Americas. We show that richness seasonally tracks the environment. By contrast, individual species’ geographical distributions do not. Rather, species occupy different sets of environmental conditions in two seasons. Our results are inconsistent with extant bottom-up hypotheses. Instead, a top-down mechanism appears to constrain the number of species that can occur in a given region.
Adaptive phenotypic plasticity and local adaptation for temperature tolerance in freshwater zooplankton
Authors: Yampolsky Lev Y. , Schaer Tobias M. M. , Ebert Dieter
Published: December 2013

Many organisms have geographical distributions extending from the tropics to near polar regions or can experience up to 30°C temperature variation within the lifespan of an individual. Two forms of evolutionary adaptation to such wide ranges in ambient temperatures are frequently discussed: local adaptation and phenotypic plasticity. The freshwater planktonic crustaceanDaphnia magna,whose range extends from South Africa to near arctic sites, shows strong phenotypic and genotypic variation in response to temperature. In this study, we useD. magnaclones from 22 populations (one clone per population) ranging from latitude 0° (Kenya) to 66° North (White Sea) to explore the contributions of phenotypic plasticity and local adaptation to high temperature tolerance. Temperature tolerance was studied as knockout time (time until immobilization,Timm) at 37°C in clones acclimatized to either 20°C or 28°C. Acclimatization to 28°C strongly increasedTimm, testifying to adaptive phenotypic plasticity. At the same time,Timmsignificantly correlated with average high temperature at the clones’ sites of origin, suggesting local adaptation. As earlier studies have found that haemoglobin expression contributes to temperature tolerance, we also quantified haemoglobin concentration in experimental animals and found that both acclimatization temperature (AccT) and temperature at the site of origin are positively correlated with haemoglobin concentration. Furthermore,Daphniafrom warmer climates upregulate haemoglobin much more strongly in response to AccT, suggesting local adaptation for plasticity in haemoglobin expression. Our results show that both local adaptation and phenotypic plasticity contribute to temperature tolerance, and elucidate a possible role of haemoglobin in mediating these effects that differs along a cold–warm gradient.
Dietary innovations spurred the diversification of ruminants during the Caenozoic
Authors: Cantalapiedra Juan L. , FitzJohn Richard G. , Kuhn Tyler S. , Fernández Manuel Hernández , DeMiguel Daniel , Azanza Beatriz , Morales Jorge , Mooers Arne Ø.
Published: December 2013

Global climate shifts and ecological flexibility are two major factors that may affect rates of speciation and extinction across clades. Here, we connect past climate to changes in diet and diversification dynamics of ruminant mammals. Using novel versions of Multi-State Speciation and Extinction models, we explore the most likely scenarios for evolutionary transitions among diets in this clade and ask whether ruminant lineages with different feeding styles (browsing, grazing and mixed feeding) underwent differential rates of diversification concomitant with global temperature change. The best model of trait change had transitions from browsers to grazers via mixed feeding, with appreciable rates of transition to and from grazing and mixed feeding. Diversification rates in mixed-feeder and grazer lineages tracked the palaeotemperature curve, exhibiting higher rates during the Miocene thermal maxima. The origination of facultative mixed diet and grazing states may have triggered two adaptive radiations—one during the Oligocene–Miocene transition and the other during Middle-to-Late Miocene. Our estimate of mixed diets for basal lineages of both bovids and cervids is congruent with fossil evidence, while the reconstruction of browser ancestors for some impoverished clades—Giraffidae and Tragulidae—is not. Our results offer model-based neontological support to previous palaeontological findings and fossil-based hypothesis highlighting the importance of dietary innovations—especially mixed feeding—in the success of ruminants during the Neogene.
Can reduced predation offset negative effects of sea louse parasites on chum salmon?
Authors: Peacock Stephanie J. , Connors Brendan M. , Krkošek Martin , Irvine James R. , Lewis Mark A.
Published: December 2013

The impact of parasites on hosts is invariably negative when considered in isolation, but may be complex and unexpected in nature. For example, if parasites make hosts less desirable to predators then gains from reduced predation may offset direct costs of being parasitized. We explore these ideas in the context of sea louse infestations on salmon. In Pacific Canada, sea lice can spread from farmed salmon to migrating juvenile wild salmon. Low numbers of sea lice can cause mortality of juvenile pink and chum salmon. For pink salmon, this has resulted in reduced productivity of river populations exposed to salmon farming. However, for chum salmon, we did not find an effect of sea louse infestations on productivity, despite high statistical power. Motivated by this unexpected result, we used a mathematical model to show how a parasite-induced shift in predation pressure from chum salmon to pink salmon could offset negative direct impacts of sea lice on chum salmon. This shift in predation is proposed to occur because predators show an innate preference for pink salmon prey. This preference may be more easily expressed when sea lice compromise juvenile salmon hosts, making them easier to catch. Our results indicate how the ecological context of host–parasite interactions may dampen, or even reverse, the expected impact of parasites on host populations.
Nucleosome-binding activities within JARID2 and EZH1 regulate the function of PRC2 on chromatin
Authors: Son Jinsook , Shen Steven S. , Margueron Raphael , Reinberg Danny
Published: December 2013

Polycomb-repressive complex 2 (PRC2) comprises specific members of the Polycomb group of epigenetic modulators. PRC2 catalyzes methylation of histone H3 at Lys 27 (H3K27me3) through its Enhancer of zeste (Ezh) constituent, of which there are two mammalian homologs: Ezh1 and Ezh2. Several ancillary factors, including Jarid2, modulate PRC2 function, with Jarid2 facilitating its recruitment to target genes. Jarid2, like Ezh2, is present in poorly differentiated and actively dividing cells, while Ezh1 associates with PRC2 in all cells, including resting cells. We found that Jarid2 exhibits nucleosome-binding activity that contributes to PRC2 stimulation. Moreover, such nucleosome-binding activity is exhibited by PRC2 comprising Ezh1 (PRC2–Ezh1), in contrast to PRC2–Ezh2. The presence of Ezh1 helps to maintain PRC2 occupancy on its target genes in myoblasts where Jarid2 is not expressed. Our findings allow us to propose a model in which PRC2–Ezh2 is important for the de novo establishment of H3K27me3 in dividing cells, whereas PRC2–Ezh1 is required for its maintenance in resting cells.
Anti-adaptors provide multiple modes for regulation of the RssB adaptor protein
Authors: Battesti Aurelia , Hoskins Joel R. , Tong Song , Milanesio Paola , Mann Jessica M. , Kravats Andrea , Tsegaye Yodit M. , Bougdour Alexandre , Wickner Sue , Gottesman Susan
Published: December 2013

RpoS, an RNA polymerase σ factor, controls the response of Escherichia coli and related bacteria to multiple stress responses. During nonstress conditions, RpoS is rapidly degraded by ClpXP, mediated by the adaptor protein RssB, a member of the response regulator family. In response to stress, RpoS degradation ceases. Small anti-adaptor proteins—IraP, IraM, and IraD, each made under a different stress condition—block RpoS degradation. RssB mutants resistant to either IraP or IraM were isolated and analyzed in vivo and in vitro. Each of the anti-adaptors is unique in its interaction with RssB and sensitivity to RssB mutants. One class of mutants defined an RssB N-terminal region close to the phosphorylation site and critical for interaction with IraP but unnecessary for IraM and IraD function. A second class, in the RssB C-terminal PP2C-like domain, led to activation of RssB function. These mutants allowed the response regulator to act in the absence of phosphorylation but did not abolish interaction with anti-adaptors. This class of mutants is broadly resistant to the anti-adaptors and bears similarity to constitutively activated mutants found in a very different PP2C protein. The mutants provide insight into how the anti-adaptors perturb RssB response regulator function and activation.
A-to-I RNA editing occurs at over a hundred million genomic sites, located in a majority of human genes
Authors: Bazak Lily , Haviv Ami , Barak Michal , Jacob-Hirsch Jasmine , Deng Patricia , Zhang Rui , Isaacs Farren J. , Rechavi Gideon , Li Jin Billy , Eisenberg Eli , Levanon Erez Y.
Published: December 2013

RNA molecules transmit the information encoded in the genome and generally reflect its content. Adenosine-to-inosine (A-to-I) RNA editing by ADAR proteins converts a genomically encoded adenosine into inosine. It is known that most RNA editing in human takes place in the primate-specific Alu sequences, but the extent of this phenomenon and its effect on transcriptome diversity are not yet clear. Here, we analyzed large-scale RNA-seq data and detected ∼1.6 million editing sites. As detection sensitivity increases with sequencing coverage, we performed ultradeep sequencing of selected Alu sequences and showed that the scope of editing is much larger than anticipated. We found that virtually all adenosines within Alu repeats that form double-stranded RNA undergo A-to-I editing, although most sites exhibit editing at only low levels (<1%). Moreover, using high coverage sequencing, we observed editing of transcripts resulting from residual antisense expression, doubling the number of edited sites in the human genome. Based on bioinformatic analyses and deep targeted sequencing, we estimate that there are over 100 million human Alu RNA editing sites, located in the majority of human genes. These findings set the stage for exploring how this primate-specific massive diversification of the transcriptome is utilized.
Overexpression of an Isoprenyl Diphosphate Synthase in Spruce Leads to Unexpected Terpene Diversion Products That Function in Plant Defense
Authors: Nagel Raimund , Berasategui Aileen , Paetz Christian , Gershenzon Jonathan , Schmidt Axel
Published: December 2013

Spruce (Picea spp.) and other conifers employ terpenoid-based oleoresin as part of their defense against herbivores and pathogens. The short-chain isoprenyl diphosphate synthases (IDS) are situated at critical branch points in terpene biosynthesis, producing the precursors of the different terpenoid classes. To determine the role of IDS and to create altered terpene phenotypes for assessing the defensive role of terpenoids, we overexpressed a bifunctional spruce IDS, a geranyl diphosphate and geranylgeranyl diphosphate synthase in white spruce (Picea glauca) saplings. While transcript level (350-fold), enzyme activity level (7-fold), and in planta geranyl diphosphate and geranylgeranyl diphosphate levels (4- to 8-fold) were significantly increased in the needles of transgenic plants, there was no increase in the major monoterpenes and diterpene acids of the resin and no change in primary isoprenoids, such as sterols, chlorophylls, and carotenoids. Instead, large amounts of geranylgeranyl fatty acid esters, known from various gymnosperm and angiosperm plant species, accumulated in needles and were shown to act defensively in reducing the performance of larvae of the nun moth (Lymantria monacha), a conifer pest in Eurasia. These results show the impact of overexpression of an IDS and the defensive role of an unexpected accumulation product of terpenoid biosynthesis with the potential for a broader function in plant protection.
An empirical study of the impact of lean construction techniques on sustainable construction in the UK
Authors: Ogunbiyi Oyedolapo , Goulding Jack Steven , Oladapo Adebayo
Published: December 2013

Purpose

– The contribution of lean construction techniques in sustainable construction cannot be over emphasised, as sustainable development is now enshrined in government policy. In addition, lean construction is now faced with the challenges of sustainable development, continuous improvement, waste elimination, a stronger user focus, increased value for money along with high quality management of projects and supply chains, and improved communications. This paper presents an exploratory study from extant literature and the results of the use of questionnaire survey among construction participants to explore the contribution of implementing lean construction techniques in sustainable construction.

Design/methodology/approach

– Surveys of UK-based construction professional were conducted. The data collected were analysed with SPSS 19.0 version software using the percentile method, Cronbach ' sαreliability test, Kruskal Wallis test, Kendall ' s coefficient of concordance and one samplet-test.

Findings

– Results from this study indicate that there are several benefits associated with implementation of lean construction and sustainable construction. The overall perspective of professionals within the construction industry, according to questionnaire survey, shows that benefits such as improved corporate image and sustainable competitive advantage, improved process flow and productivity, improvement in environmental quality and increased compliance with customer ' s expectations are realised following integration of principles of lean construction and sustainable construction within construction industry. Just-in-time, visualisation tool, value analysis, daily huddle meetings and value stream mapping are the most common lean tools/techniques for enabling sustainability. This study also identified several areas of linkage between lean and sustainability such as waste reduction, environmental management, value maximisation, and health and safety improvement among others.

Originality/value

– The originality of this paper lies in its consideration of lean construction principles to better understand its impact on sustainable construction. This research contributes to the awareness of the benefits that can be derived from the implementation of lean construction in sustainable construction within the construction industry.
Future perspectives on product data management in building information modeling
Authors: Palos Salla , Kiviniemi Arto , Kuusisto Johanna
Published: December 2013

Purpose

– It has been argued that product data libraries have the potential to improve global real-estate development and increase productivity. Product data libraries provide the basis to support diverse national classification systems and different languages. The aim of this paper is to identify product data management (PDM) systematics and recommend future development needs to building product libraries, focusing on the functional shortcomings and data processing deficiencies found in the current libraries.

Design/methodology/approach

– A literature review of state-of-the-art practices of BIM within the construction industry was conducted including product libraries, supply chains, guidelines, industry tools and practices, and general use of BIM. Findings from the literature review were complemented with insights from the academia and industry by obtaining data through focused interviews with experts who were chosen based on their prestige and reference.

Findings

– As a result of the studies performed for this article, roadmaps are proposed for product library implementation globally. The role of standardization in implementing BIM-compatible product libraries is highlighted.

Originality/value

– This article covers the state-of-the-art practices of PDM in BIM libraries, which is useful for the development of coherent BIM libraries for the AEC industry worldwide.
Integrating risk management in the innovation project
Authors: Bowers John , Khorakian Alireza
Published: December 2013

Purpose

– While innovation has many similarities to other forms of projects it is characterised by a high failure rate and the need to stimulate creativity. More explicit risk management could help in achieving success in innovation projects. However, too much or inappropriate risk management might stifle the creativity that is core to innovation. So, what project risk management should be applied and where in the innovation project?

Design/methodology/approach

– A theoretical framework is proposed which combines the generic innovation process with project risk management. The framework was used to analyse the current attitudes to managing innovation risk in a series of companies.

Findings

– The decision points of the stage-gate innovation process model provide an effective interface for incorporating project risk concepts. The general concepts appear most relevant to innovation management though it is useful to customise them to emphasise the particular characteristics of innovation projects. The experience of using the resultant combined model in a number of diverse case studies indicates the relevance of the model in understanding attitudes towards risk management in innovation. The analysis of the case study companies suggested that risk management needs to be applied in differential manner: simple, unobtrusive techniques early in the innovation life cycle with more substantial, quantitative methods being considered for later stages.

Research limitations/implications

– It would be useful to extend this research by examining more case studies from other countries and industries.

Practical implications

– The combined innovation and risk management model provides a framework that diverse companies can appreciate. The framework offers a basis for discussing the most appropriate form of risk management in different innovation-based industries.

Originality/value

– Although there are many separate models for innovation and project risk management described in the literature, there is very little discussion about explicitly combining these theories. This paper aims to help fill this gap in the knowledge.
Influence of risk on technology adoption: inertia strategy in the space industry
Authors: Dos Santos Paulino Victor
Published: December 2013

Purpose

– The topic of the risk associated with innovation is being investigated through the influence of technological risk on technology adoption.

Design/methodology/approach

– The paper analyses the dynamics of technology adoption in high technology products thanks to several regressions. The paper uses data gathered from a major European space integrator.

Findings

– The paper shows that a firm may implement a reliability-based inertia strategy under a specific context. This type of inertia strategy is rational and leads a firm to limit the adoption of new technologies and favours the reuse of proven technologies. This strategy is relevant to facing a risk of decrease in technical reliability.

Research limitations/implications

– While the space industry displays some similarities with other capital good industries, it remains specific compared to mass production industries. The current paper should be considered as a preliminary research that aims at structuring the notion of inertia strategy.

Practical implications

– In order to increase the commercial demand, the paper proposes that satellite manufactures adopt more intensive reliability-based inertia strategy and institutional demand asks for less experimental satellites.

Originality/value

– This paper contributes to show that delays in technology adoption should not systematically be regarded as a weakness. Implementing a strategy that aims at slowing down technology adoption may sometimes improve firm survival. The paper also intends to provide a new insight to the paradoxical nature of change.