bluuebunny/crossref_metadata_2025_split huggingface dataset:
Asymptotic behaviour of Stokes flow in a thin domain with a moving rough boundary
Authors: Fabricius J. , Koroleva Y. O. , Tsandzana A. , Wall P. 
Published: May 2014

We consider a problem that models fluid flow in a thin domain bounded by two surfaces. One of the surfaces is rough and moving, whereas the other is flat and stationary. The problem involves two small parameters
ϵ
and
μ
that describe film thickness and roughness wavelength, respectively. Depending on the ratio λ=
ϵ
/
μ
, three different flow regimes are obtained in the limit as both of them tend to zero. Time-dependent equations of Reynolds type are obtained in all three cases (Stokes roughness, Reynolds roughness and high-frequency roughness regime). The derivations of the limiting equations are based on formal expansions in the parameters
ϵ
and
μ
.
Stitching together the Multiple Dimensions of Autophagy Using Metabolomics and Transcriptomics Reveals Impacts on Metabolism, Development, and Plant Responses to the Environment inArabidopsis
Authors: Masclaux-Daubresse Céline , Clément Gilles , Anne Pauline , Routaboul Jean-Marc , Guiboileau Anne , Soulay Fabienne , Shirasu Ken , Yoshimoto Kohki 
Published: May 2014

AbstractAutophagy is a fundamental process in the plant life story, playing a key role in immunity, senescence, nutrient recycling, and adaptation to the environment. Transcriptomics and metabolomics of the rosette leaves of Arabidopsis thaliana autophagy mutants (atg) show that autophagy is essential for cell homeostasis and stress responses and that several metabolic pathways are affected. Depletion of hexoses, quercetins, and anthocyanins parallel the overaccumulation of several amino acids and related compounds, such as glutamate, methionine, glutathione, pipecolate, and 2-aminoadipate. Transcriptomic data show that the pathways for glutathione, methionine, raffinose, galacturonate, and anthocyanin are perturbed. Anthocyanin depletion in atg mutants, which was previously reported as a possible defect in flavonoid trafficking to the vacuole, appears due to the downregulation of the master genes encoding the enzymes and regulatory proteins involved in flavonoid biosynthesis. Overexpression of the PRODUCTION OF ANTHOCYANIN PIGMENT1 transcription factor restores anthocyanin accumulation in vacuoles of atg mutants. Transcriptome analyses reveal connections between autophagy and (1) salicylic acid biosynthesis and response, (2) cytokinin perception, (3) oxidative stress and plant defense, and possible interactions between autophagy and the COP9 signalosome machinery. The metabolic and transcriptomic signatures identified for the autophagy mutants are discussed and show consistencies with the observed phenotypes.
Trias of keratosis pilaris, ulerythema ophryogenes and 18p monosomy: Zouboulis syndrome
Authors: Liakou Aikaterini I. , Esteves de Carvalho André V. , Nazarenko Lujdmila P. 
Published: May 2014

AbstractKeratosis pilaris and ulerythema ophryogenes (keratosis pilaris atrophicans faciei) are part of a group of hereditary disorders of hair follicle keratinization involving follicular inflammation and subsequent atrophy. Monosomy 18p refers to a chromosomal disorder resulting from the deletion of all or part of the short arm of chromosome 18. This trias was first described in a patient by Zouboulis et al. (1994) and has been reported by different authors in four additional patients since then. We have reviewed the five almost identical cases that have been reported in 20 years and we suggest the existence of a new rare syndrome characterized by the trias keratosis pilaris, ulerythema ophryogenes and monosomy 18p. Recognition of the syndrome could assist in early diagnosis of monosomy 18p in these patients.
Infantile generalized pustular psoriasis: Successful disease control with intermittent etretinate
Authors: Namba Chika , Murakami Masamoto , Hanakawa Yasushi , Tohyama Mikiko , Shirakata Yuji , Tauchi Hisamichi , Sayama Koji 
Published: May 2014

AbstractInfantile generalized pustular psoriasis is a rare form of psoriasis and the best treatment is controversial. We experienced a 2‐year‐old female with erythema on her neck and axilla starting at 3 months of age. She presented with recurrent annular and geographic scaly erythema with a few pustules on the neck, precordium and axilla, but no fever. The histopathology revealed subcorneal neutrophilic infiltration and microabscesses without Kogoj's spongiform pustules. The initial diagnosis was subcorneal pustular dermatosis. However, she developed widespread geographic erythema and numerous pustules over her entire body with a fever when she got a cold. A second skin biopsy revealed monolocular pustules and Kogoj's spongiform pustules in the subcorneal layer. Etretinate was administrated after a diagnosis of pustular psoriasis was made and her condition improved gradually. The choice of treatment depends on patient age, general condition and the disease severity.
Histological studies of facial acne and atrophic acne scars treated with a bipolar fractional radiofrequency system
Authors: Kaminaka Chikako , Uede Mikiko , Nakamura Yasushi , Furukawa Fukumi , Yamamoto Yuki 
Published: May 2014

AbstractVarious fractional radiofrequency (FRF) treatments have demonstrated significant beneficial effects and minor side‐effects on atrophic acne scars and acne vulgaris by creating micro‐thermal injuries in the skins. However, histological studies to identify the precise mechanism responsible for the success of bipolar FRF treatments are lacking. In this study, six human subjects with these diseases were histologically analyzed after treatment with a bipolar FRF system (eMatrix; Syneron, Yokneam, Israel) and the effects of multiple passes were compared. Histopathological results showed that two‐pass FRF treatment created deeper dermal thermal injury zones compared to one‐pass treatment. Periadnexal collagen was coagulated, as well as that in the sebaceous glands, as evaluated in all cases with two‐pass FRF treatment. No severe side‐effects were observed after treatment. Our experience suggests that the level of dermal thermal injury is directly related to the number of passes, and that a large benefit of this treatment for these diseases is the preservation of adnexal structures.
Land sharing vs. land sparing: does the compact city reconcile urban development and biodiversity conservation?
Authors: Soga Masashi , Yamaura Yuichi , Koike Shinsuke , Gaston Kevin J. 
Published: May 2014

SummaryAs cities around the world rapidly expand, there is an urgent need to implement the best development form to minimize the negative impacts of urbanization on native biodiversity. Two divergent forms for the expansion of cities are land‐sharing and land‐sparing developments. To date, their relative benefits for biodiversity conservation are poorly understood.We quantified the relative conservation benefits of land‐sharing and land‐sparing developments for butterflies and ground beetles inTokyo,Japan. For each insect species, we determined which approach resulted in a larger total population size.At a higher level of urbanization (higher number of buildings in a landscape), land sparing rather than land sharing resulted in a higher total population size for the majority species of both taxa. However, at a lower level of urbanization, butterflies and ground beetles showed different responses to city development forms. Ground beetles had their highest total population sizes under land sparing, whereas for butterflies, especially open‐land and matrix‐dwelling species, larger populations were achieved under land sharing.The negative impacts of urbanization on biodiversity differ greatly between land‐sharing and land‐sparing development forms. We also revealed that the relative conservation benefits of land sharing and land sparing depend on the level of urbanization.Synthesis and applications. In areas that will be heavily urbanized in the future, city planners and policymakers should adopt approaches that follow a land‐sparing strategy and that keep large blocks of greenspace free from development. At lower levels of urbanization, on the other hand, as land sharing was suggested to be the better strategy for many butterfly species, a hybrid development form could be adopted that integrates areas of land sharing and land sparing, which might have the additional benefit of enhancing the delivery of some ecosystem services by bringing nature and people closer together in some areas.
Controls of vegetation structure and net primary production in restored grasslands
Authors: Munson Seth M. , Lauenroth William K. 
Published: May 2014

Summary

Vegetation structure and net primary production (NPP) are fundamental properties of ecosystems. Understanding how restoration practices following disturbance interact with environmental factors to control these properties can provide insight on how ecosystems recover and guide management efforts.

We assessed the relative contribution of environmental and restoration factors in controlling vegetation structure, above‐ and below‐ground investment in production across a chronosequence of semi‐arid Conservation Reserve Program (CRP) fields recovering from dry land wheat cropping relative to undisturbed grassland. Importantly, we determined the role of plant diversity and how seeding either native or introduced perennial grasses influenced the recovery of vegetation properties.

Plant basal cover increased with field age and was highest in CRP fields seeded with native perennial grasses. In contrast, fields seeded with introduced perennial grasses had tall‐growing plants with relatively low basal cover. These vegetation structural characteristics interacted with precipitation, but not soil characteristics, to influence above‐ground NPP (ANPP). Fields enrolled in the CRP for >7 years supported twice as much ANPP as undisturbed shortgrass steppe in the first wet year of the study, but all CRP fields converged on a common low amount of ANPP in the following dry year and invested less than half as much as the shortgrass steppe in below‐ground biomass.

ANPP in CRP fields seeded with native perennial grasses for > 7 years was positively related to species richness, whereas ANPP in CRP fields seeded with introduced perennial grasses was controlled more by dominant species.

Synthesis and applications. Seeding with introduced, instead of native, perennial grasses had a strong direct influence on vegetation structure, including species richness, which indirectly affected NPP through time. However, the effects of restoring either native or introduced grasses on NPP were secondary to low water availability. Therefore, restoration strategies that maximize basal cover and below‐ground biomass, which promote water acquisition, may lead to high resilience in semi‐arid and arid regions.
Shaping the microenvironment: evidence for the influence of a host galaxin on symbiont acquisition and maintenance in the squid‐vibrio symbiosis
Authors: Heath‐Heckman Elizabeth A. C. , Gillette Amani A. , Augustin René , Gillette Miles X. , Goldman William E. , McFall‐Ngai Margaret J. 
Published: May 2014

SummaryMost bacterial species make transitions between habitats, such as switching from free living to symbiotic niches. We provide evidence that a galaxin protein, EsGal1, of the squid Euprymna scolopes participates in both: (i) selection of the specific partner Vibrio fischeri from the bacterioplankton during symbiosis onset and, (ii) modulation of V. fischeri growth in symbiotic maintenance. We identified two galaxins in transcriptomic databases and showed by quantitative reverse‐transcriptase polymerase chain reaction that one (esgal1) was dominant in the light organ. Further, esgal1 expression was upregulated by symbiosis, a response that was partially achieved with exposure to symbiont cell‐envelope molecules. Confocal immunocytochemistry of juvenile animals localized EsGal1 to the apical surfaces of light‐organ epithelia and surrounding mucus, the environment in which V. fischeri cells aggregate before migration into the organ. Growth assays revealed that one repeat of EsGal1 arrested growth of Gram‐positive bacterial cells, which represent the cell type first ‘winnowed’ during initial selection of the symbiont. The EsGal1‐derived peptide also significantly decreased the growth rate of V. fischeri in culture. Further, when animals were exposed to an anti‐EsGal1 antibody, symbiont population growth was significantly increased. These data provide a window into how hosts select symbionts from a rich environment and govern their growth in symbiosis.
The Crc and Hfq proteins of Pseudomonas putida cooperate in catabolite repression and formation of ribonucleic acid complexes with specific target motifs
Authors: Moreno Renata , Hernández‐Arranz Sofía , La Rosa Ruggero , Yuste Luis , Madhushani Anjana , Shingler Victoria , Rojo Fernando 
Published: May 2014

SummaryThe Crc protein is a global regulator that has a key role in catabolite repression and optimization of metabolism in Pseudomonads. Crc inhibits gene expression post‐transcriptionally, preventing translation of mRNAs bearing an AAnAAnAA motif [the catabolite activity (CA) motif] close to the translation start site. Although Crc was initially believed to bind RNA by itself, this idea was recently challenged by results suggesting that a protein co‐purifying with Crc, presumably the Hfq protein, could account for the detected RNA‐binding activity. Hfq is an abundant protein that has a central role in post‐transcriptional gene regulation. Herein, we show that the Pseudomonas putida Hfq protein can recognize the CA motifs of RNAs through its distal face and that Crc facilitates formation of a more stable complex at these targets. Crc was unable to bind RNA in the absence of Hfq. However, pull‐down assays showed that Crc and Hfq can form a co‐complex with RNA containing a CA motif in vitro. Inactivation of the hfq or the crc gene impaired catabolite repression to a similar extent. We propose that Crc and Hfq cooperate in catabolite repression, probably through forming a stable co‐complex with RNAs containing CA motifs to result in inhibition of translation initiation.
Mannitol‐1‐phosphate dehydrogenases/phosphatases: a family of novel bifunctional enzymes for bacterial adaptation to osmotic stress
Authors: Sand Miriam , Rodrigues Marta , González José M. , de Crécy‐Lagard Valérie , Santos Helena , Müller Volker , Averhoff Beate 
Published: May 2014

SummaryThe nutritionally versatile soil bacteriumAcinetobacter baylyi ADP1 copes with salt stress by the accumulation of compatible solutes, a strategy that is widespread in nature. This bacterium synthesizes the sugar alcohol mannitolde novoin response to osmotic stress. In a previous study, we identifiedMtlD, a mannitol‐1‐phosphate dehydrogenase, which is essential for mannitol biosynthesis and which catalyses the first step in mannitol biosynthesis, the reduction of fructose‐6‐phosphate (F‐6‐P) to the intermediate mannitol‐1‐phosphate (Mtl‐1‐P). Until now, the identity of the second enzyme, the phosphatase that catalyses the dephosphorylation ofMtl‐1‐Pto mannitol, was elusive. Here we show thatMtlDhas a unique sequence among known mannitol‐1‐phosphate dehydrogenases with a haloacid dehalogenase (HAD)‐like phosphatase domain at theN‐terminus. This domain is indeed shown to have a phosphatase activity. Phosphatase activity is strictlyMg2+dependent. Nuclear magnetic resonance analysis revealed that purifiedMtlDcatalyses not only reduction ofF‐6‐Pbut also dephosphorylation ofMtl‐1‐P.MtlDofA. baylyiis the first bifunctional enzyme of mannitol biosynthesis that combinesMtl‐1‐Pdehydrogenase and phosphatase activities in a single polypeptide chain. Bioinformatic analysis revealed that the bifunctional enzyme is widespread amongAcinetobacterstrains but only rarely present in other phylogenetic tribes.
The type Tánicc in the Old Irish glosses: affix ordering, frequency and phonotactics
Authors: García‐Castillero Carlos 
Published: May 2014

AbstractIn this paper I investigate OIr. lexical compound verbs with the basic deuterotonic (deut.) shape CV·VC‐, of the type of expected *do·ánicc ‘he, she came’ or ‘who came’ which actually occurs in the prototonic (prot.) form tánicc. On the basis of the notions of affix ordering, frequency and junctural phonotactics developed in recent works on experimental psycholinguistics, the OIr. forms of the type tánicc are explained as relatively late innovations in which the deut. are replaced by prot. forms. The extension of the prot. form in those lexical compound verbs at the expense of the deut. form is due to the phonotactically problematic hiatus of the latter and depends mainly on grammatical (in leniting relative clause forms) and lexical (in the most frequent verbs) criteria.
Does a Nearby Murder Affect Housing Prices and Rents? The Case of Sydney
Authors: Klimova Anastasia , Lee Adrian D. 
Published: May 2014

We measure the impact of murders on prices and rents of homes in Sydney. We find that housing prices fall by 3.9 per cent for homes within 0.2 miles of the murder in the year following the murder, and weaker results in the second year after a murder. We do not find any effects of murders on rents. Higher media coverage and being located closer to the murder (within 0.1 mile) have no additional effect on prices. Taken together, our findings suggest that proximity to a murder affects nearby property prices, particularly in the first year after the incident.
Rapid Differentiation of Listeria monocytogenes Epidemic Clones III and IV and Their Intact Compared with Heat‐Killed Populations Using Fourier Transform Infrared Spectroscopy and Chemometrics
Authors: Nyarko Esmond B. , Puzey Kenneth A. , Donnelly Catherine W. 
Published: May 2014

AbstractThe objectives of this study were to determine if Fourier transform infrared (FT‐IR) spectroscopy and multivariate statistical analysis (chemometrics) could be used to rapidly differentiate epidemic clones (ECs) of Listeria monocytogenes, as well as their intact compared with heat‐killed populations. FT‐IR spectra were collected from dried thin smears on infrared slides prepared from aliquots of 10 μL of each L. monocytogenes ECs (ECIII: J1‐101 and R2‐499; ECIV: J1‐129 and J1‐220), and also from intact and heat‐killed cell populations of each EC strain using 250 scans at a resolution of 4 cm−1 in the mid‐infrared region in a reflectance mode. Chemometric analysis of spectra involved the application of the multivariate discriminant method for canonical variate analysis (CVA) and linear discriminant analysis (LDA). CVA of the spectra in the wavelength region 4000 to 600 cm−1 separated the EC strains while LDA resulted in a 100% accurate classification of all spectra in the data set. Further, CVA separated intact and heat‐killed cells of each EC strain and there was 100% accuracy in the classification of all spectra when LDA was applied. FT‐IR spectral wavenumbers 1650 to 1390 cm−1 were used to separate heat‐killed and intact populations of L. monocytogenes. The FT‐IR spectroscopy method allowed discrimination between strains that belong to the same EC. FT‐IR is a highly discriminatory and reproducible method that can be used for the rapid subtyping of L. monocytogenes, as well as for the detection of live compared with dead populations of the organism.
SimRAD: an R package for simulation‐based prediction of the number of loci expected in RADseq and similar genotyping by sequencing approaches
Authors: Lepais Olivier , Weir Jason T. 
Published: May 2014

AbstractApplication of high‐throughput sequencing platforms in the field of ecology and evolutionary biology is developing quickly with the introduction of efficient methods to reduce genome complexity. Numerous approaches for genome complexity reduction have been developed using different combinations of restriction enzymes, library construction strategies and fragment size selection. As a result, the choice of which techniques to use may become cumbersome, because it is difficult to anticipate the number of loci resulting from each method. We developed SimRAD, an R package that performs in silico restriction enzyme digests and fragment size selection as implemented in most restriction site associated DNA polymorphism and genotyping by sequencing methods. In silico digestion is performed on a reference genome or on a randomly generated DNA sequence when no reference genome sequence is available. SimRAD accurately predicts the number of loci under alternative protocols when a reference genome sequence is available for the targeted species (or a close relative) but may be unreliable when no reference genome is available. SimRAD is also useful for fine‐tuning a given protocol to adjust the number of targeted loci. Here, we outline the functionality of SimRAD and provide an illustrative example of the use of the package (available on the CRAN at http://cran.r-project.org/web/packages/SimRAD).
Evidence of nickel (Ni) efflux in Ni‐tolerant ectomycorhizal Pisolithus albus isolated from ultramafic soil
Authors: Majorel Clarisse , Hannibal Laure , Ducousso Marc , Lebrun Michel , Jourand Philippe 
Published: May 2014

SummaryNickel (Ni)‐tolerant ectomycorrhizal Pisolithus albus was isolated from extreme ultramafic soils that are naturally rich in heavy metals. This study aimed to identify the specific molecular mechanisms associated with the response of P. albus to nickel. In presence of high concentration of nickel, P. albus Ni‐tolerant isolate showed a low basal accumulation of nickel in its fungal tissues and was able to perform a metal efflux mechanism. Three genes putatively involved in metal efflux were identified from the P. albus transcriptome, and their overexpression was confirmed in the mycelium that was cultivated in vitro in the presence of nickel and in fungal tissues that were sampled in situ. Cloning these genes in yeast provided significant advantages in terms of nickel tolerance (+ 31% Ni EC50) and growth (+ 83% μ) compared with controls. Furthermore, nickel efflux was also detected in the transformed yeast cells. Protein sequence analysis indicated that the genes encoded a P‐type‐ATPase, an ABC transporter and a major facilitator superfamily permease (MFS). This study sheds light on a global mechanism of metal efflux by P. albus cells that supports nickel tolerance. These specific responses to nickel might contribute to the fungal adaptation in ultramafic soil.