bluuebunny/crossref_metadata_2025 huggingface dataset:
Phylogenetic eigenvectors and nonstationarity in the evolution of theropod dinosaur skulls
Authors: Diniz‐Filho J. A. F. , Alves D. M. C. C. , Villalobos F. , Sakamoto M. , Brusatte S. L. , Bini L. M.
Published: May 2015

Despite the long‐standing interest in nonstationarity of both phenotypic evolution and diversification rates, only recently have methods been developed to study this property. Here, we propose a methodological expansion of the phylogenetic signal‐representation (PSR) curve based on phylogenetic eigenvectors to test for nonstationarity. ThePSRcurve is built by plotting the coefficients of determinationR2from phylogenetic eigenvector regression (PVR) models increasing the number of phylogenetic eigenvectors against the accumulated eigenvalues. ThePSRcurve is linear under a stationary model of trait evolution (i.e. the Brownian motion model). Here we describe the distribution of shifts in the modelsR2and used a randomization procedure to compare observed and simulated shifts along thePSRcurve, which allowed detecting nonstationarity in trait evolution. As an applied example, we show that the main evolutionary pattern of variation in the theropod dinosaur skull was nonstationary, with a significant shift in evolutionary rates in derived oviraptorosaurs, an aberrant group of mostly toothless, crested, birdlike theropods. This result is also supported by a recently proposed Bayesian‐based method (AUTEUR). A significant deviation betweenCeratosaurusandLimusaurusterminal branches was also detected. We purport that our new approach is a valuable tool for evolutionary biologists, owing to its simplicity, flexibility and comprehensiveness.
An audit of nursing reports for First‐Tier Tribunals in a secure inpatient service
Authors: Haw C.
Published: May 2015

Accessible Summary

Very little research has been conducted into the role of nurses in relation to patients' mental health tribunals (known in some countries as review panels).

In England nurses are playing an increasingly important role in giving evidence at tribunals and, since October 2013, are required to provide much more detailed written reports than previously.

This is the first published study to examine the content of nursing tribunal reports.

Overall, the quality of nursing reports was patchy and not as good as those of psychiatrists or social workers, but there was improvement when the audit was repeated.

Writing reports for tribunals is a comparatively new and perhaps unfamiliar requirement for nursing staff.

Nurses need training in report writing and protected time and a quiet area to write reports. Providing these things is a real challenge on busy inpatient wards.

In October 2013, the Tribunals Judiciary of England issued a new practice direction stipulating how tribunal reports should be completed. This paper aimed to study the quality of nursing tribunal reports in a secure inpatient service before and after the introduction of the latest practice direction and the issuing of a local template to aid report writing. A total of 160 reports (80 written in 2013 and 80 in 2014) were scored on the presence of 24 key items derived from the latest practice direction. The quality of nursing reports improved in the re‐audit from an average of 36.3% of key items present to 51.3% but still lagged behind that of medical and social circumstances reports. Even in the second audit, few reports were signed or commented on why the patient should remain detained. Report length increased from a mean of 2.9 to 4.0 pages but only 27.5% of reports used the template despite widespread publicity. Use of the template resulted in better quality reports. Among other interventions, a training programme in report writing is now underway to assist nurses with meeting the new practice direction requirements. Nurses also need supervision, protected time and a quiet area for report writing.
Evaluation of the ventro 20° rostral‐dorsocaudal oblique radiographic projection for the investigation of canine nasal disease
Authors: Finck M. , Durand A. , Hammond G. , Sullivan M. , King A.
Published: May 2015

OBJECTIVE

To assess the ventro 20° rostral‐dorsocaudal oblique projection for canine nasal disease as an alternative to the dorsoventral intra‐oral view.

MATERIALS AND METHODS

Thirty‐one dogs with nasal disease underwent radiography and computed tomography with a final diagnosis of underlying cause achieved through rhinoscopy, biopsy or cytology. Three independent observers, blinded to diagnosis, reviewed the nasal radiographs on two separate occasions. Intra‐ and inter‐observer agreement and level of confidence on radiographic diagnosis were evaluated and radiographic diagnosis was compared with computed tomography and definitive diagnosis.

RESULTS

The ventro 20° rostral‐dorsocaudal oblique projection of canine nasal cavities was feasible in anaesthetised dogs and gave diagnostic quality images in most dogs. Assessment of this view showed moderate to substantial agreement with computed tomography diagnosis but gave lower confidence in diagnosis. Interpretation of this radiographic projection had substantial to almost perfect repeatability but moderate reproducibility.

CLINICAL SIGNIFICANCE

The ventro 20° rostral‐dorsocaudal oblique projection may be used as a valuable initial screening tool for canine nasal pathology in practices without access to advanced imaging, although computed tomography is still likely to provide greater diagnostic information.
So Many Recalls, So Little Research: A Review of the Literature and Road map for Future Research
Authors: Wowak Kaitlin D. , Boone Christopher A.
Published: May 2015

Although the literature on product recalls is informative, our understanding of these events is still in its infancy. To promote and guide future research in this nascent area, we engaged in a two‐step process that included a systematic review and categorization of product recall‐related literature and interviews with executives from along the entire supply chain. By oscillating between findings in the literature and themes that emerged during our interactions with executives, we discovered several research opportunities that have yet to be systematically examined by scholars. We also highlight four underutilized theories in supply chain management research—upper echelons theory, punctuated equilibrium theory, enactment theory, and justice theory—that could help guide future research in this area. For managers, this study reveals insights related to four key aspects of product recalls: (1) recall precursors (factors that may lead to recalls); (2) the recall process; (3) the impact of recalls; and (4) mitigation approaches (mechanisms firms can employ to reduce the impact of recalls). For scholars, our study identifies several emergent research opportunities and theoretical lenses in the same four areas and thus serves as a road map for future product recall research.
Tagore and Gandhi: The Way of the Artist and the Way of the Ascetic
Authors: Grbić Igor
Published: May 2015

Rabindranath Tagore and Mahatma Gandhi were the most world‐famous Indians of their time. Their relationship was one of great mutual respect, but it was also troubled by clashes of two very disparate sensitivities and spiritual frames. The subject has been noticed and explored by authors dealing with either of the two grand men. The present paper aims, however, at showing that not only were Tagore and Gandhi as different as they were but also that the various ways of the spirit came close to be concentrated in the two of them, making each one of its two poles: Gandhi stood for the spirit manifesting itself as renunciation, constant negation, the Apollonian − even Thanatotic − logos sustained by a strictly religious mind, while Tagore incarnated the spirit operating as the all‐embracing force of eternal affirmation, the Dionysian eros upheld by an unchecked artistic imagination. The opposition is mythically paradigmatic: one can sense in it another enactment of the irreconcilable strife between the will to create and explode towards proliferation and the will to annihilate and implode into nullity. It is the via positiva versus via negativa. At the deepest level, their ends overlap perfectly.
Was Tagore a Feminist? Re‐evaluating Selected Fiction and Their Film Adaptations
Authors: Mandal Somdatta
Published: May 2015

This paper focuses on the stories of Tagore that profess strong feminist values and also their representations in certain cinematic adaptations of the same. Although Tagore was a visionary and believed in many ideas that were much ahead of his time, the paper discusses how Tagore's feminist beliefs and his treatment of women characters were not consistent throughout his writing career. As far as the point of view of women was concerned, it moved between conservatism and radicalism, and so, in some stories, the marginalized woman finds a voice and challenges her position, while in others, she is compelled to conform to patriarchal boundaries. As this study shows, the film adaptations in Bengali cinema that continue to be inspired by Tagore's fiction illustrate the modern day relevance of Tagore's concerns and ideas in relation to a woman's position in society and the challenges she offers to social expectations of her gendered role and at the same time also embodies the ambivalent attitude to women that is evident in society today.
Towards a Tagorean Utopia: From Rural Reconstruction to Transition Towns
Authors: Marsh Christine
Published: May 2015

Rabindranath Tagore was ‘a poet who was an indefatigable man of action’ (Uma Das Gupta, A Biography ix). Over eighty years ago, Tagore saw the world environment collapsing due to ‘an epidemic of voracity that has infected the total area of civilization’ (‘City and Village’ 310). His practical activities involved a progressive school and university, integrated with research and assistance concerned with village revival and rebuilding the local economy and community. It is timely to re‐examine what Tagore tried to achieve. Information about these initiatives, together with a study of Tagore's insights as expressed in his essays, those written in English and those translated from Bengali, can yield an understanding of the form of local and global community he envisaged and tried to bring into being. That vision is compatible with the aims and development of the Transition Movement, which is motivated by a recognition that the capitalist machine is running out of control, to the detriment of planet and people. This reading of Tagore reveals that, in effect, he advocated a withdrawal from the capitalist system, ‘back to the future’, not to a rustic existence bound by rigid cultural constraints, but to local cooperative farming and industry, progressive education and renewed culture and creativity.
Rabindranath Tagore's Global Vision
Authors: Fraser Bashabi
Published: May 2015

This ‘Introduction’ to a special issue on Rabindranath Tagore affirms his position as an Indian Renaissance man and assesses his stature as a leading world writer, philosopher, educationist, environmentalist, rural reconstructionist, activist and pragmatist who embodies India's ‘modern consciousness’ (Nandy, ). Tagore's international impact was phenomenal in his lifetime and his global vision continues to have universal resonance today. This project seeks to move beyond the initial response to Tagore as an ‘Eastern Sage’ on the world stage to Tagore as the knowledgeable intellectual (Bhattacharya, ) who challenges the binarism of the East and the West and seeks to facilitate a dialogue between disparate nations and peoples. Tagore's implicit belief in humankind's creative principle is a confirmation of his vision of the ‘universal man’ prevailing in spite of the conflict of his times. A state‐of‐the field account is offered as the continuing interest amongst scholars, researchers and translators of Tagore is documented and the compilation of articles illustrates an impetus to Tagore Studies that is bound to endure beyond ‘a hundred years from now’ (Tagore, 1896).
Co‐operation and Co‐operatives: The global dilemmas of Tagore's Rural Democracy
Authors: Datta Pradip Kumar
Published: May 2015

Rabindranath Tagore experimented with co‐operatives as part of his commitment to the ethic of co‐operation that, he believed, could rescue the world from self‐destructive competition. Co‐operatives were an important part of the program of rural reconstruction at Sriniketan, a part of Viswabharati. Tagore's co‐operatives seek to activate a social ethic that can establish symmetrical relationships within and between the global, national, and local. They impinge on the desire for a substantive culture of democracy. Tagore's efforts are undertaken as part of a global network of ideas and practices, especially those formed in Ireland. Sriniketan gives practical shape to this co‐operative program and in doing so, runs into problems. These are actually profound dilemmas that have major implications for an alternate vision of a shared world.
Random mutagenesis of the nucleotide‐binding domain of NRC1 (NB‐LRR Required for Hypersensitive Response‐Associated Cell Death‐1), a downstream signalling nucleotide‐binding, leucine‐rich repeat (NB‐LRR) protein, identifies gain‐of‐function mutations in the nucleotide‐binding pocket
Authors: Sueldo Daniela J. , Shimels Mahdere , Spiridon Laurentiu N. , Caldararu Octav , Petrescu Andrei‐Jose , Joosten Matthieu H. A. J. , Tameling Wladimir I. L.
Published: May 2015

Plant nucleotide‐binding, leucine‐rich repeat (NB‐LRR) proteins confer immunity to pathogens possessing the corresponding avirulence proteins. Activation of NB‐LRR proteins is often associated with induction of the hypersensitive response (HR), a form of programmed cell death.

NRC1 (NB‐LRR Required for HR‐Associated Cell Death‐1) is a tomato (Solanum lycopersicum) NB‐LRR protein that participates in the signalling cascade leading to resistance to the pathogens Cladosporium fulvum and Verticillium dahliae.

To identify mutations in NRC1 that cause increased signalling activity, we generated a random library of NRC1 variants mutated in their nucleotide‐binding domain and screened them for the ability to induce an elicitor‐independent HR in Nicotiana tabacum. Screening of 1920 clones retrieved 11 gain‐of‐function mutants, with 10 of them caused by a single amino acid substitution.

All substitutions are located in or very close to highly conserved motifs within the nucleotide‐binding domain, suggesting modulation of the signalling activity of NRC1. Three‐dimensional modelling of the nucleotide‐binding domain of NRC1 revealed that the targeted residues are centred around the bound nucleotide. Our mutational approach has generated a wide set of novel gain‐of‐function mutations in NRC1 and provides insight into how the activity of this NB‐LRR is regulated.
Self‐Legislation and Self‐Command in Kant's Ethics
Authors: Wilson Eric Entrican
Published: May 2015

In his later writings, Kant distinguishes between autonomy and self‐mastery or self‐command. My article explains the relation between these two ideas, both of which are integral to his understanding of moral agency and the pursuit of virtue. I point to problems with other interpretations of this relation and offer an alternative. On my view, self‐command is a condition or state achieved by those agents who become proficient at solving problems presented by the passions. Such agents are able to stick to the results of self‐legislation over time and thereby achieve a form of temporally extended freedom.
Surgical Site Infection 18 Months Following Intrathecal Pump Placement Secondary to an Asymptomatic Bowel Injury
Authors: Deibert Christopher P. , Gandhoke Gurpreet S. , Forsythe Raquel M. , Moossy John J.
Published: May 2015

Surgical site infections following the implantation of intrathecal drug delivery systems typically present during the first 1 to 2 months following surgery. Surgical site infections occurring outside of this window are rare entities and require special attention to identify the source or underlying cause. In this report, we present a case of pump pocket infection 18 months following implantation due to an asymptomatic and unrecognized bowel injury associated with the catheter. This case highlights the need for a thorough evaluation in a patient with suspected infections more than 2 months after surgery to ensure adequate treatment.
Explaining and mapping total phosphorus content in French topsoils
Authors: Delmas M. , Saby N. , Arrouays D. , Dupas R. , Lemercier B. , Pellerin S. , Gascuel‐Odoux C.
Published: May 2015

Total phosphorus (TP) build‐up in agricultural soils represents both a threat to aquatic ecosystems and a valuable resource for future crop production, given the context of increasing food demand combined with the rapid depletion of the world's phosphate reserves. Therefore, it is crucially important (i) to identify the main factors controlling topsoil TP and (ii) to develop methods for mapping its spatial distribution. Multiple linear regression models were used with two distinct approaches to calculate TP and covariates linked to the P cycle. Firstly, covariates were selected from the Réseau de Mesures de la Qualité des Sols database, the French soil monitoring network, which consists of soil samples collected from 2158 sites on a 16‐km regular grid. Secondly, covariates were selected to map TP from spatially exhaustive datasets in France. The first approach explains 80% of variability in topsoil TP. The variables selected are linked to the autochthonous origin of P (parent material), to allochthonous origin (organic carbon and nitrogen contents) and to the retention capacity of soil (Al, Fe, Ca and clay contents). The predicted map obtained from the second approach provides a mean TP of 0.76 g/kg. This study demonstrates that creating national scale maps of TP, based on detailed soil sampling and many variables, is feasible and can be used to model the P cycle and P transfer processes. Such maps can be used in P erosion and transfer models over river basins, and therefore to predict P exports to surface waters.
Operational characteristics of a graphene-based electron field emitter
Authors: Bocharov Gregory S. , Eletskii Alexander V. , Kvashnin Dmitry G. , Chernozatonskii Leonid A.
Published: May 2015

The electron work function for graphene fragments with pure edges and those functionalized by hydrogen atoms is calculated using the density functional theory method, and the obtained results are used to evaluate the current–voltage (I-V) characteristics of a vertically aligned rectangular graphene sheet. The calculated results of the electric potential spatial distribution in the vicinity of the graphene layer indicates a highly inhomogeneous distribution of the electric field amplification factor along its external edge, so that the maximum amplification occurs near the vertices of the layer. Such an inhomogeneity promotes a highly inhomogeneous distribution of the emission current along the graphene layer edge. At relatively low voltages, the emission is provided mainly by the region near the vertices of the layer, where the relative contribution of this region decreases with an increase in applied voltage. This effect manifests itself in a deviation of the emission I-V characteristics from the classical Fowler–Nordheim dependence, a deviation that has been observed in recent experiments. This study shows the possibility of decreasing the degree of emission current inhomogeneity along the graphene layer edge by giving it a rounded shape.
Biomechanical Analysis of a Change-of-Direction Task in College Soccer Players
Authors: Condello Giancarlo , Kernozek Thomas W. , Tessitore Antonio , Foster Carl
Published: May 2015

This study aimed to investigate biomechanical parameters during a change-of-direction task in college soccer players. Fourteen male and 12 female players performed a 10-m sprint with a 60° change of direction at 5 m. Vertical and mediolateral groundreaction force (GRF) and contact time were measured by having the subjects run in both directions while contacting a force plate with either their preferred (kicking) or nonpreferred leg. Using the midpoint between 2 pelvic markers, further parameters were evaluated: performance cutting angle and horizontal distance. Relationships between parameters, sex, and leg preference were analyzed. Significant correlations emerged between vertical and mediolateral GRF (r = .660–.909) and between contact time and performance cutting angle (r = –.598 to –.793). Sex differences were found for mediolateral GRF (P = .005), performance cutting angle (P = .043), and horizontal distance (P = .020). Leg differences were observed for vertical GRF (P = .029), performance cutting angle (P = .011), and horizontal distance (P = .012). This study showed that a sharper change of direction corresponded to a longer contact time, while no relationships were found with GRF. Moreover, measuring the angle revealed that the real path traveled was different from the theoretical one, highlighting the performance of sharper or more rounded execution. In conclusion, this study showed that specific biomechanical measurements can provide details about the execution of a change of direction, highlighting the ability of the nonpreferred leg to perform better directional changes.
Examining Impulse-Variability in Kicking
Authors: Chappell Andrew , Molina Sergio L. , McKibben Jonathon , Stodden David F.
Published: May 2015

This study examined variability in kicking speed and spatial accuracy to test the impulse-variability theory prediction of an inverted-U function and the speed-accuracy trade-off. Twenty-eight 18- to 25-year-old adults kicked a playground ball at various percentages (50–100%) of their maximum speed at a wall target. Speed variability and spatial error were analyzed using repeated-measures ANOVA with built-in polynomial contrasts. Results indicated a significant inverse linear trajectory for speed variability (p < .001, η2= .345) where 50% and 60% maximum speed had significantly higher variability than the 100% condition. A significant quadratic fit was found for spatial error scores of mean radial error (p < .0001, η2 = .474) and subject-centroid radial error (p < .0001, η2 = .453). Findings suggest variability and accuracy of multijoint, ballistic skill performance may not follow the general principles of impulse-variability theory or the speed-accuracy trade-off.
Syllable Repetition vs. Finger Tapping: Aspects of Motor Timing in 100 Healthy Adults
Authors: Sundqvist Maria , Johnels Jakob Åsberg , Lindh Jonas , Laakso Katja , Hartelius Lena
Published: May 2015

In this study we systematically compared syllable repetition and finger tapping in healthy adults, and explored possible impacts of tempi, metronome, musical experience, and age on motor timing ability. One hundred healthy adults used finger-tapping and syllable repetition to perform an isochronous pulse in three different tempi, with and without a metronome. Results showed that the motor timing was more accurate with finger tapping than with syllable repetition in the slowest tempo, and the motor timing ability was better with the metronome than without. Persons with musical experience showed better motor timing accuracy than persons without such experience, and the timing asynchrony increased with increasing age. The slowest tempo 90 bpm posed extra challenges to the participants. We speculate that this pattern reflects the fact that the slow tempo lies outside the 3–8 Hz syllable rate of natural speech, which in turn has been linked to theta-based oscillations in the brain.
Radiolabeled Antibodies for Therapy of Infectious Diseases
Authors: Dadachova Ekaterina , Casadevall Arturo
Published: May 2015

Novel approaches to the treatment of infectious diseases are urgently needed. This need has resulted in renewing the interest in antibodies for therapy of infectious diseases. Radioimmunotherapy (RIT) is a cancer treatment modality that utilizes radiolabeled monoclonal antibodies. During the last decade we have translated RIT into the field of experimental fungal, bacterial, and HIV infections. In addition, successful proof of principle experiments with radiolabeled pan-antibodies that bind to antigens shared by major pathogenic fungi have been performed
in vitro
. The armamentarium of pan-antibodies would result in reducing our dependence on microorganism-specific antibodies and thus would speed up the development of RIT for infections. We believe that the time is ripe for deploying RIT in the clinic to combat infectious diseases.
Division of Labor in Biofilms: the Ecology of Cell Differentiation
Authors: van Gestel Jordi , Vlamakis Hera , Kolter Roberto
Published: May 2015

The dense aggregation of cells on a surface, as seen in biofilms, inevitably results in both environmental and cellular heterogeneity. For example, nutrient gradients can trigger cells to differentiate into various phenotypic states. Not only do cells adapt physiologically to the local environmental conditions, but they also differentiate into cell types that interact with each other. This allows for task differentiation and, hence, the division of labor. In this article, we focus on cell differentiation and the division of labor in three bacterial species:
Myxococcus xanthus, Bacillus subtilis
, and
Pseudomonas aeruginosa
. During biofilm formation each of these species differentiates into distinct cell types, in some cases leading to cooperative interactions. The division of labor and the cooperative interactions between cell types are assumed to yield an emergent ecological benefit. Yet in most cases the ecological benefits have yet to be elucidated. A notable exception is
M. xanthus
, in which cell differentiation within fruiting bodies facilitates the dispersal of spores. We argue that the ecological benefits of the division of labor might best be understood when we consider the dynamic nature of both biofilm formation and degradation.
P Transposable Elements in
Drosophila
and other Eukaryotic Organisms
Authors: Majumdar* Sharmistha , Rio Donald C.
Published: May 2015

P transposable elements were discovered in Drosophila as the causative agents of a syndrome of genetic traits called hybrid dysgenesis. Hybrid dysgenesis exhibits a unique pattern of maternal inheritance linked to the germline-specific small RNA piwi-interacting (piRNA) pathway. The use of P transposable elements as vectors for gene transfer and as genetic tools revolutionized the field of Drosophila molecular genetics. P element transposons have served as a useful model to investigate mechanisms of cut-and-paste transposition in eukaryotes. Biochemical studies have revealed new and unexpected insights into how eukaryotic DNA-based transposons are mobilized. For example, the P element transposase makes unusual 17nt-3′ extended double-strand DNA breaks at the transposon termini and uses guanosine triphosphate (GTP) as a cofactor to promote synapsis of the two transposon ends early in the transposition pathway. The N-terminal DNA binding domain of the P element transposase, called a THAP domain, contains a C
2
CH zinc-coordinating motif and is the founding member of a large family of animal-specific site-specific DNA binding proteins. Over the past decade genome sequencing efforts have revealed the presence of P element-like transposable elements or P element transposase-like genes (called THAP9) in many eukaryotic genomes, including vertebrates, such as primates including humans, zebrafish and Xenopus, as well as the human parasite
Trichomonas vaginalis
, the sea squirt
Ciona
, sea urchin and hydra. Surprisingly, the human and zebrafish P element transposase-related THAP9 genes promote transposition of the
Drosophila
P element transposon DNA in human and
Drosophila
cells, indicating that the THAP9 genes encode active P element “transposase” proteins.
Mating-type Gene Switching in
Saccharomyces cerevisiae
Authors: Lee Cheng-Sheng , Haber James E.
Published: May 2015

The budding yeast
Saccharomyces cerevisiae
has two alternative mating types designated
MAT
a
and
MAT
α. These are distinguished by about 700 bp of unique sequences, Y
a
or Yα, including divergent promoter sequences and part of the open reading frames of genes that regulate mating phenotype. Homothallic budding yeast, carrying an active HO endonuclease gene,
HO
, can switch mating type through a recombination process known as gene conversion, in which a site-specific double-strand break (DSB) created immediately adjacent to the Y region results in replacement of the Y sequences with a copy of the opposite mating type information, which is harbored in one of two heterochromatic donor loci,
HML
α or
HMR
a
. HO gene expression is tightly regulated to ensure that only half of the cells in a lineage switch to the opposite
MAT
allele, thus promoting conjugation and diploid formation. Study of the silencing of these loci has provided a great deal of information about the role of the Sir2 histone deacetylase and its associated Sir3 and Sir4 proteins in creating heterochromatic regions.
MAT
switching has been examined in great detail to learn about the steps in homologous recombination.
MAT
switching is remarkably directional, with
MAT
a
recombining preferentially with
HML
α and
MAT
α using
HMR
a
. Donor preference is controlled by a
cis
-acting recombination enhancer located near
HML
. RE is turned off in
MAT
α cells but in
MAT
a
binds multiple copies of the Fkh1 transcription factor whose forkhead-associated phosphothreonine binding domain localizes at the DSB, bringing
HML
into conjunction with
MAT
a
.
piggyBacTransposon
Authors: Yusa Kosuke
Published: May 2015

ThepiggyBactransposon was originally isolated from the cabbage looper moth,Trichoplusia ni, in the 1980s. Despite its early discovery and dissimilarity to the other DNA transposon families, thepiggyBactransposon was not recognized as a member of a large transposon superfamily for a long time. Initially, thepiggyBactransposon was thought to be a rare transposon. This view, however, has now been completely revised as a number of fully sequenced genomes have revealed the presence ofpiggyBac-like repetitive elements. The isolation of active copies of thepiggyBac-like elements from several distinct species further supported this revision. This includes the first isolation of an active mammalian DNA transposon identified in the bat genome. To date, thepiggyBactransposon has been deeply characterized and it represents a number of unique characteristics. In general, all members of thepiggyBacsuperfamily use TTAA as their integration target sites. In addition, thepiggyBactransposon shows precise excision, i.e., restoring the sequence to its preintegration state, and can transpose in a variety of organisms such as yeasts, malaria parasites, insects, mammals, and even in plants. Biochemical analysis of the chemical steps of transposition revealed thatpiggyBacdoes not require DNA synthesis during the actual transposition event. The broad host range has attracted researchers from many different fields, and thepiggyBactransposon is currently the most widely used transposon system for genetic manipulations.
Mechanisms of DNA Transposition
Authors: Hickman Alison B. , Dyda Fred
Published: May 2015

DNA transposases use a limited repertoire of structurally and mechanistically distinct nuclease domains to catalyze the DNA strand breaking and rejoining reactions that comprise DNA transposition. Here, we review the mechanisms of the four known types of transposition reactions catalyzed by (1) RNase H-like transposases (also known as DD(E/D) enzymes); (2) HUH single-stranded DNA transposases; (3) serine transposases; and (4) tyrosine transposases. The large body of accumulated biochemical and structural data, particularly for the RNase H-like transposases, has revealed not only the distinguishing features of each transposon family, but also some emerging themes that appear conserved across all families. The more-recently characterized single-stranded DNA transposases provide insight into how an ancient HUH domain fold has been adapted for transposition to accomplish excision and then site-specific integration. The serine and tyrosine transposases are structurally and mechanistically related to their cousins, the serine and tyrosine site-specific recombinases, but have to date been less intensively studied. These types of enzymes are particularly intriguing as in the context of site-specific recombination they require strict homology between recombining sites, yet for transposition can catalyze the joining of transposon ends to form an excised circle and then integration into a genomic site with much relaxed sequence specificity.
Serine Resolvases
Authors: Rice Phoebe A.
Published: May 2015

Serine resolvases are an interesting group of site-specific recombinases that, in their native contexts, resolve large fused replicons into smaller separated ones. Some resolvases are encoded by replicative transposons and resolve the transposition product, in which the donor and recipient molecules are fused, into separate replicons. Other resolvases are encoded by plasmids and function to resolve plasmid dimers into monomers. Both types are therefore involved in the spread and maintenance of antibiotic-resistance genes. Resolvases and the closely related invertases were the first serine recombinases to be studied in detail, and much of our understanding of the unusual strand exchange mechanism of serine recombinases is owed to those early studies. Resolvases and invertases have also served as paradigms for understanding how DNA topology can be harnessed to regulate enzyme activity. Finally, their relatively modular structure, combined with a wealth of structural and biochemical data, has made them good choices for engineering chimeric recombinases with designer specificity. This chapter focuses on the current understanding of serine resolvases, with a focus on the contributions of structural studies.
Mobile Bacterial Group II Introns at the Crux of Eukaryotic Evolution
Authors: Lambowitz Alan M. , Belfort Marlene
Published: May 2015

This review focuses on recent developments in our understanding of group II intron function, the relationships of these introns to retrotransposons and spliceosomes, and how their common features have informed thinking about bacterial group II introns as key elements in eukaryotic evolution. Reverse transcriptase-mediated and host factor-aided intron retrohoming pathways are considered along with retrotransposition mechanisms to novel sites in bacteria, where group II introns are thought to have originated. DNA target recognition and movement by target-primed reverse transcription infer an evolutionary relationship among group II introns, non-LTR retrotransposons, such as LINE elements, and telomerase. Additionally, group II introns are almost certainly the progenitors of spliceosomal introns. Their profound similarities include splicing chemistry extending to RNA catalysis, reaction stereochemistry, and the position of two divalent metals that perform catalysis at the RNA active site. There are also sequence and structural similarities between group II introns and the spliceosome's small nuclear RNAs (snRNAs) and between a highly conserved core spliceosomal protein Prp8 and a group II intron-like reverse transcriptase. It has been proposed that group II introns entered eukaryotes during bacterial endosymbiosis or bacterial-archaeal fusion, proliferated within the nuclear genome, necessitating evolution of the nuclear envelope, and fragmented giving rise to spliceosomal introns. Thus, these bacterial self-splicing mobile elements have fundamentally impacted the composition of extant eukaryotic genomes, including the human genome, most of which is derived from close relatives of mobile group II introns.
The Ty1 LTR-Retrotransposon of Budding Yeast,Saccharomyces cerevisiae
Authors: Curcio M. Joan , Lutz Sheila , Lesage Pascale
Published: May 2015

Long-terminal repeat (LTR)-retrotransposons generate a copy of their DNA (cDNA) by reverse transcription of their RNA genome in cytoplasmic nucleocapsids. They are widespread in the eukaryotic kingdom and are the evolutionary progenitors of retroviruses. The Ty1 element of the budding yeastSaccharomyces cerevisiaewas the first LTR-retrotransposon demonstrated to mobilize through an RNA intermediate, and not surprisingly, is the best studied. The depth of our knowledge of Ty1 biology stems not only from the predominance of active Ty1 elements in theS. cerevisiaegenome but also the ease and breadth of genomic, biochemical, and cell biology approaches available to study cellular processes in yeast. This review describes the basic structure of Ty1 and its gene products, the replication cycle, the rapidly expanding compendium of host cofactors known to influence retrotransposition, and the nature of Ty1's elaborate symbiosis with its host. Our goal is to illuminate the value of Ty1 as a paradigm to explore the biology of LTR-retrotransposons in multicellular organisms, where the low frequency of retrotransposition events presents a formidable barrier to investigations of retrotransposon biology.
Mining Environmental Plasmids for Synthetic Biology Parts and Devices
Authors: Martínez-García Esteban , Benedetti Ilaria , Hueso Angeles , De Lorenzo Víctor
Published: May 2015

The scientific and technical ambition of contemporary synthetic biology is the engineering of biological objects with a degree of predictability comparable to those made through electric and industrial manufacturing. To this end, biological parts with given specifications are sequence-edited, standardized, and combined into devices, which are assembled into complete systems. This goal, however, faces the customary context dependency of biological ingredients and their amenability to mutation. Biological orthogonality (i.e., the ability to run a function in a fashion minimally influenced by the host) is thus a desirable trait in any deeply engineered construct. Promiscuous conjugative plasmids found in environmental bacteria have evolved precisely to autonomously deploy their encoded activities in a variety of hosts, and thus they become excellent sources of basic building blocks for genetic and metabolic circuits. In this article we review a number of such reusable functions that originated in environmental plasmids and keep their properties and functional parameters in a variety of hosts. The properties encoded in the corresponding sequences include
inter alia
origins of replication, DNA transfer machineries, toxin-antitoxin systems, antibiotic selection markers, site-specific recombinases, effector-dependent transcriptional regulators (with their cognate promoters), and metabolic genes and operons. Several of these sequences have been standardized as BioBricks and/or as components of the SEVA (Standard European Vector Architecture) collection. Such formatting facilitates their physical composability, which is aimed at designing and deploying complex genetic constructs with new-to-nature properties.
Web-based therapy for hemianopic alexia is syndrome-specific
Authors: Woodhead Zoe V J , Ong Yean-Hoon , Leff Alex P
Published: May 2015

Rehabilitation studies rarely test the specificity of an intervention by using a control group who are matched to the therapy group in terms of baseline impairment, but who do not have the same causative syndrome. In this study, we tested the specificity of an eye movement therapy for a common, acquired reading disorder called hemianopic alexia, by comparing hemianopic participants with slow text reading, to age and reading speed matched controls without hemianopia. The study was carried out using an online therapy programme called ‘Read-Right’ that contains validated tests of the visual field and text reading speed, as well as an eye movement therapy: laterally scrolling text. 201 self-selected participants completed at least 5 h of online therapy. After excluding those with reading speeds incompatible with hemianopic alexia and those with bilateral abnormalities on their visual field test, we were left with 105 who were then classified into one of three groups depending on their visual field: (1) right-sided hemianopia (n=47); (2) left-sided hemianopia (n=36); (3) no hemianopia (n=22, control group). The three groups did not differ in terms of baseline text reading speed, but they were all significantly slower than expected based on normative data from the same age range. A repeated-measures analysis of variance showed a significant therapy by group interaction (p=0.039). Post hoc, paired t tests revealed that this was driven by reading speed improvements for the right-sided and left-sided hemianopic alexic groups but not the controls. This result demonstrates that a clinically validated therapy for hemianopic alexia improves text reading speed in hemianopic patients but not in participants matched for slow text reading but without hemianopia. This adds weight to the hypothesis that eye movement therapies are syndrome-specific. It also demonstrates an advantage of using web-based vehicles to deliver syndrome-specific therapies that can be accessed by patients worldwide.
Between compliance and resistance: exploring discourses on family planning in Community Health Committees in Mozambique
Authors: Capurchande Rehana Dauto , Coene Gily , Roelens Kristien , Meulemans Herman
Published: May 2015

Objectives

Although the Mozambican government has implemented a community-based approach to family planning (FP), little is known about the appropriateness of this process. We explore how members of Community Health Committees (CHCs) address and act regarding FP.

Methods/settings

An in-depth qualitative study of CHCs was conducted at two sites in Maputo province—Ndlavela and Boane—using focus group discussions (n=6), informal conversations (n=4) and observation. The analysis followed a phenomenological approach.

Results

CHCs in Ndlavela appeared to transfer more of the expected information than those in Boane. However, in the CHCs at both study sites, we found heterogeneity in CHCs’ perspectives leading to conflicting views among committee members (CMs). Arising issues included contraceptive type, target groups, the desirable number of children per family as well as the way FP was to be represented. Moreover, weak communication between CMs and health workers, and lack of payment for CMs’ activities influenced promotion of FP.

Conclusions

The two CHCs framed FP in different ways leading to inconsistent participation of CHC members in promoting FP. Policymakers should consider the diversity of discourses and aspirations of these committees when delivering information to them.
Defining a safe player run-off zone around rugby union playing areas
Authors: Fuller Colin W , Jones Rhys , Fuller Andrew D
Published: May 2015

Objectives

To identify the circumstances in which international rugby players exit the playing area during match activities and to define a safe run-off distance around the playing area.

Method

An observational study using video recordings of 102 matches associated with the Rugby World Cup (2011), Rugby Championship (2013, 2014) and Six Nations Championship (2013, 2014) were used to analyse every event in which one or more players exited the playing area during normal match activities. The circumstances in which a player exited the playing area were categorised using a range of parameters: playing position, location, out-of-play region, match activity, distance travelled over the touchline, contacts made with pitchside fixtures and fittings.

Results

Ninety-five per cent of player-excursions took place within 5.2 m of the touchline. Players exiting the playing area were nearly three times more likely to be a back than a forward (p<0.001) and the event was more likely to take place when a team was defending than attacking (p<0.001). Being forced out of play during a contact event (70%) was the major reason for players exiting the playing area. Most players (88%) exiting the playing area only made contact with the perimeter area surface; a small proportion of players contacted touchline flags (6.1%), advertising boards (2.3%) and TV cameras/equipment (1.0%).

Conclusions

A minimum hazard-free distance of 5 m around a Rugby pitch is proposed based on the 95% percentile frequency distribution of player-excursion events into the areas contiguous with the playing area.
Trends in treatment and outcomes of ankylosing spondylitis in outpatient rheumatological care in Germany between 2000 and 2012
Authors: Huscher Dörte , Thiele Katja , Rudwaleit Martin , Albrecht Katinka Charlotte , Bischoff Sascha , Krause Andreas , Karberg Kirsten , Wassenberg Siegfried , Zink Angela
Published: May 2015

Objectives

To describe changes in drug treatment and clinical outcomes of ankylosing spondylitis (AS) during the past decade.

Methods

The national database of the German collaborative arthritis centres collects clinical and patient-derived data from unselected outpatients with inflammatory rheumatic diseases. Cross-sectional data from 2000 to 2012 of around 1000 patients with AS per year were compared with regard to clinical presentation and quality of life indicators.

Results

Non-steroidal anti-inflammatory drugs (NSAIDs) have been the predominant treatment choice in AS over the years with a prescription rate of 67% of patients in 2012. Currently, almost half of the patients with AS in German rheumatology centres are treated with tumour necrosis factor inhibitors (TNFi). Often, both treatments are used in combination (33%), followed by combinations of NSAIDs and synthetic disease modifying antirheumatic drugs (sDMARDs) with 23% or TNFi alone (21%). In 2012, 10% of patients each received NSAID or sDMARD monotherapy. Methotrexate, sulfasalazine, glucocorticoids and analgaesics alone or in combination with other treatments were given to 10% of patients, respectively. Over the years, we have seen remarkable improvements in disease control and patient reported outcomes. These developments are consistent with enhanced functional status, increasing employment rates and decreasing sick leave, hospitalisation and work disability.

Conclusions

In the German rheumatology secondary/tertiary care setting, routine care of patients with AS has changed tremendously during the past decade. Increasingly, more efficacious treatment options are reflected in improved clinical outcomes, quality of life and participation in the labour force.
Performance of micropiled raft in clay subjected to vertical concentrated load: centrifuge modeling
Authors: Alnuaim A.M. , El Naggar M.H. , El Naggar H.
Published: May 2015

The overall behavior of a micropiled raft foundation (MPR) system is similar to a piled raft foundation where the load is transferred by both the raft and micropiles. However, there is no guidance available regarding the design of MPRs or indication of their performance. In this study, geotechnical centrifuge testing was conducted to investigate the behavior of MPR foundations in clay and evaluate their performance characteristics. The study evaluated the performance of MPRs compared to the isolated raft in terms of raft total and differential settlements; raft contact pressure; raft bending moment; and load sharing between the raft and the micropiles. The results showed that for the MPR configuration considered in the study, the raft carried 48% of the applied load. It was found that the Poulos–Davis–Randolph (PDR) method can be used to evaluate the performance of MPR for preliminarily design purposes with approximately 17% error.