bluuebunny/crossref_metadata_2025 huggingface dataset:
Computing exponentially faster: implementing a non-deterministic universal Turing machine using DNA
Authors: Currin Andrew , Korovin Konstantin , Ababi Maria , Roper Katherine , Kell Douglas B. , Day Philip J. , King Ross D.
Published: March 2017

The theory of computer science is based around universal Turing machines (UTMs): abstract machines able to execute all possible algorithms. Modern digital computers are physical embodiments of classical UTMs. For the most important class of problem in computer science, non-deterministic polynomial complete problems, non-deterministic UTMs (NUTMs) are theoretically exponentially faster than both classical UTMs and quantum mechanical UTMs (QUTMs). However, no attempt has previously been made to build an NUTM, and their construction has been regarded as impossible. Here, we demonstrate the first physical design of an NUTM. This design is based on Thue string rewriting systems, and thereby avoids the limitations of most previous DNA computing schemes: all the computation is local (simple edits to strings) so there is no need for communication, and there is no need to order operations. The design exploits DNA's ability to replicate to execute an exponential number of computational paths in P time. Each Thue rewriting step is embodied in a DNA edit implemented using a novel combination of polymerase chain reactions and site-directed mutagenesis. We demonstrate that the design works using both computational modelling and
in vitro
molecular biology experimentation: the design is thermodynamically favourable, microprogramming can be used to encode arbitrary Thue rules, all classes of Thue rule can be implemented, and non-deterministic rule implementation. In an NUTM, the resource limitation is space, which contrasts with classical UTMs and QUTMs where it is time. This fundamental difference enables an NUTM to trade space for time, which is significant for both theoretical computer science and physics. It is also of practical importance, for to quote Richard Feynman ‘there's plenty of room at the bottom’. This means that a desktop DNA NUTM could potentially utilize more processors than all the electronic computers in the world combined, and thereby outperform the world's current fastest supercomputer, while consuming a tiny fraction of its energy.
Sex pheromone of a coccoid insect with sexual and asexual lineages: fate of an ancestrally essential sexual signal in parthenogenetic females
Authors: Tabata Jun , Ichiki Ryoko T. , Moromizato Chie , Mori Kenji
Published: March 2017

Sex pheromones play a central role in intersexual communication for reproduction in many organisms. Particularly in insects, reproductive isolation that leads to speciation is often achieved by shifts of pheromone chemistries. However, the divergence and evolution of pheromones remain largely unknown. This study reveals a unique evolutionary consequence for terpenoid pheromones in coccoid insects. Coccoids, such as mealybugs, show clear sexual dimorphism: males are dwarf and short-lived, whereas females are wingless and almost immobile. Female pheromones are therefore indispensable for males to navigate for sexual reproduction, but some females can reproduce asexually. Interestingly, a derived asexual lineage that reproduces by parthenogenesis coexists with its ancestral lineage that reproduces sexually in a population of the pineapple mealybug,
Dysmicoccus brevipes
. Here, we isolated, characterized and synthesized a novel monoterpene, (−)-(
anti
-1,2-dimethyl-3-methylenecyclopentyl)acetaldehyde, as a pheromone of the sexual females of
D
.
brevipes
. This monoterpene aldehyde, with an irregular linkage of isoprene units, is notable, because all mealybug pheromones previously reported are carboxylic esters of terpenols. This compound was, however, never produced by the asexual females. As a consequence of acquiring parthenogenetic reproduction, the asexual females appear to have abandoned the production of the sex pheromone, which had been essential to attracting males in their ancestors.
Neuronal function of the mRNA decapping complex determines survival ofCaenorhabditis elegansat high temperature through temporal regulation of heterochronic gene expression
Authors: Borbolis Fivos , Flessa Christina-Maria , Roumelioti Fani , Diallinas George , Stravopodis Dimitrios J. , Syntichaki Popi
Published: March 2017

In response to adverse environmental cues,Caenorhabditis eleganslarvae can temporarily arrest development at the second moult and form dauers, a diapause stage that allows for long-term survival. This process is largely regulated by certain evolutionarily conserved signal transduction pathways, but it is also affected by miRNA-mediated post-transcriptional control of gene expression. The 5′–3′ mRNA decay mechanism contributes to miRNA-mediated silencing of target mRNAs in many organisms but how it affects developmental decisions during normal or stress conditions is largely unknown. Here, we show that loss of the mRNA decapping complex activity acting in the 5′–3′ mRNA decay pathway inhibits dauer formation at the stressful high temperature of 27.5°C, and instead promotes early developmental arrest. Our genetic data suggest that this arrest phenotype correlates with dysregulation of heterochronic gene expression and an aberrant stabilization oflin-14mRNA at early larval stages. Restoration of neuronaldcap-1activity was sufficient to rescue growth phenotypes ofdcap-1mutants at both high and normal temperatures, implying the involvement of common developmental timing mechanisms. Our work unveils the crucial role of 5′–3′ mRNA degradation in proper regulation of heterochronic gene expression programmes, which proved to be essential for survival under stressful conditions.
Modelling human perception processes in pedestrian dynamics: a hybrid approach
Authors: Colombi A. , Scianna M.
Published: March 2017

In this paper, we present a hybrid mathematical model describing crowd dynamics. More specifically, our approach is based on the well-established Helbing-like discrete model, where each pedestrian is individually represented as a dimensionless point and set to move in order to reach a target destination, with deviations deriving from both physical and social forces. In particular, physical forces account for interpersonal collisions, whereas social components include the individual desire to remain sufficiently far from other walkers (the so-called territorial effect). In this respect, the repulsive behaviour of pedestrians is here set to be different from traditional Helbing-like methods, as it is assumed to be largely determined by how they perceive the presence and the position of neighbouring individuals, i.e. either objectively as pointwise/localized entities or subjectively as spatially distributed masses. The resulting modelling environment is then applied to specific scenarios, that first reproduce a real-world experiment, specifically designed to derive our model hypothesis. Sets of numerical realizations are also run to analyse in more details the pedestrian paths resulting from different types of perception of small groups of static individuals. Finally, analytical investigations formalize and validate from a mathematical point of view selected simulation outcomes.
Face familiarity promotes stable identity recognition: exploring face perception using serial dependence
Authors: Kok Rebecca , Taubert Jessica , Van der Burg Erik , Rhodes Gillian , Alais David
Published: March 2017

Studies suggest that familiar faces are processed in a manner distinct from unfamiliar faces and that familiarity with a face confers an advantage in identity recognition. Our visual system seems to capitalize on experience to build stable face representations that are impervious to variation in retinal input that may occur due to changes in lighting, viewpoint, viewing distance, eye movements, etc. Emerging evidence also suggests that our visual system maintains a continuous perception of a face's identity from one moment to the next despite the retinal input variations through serial dependence. This study investigates whether interactions occur between face familiarity and serial dependence. In two experiments, participants used a continuous scale to rate attractiveness of unfamiliar and familiar faces (either experimentally learned or famous) presented in rapid sequences. Both experiments revealed robust inter-trial effects in which attractiveness ratings for a given face depended on the preceding face's attractiveness. This inter-trial attractiveness effect was most pronounced for unfamiliar faces. Indeed, when participants were familiar with a given face, attractiveness ratings showed significantly less serial dependence. These results represent the first evidence that familiar faces can resist the temporal integration seen in sequential dependencies and highlight the importance of familiarity to visual cognition.
A modified ‘NanoSuit®’ preserves wet samples in high vacuum: direct observations on cells and tissues in field-emission scanning electron microscopy
Authors: Takaku Yasuharu , Suzuki Hiroshi , Kawasaki Hideya , Ohta Isao , Ishii Daisuke , Hirakawa Satoshi , Tsutsui Takami , Matsumoto Haruko , Takehara Sayuri , Nakane Chinatsu , Sakaida Kana , Suzuki Chiaki , Muranaka Yoshinori , Kikuchi Hirotoshi , Konno Hiroyuki , Shimomura Masatsugu , Hariyama Takahiko
Published: March 2017

Although field-emission scanning electron microscopy (FE-SEM) has proven very useful in biomedical research, the high vacuum required (10
−3
to 10
−7
 Pa) precludes direct observations of living cells and tissues at high resolution and often produces unwanted structural changes. We have previously described a method that allows the investigator to keep a variety of insect larvae alive in the high vacuum environment of the electron microscope by encasing the organisms in a thin, vacuum-proof suit, the ‘NanoSuit®'. However, it was impossible to protect wet tissues freshly excised from intact organisms or cultured cells. Here we describe an improved ‘NanoSuit' technique to overcome this limitation. We protected the specimens with a surface shield enhancer (SSE) solution that consists of glycerine and electrolytes and found that the fine structure of the SSE-treated specimens is superior to that of conventionally prepared specimens. The SSE-based NanoSuit affords a much stronger barrier to gas and/or liquid loss than the previous NanoSuit did and, since it allows more detailed images, it could significantly help to elucidate the ‘real' organization of cells and their functions.
Efficient computation of null geodesics with applications to coherent vortex detection
Authors: Serra Mattia , Haller George
Published: March 2017

Recent results suggest that boundaries of coherent fluid vortices (elliptic coherent structures) can be identified as closed null geodesics of appropriate Lorentzian metrics defined on the flow domain. Here we derive an automated method for computing such null geodesics based on the geometry of the underlying geodesic flow. Our approach simplifies and improves existing procedures for computing variationally defined Eulerian and Lagrangian vortex boundaries. As an illustration, we compute objective vortex boundaries from satellite-inferred ocean velocity data. A MATLAB implementation of our method is available at
https://github.com/MattiaSerra/Closed-Null-Geodesics-2D
.
Sexual conflict over remating interval is modulated by the
sex peptide
pathway
Authors: Smith Damian T. , Clarke Naomi V. E. , Boone James M. , Fricke Claudia , Chapman Tracey
Published: March 2017

Sexual conflict, in which the evolutionary interests of males and females diverge, shapes the evolution of reproductive systems across diverse taxa. Here, we used the fruit fly to study sexual conflict in natural, three-way interactions comprising a female, her current and previous mates. We manipulated the potential for sexual conflict by using
sex peptide receptor
(
SPR
) null females and by varying remating from 3 to 48 h, a period during which natural rematings frequently occur.
SPR
-lacking females do not respond to sex peptide (SP) transferred during mating and maintain virgin levels of high receptivity and low fecundity. In the absence of SPR, there was a convergence of fitness interests, with all individuals gaining highest productivity at 5 h remating. This suggests that the expression of sexual conflict was reduced. We observed an unexpected second male-specific advantage to early remating, resulting from an increase in the efficiency of second male sperm use. This early window of opportunity for exploitation by second males depended on the presence of
SPR
. The results suggest that the SP pathway can modulate the expression of sexual conflict in this system, and show how variation in the selective forces that shape conflict and cooperation can be maintained.
Vine tendrils use contact chemoreception to avoid conspecific leaves
Authors: Fukano Yuya
Published: March 2017

Movement and growth habit of climbing plants have attracted attention since the time of Charles Darwin; however, there are no reports on whether plants can choose suitable hosts or avoid unsuitable ones based on chemoreception. Here, I show that the tendrils of
Cayratia japonica
(Vitaceae) appear to avoid conspecific leaves using contact chemoreception for oxalates, which are highly concentrated in
C. japonica
leaves. The coiling experiments show that
C. japonica
has a flexible plastic response to avoid coiling around conspecific leaves. The coiling response is negatively correlated with the oxalate content in the contacted leaves. Experiments using laboratory chemicals indicate that the tendrils avoid oxalate-coated plastic sticks. These results indicate that the tendrils of
C. japonica
avoid coiling around a conspecific leaf based on contact chemoreception for oxalate compounds. The tendrils of climbing plants may function as a chemoreceptor system to detect the chemical cues of a contacted plant.
Tbxl repressesMef2cgene expression by inducing histone 3 deacetylation of the anterior heart field enhancer
Authors: Pane Luna Simona , Fulcoli Filomena Gabriella , Cirino Andrea , Altomonte Alessandra , Ferrentino Rosa , Bilio Marchesa , Baldini Antonio
Published: March 2017

TheTBX1gene is haploinsufficient in the 22q11.2 deletion syndrome (22q11.2DS), and genetic evidence from human patients and mouse models points to a major role of this gene in the pathogenesis of this syndrome. Tbx1 can activate and repress transcription and previous work has shown that one of its functions is to negatively modulate cardiomyocyte differentiation. Tbx1 occupies the anterior heart field (AHF) enhancer of theMef2cgene, which encodes a key cardiac differentiation transcription factor. Here we show that increased dosage ofTbx1is associated with down regulation ofMef2cexpression and reduced acetylation of its AHF enhancer in cultured mouse myoblasts. Consistently, 22q11.2DS-derived and in vitro differentiated induced pluripotent stem cells (hiPSCs) expressed higher levels ofMef2cand showed increased AHF acetylation, compared to hiPSCs from a healthy donor. Most importantly, we show that in mouse embryos, loss ofTbx1enhances the expression of the Mef2c-AHF-Cre transgene in a specific region of the splanchnic mesoderm, and in a dosage-dependent manner, providing anin vivocorrelate of our cell culture data. These results indicate that Tbx1 regulates the Mef2c-AHF enhancer by inducing histone deacetylation.
Conflicting evolutionary histories of the mitochondrial and nuclear genomes in New WorldMyotisbats
Authors: Platt Roy N. , Faircloth Brant C. , Sullivan Kevin A.M. , Kieran Troy , Glenn Travis C. , Vandewege Michael W. , Lee Thomas E. , Baker Robert J. , Stevens Richard D. , Ray David A.
Published: March 2017

The rapid diversification ofMyotisbats into more than 100 species is one of the most extensive mammalian radiations available for study. Efforts to understand relationships withinMyotishave primarily utilized mitochondrial markers and trees inferred from nuclear markers lacked resolution. Our current understanding of relationships withinMyotisis therefore biased towards a set of phylogenetic markers that may not reflect the history of the nuclear genome. To resolve this, we sequenced the full mitochondrial genomes of 37 representativeMyotis,primarily from the New World, in conjunction with targeted sequencing of 3,648 ultraconserved elements (UCEs). We inferred the phylogeny and explored the effects of concatenation and summary phylogenetic methods, as well as combinations of markers based on informativeness or levels of missing data, on our results. Of the 294 phylogenies generated from the nuclear UCE data, all are significantly different from phylogenies inferred using mitochondrial genomes. Even within the nuclear data, quartet frequencies indicate that around half of all UCE loci conflict with the estimated species tree. Several factors can drive such conflict, including incomplete lineage sorting, introgressive hybridization, or even phylogenetic error. Despite the degree of discordance between nuclear UCE loci and the mitochondrial genome and among UCE loci themselves, the most common nuclear topology is recovered in one quarter of all analyses with strong nodal support. Based on these results, we re-examine the evolutionary history ofMyotisto better understand the phenomena driving their unique nuclear, mitochondrial, and biogeographic histories.
An exome sequencing study of Moebius syndrome including atypical cases reveals an individual with CFEOM3A and aTUBB3mutation
Authors: Patel Ronak M. , Liu David , Gonzaga-Jauregui Claudia , Jhangiani Shalini , Lu James T. , Sutton V. Reid , Fernbach Susan D. , Azamian Mahshid , White Lisa , Edmond Jane C. , Paysse Evelyn A. , Belmont John W. , Muzny Donna , Lupski James R. , Gibbs Richard A. , Lewis Richard Alan , Lee Brendan H. , Lalani Seema R. , Campeau Philippe M.
Published: March 2017

Moebius syndrome is characterized by congenital unilateral or bilateral facial and abducens nerve palsies (sixth and seventh cranial nerves) causing facial weakness, feeding difficulties, and restricted ocular movements. Abnormalities of the chest wall such as Poland anomaly and variable limb defects are frequently associated with this syndrome. Most cases are isolated; however, rare families with autosomal dominant transmission with incomplete penetrance and variable expressivity have been described. The genetic basis of this condition remains unknown. In a cohort study of nine individuals suspected to have Moebius syndrome (six typical, three atypical), we performed whole-exome sequencing to try to identify a commonly mutated gene. Although no such gene was identified and we did not find mutations inPLXND1andREV3L, we found a de novo heterozygous mutation, p.E410K, in the gene encoding tubulin beta 3 class III (TUBB3), in an individual with atypical Moebius syndrome. This individual was diagnosed with near-complete ophthalmoplegia, agenesis of the corpus callosum, and absence of the septum pellucidum. No substantial limb abnormalities were noted. Mutations inTUBB3have been associated with complex cortical dysplasia and other brain malformations and congenital fibrosis of extraocular muscles type 3A (CFEOM3A). Our report highlights the overlap of genetic etiology and clinical differences between CFEOM and Moebius syndrome and describes our approach to identifying candidate genes for typical and atypical Moebius syndrome.
Methods to Synthesize Large DNA Fragments for a Synthetic Yeast Genome
Authors: Cai Yizhi , Dai Junbiao
Published: March 2017

De novo DNA synthesis is one of the key enabling technologies for synthetic biology. Methods for large-scale DNA synthesis, in particular, have transformed many facets of life science research, supporting new discoveries in biology through the design of novel synthetic biological systems. This protocol describes in detail the methods currently being used to synthesize and assemble large pieces of DNA for the synthetic yeast genome project. The protocol includes instructions for building block synthesis as well as chunk assembly, each of which can be used as a stand-alone procedure to generate a synthetic DNA of interest.
Analyzing Microarray Data
Authors: Hung Jui-Hung , Weng Zhiping
Published: March 2017

Because there is no widely used software for analyzing RNA-seq data that has a graphical user interface, this protocol provides an example of analyzing microarray data using Babelomics. This analysis entails performing quantile normalization and then detecting differentially expressed genes associated with the transgenesis of a human oncogene c-Myc in mice. Finally, hierarchical clustering is performed on the differentially expressed genes using the Cluster program, and the results are visualized using TreeView.
Structure of epitaxial SrIrO3 perovskite studied by interference between X-ray waves diffracted by the substrate and the thin film
Authors: Horák Lukáš , Kriegner Dominik , Liu Jian , Frontera Carlos , Marti Xavier , Holý Václav
Published: March 2017

A high-pressure metastable orthorhombic phase of SrIrO3 perovskite has been epitaxially stabilized on several substrates (DyScO3, GdScO3, NdScO3 and SrTiO3) in the form of thin monocrystalline layers with (110) surface orientation. The unit-cell parameters of the pseudomorphic thin SrIrO3 layers depend on the biaxial strain imposed by the various substrates due to the different lattice mismatches of the particular substrate and the bulk orthorhombic SrIrO3 structure. Using X-ray diffractometry, it is shown that both compressive and tensile strain increase the lattice parameters a and b, while the angle γ scales with the applied strain, being smaller or larger than 90° for compressive or tensile strain, respectively, resulting in a small monoclinic distortion of the layer unit cell. Owing to the similarity of the substrate and layer lattices, the diffraction signals from the two structures overlap partially, which complicates structure determination by standard refinement methods using measured integrated intensities. The measured signal is composed of two interfering components corresponding to the waves diffracted by the substrate and by the layer, where the first component is calculated exactly using the known substrate structure, while the second one is determined by the unknown unit-cell parameters of the layer. The unit-cell parameters were refined in order to fit the experimental data with the simulation. The fractional coordinates of the atoms in the unit cell resulting from the fit are similar to those in the bulk structure.
So long, and thanks for only using readily available scripts
Authors: Holm Hannes , Sommestad Teodor
Published: March 2017

Purpose

It is often argued that the increased automation and availability of offensive cyber tools has decreased the skill and knowledge required by attackers. Some say that all it takes to succeed with an attack is to follow some instructions and push some buttons. This paper aims to tests this idea empirically through live exploits and vulnerable machines in a cyber range.

Design/methodology/approach

The experiment involved 204 vulnerable machines in a cyber range. Exploits were chosen based on the results of automated vulnerability scanning. Each exploit was executed following a set of carefully planned actions that enabled reliable tests. A total of 1,223 exploitation attempts were performed.

Findings

A mere eight exploitation attempts succeeded. All these involved the same exploit module (ms08_067_netapi). It is concluded that server-side attacks still are too complicated for novices who lack the skill or knowledge to tune their attacks.

Originality/value

This paper presents the largest conducted test of exploit effectiveness to date. It also presents a sound method for reliable tests of exploit effectiveness (or system vulnerability).
Chief financial officer (CFO) characteristics and ERP system adoption
Authors: Hiebl Martin R.W. , Gärtner Bernhard , Duller Christine
Published: March 2017

Purpose

This paper aims to examine the relationship between characteristics of chief financial officers (CFOs) and enterprise resource planning (ERP) system adoption. Following upper echelons theory, the authors theorize that CFO age, education, tenure and recruitment influence ERP system adoption, and that this relationship is moderated by the CFO being responsible for firm-wide information technology (IT) functions.

Design/methodology/approach

The empirical analysis is based on a survey of 296 large and medium-sized Austrian firms. Logistic regression analyses were used to test the association between CFO characteristics and ERP system adoption.

Findings

The authors find that firms with externally recruited CFOs have adopted ERP systems significantly more often than firms with internally promoted CFOs. Surprisingly, the results indicate that firms with less educated CFOs more often adopted an ERP system, and that the relationship between CFO characteristics and ERP system adoption is not moderated by the CFO being responsible for IT.

Research limitations/implications

This paper adds to the literature by corroborating case-based evidence that CFOs and their characteristics influence ERP system adoption. Extending previous research which indicates that CFO characteristics influence accounting practices, the authors show that CFO characteristics also influence technological innovation such as the adoption of ERP systems. Future research on technological innovation may therefore pay closer attention to the influence of CFOs.

Originality/value

This paper is the first to quantitatively test the influence of CFO characteristics on ERP system adoption.
Advancing sustainable business through discourse: a conceptual framework
Authors: Gauthier Jeffrey
Published: March 2017

Purpose

The purpose of this paper is to explore the relationship between individuals’ discursive practices and organizational-level strategic change with respect to sustainability strategy.

Design/methodology/approach

The approach taken integrates Hart’s natural resource-based view of the firm with discourse theory.

Findings

A conceptual model of the relationship between discursive practices and strategic change is proposed.

Research limitations/implications

The paper’s model serves as a foundation on which future empirical research on the effectiveness of specific discursive practices can be conducted.

Originality/value

Much of strategy research is notable for the absence of discussion on human actors and actions. The paper helps to fill this gap, contributing to existing scholarship by examining the micro-foundations of sustainability strategy through the fundamental role of individuals’ discursive practices.
CSR practices, ISO 26000 and performance among Malaysian automotive suppliers
Authors: Mohd Fuzi Nursyazwani , Habidin Nurul Fadly , Hibadullah Siti Norhafizan , Ong Sharon Yong Yee
Published: March 2017

Purpose

The purpose of this study is to examine the relationship between corporate social responsibility (CSR) practices, ISO 26000 and corporate social responsibility performance (CSRP) among Malaysian automotive suppliers.

Design/methodology/approach

For this research purpose, 400 questionnaires were given simultaneously to each Proton and Perodua automotive supplier by the researcher. In all, 288 sets of questionnaire were successfully collected, which showed a 72 per cent response rate for the 400 questionnaires distributed to Proton and Perodua automotive suppliers. In this study, the structural equation modeling (SEM) technique was utilized to perform the required statistical analysis of the data survey. To test the reliability and validity of the instruments, exploratory factor analysis, reliability analysis and confirmatory factor analysis were performed.

Findings

The findings indicate that the relationship between CSR practices and CSRP was positive and significant, and the relationship between CSR practices and ISO 26000 was also positive and significant. ISO 26000 has a direct positive and significant relationship with CSRP. Therefore, ISO 26000 mediates the relationship between CSR practices and CSRP. The results indicate that ISO 26000 could be considered as a partial mediator. Therefore, the impact of implementation of CSR practices on performance increases with ISO 26000 as a mediator among Malaysian automotive suppliers.

Practical implications

This research provides important guidelines for automotive and related companies to implement CSR practices and ISO 26000 to improve CSRP. Malaysian automotive suppliers may need to consider the measurement of CSR practices, ISO 26000 and CSRP as beneficial to their company. Based on the findings, Malaysian automotive suppliers can apply the ISO 26000 as the guideline for CSR practices to increase the CSRP.

Originality/value

This research makes a new contribution to ISO 26000 between CSR practices and CSRP, especially for Malaysian automotive suppliers, by using the SEM technique. This research provides important information for decision-makers involved in CSR practices, ISO 26000 and CSRP implementation and also provides useful reference for future researchers in this research area.
Extraintestinal infection of Helicobacter cinaedi induced by oral administration to Balb/c mice
Authors: Taniguchi Takako , Saeki Yuji , Okayama Akihiko , Hayashi Tetsuya , Misawa Naoaki
Published: March 2017

Although Helicobacter cinaedi was initially considered an opportunistic pathogen in immunocompromised patients, it was later shown to also infect immunocompetent and healthy individuals. Sporadic bacteremia due to H. cinaedi has frequently been reported; however, whether the bacterium can be translocated after passage through the intestinal mucosa remains unclear. In the present study, a preclinical small animal model that faithfully reproduces H. cinaedi infection in humans was developed. Balb/c male mice were orally inoculated with a single dose of 6.8 × 107 CFU of a human clinical H. cinaedi strain. The organism persistently colonized the intestinal tract of the mice, particularly the cecum and colon, for at least 56 days, and the bacteria were excreted in the feces. Although inoculated bacteria were recovered from the spleen, liver, kidney, lung, bladder and mesenteric lymph nodes during the first 2 weeks of bacteremia, the organism was not isolated from these organs after 4 weeks, suggesting that complement‐ and antibody‐mediated serum sensitivity account for the relatively low frequency of systemic infection. However, H. cinaedi was isolated from the biceps femoris, triceps branchii, latissimus dorsi, and trapezius muscles beyond 2 weeks after infection and after production of specific anti‐H. cinaedi IgM and IgG antibodies. The present findings suggest that experimental infection of Balb/c mice with H. cinaedi may be a useful model for further studies of H. cinaedi pathogenesis, prophylaxis or therapeutic interventions in vivo.
Increasing drought effects on five European pines modulate Δ13C‐growth coupling along a Mediterranean altitudinal gradient
Authors: Shestakova Tatiana A. , Camarero Jesús Julio , Ferrio Juan Pedro , Knorre Anastasia A. , Gutiérrez Emilia , Voltas Jordi
Published: March 2017

Climate warming increases vulnerability to drought in Mediterranean water‐limited forests. However, we still lack knowledge of the long‐term physiological responses of coexisting pine species in these forests regarding their ability to cope with warming‐induced drought stress.

We investigated spatiotemporal patterns of tree performance for five isohydric pines with partially overlapping ecological niches in the eastern Iberian Peninsula along an altitudinal gradient:Pinus halepensis = Pinus pinaster ≤ Pinus nigra ≤ Pinus sylvestris ≤ Pinus uncinata.

Using indexed tree‐ring widths (TRWi), we assessed the changes in the temporal coherence of radial growth (growth synchrony,âC) over the period 1902–2011 across three elevation belts: low ≈1100 m; mid = 1615 m; high = 2020 m. We also examined by mixed modelling whetherTRWishowed an increased coupling with leaf‐level gas exchange (inferred from indexed carbon isotope discrimination, Δ13Ci) by enhanced stomatal regulation in response to an amplified regional drought stress.

Increasingly negative annual water balances (decrease in annual precipitation minus evapotranspiration = −4·8 mm year−1; 1970–2011) prompted more synchronous growth of coexisting pines between low‐ and mid‐elevation belts, withâCrising from 0·25 ± 0·04 (1902–1951) to 0·62 ± 0·05 (1962–2011). This effect was coupled with tighter stomatal regulation at mid‐elevation as indicated by high correlations betweenTRWiand Δ13Ci(>0·60 from the mid‐1970s onwards) which resembled those found at low elevation. Simultaneously,TRWivs. Δ13Ciuncoupling occurred at the high‐elevation belt across species.

Weaker growth‐climate relationships as elevation increased highlighted the major role of the altitude‐dependent thermal gradient in growth responsiveness to drought; however, an intensified Δ13Ciresponse to spring water availability across elevation belts observed from mid‐1970s onwards suggested regional shifts in tree physiological activity linked to earlier seasonal drought impacts. Warming‐induced drought stress is spreading to higher altitudes in Iberian pinewoods as multispecies growth is linked to progressively tighter stomatal control of water losses reflected in wood Δ13C.
Linking animal contests and community structure using rockpool fishes as a model system
Authors: Paijmans Kai C. , Wong Marian Y. L.
Published: March 2017

Competition for limiting resources is a fundamental and well‐established driver of niche partitioning, which in turn promotes species coexistence and biodiversity. Although contests are a well‐known behavioural mechanism by which organisms compete over limiting resources, there has been surprisingly little application of contest theory to understanding interspecific interactions, niche partitioning, species coexistence and biodiversity.

We investigated the link between contest dynamics and community structure using two intertidal rockpool fishes,Bathygobius cocosensis(Gobiidae) andLepidoblennius haplodactylus(Tripterygiidae), as model species. We assessed the abundance and distribution of the two species on intertidal rocky shores of South‐East Australia, and whether distribution patterns were related to abiotic variables. We then conducted interspecific contest experiments between pairs ofB. cocosensisandL. haplodactylusof varying size and sex under high and low dissolved oxygen levels to assess the competitive dominance of the species. To relate these results to community structure, we quantified temporal patterns of rockpool fidelity of each speciesin situ.

Field surveys revealed thatB. cocosensiswas most prevalent in rockpools with higher dissolved oxygen, andL. haplodactyluswas most prevalent in rockpools that contained noB. cocosensis. Contest experiments revealed thatB. cocosensisdisplayed higher resource holding power thanL. haplodactylusregardless of size asymmetry, sex or dissolved oxygen concentration, although contest intensity was influenced by relative body size of competing individuals. Furthermore, the microhabitat preference ofL. haplodactyluswas modulated in the presence ofB. cocosensis. In the field,B. cocosensisdisplayed higher rockpool fidelity thanL. haplodactylus.

In light of these findings, we propose thatB. cocosensisis the superior competitor but persistence of both species is likely facilitated by low‐cost contest resolution strategies, plasticity in microhabitat preference, negative spatial co‐variation and interspecific variation in dispersal and corresponding home range sizes.

By using contest theory to understand the dynamics of interspecific contests, insight has been gained into how habitat is partitioned, species coexist and ultimately how biodiversity is maintained.

Alay summaryis available for this article.
Interactions between rainfall, fire and herbivory drive resprouter vital rates in a semi‐arid ecosystem
Authors: Giljohann Katherine M. , McCarthy Michael A. , Keith David A. , Kelly Luke T. , Tozer Mark G. , Regan Tracey J.
Published: March 2017

Global change is threatening ecosystems and biodiversity world‐wide, creating a pressing need to understand how climate and disturbance regimes interact and influence the persistence of species. We quantify how three ecosystem drivers – rainfall, fire and herbivory – influence vital rates in the perennial resprouting graminoid, Triodia scariosa, a foundation species of semi‐arid Australia.

We used an 11‐year dataset from a fire and herbivore exclosure experiment, to model flowering, post‐fire recruitment and the post‐fire survival of seedlings and resprouting plants. Regression modelling quantified the effect of rainfall, inter‐fire interval, fire type (wildfire or prescribed fire), grazing by herbivores (native and feral) and an interaction between fire type and herbivory on T. scariosa populations.

Rainfall, fire and herbivory had significant effects on post‐fire recruitment and the survival of seedlings and resprouting plants, including strong interactions between these drivers. Herbivory following wildfire had a minor effect, but in years of below‐average rainfall herbivory following prescribed fire had a large effect, reducing the survival of seedlings and resprouting plants by 20% and over 50% respectively, relative to post‐fire survival under average rainfall conditions.

Variation in rainfall underpinned significant variation in post‐fire resprouting and seedling survival, thus we postulate rainfall primarily drives the dynamics of T. scariosa populations.

Synthesis. This study highlights the importance of modelling interactions between key ecosystem drivers when predicting how changes in global climate and disturbance regimes influence plant vital rates. Relatively small changes to disturbance regimes can substantially alter population processes, even in perennial resprouting species. This work suggests that conservation of foundation species, such as T. scariosa, will benefit if fire management decisions are better integrated with inter‐annual weather forecasts and herbivore management.
Uncertainty and Monetary Policy
Authors: Kent Christopher
Published: March 2017

This article presents three dimensions of uncertainty that policy‐makers face when making policy decisions: data uncertainty, model uncertainty and unexpected events. Data uncertainty relates to both revisions and other measurement problems that imply that data are subject to a degree of ‘noise’. Model uncertainty relates to the imperfect knowledge we have on the structure of the economy, including the transmission mechanism of monetary policy and the effect of macroeconomic shocks. Unexpected events or shocks contribute to uncertainty about the future, along with the potential for the structure of the economy to evolve over time, which makes the past a poor guide to the future. The article discusses how these different dimensions of uncertainty can influence monetary policy decisions.
Observations on Uncertainty
Authors: Bloom Nicholas
Published: March 2017

I discuss three phenomena which appear important for modelling the impact of uncertainty on growth. The first is international spillovers in uncertainty, which arise even in large countries like the United States and particularly in smaller countries like Australia. Second, that the main channel for uncertainty to impact gross domestic product growth is through investment, which responds much more strongly and rapidly than consumption expenditure. This is possibly because firms are more forward‐looking than consumers, so respond more strongly to changes in future expectations of business conditions. Third, I discuss how recently uncertainty has spiked in three waves: the great recession of 2008–2009, the fiscal crises in the United States and Europe from 2010 to 2012 and recently after the Brexit and Trump votes.
Accounting for Uncertainty in Public Debt Targets
Authors: Fukač Martin , Kirkby Robert
Published: March 2017

We use a semi‐structural fan‐chart approach to measure the changing nature of uncertainty for public debt targets in New Zealand. We find that economic and fiscal factors dominate the uncertainty landscape over the 3 year and longer time horizons. The near term tends to be dominated by non‐fundamental factors, such as measurement errors, that are typically outside of reasonable policy responses. We conclude that medium‐term fiscal targets are better placed to support macroeconomic stability than short‐term targets. We also quantify the fiscal buffers that may be needed to offset some of the future uncertainty, if policy‐makers choose to do so. The analysis is intended to support contingency planning in fiscal management and communication strategy of fiscal targets.
An ‘Unpleasant Dilemma’: The Portsmouth Volunteers and the Limits of Loyalism, 1803‐5
Authors: Linch Kevin
Published: March 2017

This article takes up Matthew McCormack's appeal for the closer scrutiny of loyalism across the eighteenth century through a case study of the Portsmouth Volunteers at the height of the 1803‐5 invasion scare. The part‐time military forces of the town were riven by a dispute between its officers and the garrison's military governor that ultimately shattered the unit. Utilising the extensive correspondence regarding the case, this article argues that loyalism had robust legalist and associational features that were employed as a bastion against the potential of unbridled military control inherent within mass‐mobilisation.
Property, Patriotism and Independence: The Figure of the ‘Freeholder’ in Eighteenth‐Century Partisan Print
Authors: Smith Adam James
Published: March 2017

This article accounts for the changing usage of the term ‘freeholder’ across a series of political battles fought throughout the eighteenth century, tracking its implementation in both cheap and privileged print from the end of Queen Anne's reign to the dawn of the America Revolution. Analysis of the term offers an insightful perspective on the epistemic reconfigurations of the associative links between property, patriotism, partisanship and public responsibility throughout the eighteenth century. Considering ballads, pamphlets and periodicals produced by Whigs, Tories and the opposition, this article focuses particularly on the writing of Joseph Addison, Francis Atterbury and Henry St John.
Using Factor Mixture Models to Evaluate the Type A/B Classification of Alcohol Use Disorders in a Heterogeneous Treatment Sample
Authors: Hildebrandt Tom , Epstein Elizabeth E. , Sysko Robyn , Bux Donald A.
Published: March 2017

Background

The type A/B classification model for alcohol use disorders (AUDs) has received considerable empirical support. However, few studies examine the underlying latent structure of this subtyping model, which has been challenged as a dichotomization of a single drinking severity dimension. Type B, relative to type A, alcoholics represent those with early age of onset, greater familial risk, and worse outcomes from alcohol use.

Methods

We examined the latent structure of the type A/B model using categorical, dimensional, and factor mixture models in a mixed‐gender community treatment‐seeking sample of adults with an AUD.

Results

Factor analytic models identified 2 factors (drinking severity/externalizing psychopathology and internalizing psychopathology) underlying the type A/B indicators. A factor mixture model with 2 dimensions and 3 classes emerged as the best overall fitting model. The classes reflected a type A class and 2 type B classes (B1 and B2) that differed on the respective level of drinking severity/externalizing pathology and internalizing pathology. Type B1 had a greater prevalence of women and more internalizing pathology and B2 had a greater prevalence of men and more drinking severity/externalizing pathology. The 2‐factor, 3‐class model also exhibited predictive validity by explaining significant variance in 12‐month drinking and drug use outcomes.

Conclusions

The model identified in this study may provide a basis for examining different sources of heterogeneity in the course and outcome of AUDs.
On the relationships in rhesus macaques between chronic ethanol consumption and the brain transcriptome
Authors: Iancu Ovidiu D. , Colville Alexander , Walter Nicole A.R. , Darakjian Priscila , Oberbeck Denesa L. , Daunais James B. , Zheng Christina L. , Searles Robert P. , McWeeney Shannon K. , Grant Kathleen A. , Hitzemann Robert
Published: March 2017

This is the first description of the relationship between chronic ethanol self‐administration and the brain transcriptome in a non‐human primate (rhesus macaque). Thirty‐one male animals self‐administered ethanol on a daily basis for over 12 months. Gene transcription was quantified with RNA‐Seq in the central nucleus of the amygdala (CeA) and cortical Area 32. We constructed coexpression and cosplicing networks, and we identified areas of preservation and areas of differentiation between regions and network types. Correlations between intake and transcription included largely distinct gene sets and annotation categories across brain regions and between expression and splicing; positive and negative correlations were also associated with distinct annotation groups. Membrane, synaptic and splicing annotation categories were over‐represented in the modules (gene clusters) enriched in positive correlations (CeA); our cosplicing analysis further identified the genes affected only at the exon inclusion level. In the CeA coexpression network, we identified Rab6b, Cdk18 and Igsf21 among the intake‐correlated hubs, while in the Area 32, we identified a distinct hub set that included Ppp3r1 and Myeov2. Overall, the data illustrate that excessive ethanol self‐administration is associated with broad expression and splicing mechanisms that involve membrane and synapse genes.
Congenital erosive and vesicular dermatosis with reticulated supple scarring
Authors: Wong Vincent , Fischer Gayle
Published: March 2017

Congenital erosive and vesicular dermatosis with reticulated supple scarring is a rare cutaneous disorder of unknown aetiology first described by Cohen and colleagues in 1985. It classically presents in the neonate as erosions and vesicles that heal within the first months of life, with supple scarring of a reticulated pattern. Along with a review of the literature, this article presents two atypical cases of congenital erosive and vesicular dermatosis with reticulated supple scarring. Patient one presented with neither erosions nor vesicles at birth, yet continued to experience sporadic blistering at the age of 15 months and patient two is the second documented case to develop congenital erosive and vesicular dermatosis after birth.