bluuebunny/crossref_metadata_2025 huggingface dataset:
Statistical Significance Testing in Second Language Research: Basic Problems and Suggestions for Reform
Authors: Norris John M.
Published: May 2015

Traditions of statistical significance testing in second language (L2) quantitative research are strongly entrenched in how researchers design studies, select analyses, and interpret results. However, statistical significance tests using p values are commonly misinterpreted by researchers, reviewers, readers, and others, leading to confusion regarding the actual findings of primary studies and critical challenges for the accumulation of meaningful knowledge about language learning research. This paper outlines the basic challenges of accurately calculating and interpreting statistical significance tests, explores common examples of incorrect interpretations in L2 research, and proposes strategies for resolving these problems.
Structural Equation Modeling: Possibilities for Language Learning Researchers1
Authors: Hancock Gregory R. , Schoonen Rob
Published: May 2015

Although classical statistical techniques have been a valuable tool in second language (L2) research, L2 research questions have started to grow beyond those techniques’ capabilities, and indeed are often limited by them. Questions about how complex constructs relate to each other or to constituent subskills, about longitudinal development in those constructs and factors affecting that development, and about differences among populations in average amounts of complex constructs or in their relations require a broader analytical framework. Fortunately, that of structural equation modeling (SEM), a versatile and ever‐expanding family of techniques, is able to accommodate such questions and many more. The current article describes some of the questions that can be addressed by SEM, presents some research examples within the existing L2 literature, and then provides examples of the incredible potential of SEM, cautions in its practice, and resources for further information.
Colonization of a novel depauperate habitat leads to trophic niche shifts in three desert lizard species
Authors: Des Roches Simone , Harmon Luke J. , Rosenblum Erica B.
Published: May 2015

In a novel, depauperate ecosystem, colonizing species may experience changes in their trophic niche as a result of a new resource base and fewer competitors and predators. To examine trophic niche shifts of recent colonists, we focused on three ecologically and phylogenetically divergent lizard species that inhabit both the geologically distinctive depauperate habitat of White Sands and the surrounding Chihuahuan ‘dark soil’ desert in New Mexico. In White Sands the three species comprise the entire lizard community, whereas in the dark soils habitat, they constitute less than half of the lizard community abundance. As a result, we hypothesized that the three focal species would collectively represent a greater variety of trophic positions in the White Sands habitat than in the dark soils habitat. We hypothesized that the extent of shifts in each species’ trophic position would parallel diet and ecomorphology differences between habitats. To test these hypotheses, we combined analysis of lizard stomach contents with carbon and nitrogen stable isotopes in the context of previously published ecomorphology measurements. Stable isotope data indicated that as predicted, species were more different from one another in White Sands than in dark soils, suggesting community‐wide ecological release. Overall, all species were lower on the White Sands food chain; however, only one species decreased trophic level significantly, one increased trophic level variance, and one did not change significantly. Furthermore, stomach content data paralleled both stable isotope and ecomorphological data, showing different degrees of dietary overlap between habitats, depending on the species. That species’ differences in trophic ecology also correspond with ecomorphological differences suggests that these factors are either causally linked or collectively responding to similar ecological pressures, such as competition. By examining diet, trophic position, and ecomorphology of three colonist species, we demonstrate both species‐specific and community‐wide trophic differences in adjacent, but distinct habitats.
Growth, developmental and stress responses of larvae of the clouded sulphur butterfly Colias eriphyle to repeated exposure to high, sub‐lethal temperatures
Authors: Higgins Jessica K. , MacLean Heidi J. , Buckley Lauren B. , Kingsolver Joel G.
Published: May 2015

The optimal temperature at which an organism grows and develops is commonly correlated with latitude and elevation; however, the maximum temperature for physiological performance often is not. This makes performance at temperatures between the optimum and the maximum of particular interest. Temperature can influence long‐term performance (growth and development), as well as short‐term performance (heat shock protein) responses differentially. In the present study, two populations of the clouded sulphur butterfly Colias eriphyle Edwards that differ in elevation, thermal regime and optimal and maximum temperatures are studied to quantify their responses to repeated, sub‐lethal heat treatments early in development (second instar). Heat treatments accelerate development during the second to fourth instars in both populations initially, although this effect disappears by pupation. Heat treatment decreases pupal mass in the lower elevation population, suggesting that repeated exposure to high temperatures early in development may reduce final size and fecundity in this population. Heat shock protein gene (hsp70) expression levels in the lower elevation (1633 m a.s.l.) population are highest 24 h after the start of the heat treatment and then the fall to pre‐exposure levels by 36–72 h, suggesting a rapid response to stressful temperatures. By contrast, heat treatment has no significant effect on pupal mass in the higher elevation (2347 m a.s.l.) population. This population has higher levels of hsp70 expression overall but constant expression levels, suggesting that the temperature treatments used are insufficient to elicit a heat stress response. Overall, the effects of repeated exposure to sub‐lethal high temperatures early in development on growth, final size and gene expression differ between populations that differ in thermal sensitivity.
The Effect of Surface Charge Saturation on Heat‐induced Aggregation of Firefly Luciferase
Authors: Gharanlar Jamileh , Hosseinkhani Saman , Sajedi Reza H. , Yaghmaei Parichehr
Published: May 2015

We present here the effect of firefly luciferase surface charge saturation and the presence of some additives on its thermal‐induced aggregation. Three mutants of firefly luciferase prepared by introduction of surface Arg residues named as 2R, 3R and 5R have two, three and five additional arginine residues substituted at their surface compared to native luciferase; respectively. Turbidimetric study of heat‐induced aggregation indicates that all three mutants were reproducibly aggregated at higher rates relative to wild type in spite of their higher thermostability. Among them, 2R had most evaluated propensity to heat‐induced aggregation. Therefore, the hydrophilization followed by appearing of more substituted arginine residues with positive charge on the firefly luciferase surface was not reduced its thermal aggregation. Nevertheless, at the same condition in the presence of charged amino acids, e.g. Arg, Lys and Glu, as well as a hydrophobic amino acid, e.g. Val, the heat‐induced aggregation of wild type and mutants of firefly luciferases was markedly decelerated than those in the absence of additives. On the basis of obtained results it seems, relinquishment of variety in charge of amino acid side chains, they via local interactions with proteins cause to decrease rate and extent of their thermal aggregation.
Two WUSCHEL‐related HOMEOBOX genes, PeWOX11a and PeWOX11b, are involved in adventitious root formation of poplar
Authors: Xu Meng , Xie Wenfan , Huang Minren
Published: May 2015

The plant‐specific WUSCHEL‐related HOMEOBOX (WOX) transcription factors play important roles in key developmental processes, but knowledge regarding functional characterization of WOX genes in poplar remains limited. To reveal genes and signaling pathways associated with adventitious rooting in poplar, here we isolated and characterized two WOX genes through the rapid amplification of cDNA ends (RACE), sequence aligning, expression profiling, protoplast transfection and poplar transformation. Detailed information about the sequence similarity, structural features, evolutionary relationships, expression patterns and subcellular localization of the two genes were revealed. Overexpression of either PeWOX11a or PeWOX11b not only increased the number of adventitious roots on the cuttings but also induced ectopic roots in the aerial parts of transgenic poplars. Meanwhile, their overexpression in transgenic poplars affected axillary bud and leaf development. These results suggest that PeWOX11a and PeWOX11b were involved in multiple developmental processes of poplar, especially in adventitious root formation. Our results provide new insights into the molecular mechanisms underlying adventitious root formation of poplar.
Modulation of the attentional span by foveal and parafoveal task load: An ERP study using attentional probes
Authors: Kornrumpf Benthe , Sommer Werner
Published: May 2015

Due to capacity limitation, visual attention must be focused to a limited region of the visual field. Nevertheless, it is assumed that the size of that region may vary with task demands. We aimed to obtain direct evidence for the modulation of visuospatial attention as a function of foveal and parafoveal task load. Participants were required to fixate the center word of word triplets. In separate task blocks, either just the fixated word or both the fixated and the parafoveal word to the right should be semantically classified. The spatiotemporal distribution of attention was assessed with task‐irrelevant probes flashed briefly at center or parafoveal positions, during or in between word presentation trials. The N1 component of the ERP elicited by intertrial probes at possible target positions increased with task demands within a block. These results suggest the recruitment of additional attentional resources rather than a redistribution of a fixed resource pool, which persists across trials.
A GIS‐based decision‐making approach for prioritizing seabird management following predator eradication
Authors: Borrelle Stephanie B. , Buxton Rachel T. , Jones Holly P. , Towns David R.
Published: May 2015

Given that 29% of seabird species are threatened with extinction, protecting seabird colonies on offshore islands is a global conservation priority. Seabirds are vulnerable to non‐native predator invasions, which reduce or eliminate colonies. Accordingly, conservation efforts have focused on predator eradication. However, affected populations are often left to passively recover following eradications. Although seabirds are highly mobile, their life history traits such as philopatry can limit passive recolonization of newly predator‐free habitat. In such cases, seabird colonies can potentially be re‐instated with active restoration via chick translocations or social attraction methods, which can be risky and expensive. We used biogeographic and species‐specific behavioral data in the Hauraki Gulf, New Zealand, a global hotspot of seabird diversity and predator eradications, to illustrate the use of geographic information systems multi‐criteria decision analysis to prioritize islands for active seabird restoration. We identified nine islands with low observed passive recovery of seabirds posteradication over a 50‐year timeframe, and classified these as sites where active seabird management could be prioritized. Such spatially explicit tools are flexible, allowing for managers to choose case‐specific criteria such as time, funding, and goals constrained for their conservation needs. Furthermore, this flexibility can also be applied to threatened species management by customizing the decision criteria for individual species' capacity to passively recolonize islands. On islands with complex restoration challenges, decision tools that help island restoration practitioners decide whether active seabird management should be paired with eradication can optimize restoration outcomes and ecosystem recovery.
A Note on the New Rule for the Current Account
Authors: Erauskin Iñaki
Published: May 2015

In this note, we show that the two main concerns against the new rule for the current account are flawed. The new rule states that the impact of a transitory income shock on the current account is given by the savings generated by the shock multiplied by the ratio of the net foreign asset position to domestic wealth. First, we adapt the new rule to distinguish between gross and net foreign asset positions. Second, we demonstrate that the results for the new rule are driven neither by an accounting‐based “approximate” regression nor a steady state.
A simple method for measuring power, force, velocity properties, and mechanical effectiveness in sprint running
Authors: Samozino P. , Rabita G. , Dorel S. , Slawinski J. , Peyrot N. , Saez de Villarreal E. , Morin J.‐B.
Published: May 2015

This study aimed to validate a simple field method for determining force– and power–velocity relationships and mechanical effectiveness of force application during sprint running. The proposed method, based on an inverse dynamic approach applied to the body center of mass, estimates the step‐averaged ground reaction forces in runner's sagittal plane of motion during overground sprint acceleration from only anthropometric and spatiotemporal data. Force– and power–velocity relationships, the associated variables, and mechanical effectiveness were determined (a) on nine sprinters using both the proposed method and force plate measurements and (b) on six other sprinters using the proposed method during several consecutive trials to assess the inter‐trial reliability. The low bias (<5%) and narrow limits of agreement between both methods for maximal horizontal force (638 ± 84 N), velocity (10.5 ± 0.74 m/s), and power output (1680 ± 280 W); for the slope of the force–velocity relationships; and for the mechanical effectiveness of force application showed high concurrent validity of the proposed method. The low standard errors of measurements between trials (<5%) highlighted the high reliability of the method. These findings support the validity of the proposed simple method, convenient for field use, to determine power, force, velocity properties, and mechanical effectiveness in sprint running.
Sensitivity of Echinochloa crus‐galli populations to maize herbicides: a comparison between cropping systems
Authors: Claerhout S , Reheul D , De Cauwer B
Published: May 2015

Echinochloa crus‐galli is an important maize weed with significant variation in herbicide sensitivity. This differential response may reflect differences in selection pressure caused by years of cropping system‐related herbicide usage. The herbicide sensitivity of E. crus‐galli populations from three divergent cropping systems was evaluated in dose–response pot experiments. Populations were collected from sandy fields with (i) a long‐term organic cropping system, (ii) a conventional cropping system with maize in the crop rotation or (iii) a conventional cropping system with long‐term monocropping of maize. Each cropping system was represented by six E. crus‐galli populations. The effectiveness of three foliar‐applied maize herbicides (nicosulfuron, cycloxydim and topramezone) and two soil‐applied maize herbicides (S‐metolachlor and dimethenamid‐P) was tested at three doses and two runs. Foliar‐applied herbicides were applied at the three true leaves stage. Soil‐applied herbicides were applied immediately after sowing. The foliage dry weight per pot was determined 4 weeks after treatment. Plant responses were expressed as biomass reduction. Herbicide sensitivity was consistently lowest for populations from maize monocropping systems. Compared with populations from organic cropping systems, populations from monocropping systems showed 6.9%, 9.8% and 29.3% lower sensitivity to cycloxydim, topramezone and nicosulfuron respectively. Populations from the conventional crop rotation system showed intermediate sensitivity levels, which did not significantly differ from sensitivity levels of populations from the other cropping systems. Sensitivity to dimethenamid‐P and S‐metolachlor was not affected by cropping system. Environmental conditions influenced herbicidal response. This study indicated that integrated weed management may be necessary to preserve herbicide efficacy over the long term.
Reversed electrogenic sodium bicarbonate cotransporter 1 is the major acid loader during recovery from cytosolic alkalosis in mouse cortical astrocytes
Authors: Theparambil Shefeeq M. , Naoshin Zinnia , Thyssen Anne , Deitmer Joachim W.
Published: May 2015

Key points

The regulation of H+i from cytosolic alkalosis has generally been attributed to the activity of Cl–‐coupled acid loaders/base extruders in most cell types, including brain cells.

The present study demonstrates that outwardly‐directed sodium bicarbonate cotransport via electrogenic sodium bicarbonate cotransporter 1 (NBCe1) mediates the major fraction of H+i regulation from cytosolic alkalosis in mouse cortical astrocytes.

Cl–‐coupled acid‐loading transporters play only a minor role in the regulation of H+i from alkalosis in mouse cortical astrocytes.

NBCe1‐mediated H+i regulation from alkalosis was dominant, with the support of intracellular carbonic anhydrase II, even when the intra‐ and extracellular [HCO3–] was very low (<1mM), as in nominally CO2/HCO3– free condition.

A reversed NBCe1 in astrocytes may also be significant for stabilizing extracellular pH in brain tissue.

Recovery of intracellular pH from cytosolic alkalosis has been attributed primarily to Cl– coupled acid loaders/base extruders such as Cl–/HCO3– or Cl–/OH– exchangers. We have studied this process in cortical astrocytes from wild‐type and transgenic mouse models with gene deletion for the electrogenic sodium bicarbonate cotransporter 1 (NBCe1) and for carbonic anhydrase (CA) isoform II. An acute cytosolic alkalosis was induced by the removal of either CO2/HCO3– or butyric acid, and the subsequent acid loading was analysed by monitoring changes in cytosolic H+ or Na+ using ion‐sensitive fluorescent dyes. We have identified that NBCe1 reverses during alkalosis and contributes more than 70% to the rate of recovery from alkalosis by extruding Na+ and HCO3–. After CA inhibition or in CAII‐knockout (KO) cells, the rate of recovery was reduced by 40%, and even by 70% in the nominal absence of CO2/HCO3–. Increasing the extracellular K+ concentration modulated the rate of acid loading in wild‐type cells, but not in NBCe1‐KO cells. Removing chloride had only a minor effect on the recovery from alkalosis. Reversal of NBCe1 by reducing pH/[HCO3–] was demonstrated in astrocytes and in Xenopus oocytes, in which human NBCe1 was heterologously expressed. The results obtained suggest that reversed NBCe1, supported by CAII activity, plays a major role in acid‐loading cortical astrocytes to support recovery from cytosolic alkalosis.
cAMP‐dependent protein kinase inhibits α7 nicotinic receptor activity in layer 1 cortical interneurons through activation of D1/D5 dopamine receptors
Authors: Komal Pragya , Estakhr Jasem , Kamran Melad , Renda Anthony , Nashmi Raad
Published: May 2015

Key points

Protein kinases can modify the function of many proteins including ion channels.

However, the role of protein kinase A in modifying nicotinic receptors in the CNS has never been investigated.

We showed through whole‐cell recordings of layer 1 prefrontal cortical interneurons that α7 nicotinic responses are negatively modulated by protein kinase A.

Furthermore, we show that stimulation of dopamine receptors can similarly attenuate α7 nicotinic responses through the activation of protein kinase A.

These results suggest how the interaction of the cholinergic and dopaminergic systems may influence neuronal excitability in the brain.

Phosphorylation of ion channels, including nicotinic acetylcholine receptors (nAChRs), by protein kinases plays a key role in the modification of synaptic transmission and neuronal excitability. α7 nAChRs are the second most prevalent nAChR subtype in the CNS following α4β2. Serine 365 in the M3–M4 cytoplasmic loop of the α7 nAChR is a phosphorylation site for protein kinase A (PKA). D1/D5 dopamine receptors signal through the adenylate cyclase–PKA pathway and play a key role in working memory and attention in the prefrontal cortex. Thus, we examined whether the dopaminergic system, mediated through PKA, functionally interacts with the α7‐dependent cholinergic neurotransmission. In layer 1 interneurons of mouse prefrontal cortex, α7 nicotinic currents were decreased upon stimulation with 8‐Br‐cAMP, a PKA activator. In HEK 293T cells, dominant negative PKA abolished 8‐Br‐cAMP's effect of diminishing α7 nicotinic currents, while a constitutively active PKA catalytic subunit decreased α7 currents. In brain slices, the PKA inhibitor KT‐5720 nullified 8‐Br‐cAMP's effect of attenuating α7 nicotinic responses, while applying a PKA catalytic subunit in the pipette solution decreased α7 currents. 8‐Br‐cAMP stimulation reduced surface expression of α7 nAChRs, but there was no change in single‐channel conductance. The D1/D5 dopamine receptor agonist SKF 83822 similarly attenuated α7 nicotinic currents from layer 1 interneurons and this attenuation of nicotinic current was prevented by KT‐5720. These results demonstrate that dopamine receptor‐mediated activation of PKA negatively modulates nicotinic neurotransmission in prefrontal cortical interneurons, which may be a contributing mechanism of dopamine modulation of cognitive behaviours such as attention or working memory.
The ambiguity of “distinguishability” in statistical mechanics
Authors: Swendsen Robert H.
Published: May 2015

Differences of opinion concerning fundamental issues in statistical mechanics directly related to the thermodynamic entropy have persisted through more than a century of debate. One reason is the lack of consensus on the definitions of key terms, especially the terms “distinguishable,” “indistinguishable,” and “identical.” Several definitions occur in the literature, but are not always made explicit. The multiplicity of definitions has created confusion about the basic conditions under which entropy is to be defined. In this paper, I present an overview of definitions in current use for terms associated with distinguishability and relate them to various definitions that have been suggested for entropy. My hope is that consensus will be achievable if the definitions are clarified and agreed upon.
A reformulation of the Λ−Φ diagram for the prediction of ocean acoustic fluctuation regimes
Authors: Colosi John A.
Published: May 2015

The Λ−Φ diagram was a tool introduced in the late 1970s to predict ocean acoustic fluctuation regimes termed unsaturated, partially saturated, and fully saturated, where internal wave sound speed fluctuations play a dominant role. The Λ−Φ parameters reflect, respectively, the strength of diffraction and the root-mean-square phase fluctuation along a ray path. Oceanographic knowledge of the small scale part of the internal wave spectrum and high angle Fresnel zone formulations now allow a more stable and accurate calculation of these parameters. An empirical relation between the variance of log-intensity and Λ−Φ provides a more accurate border between the unsaturated regime and stronger fluctuations. The diagram is consistent with six short range, deep water experiments in the Pacific, Atlantic, and Arctic oceans with frequencies ranging from 75 to 16 000 Hz. The utility of the Λ−Φ diagram is that it provides one of the few means to inter-compare experiments at different geographic locations, and at different frequencies and ranges.
Speech timing and linguistic rhythm: On the acoustic bases of rhythm typologies
Authors: Rathcke Tamara V. , Smith Rachel H.
Published: May 2015

Research into linguistic rhythm has been dominated by the idea that languages can be classified according to rhythmic templates, amenable to assessment by acoustic measures of vowel and consonant durations. This study tested predictions of two proposals explaining the bases of rhythmic typologies: the Rhythm Class Hypothesis which assumes that the templates arise from an extensive vs a limited use of durational contrasts, and the Control and Compensation Hypothesis which proposes that the templates are rooted in more vs less flexible speech production strategies. Temporal properties of segments, syllables and rhythmic feet were examined in two accents of British English, a “stress-timed” variety from Leeds, and a “syllable-timed” variety spoken by Panjabi-English bilinguals from Bradford. Rhythm metrics were calculated. A perception study confirmed that the speakers of the two varieties differed in their perceived rhythm. The results revealed that both typologies were informative in that to a certain degree, they predicted temporal patterns of the two varieties. None of the metrics tested was capable of adequately reflecting the temporal complexity found in the durational data. These findings contribute to the critical evaluation of the explanatory adequacy of rhythm metrics. Acoustic bases and limitations of the traditional rhythmic typologies are discussed.
Low frequency finite element models of the acoustical behavior of earmuffs
Authors: Boyer Sylvain , Doutres Olivier , Sgard Franck , Laville Frédéric , Boutin Jérôme
Published: May 2015

This paper compares different approaches to model the vibroacoustic behavior of earmuffs at low frequency and investigates their accuracy by comparison with objective insertion loss measurements recently carried out by Boyer et al. [(2014). Appl. Acoust. 83, 76–85]. Two models based on the finite element (FE) method where the cushion is either modeled as a spring foundation (SF) or as an equivalent solid (ES), and the well-known lumped parameters model (LPM) are investigated. Modeling results show that: (i) all modeling strategies are in good agreement with measurements, providing that the characterization of the cushion equivalent mechanical properties are performed with great care and as close as possible to in situ loading, boundary, and environmental conditions and that the frequency dependence of the mechanical properties is taken into account, (ii) the LPM is the most simple modeling strategy, but the air volume enclosed by the earmuff must be correctly estimated, which is not as straightforward as it may seem, (iii) similar results are obtained with the SF and the ES FE-models of the cushion, but the SF should be preferred to predict the earmuff acoustic response at low frequency since it requires less parameters and a less complex characterization procedure.
Sound source identification and sound radiation modeling in a moving medium using the time-domain equivalent source method
Authors: Zhang Xiao-Zheng , Bi Chuan-Xing , Zhang Yong-Bin , Xu Liang
Published: May 2015

Planar near-field acoustic holography has been successfully extended to reconstruct the sound field in a moving medium, however, the reconstructed field still contains the convection effect that might lead to the wrong identification of sound sources. In order to accurately identify sound sources in a moving medium, a time-domain equivalent source method is developed. In the method, the real source is replaced by a series of time-domain equivalent sources whose strengths are solved iteratively by utilizing the measured pressure and the known convective time-domain Green's function, and time averaging is used to reduce the instability in the iterative solving process. Since these solved equivalent source strengths are independent of the convection effect, they can be used not only to identify sound sources but also to model sound radiations in both moving and static media. Numerical simulations are performed to investigate the influence of noise on the solved equivalent source strengths and the effect of time averaging on reducing the instability, and to demonstrate the advantages of the proposed method on the source identification and sound radiation modeling.
A Reciprocal Effects Model of the Temporal Ordering of Basic Psychological Needs and Motivation
Authors: Martinent Guillaume , Guillet-Descas Emma , Moiret Sophie
Published: May 2015

Using self-determination theory as the framework, we examined the temporal ordering between satisfaction and thwarting of basic psychological needs and motivation. We accomplished this goal by using a two-wave 7-month partial least squares path modeling approach (PLS-PM) among a sample of 94 adolescent athletes (Mage = 15.96) in an intensive training setting. The PLS-PM results showed significant paths leading: (a) from T1 satisfaction of basic psychological need for competence to T2 identified regulation, (b) from T1 external regulation to T2 thwarting and satisfaction of basic psychological need for competence, and (c) from T1 amotivation to T2 satisfaction of basic psychological need for relatedness. Overall, our results suggest that the relationship between basic psychological need and motivation varied depending on the type of basic need and motivation assessed. Basic psychological need for competence predicted identified regulation over time whereas amotivation and external regulation predicted basic psychological need for relatedness or competence over time.
Scratching the surface: Alterations of skin microbiota in the initiation of eczematous dermatitis
Authors: Singh Anne Marie
Published: May 2015

Naturally occurring
S. aureus
and
C. bovis
drive inflammation and immune deviation in murine eczematous dermatitis.
Unexpected innate immunity targets for cancer
Authors: Beswick Ellen J.
Published: May 2015

Blocking the innate immune receptor TLR2 shows promise for treating head and neck cancer.
Synthetic and Evolutionary Construction of a Chlorate-Reducing Shewanella oneidensis MR-1
Authors: Clark Iain C. , Melnyk Ryan A. , Youngblut Matthew D. , Carlson Hans K. , Iavarone Anthony T. , Coates John D.
Published: May 2015

Despite evidence for the prevalence of horizontal gene transfer of respiratory genes, little is known about how pathways functionally integrate within new hosts. One example of a mobile respiratory metabolism is bacterial chlorate reduction, which is frequently encoded on composite transposons. This implies that the essential components of the metabolism are encoded on these mobile elements. To test this, we heterologously expressed genes for chlorate reduction from

Shewanella alga
e

ACDC in the non-chlorate-reducing
Shewanella oneidensis
MR-1. The construct that ultimately endowed robust growth on chlorate included
cld
, a cytochrome
c
gene,
clrABDC
, and two genes of unknown function. Although strain MR-1 was unable to grow on chlorate after initial insertion of these genes into the chromosome, 11 derived strains capable of chlorate respiration were obtained through adaptive evolution. Genome resequencing indicated that all of the evolved chlorate-reducing strains replicated a large genomic region containing chlorate reduction genes. Contraction in copy number and loss of the ability to reduce chlorate were also observed, indicating that this phenomenon was extremely dynamic. Although most strains contained more than six copies of the replicated region, a single strain with less duplication also grew rapidly. This strain contained three additional mutations that we hypothesized compensated for the low copy number. We remade the mutations combinatorially in the unevolved strain and determined that a single nucleotide polymorphism (SNP) upstream of
cld
enabled growth on chlorate and was epistatic to a second base pair change in the NarP binding sequence between
narQP
and
nrfA
that enhanced growth.

IMPORTANCE
The ability of chlorate reduction composite transposons to form functional metabolisms after transfer to a new host is an important part of their propagation. To study this phenomenon, we engineered
Shewanella oneidensis
MR-1 into a chlorate reducer. We defined a set of genes sufficient to endow growth on chlorate from a plasmid, but found that chromosomal insertion of these genes was nonfunctional. Evolution of this inoperative strain into a chlorate reducer showed that tandem duplication was a dominant mechanism of activation. While copy number changes are a relatively rapid way of increasing gene dosage, replicating almost 1 megabase of extra DNA is costly. Mutations that alleviate the need for high copy number are expected to arise and eventually predominate, and we identified a single nucleotide polymorphism (SNP) that relieved the copy number requirement. This study uses both rational and evolutionary approaches to gain insight into the evolution of a fascinating respiratory metabolism.
Gut Microbial Succession Follows Acute Secretory Diarrhea in Humans
Authors: David Lawrence A. , Weil Ana , Ryan Edward T. , Calderwood Stephen B. , Harris Jason B. , Chowdhury Fahima , Begum Yasmin , Qadri Firdausi , LaRocque Regina C. , Turnbaugh Peter J.
Published: May 2015

Disability after childhood diarrhea is an important burden on global productivity. Recent studies suggest that gut bacterial communities influence how humans recover from infectious diarrhea, but we still lack extensive data and mechanistic hypotheses for how these bacterial communities respond to diarrheal disease and its treatment. Here, we report that after
Vibrio cholerae
infection, the human gut microbiota undergoes an orderly and reproducible succession that features transient reversals in relative levels of enteric
Bacteroides
and
Prevotella
. Elements of this succession may be a common feature in microbiota recovery from acute secretory diarrhea, as we observed similar successional dynamics after enterotoxigenic
Escherichia coli
(ETEC) infection. Our metagenomic analyses suggest that multiple mechanisms drive microbial succession after cholera, including bacterial dispersal properties, changing enteric oxygen and carbohydrate levels, and phage dynamics. Thus, gut microbiota recovery after cholera may be predictable at the level of community structure but is driven by a complex set of temporally varying ecological processes. Our findings suggest opportunities for diagnostics and therapies targeting the gut microbiota in humans recovering from infectious diarrhea.

IMPORTANCE
Disability after diarrhea is a major burden on public health in the developing world. Gut bacteria may affect this recovery, but it remains incompletely understood how resident microbes in the digestive tract respond to diarrheal illness. Here, we observed an orderly and reproducible succession of gut bacterial groups after cholera in humans. Genomic analyses associated the succession with bacterial dispersal in food, an altered microbial environment, and changing phage levels. Our findings suggest that it may one day be feasible to manage resident bacterial populations in the gut after infectious diarrhea.
Genome-Wide siRNA Screen Identifies Complementary Signaling Pathways Involved in
Listeria
Infection and Reveals Different Actin Nucleation Mechanisms during
Listeria
Cell Invasion and Actin Comet Tail Formation
Authors: Kühbacher Andreas , Emmenlauer Mario , Rämo Pauli , Kafai Natasha , Dehio Christoph , Cossart Pascale , Pizarro-Cerdá Javier
Published: May 2015

Listeria monocytogenes
enters nonphagocytic cells by a receptor-mediated mechanism that is dependent on a clathrin-based molecular machinery and actin rearrangements. Bacterial intra- and intercellular movements are also actin dependent and rely on the actin nucleating Arp2/3 complex, which is activated by host-derived nucleation-promoting factors downstream of the cell receptor Met during entry and by the bacterial nucleation-promoting factor ActA during comet tail formation. By genome-wide small interfering RNA (siRNA) screening for host factors involved in bacterial infection, we identified diverse cellular signaling networks and protein complexes that support or limit these processes. In addition, we could precise previously described molecular pathways involved in
Listeria
invasion. In particular our results show that the requirements for actin nucleators during
Listeria
entry and actin comet tail formation are different. Knockdown of several actin nucleators, including SPIRE2, reduced bacterial invasion while not affecting the generation of comet tails. Most interestingly, we observed that in contrast to our expectations, not all of the seven subunits of the Arp2/3 complex are required for
Listeria
entry into cells or actin tail formation and that the subunit requirements for each of these processes differ, highlighting a previously unsuspected versatility in Arp2/3 complex composition and function.

IMPORTANCE
Listeria
is a bacterial pathogen that induces its internalization within the cytoplasm of human cells and has been used for decades as a major molecular tool to manipulate cells in order to explore and discover cellular functions. We have inactivated individually, for the first time in epithelial cells, all the genes of the human genome to investigate whether each gene modifies positively or negatively the
Listeria
infectious process. We identified novel signaling cascades that have never been associated with
Listeria
infection. We have also revisited the role of the molecular complex Arp2/3 involved in the polymerization of the actin cytoskeleton, which was shown previously to be required for
Listeria
entry and movement inside host cells, and we demonstrate that contrary to the general dogma, some subunits of the complex are dispensable for both
Listeria
entry and bacterial movement.
Use of antibiotics in paediatric primary care settings in Serbia
Authors: Bozic Bojana , Bajcetic Milica
Published: May 2015

Objective

The aim of the study was to compare the quality of antibiotic use among children in primary settings with the internationally developed disease-specific quality indicators and with National Guidelines.

Design

Prescriptions of systemic antibiotics to the paediatric population (<18 years) at the primary level of healthcare for the period between 2011 and 2013 were analysed by using the National Health Insurance Fund's outpatient reimbursement database.

Results

The mean annual number of antibiotic prescriptions was 1.887.615, while the mean annual number of children receiving antibiotics was 728.285. The prescription rate slightly decreased by 10% from 1.516 antibiotic prescriptions per 1000 persons per year in 2011 to 1.365 in 2013. The highest percentage of prescribed antibiotics was observed in the group of children aged 2–23 months. The mean annual prevalence of antibiotic prescriptions was 54%. The percentage of patients prescribed an antibiotic for acute upper respiratory tract infections, acute tonsillitis and acute otitis media (AOM) was above the proposed range (≤20), 87% –96%. These three diagnoses represent more than 69% of all indications for prescribing antibiotics. The percentage of patients prescribed a recommended antibiotic was below the proposed range (≥80%), 1% –17%, while the adherence rate to National Guidelines was low, 19%–28%. The percentage of patients prescribed quinolones was above the proposed range for AOM (≤5%), 7%. There were no significant differences in indicators value at the regional level in Serbia.

Conclusions

Antibiotic use among children in Serbia is extremely high compared with that in most other European countries. Major problems are frequent use of antibiotics for indications that usually receive no benefit from this treatment and the use of broad-spectrum antibiotics.
Thyrotoxicosis: an under-recognised aetiology
Authors: Dave Anjalee , Ludlow Jason , Malaty John
Published: May 2015

A 53-year-old woman presented for evaluation of dizziness, shortness of breath and chest pain. She was found to be in atrial fibrillation with rapid ventricular response that was determined to be caused by iodine-induced thyrotoxicosis (from a CT scan with intravenous contrast 2 months prior to presentation). Jod-Basedow syndrome (iodine-induced hyperthyroidism) is infrequently considered as a cause of thyrotoxicosis, even when typical risk factors are present. However, this patient did not have typical risk factors: she did not reside in an iodine deficient area, did not have a prior diagnosis of thyroid disorder or goitre, had never been treated with thyroid medications or medications known to cause thyroid dysfunction and she presented later than is typical with this syndrome (2 months after receiving iodinated contrast). She had complete resolution of hyperthyroidism and atrial fibrillation 2 weeks later with no recurrence over the following 7 months.
Psoas muscle pyogenic abscess in association with infected hip arthroplasty: a rare case of simultaneous bilateral presentation
Authors: Volpin Andrea , Kini Sunil Gurpur , Berizzi Antonio
Published: May 2015

Simultaneous bilateral presentation of psoas abscess with prosthetic joint involvement is extremely rare. A 68-year-old woman presented to us with bilateral dull aching groin pain of 6 months’ duration, which flared up in the past month, associated with pyrexial symptoms. She had undergone bilateral hip replacements in the past with uneventful recovery. MRI showed bilateral psoas muscle collection in communication with the hip joints. Preoperative hip aspirate demonstrated frank pus with positivity on Gram stain and radiographs confirmed prosthetic loosening of bilateral hips. The patient subsequently underwent two-stage revision arthroplasty of both infected hip implants. At 5-year follow-up, the patient remains asymptomatic with good functional outcome and no recurrence on serial MRI.
Patients’ adherence-related beliefs about methotrexate: a qualitative study of the role of written patient information
Authors: Hayden Charlotte , Neame Rebecca , Tarrant Carolyn
Published: May 2015

Objectives

Methotrexate is effective in treating inflammatory arthritis, but both underadherence and overadherence can put patients at risk. Patients may fail to adhere due to practicalities including the unusual weekly dosing regimen, but medication beliefs also play a role. This study explored how both beliefs about necessity and concerns about methotrexate become established in patients with inflammatory arthritis and how patients use information in managing their beliefs and concerns.

Design

Semistructured interviews were conducted with patients taking oral methotrexate for inflammatory arthritis. Interviews were transcribed verbatim and analysed thematically.

Setting

Participants were recruited from a single Trust in the East Midlands.

Participants

Fifteen patients (4 male, 11 female) with inflammatory arthritis.

Results

Methotrexate was commonly prescribed at the time of diagnosis; at this point, experience of illness was influential for beliefs about medication necessity. Following prescription, patients absorbed information from written and verbal sources which reinforced beliefs about necessity but also raised concerns, including fear of side effects. Over time, beliefs were modified on the basis of personal experience, particularly of medication effectiveness and side effects. Some patients described tensions and dissonance in their beliefs and experiences of methotrexate, which put them at risk of non-adherence. Patients used information-seeking and information-avoidance as strategies to resolve these tensions. The available information did little to help suppress dissonance and sometimes exacerbated it.

Conclusions

Patients’ experiences of coming to terms with taking methotrexate are complex, and their experiences of dissonance are particularly problematic. Experiences might be improved by supporting patients to assess necessity (particularly in the presence of side effects) and by providing information to moderate unnecessary concerns. Improving recording and sharing of monitoring results may be one way to meet these needs.
Perspectives from health, social care and policy stakeholders on the value of a single self-report outcome measure across long-term conditions: a qualitative study
Authors: Hunter Cheryl , Fitzpatrick Ray , Jenkinson Crispin , Darlington Anne-Sophie Emma , Coulter Angela , Forder Julien E , Peters Michele
Published: May 2015

Objectives

To explore the views of a range of stakeholders regarding whether patient-reported outcome measures (PROMs) can be developed to measure key attributes of long-term conditions (LTCs) care in England, and the potential value of a single generic measure.

Design

Qualitative semistructured interview study, analysed using a framework approach.

Participants and setting

Interviews with 31 stakeholders from primary care, secondary care, social care, policy and patient-focused voluntary organisations in England.

Results

There was broad support for a single PROM that could be used to measure outcomes for patients with any LTCs in any health or social care setting. Interviewees identified three desired uses for a PROM: to improve the quality of individual care; to increase people's engagement in their own care; and to monitor the performance of services. Interviewees felt that a PROM for LTCs should incorporate a mixture of traditional and non-traditional domains, such as functioning, empowerment and social participation, and be codesigned with patients and professional end-users. Stakeholders emphasised the need for a PROM to be feasible for practical implementation at the individual clinical level as a first priority. A number of concerns and potential problems were identified in relation to the application and interpretation of an LTC PROM.

Conclusions

This study has demonstrated support for a single self-report outcome measure that reflects the priorities of people with LTCs, if such a measure can be shown to be meaningful and useful at the individual level. People with LTCs and professional end-users in health and social care should be involved in the development and evaluation of such a measure.
Why do patients with ‘primary care sensitive’ problems access ambulance services? A systematic mapping review of the literature
Authors: Booker Matthew J , Shaw Ali R G , Purdy Sarah
Published: May 2015

Objective

Emergency ambulance use for problems that could be managed in primary care continues to rise owing to complex reasons that are poorly understood. The objective of this systematic review is to draw together published evidence across a variety of study methodologies and settings to gain a better understanding of why patients seek help from ambulance services for these problems.

Design

Systematic searches were undertaken across the MEDLINE, EMBASE, PsychINFO, CINAHL, Health Management Information Consortium and Health Management Information Service publication databases. Google Scholar, Web of Science, OpenSigle, EThOS and DART databases were also systematically searched for reports, proceedings, book chapters and theses, along with hand-searching of grey literature sources. Studies were included if they reported on findings examining patient, carer, health professional or service management interactions with ambulance services for primary care problems. All study methodologies and perspectives were of interest. Data were extracted, quality assessed and systematically mapped according to key findings through generation of an iterative framework.

Results

A total of 31 studies met inclusion criteria. Findings were summarised across 5 broad categories: factors associated with individual patients; actions of care-givers and bystanders; population-level factors; health infrastructure factors; challenges faced by health professionals. A number of subcategories were developed to explore these factors in more detail.

Conclusions

This review reports important factors that may impact on ambulance use for primary care problems across a global setting, including demographic measures associated with deprivation, minority status and individual social circumstances. Categorising ambulance calls for primary care problems as ‘inappropriate’ is context dependant and may be unhelpful. Potential implications for triage and risk management strategies are discussed.