bluuebunny/crossref_metadata_2025 huggingface dataset:
Five Factor Model and Personality Disorder
Authors: Widiger Thomas A. , Gore Whitney L. , Crego Cristina , Rojas Stephanie L. , Oltmanns Joshua R.
Published: March 2016

The purpose of this chapter is to provide an overview of the relationship of the Five Factor Model (FFM) to personality disorder. The FFM has traditionally been viewed as a dimensional model of normal personality structure. However, it should probably be viewed as a dimensional model of general personality structure, including maladaptive as well as adaptive personality traits. Discussed herein is the empirical support for the coverage of personality disorders within the FFM; the ability of the FFM to explain the convergence and divergence among personality disorder scales; the relationship of the FFM to the DSM-5 dimensional trait model; the empirical support for maladaptivity within both poles of each FFM domain (focusing in particular on agreeableness, conscientiousness, and openness); and the development of scales for the assessment of maladaptive variants of the FFM.
Interventions for the Reduction of Violence by Persons with Serious Mental Illnesses
Authors: Douglas Kevin S. , Nicholls Tonia L. , Brink Johann
Published: March 2016

Violence perpetrated by persons with serious mental illness (SMI), although certainly not the norm among this group, is of clinical and legal import in numerous legal settings. Among these are civil commitment, forensic psychiatry (insanity acquittees), and the criminal justice system. In this chapter, we provide a critical review of interventions and their empirical support that are used to reduce violence among persons with SMI. Promising findings support the use of cognitive behavioral, social learning, and cognitive skills approaches that are consistent with the Risk-Need-Responsivity (RNR) approach to crime and violence prevention. Anger management remains a promising, focused intervention with reasonable support in the literature. Dialectical behavioral therapy (DBT) has substantial general support. Community-based mandatory service programs such as outpatient commitment and mental health courts appear effective. Finally, the evidence base for the violence-reducing effect of certain psychotropic medication, particularly clozapine, is promising yet inconsistent.
Optimism
Authors: Mens Maria G. , Scheier Michael F. , Carver Charles S.
Published: March 2016

Optimism is expecting good things to occur in your life. Such positive expectations are associated with higher levels of subjective well-being, better physical health, and a higher quality and quantity of social relationships. The benefits of optimism are partially attributable to the manner in which optimists and pessimists cope with adversity. Optimists tend to cope with adversity actively, attempting to solve problems when they can, accepting problems that they cannot resolve, and focusing on the positive aspects of their experiences. In addition to coping with adversity better, optimists also appear to engage in proactive efforts to prevent problems in the future, including taking actions to minimize various kinds of health risks. Although previous research has clearly demonstrated the benefits of optimism across a wide array of outcomes, there remains several unresolved issues concerning the effects of optimism and how optimism should be conceptualized, which are discussed.
Etruscan
Authors: Bonfante Larissa
Published: March 2016

This article provides an overview of Etruscan literature. It considers how the Greek innovations of myth and writing came into Etruria, how the Etruscans viewed early writing as magical, and how Etruscan culture developed its own identity. It discusses the Etruscan language, written documents, and inscriptions, as well as religious ritual, divination, and prophecy. It also examines Etruscan historical epic and myth, theatre, and imagery. Finally, it examines the influence of Etruscan culture in the Roman world: the Romans derived their alphabet from the Etruscans and adopted Etruscan dress and musical instruments, along with the organization of the army. The article shows the significance of such Etruscan influence to Roman culture and life even as the Romans maintained their own religion and language, and the eventual death of the Etruscan language by the time of the Roman Empire.
Environmental Ethics, Sustainability Science, and the Recovery of Pragmatism
Authors: Minteer Ben A.
Published: March 2016

The recent emergence of sustainability science has created opportunities and challenges for environmental ethics. On the one hand, the fast growth and increasing influence of sustainability science in environmental management and policy circles—and its normative character as a goal-directed enterprise focused on moving society toward a more durable socio-ecological relationship—provides an opening for environmental ethics to contribute to the development of this new transdisciplinary science. Yet traditional (and historically dominant) nonanthropocentric ethics will prove difficult to reconcile with sustainability science’s strong emphasis on the anthropocentric goals of improving human welfare and well-being. A more explicitly pragmatic understanding of environmental ethics, a view that combines respect for nature with a wider sense of value pluralism (including more human-directed values) in the cautious shaping of ecological systems for conservation and human benefit, has the potential to draw the two fields closer together at this critical stage in their developmental trajectories.
Origin of the broad iron line feature and the soft X-ray variation in Seyfert galaxies
Authors: Iso Naoki , Ebisawa Ken , Sameshima Hiroaki , Mizumoto Misaki , Miyakawa Takehiro , Inoue Hajime , Yamasaki Hiroki
Published: March 2016

Many Seyfert galaxies are known to exhibit significant X-ray spectral variations and seemingly broad iron K-emission line features. In this paper, we show that the “variable partial covering model,” which has been successfully proposed for MCG −6–30–15 (Miyakawa et al. 2012, PASJ, 64, 140) and 1H 0707−495 (Mizumoto et al. 2014, PASJ, 66, 122), can also explain the spectral variations in 2–10 keV as well as the broad iron line features in 20 other Seyfert galaxies observed with Suzaku. In this model, the absorbed spectral component through the optically thick absorbing clouds has a significant iron K-edge, which primarily accounts for the observed, seemingly broad iron line feature. Fluctuation of the absorbing clouds in the line of sight of the extended X-ray source results in variation of the partial covering fraction, which causes an anti-correlation between the direct (not covered) spectral component and the absorbed (covered) spectral component below ∼10 keV. Observed spectral variation in 2–10 keV in a timescale of less than ∼1 day is primarily explained by such variations of the partial covering fraction, while the intrinsic soft X-ray luminosity is hardly variable.
Do female
Nicrophorus vespilloides
reduce direct costs by choosing males that mate less frequently?
Authors: Hopwood P. E. , Mazué G. P. F. , Carter M. J. , Head M. L. , Moore A. J. , Royle N. J.
Published: March 2016

Sexual conflict occurs when selection to maximize fitness in one sex does so at the expense of the other sex. In the burying beetle
Nicrophorus vespilloides
, repeated mating provides assurance of paternity at a direct cost to female reproductive productivity. To reduce this cost, females could choose males with low repeated mating rates or smaller, servile males. We tested this by offering females a dichotomous choice between males from lines selected for high or low mating rate. Each female was then allocated her preferred or non-preferred male to breed. Females showed no preference for males based on whether they came from lines selected for high or low mating rates. Pairs containing males from high mating rate lines copulated more often than those with low line males but there was a negative relationship between female size and number of times she mated with a non-preferred male. When females bred with their preferred male the number of offspring reared increased with female size but there was no such increase when breeding with non-preferred males. Females thus benefited from being choosy, but this was not directly attributable to avoidance of costly male repeated mating.
Market analyses of livestock trade networks to inform the prevention of joint economic and epidemiological risks
Authors: Moslonka-Lefebvre Mathieu , Gilligan Christopher A. , Monod Hervé , Belloc Catherine , Ezanno Pauline , Filipe João A. N. , Vergu Elisabeta
Published: March 2016

Conventional epidemiological studies of infections spreading through trade networks, e.g. via livestock movements, generally show that central large-size holdings (hubs) should be preferentially surveyed and controlled in order to reduce epidemic spread. However, epidemiological strategies alone may not be economically optimal when costs of control are factored in together with risks of market disruption from targeting core holdings in a supply chain. Using extensive data on animal movements in supply chains for cattle and swine in France, we introduce a method to identify effective strategies for preventing outbreaks with limited budgets while minimizing the risk of market disruptions. Our method involves the categorization of holdings based on position along the supply chain and degree of market share. Our analyses suggest that trade has a higher risk of propagating epidemics through cattle networks, which are dominated by exchanges involving wholesalers, than for swine. We assess the effectiveness of contrasting interventions from the perspectives of regulators and the market, using percolation analysis. We show that preferentially targeting minor, non-central agents can outperform targeting of hubs when the costs to stakeholders and the risks of market disturbance are considered. Our study highlights the importance of assessing joint economic–epidemiological risks in networks underlying pathogen propagation and trade.
A Balamuthia survivor
Authors: Vollmer Michael Eric , Glaser Carol
Published: March 2016

Introduction:

This case report describes a human survivor of Balamuthia mandrillaris infection. This is a free-living amoeba that can cause infection with the devastating consequence of near universally fatal encephalitis. We report this case to demonstrate the possibility of recovery.

Case presentation:

A 26-year-old Hispanic male, a landscape gardener, presented to the hospital in March 2010 with a two month history of headache, visual disturbances and new-onset seizures. Brain imaging identified two enhancing central lesions and Balamuthia mandrillaris was later identified by brain biopsy. He received several months of various antimicrobials including miltefosine, a novel use of the drug in this disease at the time. Seven weeks into therapy, considerations were made to switch him to ‘comfort care’ because of worsening clinical status and seemingly lack of response to treatment. The patient finally demonstrated clinical and radiological improvement after eight weeks with modified therapy, despite experiencing some debilitating toxic effects likely to be related to antibiotics. Two years after his initial presentation he made a complete recovery.

Conclusion:

Balamuthia mandrillaris amoebic encephalitis is considered an almost universally fatal disease; this case demonstrates the possibility of recovery. This report outlines his treatment, drug toxicities and includes additional information regarding the therapeutic use of the drug miltefosine. Whether his survival is related to the specific antimicrobials used in this case is unknown and further investigation is warranted.
Topologically associated domains are ancient features that coincide with Metazoan clusters of extreme noncoding conservation
Authors: Harmston Nathan , Ing-Simmons Elizabeth , Tan Ge , Perry Malcolm , Merkenschlager Matthias , Lenhard Boris
Published: March 2016

In vertebrates and other Metazoa, developmental genes are found surrounded by dense clusters of highly conserved noncoding elements (CNEs). CNEs exhibit extreme levels of sequence conservation of unexplained origin, with many acting as long-range enhancers during development. Clusters of CNEs, termed genomic regulatory blocks (GRBs), define the span of regulatory interactions for many important developmental regulators. The function and genomic distribution of these elements close to important regulatory genes raises the question of how they relate to the 3D conformation of these loci. We show that GRBs, defined using clusters of CNEs, coincide strongly with the patterns of topological organisation in metazoan genomes, predicting the boundaries of topologically associating domains (TADs) at hundreds of loci. The set of TADs that are associated with high levels of non-coding conservation exhibit distinct properties compared to TADs called in chromosomal regions devoid of extreme non-coding conservation. The correspondence between GRBs and TADs suggests that TADs around developmental genes are ancient, slowly evolving genomic structures, many of which have had conserved spans for hundreds of millions of years. This relationship also explains the difference in TAD numbers and sizes between genomes. While the close correspondence between extreme conservation and the boundaries of this subset of TADs does not reveal the mechanism leading to the conservation of these elements, it provides a functional framework for studying the role of TADs in long-range transcriptional regulation.
RNA-seq based analysis of population structure within the maize inbred B73
Authors: Liang Zhikai , Schnable James C.
Published: March 2016

B73 is a variety of maize (Zea mays ssp. mays) widely used in genetic, genomic, and phenotypic research around the world. B73 was also served as the reference genotype for the original maize genome sequencing project. The advent of large-scale RNA-sequencing as a method of measuring gene expression presents a unique opportunity to assess the level of relatedness among individuals identified as variety B73. The level of haplotype conservation and divergence across the genome were assessed using 27 RNA-seq data sets from 20 independent research groups in three countries. Several clearly distinct clades were identified among putatively B73 samples. A number of these blocks were defined by the presence of clearly defined genomic blocks containing a haplotype which did not match the published B73 reference genome. In a number of cases the relationship among B73 samples generated by different research groups recapitulated mentor/mentee relationships within the maize genetics community. A number of regions with distinct, dissimilar, haplotypes were identified in our study. However, when considering the age of the B73 accession – greater than 40 years – and the challenges of maintaining isogenic lines of a naturally outcrossing species, a strikingly high overall level of conservation was exhibited among B73 samples from around the globe.
Bridging the gap between genes and language deficits in schizophrenia: an oscillopathic approach
Authors: Murphy Elliot , Benítez-Burraco Antonio
Published: March 2016

Schizophrenia is characterised by marked language deficits, but it is not clear how these deficits arise from gene mutations linked to or associated with the disease. The goal of this paper is to aid the bridging of the gap between genes and schizophrenia and, ultimately, give support to the view that it represents an abnormal ontogenetic itinerary for the human faculty of language, heavily rooted in the evolutionary processes that brought about modern language. To that end we will focus on how the schizophrenia brain processes language and, particularly, on its distinctive oscillatory profile during language processing: We will argue that brain rhythms constitute the best route to interpret language deficits in this condition and map them to neural dysfunction and risk alleles of the genes. Additionally, we will show that candidate genes for schizophrenia are overrepresented among the set of genes that are believed are important for the evolution of human language. These genes crucially include (and are related to) genes involved in brain rhythmicity. We will claim that this translational effort and the links we uncover may help develop an understanding of language evolution, along with the aetiology of schizophrenia, its clinical/linguistic profile, and its high prevalence among modern populations.
Using reciprocity for relating the simulation of transcranial current stimulation to the EEG forward problem
Authors: Wagner S. , Lucka F. , Vorwerk J. , Herrmann C.S. , Nolte G. , Burger M. , Wolters C.H.
Published: March 2016

To explore the relationship between transcranial current stimulation (tCS) and the electroencephalography (EEG) forward problem, we investigate and compare accuracy and efficiency of a reciprocal and a direct EEG forward approach for dipolar primary current sources both based on the finite element method (FEM), namely the adjoint approach (AA) and the partial integration approach in conjunction with a transfer matrix concept (PI). By analyzing numerical results, comparing to analytically derived EEG forward potentials and estimating computational complexity in spherical shell models, AA turns out to be essentially identical to PI. It is then proven that AA and PI are also algebraically identical even for general head models. This relation offers a direct link between the EEG forward problem and tCS. We then demonstrate how the quasi-analytical EEG forward solutions in sphere models can be used to validate the numerical accuracies of FEM-based tCS simulation approaches. These approaches differ with respect to the ease with which they can be employed for realistic head modeling based on MRI-derived segmentations. We show that while the accuracy of the most easy to realize approach based on regular hexahedral elements is already quite high, it can be significantly improved if a geometry-adaptation of the elements is employed in conjunction with an isoparametric FEM approach. While the latter approach does not involve any additional difficulties for the user, it reaches the high accuracies of surface-segmentation based tetrahedral FEM, which is considerably more difficult to implement and topologically less flexible in practice. Finally, in a highly realistic head volume conductor model and when compared to the regular alternative, the geometry-adapted hexahedral FEM is shown to result in significant changes in tCS current flow orientation and magnitude up to 45 degrees and a factor of 1.66, respectively.
Complex ancient genetic structure and cultural transitions in southern African populations
Authors: Montinaro Francesco , Busby George BJ , Gonzalez-Santos Miguel , Oosthuitzen Ockie , Oosthuizen Erika , Anagnostou Paolo , Destro-Bisol Giovanni , Pascali Vincenzo L , Capelli Cristian
Published: March 2016

The characterization of the structure of southern Africa populations has been the subject of numerous genetic, medical, linguistic, archaeological and anthropological investigations. Current diversity in the subcontinent is the result of complex episodes of genetic admixture and cultural contact between the early inhabitants and the migrants that have arrived in the region over the last 2,000 years. Here we analyze 1,856 individuals from 91 populations, comprising novel and available genotype data to characterize the genetic ancestry profiles of 631 individuals from 51 southern African populations. Combining local ancestry and allele frequency analyses we identify a tripartite, ancient, Khoesan-related genetic structure, which correlates with geography, but not with linguistic affiliation or subsistence strategy. The fine mapping of these components in southern African populations reveals admixture dynamics and episodes of cultural reversion involving several Khoesan groups and highlights different mixtures of ancestral components in Bantu speakers and Coloured individuals.
Synlet: an R package for systemically analyzing synthetic lethal RNA interference screen data
Authors: Shao Chunxuan , Westermann Frank , Höfer Thomas
Published: March 2016

High-throughput synthetic lethal RNA interference (RNAi) screen experiments shed important insights on the filed of cancer researches and drug discovery, but a comprehensive software for analyzing the data was not available yet. We present synlet, an R package provided a complete pipeline to process the synthetic lethal RNAi screens data. Synlet provides several methods to access the screen quality, including Z’ factor and data visualization. B-score and fraction of control or samplesnormalizationmethods are implemented in the package. More importantly, synlet facilitates the process of hits selection by implementing several algorithms, providing the possibility to identify high confidence targets.

Availability

The source code is freely available in Bioconductor (http://bioconductor.org/).

Contact

c.shao@Dkfz-Heidelberg.de
GenVisR: Genomic Visualizations in R
Authors: Skidmore Zachary L , Wagner Alex H , Lesurf Robert , Campbell Katie M , Kunisaki Jason , Griffith Obi L , Griffith Malachi
Published: March 2016

Summary: Visualizing and summarizing data from genomic studies continues to be a challenge. Here we introduce the GenVisR package to addresses this challenge by providing highly customizable, publication-quality graphics focused on cohort level genome analyses. GenVisR provides a rapid and easy-to-use suite of genomic visualization tools, while maintaining a high degree of flexibility by leveraging the abilities of ggplot2 and bioconductor. Availability and Implementation: GenVisR is an R package available via bioconductor (https://bioconductor.org/packages/GenVisR) under GPLv3. Support is available via GitHub (https://github.com/griffithlab/GenVisR/issues) and the Bioconductor support website.
Hybrid Discrete-Continuum Cellular Automaton (HCA) model of Prostate to Bone Metastasis
Authors: Araujo Arturo , Basanta David
Published: March 2016

Prostate to bone metastases induce a “vicious cycle” by promoting excessive osteoclast and osteoblast mediated bone degradation and formation that in turn yields factors that drive cancer growth. Recent advances defining the molecular mechanisms that control the vicious cycle have revealed new therapeutic targeting opportunities. However, given the complex temporal and simultaneous cellular interactions occurring in the bone microenvironment, assessing the impact of putative therapies is challenging. To this end, we have integrated biological and computational approaches to generate an accurate model of normal bone matrix homeostasis and the prostate cancer-bone microenvironment. The model faithfully reproduces the basic multicellular unit (BMU) bone coupling process and introduction of a single prostate cancer cell yields a vicious cycle that is similar in cellular composition and pathophysiology to models of prostate to bone metastasis.
The evolutionary fates of a large segmental duplication in mouse
Authors: Morgan Andrew P , Holt J Matthew , McMullan Rachel C , Bell Timothy A , Clayshulte Amelia M-F , Didion John P , Yadgary Liran , Thybert David , Odom Duncan T , Flicek Paul , McMillan Leonard , de Villena Fernando Pardo-Manuel
Published: March 2016

Gene duplication and loss are major sources of genetic polymorphism in populations, and are important forces shaping the evolution of genome content and organization. We have reconstructed the origin and history of a 127 kbp segmental duplication,R2d, in the house mouse (Mus musculus). R2dcontains a single protein-coding gene,Cwc22. De novoassembly of both the ancestral (R2d1) and the derived (R2d2) copies reveals that they have been subject to non-allelic gene conversion events spanning tens of kilobases.R2d2is also a hotspot for structural variation: its diploid copy number ranges from zero in the mouse reference genome to more than 80 in wild mice sampled from around the globe. Hemizgyosity for high-copy-number alleles ofR2d2is associated inciswith meiotic drive, suppression of meiotic crossovers, and copy-number instability, with a mutation rate in excess of 1 per 100 transmissions in laboratory populations. We identify an additional 57 loci covering 0.8% of the mouse genome with patterns of sequence variation similar to those atR2d1andR2d2. Our results provide a striking example of allelic diversity generated by duplication and demonstrate the value ofde novoassembly in a phylogenetic context for understanding the mutational processes affecting duplicate genes.
Tissue culture as a source of replicates in non-model plants: variation in cold tolerance inArabidopsis lyratassp.petraea
Authors: Kenta Tanaka , Edwards Jessica E.M. , Butlin Roger K. , Burke Terry , Quick W. Paul , Urwin Peter , Davey Matthew P.
Published: March 2016

Whilst genotype–environment interaction is increasingly receiving attention by ecologists and evolutionary biologists, such studies need genetically homogeneous replicates—a challenging hurdle in outcrossing plants. This could potentially be overcome by using tissue culture techniques. However, plants regenerated from tissue culture may show aberrant phenotypes and “somaclonal” variation. Here we examined the somaclonal variation due to tissue culturing using the response of the photosynthetic efficiency (chlorophyll fluorescence measurements forFv/Fm,Fv’/Fm’ and ΦPSII, representing maximum efficiency of photosynthesis for dark‐ and light-adapted leaves, and the actual electron transport operating efficiency, respectively) to cold treatment, compared to variation among half-sibling seedlings from three different families ofArabidopsis lyratassp.petraea. Somaclonal variation was limited and we could successfully detect within-family variation in change in chlorophyll fluorescence by cold shock with the help of tissue-culture derived replicates. Icelandic and Norwegian families exhibited higher chlorophyll fluorescence, suggesting higher cold tolerance, than a Swedish family. Although the main effect of tissue culture onFv/Fm,Fv’/Fm’ and ΦPSIIwas small, there were significant interactions between tissue culture and family, suggesting that the effect of tissue culture is genotype–specific. Tissue-cultured plantlets were less affected by cold treatment than seedlings, but to a different extent in each family. These interactive effects, however, were comparable to, or much smaller than the single effect of family. These results suggest that tissue culture is a useful method for obtaining genetically homogenous replicates for studying genotype–environment interaction related to adaptively relevant phenotypes, such as cold tolerance, in non-model outcrossing plants.
A little walk from physical to biological complexity: protein folding and stability
Authors: Pucci Fabrizio , Rooman Marianne
Published: March 2016

As an example of topic where biology and physics meet, we present the issue of protein folding and stability, and the development of thermodynamics-based bioinformatics tools that predict the stability and thermal resistance of proteins and the change of these quantities upon amino acid substitutions. These methods are based on knowledge-driven statistical potentials, derived from experimental protein structures using the inverse Boltzmann law. We also describe an application of these predictors, which contributed to the understanding of the mechanisms of aggregation of a particular protein known to cause a neuronal disease.
Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet
Authors: Viner Coby , Ishak Charles A. , Johnson James , Walker Nicolas J. , Shi Hui , Sjöberg-Herrera Marcela K. , Shen Shu Yi , Lardo Santana M. , Adams David J. , Ferguson-Smith Anne C. , De Carvalho Daniel D. , Hainer Sarah J. , Bailey Timothy L. , Hoffman Michael M.
Published: March 2016

Transcription factors bind DNA in specific sequence contexts. In addition to distinguishing one nucleobase from another, some transcription factors can distinguish between unmodified and modified bases. Current models of transcription factor binding tend not take DNA modifications into account, while the recent few that do often have limitations. This makes a comprehensive and accurate profiling of transcription factor affinities difficult.

Here, we developed methods to identify transcription factor binding sites in modified DNA. Our models expand the standard A/C/G/T DNA alphabet to include cytosine modifications. We developed Cytomod to create modified genomic sequences and enhanced the Multiple EM for Motif Elicitation (MEME) Suite by adding the capacity to handle custom alphabets. We adapted the well-established position weight matrix (PWM) model of transcription factor binding affinity to this expanded DNA alphabet.

Using these methods, we identified modification-sensitive transcription factor binding motifs. We confirmed established binding preferences, such as the preference of ZFP57 and C/EBPβ for methylated motifs and the preference of c-Myc for unmethylated E-box motifs. Using known binding preferences to tune model parameters, we discovered novel modified motifs for a wide array of transcription factors. Finally, we validated predicted binding preferences of OCT4 using cleavage under targets and release using nuclease (CUT&RUN) experiments across conventional, methylation-, and hydroxymethylation-enriched sequences. Our approach readily extends to other DNA modifications. As more genome-wide single-base resolution modification data becomes available, we expect that our method will yield insights into altered transcription factor binding affinities across many different modifications.
Findingde novomethylated DNA motifs
Authors: Ngo Vu , Wang Mengchi , Wang Wei
Published: March 2016

Increasing evidence has shown that posttranslational modifications (PTMs) such as methylation and hydroxymethylation on cytosine would greatly impact the binding of transcription factors (TFs). However, there is a lack of motif finding algorithms with the function to search for motifs with PTMs. In this study, we expend on our previous motif finding pipeline Epigram to provide systematicde novomotif discovery and performance evaluation on methylated DNA motifs. Using the tool, we were able to identified methylated motifs inArabidopsisDAP-seq data that were previously demonstrated to contain such motifs1. When applied to TF ChIP-seq and DNA methylome data in H1 and GM12878, our method successfully identified novel methylated motifs that can be recognized by the TFs or their co-factors. We also observed spacing constraint between the canonical motif of the TF and the newly discovered methylated motifs, which suggests operative recognition of these cis-elements by collaborative proteins.
Amus-51RIP allele for transformation ofNeurospora crassa
Authors: Smith Zachary J. , Bedore Stacy , Spingler Stephanie , Hammond Thomas M.
Published: March 2016

This report describes the construction and characterization ofmus-51RIP70, an allele for high-efficiency targeted integration of transgenes into the genome of the model eukaryoteNeurospora crassa. Two of themus-51RIP70strains investigated in this work (RZS27.10 and RZS27.18) can be obtained from the Fungal Genetics Stock Center. The two deposited strains are, to our knowledge, genetically identical and neither one is preferred over the other for use inNeurosporaresearch.
Hierarchical Association Coefficient Algorithm
Authors: Kim Bongsong
Published: March 2016

Suppose that members in a universal set categorized based on observations, and that categories can be stratified based on the average of observations within each category. Two sorting extremes can be obtained from the perspective of arbitrariness of an order of observations. The first sorting extreme is an increasing order of observations on ascendingly stratified categories. The second sorting extreme is a decreasing order of observations on ascendingly stratified categories. Hierarchical association coefficient (HA-coefficient) algorithm is based on a principle that any order of observations in stratified categorization can be placed between the two sorting extremes. The algorithm produces a proportion of how much an order of observations in stratified categorization is close to the first sorting extreme, or how much an order of categorized observations is distant from the second sorting extreme. This paper introduces a theory about the HA-coefficient algorithm, and shows its applications with example data. In addition, proving a reliability of the algorithm is shown through a simulation.
Counterconditioned fear responses exhibit greater renewal than extinguished fear responses
Authors: Holmes Nathan M. , Leung Hiu T. , Westbrook R. Frederick
Published: March 2016

This series of experiments used rats to compare counterconditioning and extinction of conditioned fear responses (freezing) with respect to the effects of a context shift. In each experiment, a stimulus was paired with shock in context A, extinguished or counterconditioned through pairings with sucrose in context B, and then tested for renewal outside of context B. Counterconditioned fear responses exhibited greater ABA renewal than extinguished fear responses. This result was observed using a between-subjects design (Experiment 1) and a within-subject design in which counterconditioned and extinguished stimuli were equated in all respects other than their signaling of sucrose (Experiment 2). Counterconditioned fear responses also exhibited greater ABC renewal than extinguished fear responses (Experiment 3). This result was observed using a within-subject design in which context C was identical to context B in terms of its associative history, and when counterconditioned and extinguished CSs were tested in compounds matched for their association with both shock and sucrose (Experiment 4). These results are consistent with models which hold that context regulates expression of associations formed in counterconditioning and extinction, and allow the level of regulation to be greater following counterconditioning than extinction, as noted in previous studies.
An omission procedure reorganizes the microstructure of sign-tracking while preserving incentive salience
Authors: Chang Stephen E. , Smith Kyle S.
Published: March 2016

Appetitive sign-tracking, in which reward-paired cues elicit approach that can result in cue interaction, demonstrates how cues acquire motivational value. For example, rats will approach and subsequently interact with a lever insertion cue that signals food delivery upon its retraction. However, lever deflections are rapidly reduced once rats are trained on an omission schedule in which lever interactions cancel food delivery. Here we evaluated the change in sign-tracking response topography in rats exposed to such an omission procedure. Lever deflections dropped precipitously when they canceled reward. However, rats that were on an omission schedule continued to approach, sniff, and contact the lever without pressing it, and did so at comparable rates to rats that were not under an omission schedule. Thus, sign-tracking was maintained, albeit in a different manner, following omission. Such findings show that the motivational attraction to reward cues can be expressed with remarkable persistence and flexibility.
Exome sequencing results in successful diagnosis and treatment of a severe congenital anemia
Authors: Lacy Jessica N. , Ulirsch Jacob C. , Grace Rachael F. , Towne Meghan C. , Hale John , Mohandas Narla , Lux Samuel E. , Agrawal Pankaj B. , Sankaran Vijay G.
Published: March 2016

Whole-exome sequencing is increasingly used for diagnosis and identification of appropriate therapies in patients. Here, we present the case of a 3-yr-old male with a lifelong and severe transfusion-dependent anemia of unclear etiology, despite an extensive clinical workup. Given the difficulty of making the diagnosis and the potential side effects from performing interventions in patients with a congenital anemia of unknown etiology, we opted to perform whole-exome sequencing on the patient and his parents. This resulted in the identification of homozygous loss-of-function mutations in the EPB41 gene, encoding erythrocyte protein band 4.1, which therefore causes a rare and severe form of hereditary elliptocytosis in the patient. Based on prior clinical experience in similar patients, a surgical splenectomy was performed that resulted in subsequent transfusion independence in the patient. This case illustrates how whole-exome sequencing can lead to accurate diagnoses (and exclusion of diagnoses where interventions, such as splenectomy, would be contraindicated), thereby resulting in appropriate and successful therapeutic intervention—a major goal of precision medicine.
Isolation, crystallization and crystal structure determination of bovine kidney Na+,K+-ATPase
Authors: Gregersen Jonas Lindholt , Mattle Daniel , Fedosova Natalya U. , Nissen Poul , Reinhard Linda
Published: March 2016

Na+,K+-ATPase is responsible for the transport of Na+and K+across the plasma membrane in animal cells, thereby sustaining vital electrochemical gradients that energize channels and secondary transporters. The crystal structure of Na+,K+-ATPase has previously been elucidated using the enzyme from native sources such as porcine kidney and shark rectal gland. Here, the isolation, crystallization and first structure determination of bovine kidney Na+,K+-ATPase in a high-affinity E2–BeF3−–ouabain complex with bound magnesium are described. Crystals belonging to the orthorhombic space groupC2221with one molecule in the asymmetric unit exhibited anisotropic diffraction to a resolution of 3.7 Å with full completeness to a resolution of 4.2 Å. The structure was determined by molecular replacement, revealing unbiased electron-density features for bound BeF3−, ouabain and Mg2+ions.
Binding of Gd3+to the neuronal signalling protein calexcitin identifies an exchangeable Ca2+-binding site
Authors: Chataigner Lucas , Guo Jingxu , Erskine Peter T. , Coker Alun R. , Wood Steve P. , Gombos Zoltan , Cooper Jonathan B.
Published: March 2016

Calexcitin was first identified in the marine snailHermissenda crassicornisas a neuronal-specific protein that becomes upregulated and phosphorylated in associative learning. Calexcitin possesses four EF-hand motifs, but only the first three (EF-1 to EF-3) are involved in binding metal ions. Past work has indicated that under physiological conditions EF-1 and EF-2 bind Mg2+and Ca2+, while EF-3 is likely to bind only Ca2+. The fourth EF-hand is nonfunctional owing to a lack of key metal-binding residues. The aim of this study was to use a crystallographic approach to determine which of the three metal-binding sites of calexcitin is most readily replaced by exogenous metal ions, potentially shedding light on which of the EF-hands play a `sensory' role in neuronal calcium signalling. By co-crystallizing recombinant calexcitin with equimolar Gd3+in the presence of trace Ca2+, EF-1 was shown to become fully occupied by Gd3+ions, while the other two sites remain fully occupied by Ca2+. The structure of the Gd3+–calexcitin complex has been refined to anRfactor of 21.5% and anRfreeof 30.4% at 2.2 Å resolution. These findings suggest that EF-1 of calexcitin is the Ca2+-binding site with the lowest selectivity for Ca2+, and the implications of this finding for calcium sensing in neuronal signalling pathways are discussed.
Rethinking urban destination marketing
Authors: Heeley John
Published: March 2016

Purpose

– The purpose of this paper is to trace the emergence of a dominant paradigm from within which academics and practitioners alike currently describe and otherwise explain urban destination marketing. The paradigm has been dubbed the “theory of marketing competitive advantage (CA)” by the author, and by others as the “4P’s marketing paradigm”. To effectively market themselves as tourism destinations, this paradigm requires towns and cities to differentiate themselves through the provision of more or less unique products, based on which they subsequently undertake branding, market positioning, distribution and other activities through bespoke destination marketing organisations (DMOs).

Design/methodology/approach

– The paper summarises the findings of: first, a review of the academic and practitioner literature on urban destination marketing; second, an online investigation of urban destination marketing in 62 European towns and cities, consulting the corporate and consumer pages of the relevant DMO website; and third, in-depth interviews with 20 senior DMO departmental executives. Each interview was recorded digitally for subsequent transcribing, and was conducted on the basis of a semi-structured interview schedule.

Findings

– Theory, as enshrined in the “4P’s marketing paradigm” rarely holds up in practice. Irrespective of whether or not a town or city possesses CA (and few do), DMO marketing gravitates almost inexorably towards a “marketing of everything”. Moreover, much the greater part of urban destination marketing is ineffective, failing to create visitors and deliver the commercial and economic returns on which it is premised. Against a backdrop of DMO marginality and ineffectiveness and a reluctance by them to market what is special and different about places, the continued existence of DMOs and the destination marketing they undertake is thrown into serious question.

Research limitations/implications

– Interpretation is unavoidably subjective in parts, drawing on personal experience as well as research undertaken.

Originality/value

– This paper is intended to give the reader an understanding of why success is so problematic in urban destination marketing, serving as an antidote to the prevailing idealised, normative and unproblematic picture of the DMO world as this is depicted from within the prevailing “4P’s marketing paradigm”. The research method provides a basis on which to unite theory and practice in the field of urban destination marketing in a more systematic and verifiable manner than has hitherto ever been the case.
Can incivility impair team’s creative performance through paralyzing employee’s knowledge sharing? A multi-level approach
Authors: Sharifirad Mohammad Sadegh
Published: March 2016

Purpose

– The purpose of this paper is to examine how a supervisor’s incivility in teams impact team’s creative performance through the mediating factor of knowledge sharing intention among team members. Moreover, the moderating role of collaborative climate was investigated as protector against leaders’ incivility.

Design/methodology/approach

– The proposed multi-level model was tested by surveying 312 health care providers nested within 42 work units at eight large hospitals in Iran. Multi-level regression analysis was used to analyze the data.

Findings

– The findings revealed that those team members experiencing incivility from their supervisors are more likely to show reluctance to share knowledge with team members and as a consequence this response further decreases team’s creative performance. However, the climate of collaboration inside hospitals can buffer the negative impact of incivility on their readiness to share knowledge.

Practical implications

– In team-based organizations, a supervisor’s incivility can stifle the creative performance of his/her team through blocking the knowledge sharing of members. First, human resource department should have some plans to curtail incivility of supervisors. Second, establishing a climate of collaboration and trust among team members can mitigate the insidious effects of supervisors’ incivility.

Originality/value

– In prior research studies, the role of incivility on individual outcomes has been highlighted. This paper, according to the best knowledge of the author, is the first considering the negative impact of incivility on team’s performance. Moreover, collaborative climate is a novel moderator considered in this study.
What’s to argue? A comparison of opposing viewpoints in context to the updated points of view reference center, with a nod to the original points of view reference center
Authors: Nuttall Harry D.
Published: March 2016

Purpose

– The purpose of this paper is to provide an evaluative comparison of databases for argumentative/persuasive rhetoric.

Design/methodology/approach

– This paper reviews and compares the databases in terms of the organization, types of information included and the ease of use.

Findings

– To assist students in learning the rhetorical modes of argument and persuasion, some database vendors have developed proprietary electronic databases specific to this purpose. EBSCOhost’s Points of View Reference Center and Gale/Cengage’s Opposing Viewpoints in Context are two such databases. Which is better largely depends on the dominant user demographic of the educational institution. Both databases have strengths and weaknesses; therefore, the best results can be achieved by using them to complement one another. But if only one database can be selected, then that choice should most be influenced by the user demographic served.

Research limitations/implications

– These databases have value as primers and introductions to research and writing in the rhetorical mode(s) of argumentation and persuasion, but students taking advanced classes should supplement them with more sophisticated searches in standard aggregator databases, which are not examined in detail in this paper.

Originality/value

– This paper offers selectors an apples-to-apples comparison and analysis of two related resources, providing an insight about which can be used in the selection process.
A Skeletal Prototype of Surgical Arm Based on Dual-Triangular Mechanism
Authors: Liu Shao T. , Harewood Laurence , Chen Bernard , Chen Chao
Published: March 2016

The parallelogram-based remote center of motion (RCM) mechanism used for robotic minimally invasive surgery (MIS) manipulators generates a relatively large device footprint. The consequence being larger chance of interference between the robotic arms and restricted workspace, hence obstruct optimal surgical functioning. A novel mechanism with RCM, dual-triangular linkage (DT-linkage), is introduced to reduce the occupied space by the linkage while keeping sufficient space around the incision. Hence, the chance of collisions among arms and tools can be reduced. The concept of this dual-triangular linkage is proven mathematically and validated by a prototype. Auxiliary mechanisms are introduced to remove the singularity at the fully folded configuration. The characterized footprints of this new linkage and the one based on parallelograms are analyzed and compared.
Dynamic Modeling for a Flexible Spacecraft With Solar Arrays Composed of Honeycomb Panels and Its Proportional–Derivative Control With Input Shaper
Authors: Liu Lun , Cao Dengqing
Published: March 2016

A high-precision dynamic model of a flexible spacecraft installed with solar arrays, which are composed of honeycomb panels, is established based on the nonconstrained modes of flexible appendages (solar arrays), and an effective cooperative controller is designed for attitude maneuver and vibration suppression by integrating the proportional–derivative (PD) control and input shaping (IS) technique. The governing motion equations of the system and the corresponding boundary conditions are derived by using Hamiltonian Principle. Solving the linearized form of those equations with associated boundaries, the nonconstrained modes of solar arrays are obtained for deriving the discretized dynamic model. Applying this discretized model and combining the IS technique with the PD controller, a hybrid control scheme is designed to achieve the attitude maneuver of the spacecraft and vibration suppression of its flexible solar arrays. The numerical results reveal that the nonconstrained modes of the system are significantly influenced by the spacecraft flexibility and honeycomb panel parameters. Meanwhile, the differences between the nonconstrained modes and the constrained ones are growing as the spacecraft flexibility increases. Compared with the pure PD controller, the one integrating the PD control and IS technique performs much better, because it is more effective for suppressing the oscillation of attitude angular velocity and the vibration of solar array during the attitude maneuver, and reducing the residual vibration after the maneuver process.