bluuebunny/crossref_metadata_2025 huggingface dataset:
Dynamic changes in genes related to glucose uptake and utilization during pig skeletal and cardiac muscle development
Authors: Guo Yanqin , Jin Long , Wang Fengjiao , He Mengnan , Liu Rui , Li Mingzhou , Shuai Surong
Published: May 2014

Skeletal and cardiac muscle have important roles in glucose uptake and utilization. However, changes in expression of protein coding genes and miRNAs that participate in glucose metabolism during development are not fully understood. In this study, we investigated the expression of genes related to glucose metabolism during muscle development. We found an age-dependent increase in gene expression in cardiac muscle, with enrichment in heart development- and energy-related metabolic processes. A subset of genes that were up-regulated until 30 or 180 days postnatally, and then down-regulated in psoas major muscle was significantly enriched in mitochondrial oxidative-related processes, while genes that up-regulated in longissimus doris muscle was significantly enriched in glycolysis-related processes. Meanwhile, expression of energy-related microRNAs decreased with increasing age. In addition, we investigated the correlation between microRNAs and mRNAs in three muscle types across different stages of development and found many potential microRNA–mRNA pairs involved in regulating glucose metabolism.
On the stratification of noncommutative prime spectra
Authors: Lorenz Martin
Published: May 2014

We study rational actions of an algebraic torus

G
G

by automorphisms on an associative algebra

R
R

. The

G
G

-action on

R
R

induces a stratification of the prime spectrum

Spec
⁡
R

\operatorname {Spec} R

which was introduced by Goodearl and Letzter. For a noetherian algebra

R
R

, Goodearl and Letzter showed that the strata of

Spec
⁡
R

\operatorname {Spec} R

are isomorphic to the spectra of certain commutative Laurent polynomial algebras. The purpose of this note is to give a new proof of this result which works for arbitrary algebras

R
R

.
Computing prime divisors in an interval
Authors: Kim Minkyu , Cheon Jung Hee
Published: May 2014

We address the problem of finding a nontrivial divisor of a composite integer when it has a prime divisor in an interval. We show that this problem can be solved in time of the square root of the interval length with a similar amount of storage, by presenting two algorithms; one is probabilistic and the other is its derandomized version.
Relations on \overline{ℳ}_{ℊ,𝓃} via 3-spin structures
Authors: Pandharipande Rahul , Pixton Aaron , Zvonkine Dimitri
Published: May 2014

Witten’s class on the moduli space of 3-spin curves defines a (non-semisimple) cohomological field theory. After a canonical modification, we construct an associated semisimple CohFT with a non-trivial vanishing property obtained from the homogeneity of Witten’s class. Using the classification of semisimple CohFTs by Givental-Teleman, we derive two main results. The first is an explicit formula in the tautological ring ofM¯g,n\overline {\mathcal {M}}_{g,n}for Witten’s class. The second, using the vanishing property, is the construction of relations in the tautological ring ofM¯g,n\overline {\mathcal {M}}_{g,n}.

Pixton has previously conjectured a system of tautological relations onM¯g,n\overline {\mathcal {M}}_{g,n}(which extends the established Faber-Zagier relations onMg\mathcal {M}_{g}). Our 3-spin construction exactly yields Pixton’s conjectured relations. As the classification of CohFTs is a topological result depending upon the Madsen-Weiss theorem (Mumford’s conjecture), our construction proves relations in cohomology. The study of Witten’s class and the associated tautological relations forrr-spin curves via a parallel strategy will be taken up in a following paper.
CWig: compressed representation of Wiggle/BedGraph format
Authors: Huy Hoang Do , Sung Wing-Kin
Published: May 2014

Motivation: BigWig, a format to represent read density data, is one of the most popular data types. They can represent the peak intensity in ChIP-seq, the transcript expression in RNA-seq, the copy number variation in whole genome sequencing, etc. UCSC Encode project uses the bigWig format heavily for storage and visualization. Of 5.2 TB Encode hg19 database, 1.6 TB (31% of the total space) is used to store bigWig files. BigWig format not only saves a lot of space but also supports fast queries that are crucial for interactive analysis and browsing. In our benchmark, bigWig often has similar size to the gzipped raw data, while is still able to support ∼5000 random queries per second.

Results: Although bigWig is good enough at the moment, both storage space and query time are expected to become limited when sequencing gets cheaper. This article describes a new method to store density data named CWig. The format uses on average one-third of the size of existing bigWig files and improves random query speed up to 100 times.

Availability and implementation:  http://genome.ddns.comp.nus.edu.sg/∼cwig

Contact:  ksung@comp.nus.edu.sg

Supplementary information:  Supplementary data are available at Bioinformatics online.
MIPgen: optimized modeling and design of molecular inversion probes for targeted resequencing
Authors: Boyle Evan A. , O’Roak Brian J. , Martin Beth K. , Kumar Akash , Shendure Jay
Published: May 2014

Summary Molecular inversion probes (MIPs) enable cost-effective multiplex targeted gene resequencing in large cohorts. However, the design of individual MIPs is a critical parameter governing the performance of this technology with respect to capture uniformity and specificity. MIPgen is a user-friendly package that simplifies the process of designing custom MIP assays to arbitrary targets. New logistic and SVM-derived models enable in silico predictions of assay success, and assay redesign exhibits improved coverage uniformity relative to previous methods, which in turn improves the utility of MIPs for cost-effective targeted sequencing for candidate gene validation and for diagnostic sequencing in a clinical setting.

Availability and implementation: MIPgen is implemented in C++. Source code and accompanying Python scripts are available at http://shendurelab.github.io/MIPGEN/ .

Contact:  shendure@uw.edu or boylee@uw.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Mechanisms driving recruitment variability in fish: comparisons between the Laurentian Great Lakes and marine systems
Authors: Pritt Jeremy J. , Roseman Edward F. , O'Brien Timothy P.
Published: May 2014

In his seminal work, Hjort (in Fluctuations in the great fisheries of Northern Europe. Conseil Parmanent International Pour L'Exploration De La Mar. Rapports et Proces-Verbaux, 20: 1–228, 1914) observed that fish population levels fluctuated widely, year-class strength was set early in life, and egg production by adults could not alone explain variability in year-class strength. These observations laid the foundation for hypotheses on mechanisms driving recruitment variability in marine systems. More recently, researchers have sought to explain year-class strength of important fish in the Laurentian Great Lakes and some of the hypotheses developed for marine fisheries have been transferred to Great Lakes fish. We conducted a literature review to determine the applicability of marine recruitment hypotheses to Great Lakes fish. We found that temperature, interspecific interactions, and spawner effects (abundance, age, and condition of adults) were the most important factors in explaining recruitment variability in Great Lakes fish, whereas relatively fewer studies identified bottom-up trophodynamic factors or hydrodynamic factors as important. Next, we compared recruitment between Great Lakes and Baltic Sea fish populations and found no statistical difference in factors driving recruitment between the two systems, indicating that recruitment hypotheses may often be transferable between Great Lakes and marine systems. Many recruitment hypotheses developed for marine fish have yet to be applied to Great Lakes fish. We suggest that future research on recruitment in the Great Lakes should focus on forecasting the effects of climate change and invasive species. Further, because the Great Lakes are smaller and more enclosed than marine systems, and have abundant fishery-independent data, they are excellent candidates for future hypothesis testing on recruitment in fish.
Thermal vibration of single-walled carbon nanotubes with quantum effects
Authors: Wang Lifeng , Hu Haiyan
Published: May 2014

The thermal vibration of a single-walled carbon nanotube (SWCNT) is investigated by using the models of Euler beam and Timoshenko beam with quantum effects taken into consideration when the law of energy equipartition is unreliable. The relation between temperature and the root of mean-squared (RMS) amplitude of thermal vibration at any cross section of the SWCNT is derived via the beam models in simply supported case and cantilevered case. The RMS amplitude of thermal vibration of SWCNT predicted by using Timoshenko beam is higher than that predicted by using Euler beam. The RMS amplitude of thermal vibration of an SWCNT predicted by the quantum theory is lower than that predicted by the law of energy equipartition. The quantum effect is more important for the thermal vibration of an SWCNT in the cases of higher-order modes, short length and low temperature.
Chimaeric load among sympatric social bacteria increases with genotype richness
Authors: Mendes-Soares Helena , Chen I-Chen Kimberly , Fitzpatrick Kara , Velicer Gregory J.
Published: May 2014

The total productivity of social groups can be determined by interactions among their constituents. Chimaeric load—the reduction of group productivity caused by antagonistic within-group heterogeneity—may be common in heterogeneous microbial groups due to dysfunctional behavioural interactions between distinct individuals. However, some instances of chimaerism in social microbes can increase group productivity, thus making a general relationship between chimaerism and group-level performance non-obvious. Using genetically similar strains of the soil bacterium
Myxococcus xanthus
that were isolated from a single centimetre-scale patch of soil, we tested for a relationship between degree of chimaerism (genotype richness) and total group performance at social behaviours displayed by this species. Within-group genotype richness was found to correlate negatively with total group performance at most traits examined, including swarming in both predatory and prey-free environments and spore production during development. These results suggest that interactions between such neighbouring strains in the wild will tend to be mutually antagonistic. Negative correlations between group performance and average genetic distance among group constituents at three known social genes were not found, suggesting that divergence at other loci that govern social interaction phenotypes is responsible for the observed chimaeric load. The potential for chimaeric load to result from co-aggregation among even closely related neighbours may promote the maintenance and strengthening of kin discrimination mechanisms, such as colony-merger incompatibilities observed in
M. xanthus
. The findings reported here may thus have implications for understanding the evolution and maintenance of diversity in structured populations of soil microbes.
Low ecological disparity in Early Cretaceous birds
Authors: Mitchell Jonathan S. , Makovicky Peter J.
Published: May 2014

Ecological divergence is thought to be coupled with evolutionary radiations, yet the strength of this coupling is unclear. When birds diversified ecologically has received much less attention than their hotly debated crown divergence time. Here, we quantify how accurately skeletal morphology can predict ecology in living and extinct birds, and show that the earliest known assemblage of birds (= pygostylians) from the Jehol Biota (≈ 125 Ma) was substantially impoverished ecologically. The Jehol avifauna has few representatives of highly preservable ecomorphs (e.g. aquatic forms) and a notable lack of ecomorphological overlap with the pterosaur assemblage (e.g. no large or aerially foraging pygostylians). Comparisons of the Jehol functional diversity with modern and subfossil avian assemblages show that taphonomic bias alone cannot explain the ecomorphological impoverishment. However, evolutionary simulations suggest that the constrained ecological diversity of the Early Cretaceous pygostylians is consistent with what is expected from a relatively young radiation. Regardless of the proximate biological explanation, the anomalously low functional diversity of the Jehol birds is evidence both for ecological vacancies in Cretaceous ecosystems, which were subsequently filled by the radiation of crown Aves, and for discordance between taxonomic richness and ecological diversity in the best-known Mesozoic ecosystem.
Amphiplicatus metriothermophilus gen. nov., sp. nov., a thermotolerant alphaproteobacterium isolated from a hot spring
Authors: Zhen-Li Zhang , Xin-Qi Zhang , Nan Wu , Wen-Wu Zhang , Xu-Fen Zhu , Yi Cao , Min Wu
Published: May 2014

A thermotolerant, Gram-strain-negative, non-spore-forming and strictly aerobic bacterium, designated GU51T, was isolated from Guhai hot spring in Jimsar county, Xinjiang province, north-west China. Each cell of strain GU51T consisted of an oval body and two symmetrical long (3–6 µm) prosthecae. The strain moved by polar flagellum. Oxidase and catalase were produced. Strain GU51T grew within the ranges of 37–65 °C (optimum 48–50 °C), 0.5–7.5 % (w/v) NaCl (optimum 2–3 %) and pH 6.0–9.0 (optimum pH 7.5). The major respiratory quinone detected was ubiquinone 10 (U-10) and the genomic DNA G+C content was 66.7±0.4 mol%. Major fatty acids (>5 %) were C16 : 0, C18 : 1ω7c and 11-methyl C18 : 1ω7c. The polar lipids consisted of diphosphatidylglycerol, five glycolipids, phosphatidylglycerol and an unknown phospholipid. Phylogenetic analysis showed the closest relatives of strain GU51T were members of the genus

Parvularcula

with 92.3 % 16S rRNA gene sequence similarity. On the basis of this polyphasic taxonomic characterization, it is suggested that strain GU51T represents a novel species of a new genus in the family ‘

Parvularculaceae

’, for which the name Amphiplicatus metriothermophilus gen. nov., sp. nov. is proposed. The type strain of the type species is GU51T ( = CGMCC 1.12710T = JCM 19779T).
Paludibaculum fermentans gen. nov., sp. nov., a facultative anaerobe capable of dissimilatory iron reduction from subdivision 3 of the Acidobacteria
Authors: Kulichevskaya Irina S. , Suzina Natalia E. , Rijpstra W. Irene C. , Damsté Jaap S. Sinninghe , Dedysh Svetlana N.
Published: May 2014

A facultatively anaerobic, non-pigmented, non-spore-forming bacterium was isolated from a littoral wetland of a boreal lake located on Valaam Island, northern Russia, and designated strain P105T. Cells of this isolate were Gram-negative, non-motile rods coated by S-layers with p2 lattice symmetry. Sugars were the preferred growth substrates. Under anoxic conditions, strain P105T was capable of fermentation and dissimilatory Fe(III) reduction. End products of fermentation were acetate, propionate and H2. Strain P105T was a mildly acidophilic, mesophilic organism, capable of growth at pH 4.0–7.2 (optimum pH 5.5–6.0) and at 4–35 °C (optimum at 20–28 °C). The major fatty acids were iso-C15 : 0 and C16 : 1ω7c; the cells also contained significant amounts of 13,16-dimethyl octacosanedioic acid (isodiabolic acid). The major polar lipids were phosphocholine and phosphoethanolamine; the quinone was MK-8. The G+C content of the DNA was 60.5 mol%. 16S rRNA gene sequence analysis showed that strain P105T belongs to subdivision 3 of the

Acidobacteria

and is only distantly related (90 % sequence similarity) to the only currently characterized member of this subdivision,

Bryobacter aggregatus

. The novel isolate differs from

Bryobacter aggregatus

in its cell morphology and ability to grow under anoxic conditions and in the presence of iron- and nitrate-reducing capabilities as well as quinone and polar lipid compositions. These differences suggest that strain P105T represents a novel genus and species, for which the name Paludibaculum fermentans gen. nov., sp. nov., is proposed. The type strain of Paludibaculum fermentans is P105T ( = DSM 26340T = VKM B-2878T).
Detection of TEM-, SHV- and CTX-M-type β-lactamase production among clinical isolates of Salmonella species
Authors: Elumalai Sathishkumar , Muthu G. , Selvam R. Esther Mary , Ramesh Srivani
Published: May 2014

Enteric fever is a major public health problem in developing countries. Due to the problem of resistance to first-line drugs and fluoroquinolone, cephalosporins are currently used for treatment of enteric fever. Cephalosporin resistance in Salmonella spp. is mainly due to production of extended-spectrum β-lactamases (ESBLs). The majority of ESBLs in Salmonella are derivatives of the TEM and SHV β-lactamase families. The objectives of this study were to detect antibiotic susceptibility patterns, ESBL production and TEM-, SHV- and CTX-M-encoding genes (bla
TEM, bla
SHV and bla
CTX-M) among clinical isolates of Salmonella spp. A total of 134 Salmonella isolates [Salmonella Typhi (n = 101), Salmonella Paratyphi A (n = 31), Salmonella Paratyphi B (n = 1) and Salmonella Typhimurium (n = 1)] were included in this study. Multidrug resistance was seen in 5/134 (3.73 %) isolates, all of which belonged to serotype S. Typhi. A better susceptibility profile was observed for first-line drugs (ampicillin, chloramphenicol, co-trimoxazole and tetracycline) and cephalosporins (cefotaxime, ceftazidime, ceftriaxone, cefixime and cefepime). However, 131 (97.76 %) of the 134 isolates were resistant to nalidixic acid and one (0.75 %) was resistant to ciprofloxacin. TEM-1-type β-lactamase (bla
TEM-1) was detected in six (4.47 %) of the 134 isolates, which belonged to the serotype S. Typhi. All six TEM-positive isolates were negative for the bla
SHV gene and none of the isolates was positive for the bla
CTX-M gene. The presence of the bla
TEM gene encoding TEM-1 β-lactamase is believed to confer resistance only to penicillins and early cephalosporins; however, the resistance spectrum of TEM-1 descendants may extend to second-, third- and fourth-generation cephalosporins. The ESBLs derived from TEM-1 differ from their progenitors by as few as 1 aa, and have the ability to hydrolyse third-generation cephalosporins. Therefore, appropriate selection and rotation of antibiotics as well as continuous monitoring of antibiotic susceptibility profiles could help to control the emergence and spread of resistant strains.
Baculovirus induces host cell aggregation via a Rho/Rok-dependent mechanism
Authors: Deng Zihao , Huang Zhihong , Yuan Meijin , Yang Kai , Pang Yi
Published: May 2014

Several baculoviruses can induce host cell aggregation during infection; however, the molecular basis remains unknown. The Rho family of small GTPases, including Rho1, Racs and Cdc42, plays important roles in cell migration and cell–cell contact. Activated GTPases target actin polymerization to discrete sites on the plasma membrane, thereby inducing membrane protrusions. In this study, we demonstrated thatSpodoptera lituranucleopolyhedrovirus (SpltNPV) infection induced the amoeboid movement and aggregation of SpLi-221 cellsin vitro. The amount of Rho1-GTP increased in the infected cells, which suggested that Rho1 was activated upon infection. RNA interference and superinfection of dominant-negative recombinants revealed that the SpltNPV-induced SpLi-221 cell aggregation was dependent on the Rho1, but not Racs or Cdc42, signalling pathway. Inhibition of Rho-associated protein kinase (Rok) activity by the inhibitor Y-27632 significantly reduced SpLi-221 cell aggregation. Silencing Rho1 expression with RNA interference decreased SpltNPV propagation by approximately 40 %in vitro, when SpLi-221 cells were infected at a low, but not high, m.o.i., suggesting that the SpltNPV-induced cell aggregation may benefit SpltNPV spread.
The novel capripoxvirus vector lumpy skin disease virus efficiently boosts modified vaccinia Ankara human immunodeficiency virus responses in rhesus macaques
Authors: Burgers Wendy A. , Ginbot Zekarias , Shen Yen-Ju , Chege Gerald K. , Soares Andreia P. , Müller Tracey L. , Bunjun Rubina , Kiravu Agano , Munyanduki Henry , Douglass Nicola , Williamson Anna-Lise
Published: May 2014

Poxvirus vectors represent promising human immunodeficiency virus (HIV) vaccine candidates and were a component of the only successful HIV vaccine efficacy trial to date. We tested the immunogenicity of a novel recombinant capripoxvirus vector, lumpy skin disease virus (LSDV), in combination with modified vaccinia Ankara (MVA), both expressing genes from HIV-1. Here, we demonstrated that the combination regimen was immunogenic in rhesus macaques, inducing high-magnitude, broad and balanced CD4+ and CD8+ T-cell responses, and transient activation of the immune response. These studies support further development of LSDV as a vaccine vector.
Dynamics of a combined medea-underdominant population transformation system
Authors: Gokhale Chaitanya , Reeves Richard Guy , Reed Floyd A
Published: May 2014

Transgenic constructs intended to be stably established at high frequencies in wild popu- lations have been demonstrated to drive from low frequencies in experimental insect populations. Link- ing such population transformation constructs to genes which render them unable to transmit pathogens could eventually be used to stop the spread of vector-borne diseases like malaria and dengue. Generally, population transformation constructs with only a single transgenic drive mechanism have been envisioned. Using a theoretical modelling approach we describe the predicted properties of a construct combining autosomal Medea and underdominant population transformation systems. We show that when combined they can exhibit synergistic properties which in broad circumstances surpass those of the single systems. With combined systems, intentional population transformation and its reversal can be achieved readily. Combined constructs also enhance the capacity to geographically restrict transgenic constructs to targeted populations. It is anticipated that these properties are likely to be of particular value in attracting regulatory approval and public acceptance of this novel technology.
Suppression of Photosynthetic Gene Expression in Roots Is Required for Sustained Root Growth under Phosphate Deficiency
Authors: Kang Jun , Yu Haopeng , Tian Caihuan , Zhou Wenkun , Li Chuanyou , Jiao Yuling , Liu Dong
Published: May 2014

Plants cope with inorganic phosphate (Pi) deficiencies in their environment by adjusting their developmental programs and metabolic activities. For Arabidopsis (Arabidopsis thaliana), the developmental responses include the inhibition of primary root growth and the enhanced formation of lateral roots and root hairs. Pi deficiency also inhibits photosynthesis by suppressing the expression of photosynthetic genes. Early studies showed that photosynthetic gene expression was also suppressed in Pi-deficient roots, a nonphotosynthetic organ; however, the biological relevance of this phenomenon remains unknown. In this work, we characterized an Arabidopsis mutant, hypersensitive to Pi starvation7 (hps7), that is hypersensitive to Pi deficiency; the hypersensitivity includes an increased inhibition of root growth. HPS7 encodes a tyrosylprotein sulfotransferase. Accumulation of HPS7 proteins in root tips is enhanced by Pi deficiency. Comparative RNA sequencing analyses indicated that the expression of many photosynthetic genes is activated in roots of hps7. Under Pi deficiency, the expression of photosynthetic genes in hps7 is further increased, which leads to enhanced accumulation of chlorophyll, starch, and sucrose. Pi-deficient hps7 roots also produce a high level of reactive oxygen species. Previous research showed that the overexpression of GOLDEN-like (GLK) transcription factors in transgenic Arabidopsis activates photosynthesis in roots. The GLK overexpressing (GLK OX) lines also exhibit increased inhibition of root growth under Pi deficiency. The increased inhibition of root growth in hps7 and GLK OX lines by Pi deficiency was completely reversed by growing the plants in the dark. Based on these results, we propose that suppression of photosynthetic gene expression is required for sustained root growth under Pi deficiency.
Structure of tomato wound-induced leucine aminopeptidase sheds light on substrate specificity
Authors: Duprez Kevin , Scranton Melissa A. , Walling Linda L. , Fan Li
Published: May 2014

The acidic leucine aminopeptidase (LAP-A) from tomato is induced in response to wounding and insect feeding. Although LAP-A showsin vitropeptidase activity towards peptides and peptide analogs, it is not clear what kind of substrates LAP-A hydrolyzesin vivo. In the current study, the crystal structure of LAP-A was determined to 2.20 Å resolution. Like other LAPs in the M17 peptidase family, LAP-A is a dimer of trimers containing six monomers of bilobal structure. Each monomer contains two metal ions bridged by a water or a hydroxyl ion at the active site. Modeling of different peptides or peptide analogs in the active site of LAP-A reveals a spacious substrate-binding channel that can bind peptides of five or fewer residues with few geometric restrictions. The sequence specificity of the bound peptide is likely to be selected by the structural and chemical restrictions on the amino acid at the P1 and P1′ positions because these two amino acids have to bind perfectly at the active site for hydrolysis of the first peptide bond to occur. The hexameric assembly results in the merger of the open ends of the six substrate-binding channels from the LAP-A monomers to form a spacious central cavity allowing the hexameric LAP-A enzyme to simultaneously hydrolyze six peptides containing up to six amino acids each. The hexameric LAP-A enzyme may also hydrolyze long peptides or proteins if only one such substrate is bound to the hexamer because the substrate can extend through the central cavity and the two major solvent channels between the two LAP-A trimers.
Structural, electronic and magnetic properties of YMnO3/La0.7Sr0.3MnO3heterostructures
Authors: Paul Amitesh , Zandalazini Carlos , Esquinazi Pablo , Autieri Carmine , Sanyal Biplab , Korelis Panagiotis , Böni Peter
Published: May 2014

Heterostructures with competing magnetic interactions are often exploited for their tailored new functionalities. Exchange bias is one such outcome of interfacial coupling across ferromagnetic–antiferromagnetic, multiferroic–ferromagnetic, two antiferromagnetic, or antiferromagnetic and paramagnetic interfaces. Apart from the usual horizontal shift of the hysteresis loop (exchange bias shift), a small `vertical shift' of the hysteresis loops along the magnetization axis has also been seen, but it was always relatively small. Recently, an unusually large `vertical shift' in epitaxial bilayer heterostructures comprising ferromagnetic La0.7Sr0.3MnO3and multiferroic orthorhombic YMnO3layers was reported. Here, using polarized neutron reflectometry, the magnetic proximity effect in such bilayers has been investigated. A detailed magnetic depth profile at the interface, elucidating the intrinsic nature of the vertical shift in such heterostructures, is reported. Further corroboration of this observation has been made by means of first-principles calculations, and the structural and electronic properties of YMnO3/La0.7Sr0.3MnO3heterostructures are studied. Although in the bulk, the ground state of YMnO3is anE-type antiferromagnet, the YMnO3/La0.7Sr0.3MnO3heterostructure stabilizes the ferromagnetic phase in YMnO3in the interface region. It is found that, in the hypothetical ferromagnetic phase of bulk YMnO3, the polarization is suppressed, and owing to a large difference between the lattice constants in theabplane a strong magnetocrystalline anisotropy is present. This anisotropy produces a high coercivity of the unusual ferromagnetic YMnO3phase at the interface, which is responsible for the large vertical shift observed in experiment.
Real space crystallography of a complex metallic alloy: high-angle annular dark-field scanning transmission electron microscopy of o-Al4(Cr,Fe)
Authors: Gaspari Roberto , Erni Rolf , Arroyo Yadira , Parlinska-Wojtan Magdalena , Dshemuchadse Julia , Pignedoli Carlo A. , Passerone Daniele , Schmutz Patrik , Beni Alessandra
Published: May 2014

High-angle annular dark-field scanning transmission electron microscopy (HAADF STEM) has been performed along the low-index zone axes of the o-Al4(Cr,Fe) complex metallic alloy to obtain a real-space representation of the crystal structure and to elucidate the material's inherent structural disorder. By comparing experiments with multislice STEM simulations, the model previously suggested by X-ray diffraction is further refined to provide a new set of positions and occupancies for the transition metal atoms.Pmnbis suggested as the new space group for the o-Al4(Cr,Fe) phase. A nonperiodic layer-type modulation, averaged out in bulk diffraction methods, is detected, corroborating the need for complementing bulk diffraction analysis with real-space imaging to derive the true crystal structure of Al4(Cr,Fe).
On the calibration of high-energy X-ray diffraction setups. I. Assessing tilt and spatial distortion of the area detector
Authors: Borbely Andras , Renversade Loic , Kenesei Peter , Wright Jonathan
Published: May 2014

The geometry of high-energy X-ray diffraction setups using an area detector and a rotation axis is analysed. The present paper (part 1) describes the methodology for determining continuously varying spatial distortions and tilt of the area detector based on the reference diffraction rings of a certified powder. Analytical expressions describing the degeneration of Debye rings into ellipses are presented and a robust calibration procedure is introduced. It is emphasized that accurate detector calibration requires the introduction of spatial distortion into the equation describing the tilt. The method is applied to data sets measured at the Advanced Photon Source and at the European Synchrotron Radiation Facility using detectors with different physical characteristics, the GE 41RT flat-panel and the FReLoN4M detector, respectively. The spatial distortion of the detectors is compared with regard to their use in structural and strain tensor analysis, a subject treated in part 2 of the calibration work [Borbély, Renversade & Kenesei (2014).J. Appl. Cryst.Submitted].
Butterfly-effect for massively separated flows
Authors: Lohner Rainald , Britto Dominic , Michailski Alexander , Haug Eberhard
Published: May 2014

Purpose

– During a routine benchmarking and scalability study of CFD codes for typical large-scale wind engineering runs, it was observed that the resulting loads for buildings varied considerably with the number of parallel processors employed. The differences remained very small at the beginning of a typical run, and then grew progressively to a state of total dissimilitude. A “butterfly-effect” for such flows was suspected and later confirmed. The paper aims to discuss these issues.

Design/methodology/approach

– A series of numerical experiments was conducted for massively separated flows. The same geometry – a cube in front of an umbrella – was used to obtain the flowfields using different grids, different numbers of domains/processors, slightly different inflow conditions and different codes.

Findings

– In all of these cases the differences remained very small at the beginning of a typical run, they then grew progressively to a state of total dissimilitude. While the mean and maximum loads remained similar, the actual (deterministic) instantiations were completely different. The authors therefore suspect that for flows of this kind a “butterfly effect” is present, whereby even very small (roundoff) errors can have a pronounced effect on the actual deterministic instantiation of a flowfield.

Research limitations/implications

– This implies that for flows of this kind the CFD runs have to be carried out to much larger times than formerly expected (and done) in order to obtain statistically relevant ensembles.

Practical implications

– For practical calculations this implies running to much larger times in order to reach statistically relevant ensembles, with the associated much higher CPU time requirements.

Originality/value

– This is the first time such a finding has been reported in the numerical wind engineering context.
Does Lesson Study work?
Authors: Ming Cheung Wai , Yee Wong Wing
Published: May 2014

Purpose

– There has been rapid proliferation of Lesson Studies and Learning Studies over the world. Do they really help teachers’ professional development and student learning? The purpose of this paper is to review studies from 2000 to 2010 on Lesson Study and Learning Study to unravel their benefits on teachers and students.

Design/methodology/approach

– Relevant studies were screen and extracted on available electronic databases to evaluate outcome of Lesson Study and Learning Study. The results were based on nine studies which examined the achievement of Learning Study and Lesson Study.

Findings

– All reviews identified positive evidence supporting the benefits of Lesson Study and Learning Study as powerful tool to help teachers examine their practices and enhance student learning. Although all nine studies showed positive effects of Lesson Study and Learning Study on teaching, learning or both, different outcome measures were employed and the study designs varied in qualities.

Originality/value

– More well-controlled studies with consistent and validated outcome measures were recommended in the future to address the short- and long-term effects of Lesson Study on students, teachers, and school level. Efforts should be focussed on unveiling the relationship between what is taught and what is learned. Studies using these approaches with more vigorous procedures in randomization and blinding should be implemented.
The impact of transaction costs and institutional pressure on supplier environmental practices
Authors: L. Tate Wendy , M. Ellram Lisa , J. Dooley Kevin
Published: May 2014

Purpose

– Suppliers play a more significant role in the environmental footprint of supply chains than most final manufacturers. The purpose of this paper is to apply transaction costs and institutional theory to help understand why the more conservative, or reactive suppliers may or may not be likely to adopt environmental practices.

Design/methodology/approach

– This research builds on a prior conceptual paper and uses the results of a survey to test whether transaction costs and institutional theory can provide insight into supplier's adoption of environmental practices.

Findings

– This research finds that perceived transaction costs affect supplier cooperation in adopting environmental practices. Suppliers are more likely to adopt an environmental practice if information-seeking costs are low or the cost of adoption is considered necessary to maintain the relationship. Data did not support the hypotheses concerning institutional pressures.

Originality/value

– There is much research in the area of proactive adoption of environmental business practices. This research looks specifically at what influences the adoption of environmental business practices by suppliers that are more reactive or hesitant to be leaders in this area.
Exploring the educative potential of eating disorder memoirs
Authors: McAllister Margaret , Lee Brien Donna , Alexander June , Flynn Trudi
Published: May 2014

Purpose

– The purpose of this paper is to explore the potential benefits that books, and specifically memoirs, may offer mental health students, positing that first person testimonials may make the complex experiences of a mental health challenge, in this case eating disorders (ED), accessible to learners.

Design/methodology/approach

– The paper presents a pedagogical approach, based on transformative learning (TL), to assist in encouraging the development of a Recovery Approach in students. TL is a pedagogy that is interested in problematic practices that keep afflicting an area such as mental health, such as the imbalanced focus on learning illness rather than wellbeing, and in pondering and revising the educational solutions.

Findings

– The paper proposes that forward movement in this area will be based on considering and developing such innovative curricula, and researching its impact.

Originality/value

– By virtue of their accessibility, memoirs could offer to a large audience the benefits of universality, empathy, hope and guidance. Teachers and learners could be making use of these books in face-to-face or online activities. This paper explores the groundwork that is needed before ED memoirs can be confidently recommended as an empowering tool.
Psychological morbidity associated with ovarian cancer screening: results from more than 23 000 women in the randomised trial of ovarian cancer screening (UKCTOCS)
Authors: Barrett J , Jenkins V , Farewell V , Menon U , Jacobs I , Kilkerr J , Ryan A , Langridge C , Fallowfield L ,   UKCTOCS trialists
Published: May 2014

Objective

To examine the psychological sequelae associated with abnormal screening in the United Kingdom Collaborative Trial of Ovarian Cancer Screening (UKCTOCS).

Design

Prospective, longitudinal randomised control trial.

Setting

Sixteen UKCTOCS centres.

Sample

Women aged 50–70 years randomised to annual multimodal screening, ultrasound screening or control groups.

Methods

Two groups were followed for 7 years: (1) a random sample (n = 1339), taken from all three study groups; and (2) an events sample (n = 22 035) of women with abnormal screens resulting in the need for repeat testing of either low or higher level intensity.

Main outcome measures

Patient‐reported measures of anxiety (scores ranging from 20 to 80) and psychological morbidity.

Results

In the random sample the mean difference between anxiety scores after a repeat screening and those following an annual screening was 0.4 (95% CI −0.46, 1.27), and in the events sample it was 0.37 (95% CI 0.23, 0.51). The risk of psychological morbidity was only increased in the event sample for women requiring higher level repeat screening (OR 1.28; 95% CI 1.18, 1.39). The risk of psychological morbidity in women with ovarian cancer was higher at both 6 weeks (OR 16.2; 95% CI 9.19, 28.54) and 6 months (OR 3.32; 95% CI 1.91, 5.77) following surgery.

Conclusions

Screening does not appear to raise anxiety but psychological morbidity is elevated by more intense repeat testing following abnormal annual screens, and in women after surgical treatment for ovarian cancer.
Metamicrobiomics in herbivore beetles of the genus Cryptocephalus (Chrysomelidae): toward the understanding of ecological determinants in insect symbiosis
Authors: Montagna Matteo , Gómez‐Zurita Jesús , Giorgi Annamaria , Epis Sara , Lozzia Giuseppe , Bandi Claudio
Published: May 2014

The Cryptocephalus marginellus (Coleoptera: Chrysomelidae) complex is composed by six species that are supposed to have originated by events of allo‐ or parapatric speciation. In the present study we investigated the alternative hypotheses that the bacterial communities associated with six populations of this species complex are shaped by environmental factors, or reflect the proposed pattern of speciation. The microbiota associated with the six populations, from five species of the complex, have been characterized through 16S rRNA pyrotag sequencing. Based on a 97% sequence similarity threshold, data were clustered into 381 OTUs, which were analyzed using a variety of diversity indices. The microbiota of C. acquitanus and C. marginellus (Calanques) were the most diverse (over 100 OTUs), while that from C. zoiai yielded less bacterial diversity (45 OTUs). Taxonomic assignment revealed Proteobacteria, Tenericutes and Firmicutes as the dominant components of these beetles’ microbiota. The most abundant genera were Ralstonia, Sphingomonas, Rickettsia, and Pseudomonas. Different strains of Rickettsia were detected in C. eridani and C. renatae. The analysis of β‐diversity revealed high OTU turnover among the populations of C. marginellus complex, with only few shared species. Hierarchical clustering taking into account relative abundances of OTUs does not match the phylogeny of the beetles, therefore we hypothesize that factors other than phylogenetic constraints play a role in shaping the insects’ microbiota. Environmental factors that could potentially affect the composition of bacterial communities were tested by fitting them on the results of a multi‐dimensional scaling analysis. No significant correlations were observed towards the geographic distances or the host plants, while the composition of the microbiota appeared associated with altitude. The metabolic profiles of the microbiotas associated with each population were inferred from bacterial taxonomy, and interestingly, the obtained clustering pattern was consistent with the host phylogeny.
Distance, flow and PCR inhibition: eDNA dynamics in two headwater streams
Authors: Jane Stephen F. , Wilcox Taylor M. , McKelvey Kevin S. , Young Michael K. , Schwartz Michael K. , Lowe Winsor H. , Letcher Benjamin H. , Whiteley Andrew R.
Published: May 2014

Environmental DNA (eDNA) detection has emerged as a powerful tool for monitoring aquatic organisms, but much remains unknown about the dynamics of aquatic eDNA over a range of environmental conditions. DNA concentrations in streams and rivers will depend not only on the equilibrium between DNA entering the water and DNA leaving the system through degradation, but also on downstream transport. To improve understanding of the dynamics of eDNA concentration in lotic systems, we introduced caged trout into two fishless headwater streams and took eDNA samples at evenly spaced downstream intervals. This was repeated 18 times from mid‐summer through autumn, over flows ranging from approximately 1–96 L/s. We used quantitative PCR to relate DNA copy number to distance from source. We found that regardless of flow, there were detectable levels of DNA at 239.5 m. The main effect of flow on eDNA counts was in opposite directions in the two streams. At the lowest flows, eDNA counts were highest close to the source and quickly trailed off over distance. At the highest flows, DNA counts were relatively low both near and far from the source. Biomass was positively related to eDNA copy number in both streams. A combination of cell settling, turbulence and dilution effects is probably responsible for our observations. Additionally, during high leaf deposition periods, the presence of inhibitors resulted in no amplification for high copy number samples in the absence of an inhibition‐releasing strategy, demonstrating the necessity to carefully consider inhibition in eDNA analysis.
Pipeliner: software to evaluate the performance of bioinformatics pipelines for next‐generation resequencing
Authors: Nevado B. , Perez‐Enciso M.
Published: May 2014

The choice of technology and bioinformatics approach is critical in obtaining accurate and reliable information from next‐generation sequencing (NGS) experiments. An increasing number of software and methodological guidelines are being published, but deciding upon which approach and experimental design to use can depend on the particularities of the species and on the aims of the study. This leaves researchers unable to produce informed decisions on these central questions. To address these issues, we developed pipeliner – a tool to evaluate, by simulation, the performance of NGS pipelines in resequencing studies. Pipeliner provides a graphical interface allowing the users to write and test their own bioinformatics pipelines with publicly available or custom software. It computes a number of statistics summarizing the performance in SNP calling, including the recovery, sensitivity and false discovery rate for heterozygous and homozygous SNP genotypes. Pipeliner can be used to answer many practical questions, for example, for a limited amount of NGS effort, how many more reliable SNPs can be detected by doubling coverage and halving sample size or what is the false discovery rate provided by different SNP calling algorithms and options. Pipeliner thus allows researchers to carefully plan their study's sampling design and compare the suitability of alternative bioinformatics approaches for their specific study systems. Pipeliner is written in C++ and is freely available from http://github.com/brunonevado/Pipeliner.
Evaluation of metatranscriptomic protocols and application to the study of freshwater microbial communities
Authors: Tsementzi Despina , Poretsky Rachel , Rodriguez‐R Luis M. , Luo Chengwei , Konstantinidis Konstantinos T.
Published: May 2014

Metatranscriptomics of environmental samples enables the identification of community activities without a priori knowledge of taxonomic or functional composition. However, several technical challenges associated with the RNA preparation protocols can affect the relative representation of transcripts and data interpretation. Here, seven replicate metatranscriptomes from planktonic freshwater samples (Lake Lanier, USA) were sequenced to evaluate technical and biological reproducibility of different RNA extraction protocols. Organic versus bead‐beating extraction showed significant enrichment for low versus high G + C% mRNA populations respectively. The sequencing data were best modelled by a negative binomial distribution to account for the large technical and biological variation observed. Despite the variation, the transcriptional activities of populations that persisted in year‐round metagenomes from the same site consistently showed distinct expression patterns, reflecting different ecologic strategies and allowing us to test prevailing models on the contribution of both rare biosphere and abundant members to community activity. For instance, abundant members of the Verrucomicrobia phylum systematically showed low transcriptional activity compared with other abundant taxa. Our results provide a practical guide to the analysis of metatranscriptomes and advance understanding of the activity and ecology of abundant and rare members of temperate freshwater microbial communities.
Spatially constrained clustering of ecological networks
Authors: Miele Vincent , Picard Franck , Dray Stéphane
Published: May 2014

Spatial ecological networks are widely used to model interactions between georeferenced biological entities (e.g. populations or communities). The analysis of such data often leads to a two‐step approach where groups containing similar biological entities are firstly identified and the spatial information is used afterwards to improve the ecological interpretation.

We develop an integrative approach to retrieve groups of nodes that are geographically close and ecologically similar. Our model‐based spatially constrained method embeds the geographical information within a regularization framework by adding some constraints to the maximum likelihood estimation of parameters.

A simulation study and the analysis of two real data sets demonstrate that our approach is able to detect complex spatial patterns that are ecologically meaningful.

The model‐based framework allows us to consider external information (e.g. geographical proximities, covariates) in the analysis of ecological networks and appears to be an appealing alternative to consider such data.