bluuebunny/crossref_metadata_2025 huggingface dataset:
Implicit homophobic argument structure
Authors: van der Bom Isabelle , Coffey-Glover Laura , Jones Lucy , Mills Sara , Paterson Laura L.
Published: March 2015

This article analyses the linguistic and discursive elements which contribute to the production of implicit homophobia. Explicit homophobia has been well documented and strategies for countering discriminatory language have been developed (Baker 2014, Leap 2012). However, our interest here is in documenting implicit homophobia, where homophobic beliefs are only hinted at, are disassociated from the speaker, or are embedded within discursive and argument structures. We decided to analyse the debate in the media around the introduction of equal or same-sex marriage legislation in the UK. We focused our analysis on a series of radio programmes on BBC Radio 4,The Moral Maze(2011–2012), where the issue of same-sex marriage was debated with a team of panelists and invited guests from a range of different organisations. Different perspectives on same-sex marriage were discussed, in a seemingly objective and dispassionate way, where the interactants distanced themselves from homophobic beliefs and yet implicitly subscribed to homophobia. We used an analysis drawing on argumentation structure (Fairclough & Fairclough 2012) and through focusing on stance, recontextualisation, imaginaries, and metaphor, we developed an analysis which made the way that implicit homophobia works more visible. In this way, we hope to foreground implicit homophobia, and develop a linguistic and discursive ‘toolkit’ which will enable it to be challenged and countered.
A prospectus for pronunciation research in the 21st century
Authors: Munro Murray J. , Derwing Tracey M.
Published: March 2015

This inaugural issue of the Journal of Second Language Pronunciation, an auspicious step forward in our field, gives us an opportunity to take stock of current trends in pronunciation research with an eye to the future of this evolving field. As longtime researchers, we have learned many lessons by trial and error and wish to share our perspectives on sound methodological practices and on pitfalls to avoid. Our review follows the outline of a traditional experimental investigation, starting with the conceptualization of pronunciation research studies. We then discuss theoretical motivations, choice of constructs, and issues arising from the literature review. Next we compare several research designs and summarize types of data commonly used in pronunciation research. We then move on to consider data collection and analysis, focusing on reliability, effect sizes, and speaker variability, and to offer some caveats regarding the interpretation of results. We conclude by suggesting areas for future second language speech research, in terms of both replications and new studies.
Beyond rating data
Authors: Hayes-Harb Rachel , Hacking Jane F.
Published: March 2015

The accentedness judgment task is widely used in the study of second language speech, and has proven to elicit remarkably reliable ratings across listeners. Despite this reliability, however, we know little about how listeners arrive at accentedness ratings. In the present study we seek to illuminate the role that listener attitudes and expectations play in assessments of accentedness by probing listeners’ explicit criteria for the judgments. We asked ten native English listeners to rate the accentedness of five native Bosnian and five native English speakers, and then to justify their ratings in a semi-structured interview. Analysis of the interview data indicates that despite the elegance of quantitative accentedness data and its remarkable reliability, it appears that when making accentedness judgments, listeners may activate a complex set of attitudes and expectations about speakers that go far beyond a straightforward bottom-up analysis of the speech signal.
Quasi-neutralization in the acquisition of English coronal fricatives by native speakers of Japanese
Authors: Kaneko Emiko , Heo Younghyon , Iverson Gregory , Wilson Ian
Published: March 2015

Second language learners show various forms of mispronunciation, or modification, of target pronunciation, most perhaps due to direct native language transfer, but others, summarized here, to deflected contrast, hypercorrection and covert contrast. The present paper reports on a novel form of adaptation that we term ‘quasi-neutralization,’ in which acoustic characteristics of competing target phonemes are found within the same interlanguage segment (e.g., think [θɪŋk] pronounced as [θsiŋk]). The three English voiceless coronal fricatives /s/, /ʃ/, /θ/ were elicited from Japanese learners of English via two techniques: a wordlist reading task that encouraged participants to focus on their pronunciation, and a sentence construction task that diverted their attention from pronunciation. Among different types of modification, quasi-neutralization was observed predominantly when participants were conscious of their pronunciation, which could reflect their linguistic insecurity as learners. This research thus illuminates another of the strategies that learners employ in the acquisition of L2 pronunciation.
Do fiction writers have superior perspective taking ability?
Authors: Bischoff Theanna , Peskin Joan
Published: March 2015

In investigating the relationship between fiction writing and perspective taking, beliefs about the ability of fiction writers to correctly infer the mental states of others were assessed via survey, in comparison to other professions. Next, two groups of fiction writers (established and intermediate) and a control group were compared across different measures of perspective taking. Possible moderating variables such as age, verbal intelligence, depressive symptoms, and fiction reading were measured. Participants provided writing samples, which were scored for quality. Analyses revealed that the general public believes fiction writers demonstrate above-average perspective-taking ability; however, empirical tests revealed no significant between-group differences on the outcome measures, nor any relationship between fiction writing quality and any outcome measures. The results of the suggest that fiction writers are no better than similar individuals who do not write fiction in terms of their ability to infer others’ mental states or take their perspectives.
Lost in an iPad
Authors: Mangen Anne , Kuiken Don
Published: March 2015

The purpose of this study was to examine the effects of reading medium and a paratext manipulation on aspects of narrative engagement. In a 2 (medium: booklet vs. iPad) by 2 (paratext: fiction vs. nonfiction) between-subjects factorial design, the study combined state oriented measures of narrative engagement and a newly developed measure of interface interference. Results indicated that, independently of prior experience with reading on electronic media, readers in the iPad condition reported dislocation within the text and awkwardness in handling their medium. Also, iPad readers who believed they were reading nonfiction were less likely to report narrative coherence and transportation, while booklet readers who believed they were reading nonfiction were, if anything, more likely to report narrative coherence. Finally, booklet (but not iPad) readers were more likely to report a close association between transportation and empathy. Implications of these findings for cognitive and emotional engagement with textual narratives on paper and tablet are discussed.
From “compelling and mystical” to “makes you want to commit suicide”
Authors: Milota Megan
Published: March 2015

The exploration of what makes a story interesting remains a popular topic in narrative theory. This study aims to contribute to the study of narrative interest by analyzing of a corpus of online amateur reviews of Marilynne Robinson’s debut novelHousekeepingfrom Amazon.com, Goodreads.com, and Librarything.com. The expectation is that, even on these vast, fluid social networking sites, there will still be patterns in the content of reviews, indicating evolving or established positioning strategies and practices. This study presents a viable, replicable method for quantifying what this particular group of amateur critics value in a text, thereby arriving at a deeper understanding of online review forums and the people who use them.
Amazing but true
Authors: D. Leavitt Jonathan , Ryazanov Arseny A. , Christenfeld Nicholas J.S.
Published: March 2015

People find it important to know if a story is factual, but still the most popular stories, in such forms as books and movies, are fictional. Research suggests that a story being true may add value to the reader’s experience, but other findings suggest that fiction may increase enjoyment by providing fewer disruptions to narrative comprehension. In three studies we explored the appeal of stories when they are presented as fiction or as non-fiction. Subjects read (1) story synopses, (2) vignettes from two popular websites, or (3) narratives on relationships and war. Results indicate that readers preferred stories when they were presented, externally, as non-fiction. Readers also preferred stories that seemed internally — that is, because of how they were written — like fiction. Additionally the results suggested that readers rely more heavily on factual stories to update their notions of reality. This study contributes to a body of literature on reader enjoyment in relation to truth labels made explicit or implicit in narratives as well as on the efficacy of arts-based research.
In the eye of the recipient
Authors: Riese Katrin , Bayer Mareike , Lauer Gerhard , Schacht Annekathrin
Published: March 2015

Plot suspense is one of the most important components of narrative fiction that motivate recipients to follow fictional characters through their worlds. The present study investigates the dynamic development of narrative suspense in excerpts of literary classics from the 19th century in a multi-methodological approach. For two texts, differing in suspense as judged by a large independent sample, we collected (a) data from questionnaires, indicating different affective and cognitive dimensions of receptive engagement, (b) continuous ratings of suspense during text reception from both experts and lay recipients, and (c) registration of pupil diameter as a physiological indicator of changes in emotional arousal and attention during reception. Data analyses confirmed differences between the two texts at different dimensions of receptive engagement and, importantly, revealed significant correlations of pupil diameter and the course of suspense over time. Our findings demonstrate that changes of the pupil diameter provide a reliable ‘online’ indicator of suspense.
Relocalizing the translingual practices of young adults in Mongolia and Bangladesh
Authors: Dovchin Sender , Sultana Shaila , Pennycook Alastair
Published: March 2015

The translingual practices of young Mongolians and Bangladeshis suggest that contrary to those popular discourses which position youth as passive recipients of global culture, these young adults are better understood as actively and powerfully engaged with popular culture productions. Drawing on the examples of casual offline conversations and online Facebook interactions of university students in Mongolia and Bangladesh, this paper shows how processes of relocalization give new meanings to the translingual practices of these students as they draw on different modalities from popular culture (film, music and so on) and different linguistic and nonlinguistic resources. This transtextual and transmodal analysis enables us to show how these young adults relocalize linguistic and cultural resources in both their on- and offline interactions.
Translation universals in the oral production of bilingual children
Authors: Álvarez de la Fuente Esther , Fernández Fuertes Raquel
Published: March 2015

This paper investigates two of the most widely analysed universals in translation research, namely simplification and explicitation. We examine the oral production of bilingual children with different language pairs as available in the CHILDES project (MacWhinney 2000) (i.e. the FerFuLice, Ticio, Deuchar, Vila, Genesee and Pérez-Bazán corpora) as well as in other compilation forms (i.e. Ronjat 1913; Leopold 1939–1949; Swain 1972; Lanza 1988, 1997, 2001; Cossato 2008). We address two main issues: whether instances of simplification and explicitation appear in the production of non-instructed interpreters and, if so, how their occurrence relates to the type of data (i.e. spontaneous or experimental) and the language pair involved. The results show that children acquiring two first languages often translate and use simplification and explicitation at varying degrees irrespective of the language pair. We conclude that the analysis of acquisition data can contribute to shed light on the nature of these translation universals.
Translation in cross-language qualitative research
Authors: Piazzoli Erika C.
Published: March 2015

This paper considers some methodological implications related to translation in cross-language qualitative research. The paper takes a twofold stance: on the one hand, it argues that, provided the process is carried out with integrity and transparency, translation in cross-language research can be insightful, and can function as a phase of the analysis in itself. On the other hand, ‘interlanguage translation’, that is, the translation of non-native speakers’ utterances in the target language, should be avoided, or at least acknowledged as a limitation of the study. The article draws on a cross-language qualitative research study, conducted partly in Australia and partly in Italy, in the inter-disciplinary field of second language acquisition (SLA) drama education research. The article argues that a multi-approach to equivalence (dynamic, conceptual and dynamic equivalence) may be needed to translate different kinds of texts within the same study, offering a variety of examples to support these claims.
An overview of translanguaging
Authors: Beres Anna M.
Published: March 2015

Over the last two decades, with the increasing bilingual population across the globe, it has become clear that we need to develop new approaches to language and education. Translanguaging is a term that was originally coined in Wales to describe a kind of bilingual education in which students receive information in one language, for example English, and produce an output of their learning in their second language, for example Welsh. Since then, scholars across the globe have developed this concept and it is now argued it is the best way to educate bilingual children in the 21st century. The present article offers an overview of translanguaging from its origins in Wales to recent developments in the UK and the US. It first presents the traditional approaches to bilingualism in education, which viewed the first and second language as separate entities. Next, it explores how bilingual education can be transformed through the use of translanguaging and outlines current research in the UK. Finally, it proposes some avenues for future studies.
A mechanism for nano-titanium dioxide-induced cytotoxicity in HaCaT cells under UVA irradiation
Authors: Xue Chengbin , Luo Wen , Yang Xiang liang
Published: March 2015

Nano-TiO2 has been reported to be an efficient photocatalyst, which is able to produce reactive oxygen species (ROS) under UVA irradiation. In this study, we investigated the effects of nano-TiO2 on the cytotoxicity, induction of apoptosis, and the putative pathways of its actions in HaCaT cells. We show that nano-TiO2 is a potent inducer of apoptosis and that it transduces the apoptotic signal via ROS generation, thereby inducing mitochondrial permeability transition (MPT) and activating Caspase-3 from HaCaT cells. ROS production, mitochondrial alteration, and subsequent apoptotic cell death in nano-TiO2-treated cells were blocked by the MPT pore-blocker cyclosporin A. Taken together, our data indicate that nano-TiO2 induces the ROS-mediated MPT and resultant Caspase-3 activation.
Purification, cDNA cloning, and characterization of LysM-containing plant chitinase from horsetail (Equisetum arvense)
Authors: Inamine Saki , Onaga Shoko , Ohnuma Takayuki , Fukamizo Tamo , Taira Toki
Published: March 2015

Chitinase-A (EaChiA), molecular mass 36 kDa, was purified from the vegetative stems of a horsetail (Equisetum arvense) using a series of column chromatography. The N-terminal amino acid sequence of EaChiA was similar to the lysin motif (LysM). A cDNA encoding EaChiA was cloned by rapid amplification of cDNA ends and polymerase chain reaction. It consisted of 1320 nucleotides and encoded an open reading frame of 361 amino acid residues. The deduced amino acid sequence indicated that EaChiA is composed of a N-terminal LysM domain and a C-terminal plant class IIIb chitinase catalytic domain, belonging to the glycoside hydrolase family 18, linked by proline-rich regions. EaChiA has strong chitin-binding activity, however, no antifungal activity. This is the first report of a chitinase from Equisetopsida, a class of fern plants, and the second report of a LysM-containing chitinase from a plant.
Research on food and nutrition characteristics of conjugated fatty acids
Authors: Tsuduki Tsuyoshi
Published: March 2015

In this study, the physiological effects of fatty acids with conjugated double bonds were widely examined in vitro and in vivo. Initially, a method for determination of conjugated fatty acids in food and biological samples was established. I then clarified that the oxidative stability of conjugated fatty acids was improved by the form of triacylglycerol and addition of an antioxidant, and the influence of this effect on the metabolism and pharmacokinetics of conjugated fatty acids was clarified in vivo. In addition, antitumor, anti-angiogenesis, and antiobesity effects of conjugated fatty acids were found for the first time, thus demonstrating the usefulness of conjugated fatty acids. This communication mainly outlines the data obtained for conjugated linolenic acid. In addition, this review summarizes my research on conjugated fatty acid.
L1CAM/Neuroglian controls the axon–axon interactions establishing layered and lobular mushroom body architecture
Authors: Siegenthaler Dominique , Enneking Eva-Maria , Moreno Eliza , Pielage Jan
Published: March 2015

The establishment of neuronal circuits depends on the guidance of axons both along and in between axonal populations of different identity; however, the molecular principles controlling axon–axon interactions in vivo remain largely elusive. We demonstrate that the Drosophila melanogaster L1CAM homologue Neuroglian mediates adhesion between functionally distinct mushroom body axon populations to enforce and control appropriate projections into distinct axonal layers and lobes essential for olfactory learning and memory. We addressed the regulatory mechanisms controlling homophilic Neuroglian-mediated cell adhesion by analyzing targeted mutations of extra- and intracellular Neuroglian domains in combination with cell type–specific rescue assays in vivo. We demonstrate independent and cooperative domain requirements: intercalating growth depends on homophilic adhesion mediated by extracellular Ig domains. For functional cluster formation, intracellular Ankyrin2 association is sufficient on one side of the trans-axonal complex whereas Moesin association is likely required simultaneously in both interacting axonal populations. Together, our results provide novel mechanistic insights into cell adhesion molecule–mediated axon–axon interactions that enable precise assembly of complex neuronal circuits.
A formin-nucleated actin aster concentrates cell wall hydrolases for cell fusion in fission yeast
Authors: Dudin Omaya , Bendezú Felipe O. , Groux Raphael , Laroche Thierry , Seitz Arne , Martin Sophie G.
Published: March 2015

Cell–cell fusion is essential for fertilization. For fusion of walled cells, the cell wall must be degraded at a precise location but maintained in surrounding regions to protect against lysis. In fission yeast cells, the formin Fus1, which nucleates linear actin filaments, is essential for this process. In this paper, we show that this formin organizes a specific actin structure—the actin fusion focus. Structured illumination microscopy and live-cell imaging of Fus1, actin, and type V myosins revealed an aster of actin filaments whose barbed ends are focalized near the plasma membrane. Focalization requires Fus1 and type V myosins and happens asynchronously always in the M cell first. Type V myosins are essential for fusion and concentrate cell wall hydrolases, but not cell wall synthases, at the fusion focus. Thus, the fusion focus focalizes cell wall dissolution within a broader cell wall synthesis zone to shift from cell growth to cell fusion.
A novel role of farnesylation in targeting a mitotic checkpoint protein, human Spindly, to kinetochores
Authors: Moudgil Devinderjit K. , Westcott Nathan , Famulski Jakub K. , Patel Kinjal , Macdonald Dawn , Hang Howard , Chan Gordon K.T.
Published: March 2015

Kinetochore (KT) localization of mitotic checkpoint proteins is essential for their function during mitosis. hSpindly KT localization is dependent on the RZZ complex and hSpindly recruits the dynein–dynactin complex to KTs during mitosis, but the mechanism of hSpindly KT recruitment is unknown. Through domain-mapping studies we characterized the KT localization domain of hSpindly and discovered it undergoes farnesylation at the C-terminal cysteine residue. The N-terminal 293 residues of hSpindly are dispensable for its KT localization. Inhibition of farnesylation using a farnesyl transferase inhibitor (FTI) abrogated hSpindly KT localization without affecting RZZ complex, CENP-E, and CENP-F KT localization. We showed that hSpindly is farnesylated in vivo and farnesylation is essential for its interaction with the RZZ complex and hence KT localization. FTI treatment and hSpindly knockdown displayed the same mitotic phenotypes, indicating that hSpindly is a key FTI target in mitosis. Our data show a novel role of lipidation in targeting a checkpoint protein to KTs through protein–protein interaction.
To avoid a mating mishap, yeast focus and communicate
Authors: McClure Allison W. , Lew Daniel J.
Published: March 2015

During mating, yeast cells must perforate their rigid cell walls at the right place to allow cell–cell fusion. In this issue, Dudin et al. (2015; J. Cell Biol. http://dx.doi.org/jcb.201411124) image mating fission yeast cells with unprecedented spatiotemporal resolution. The authors find that when mating cells come into contact, they form aster-like actin structures that direct cell wall remodeling precisely to the point of contact.
Damaged mitochondria get a Parkin ticket
Authors: Short Ben
Published: March 2015

In 2008, Narendra et al. revealed that a protein associated with Parkinson’s disease promotes the turnover of dysfunctional mitochondria.
Chiara Zurzolo: GPI knows the way to go
Authors: Sedwick Caitlin
Published: March 2015

Zurzolo studies the trafficking of GPI-anchored proteins and how this links to human disease.
Two distinct effects of PIP2 underlie auxiliary subunit-dependent modulation of Slo1 BK channels
Authors: Tian Yutao , Ullrich Florian , Xu Rong , Heinemann Stefan H. , Hou Shangwei , Hoshi Toshinori
Published: March 2015

Phosphatidylinositol 4,5-bisphosphate (PIP2) plays a critical role in modulating the function of numerous ion channels, including large-conductance Ca2+- and voltage-dependent K+ (BK, Slo1) channels. Slo1 BK channel complexes include four pore-forming Slo1 (α) subunits as well as various regulatory auxiliary subunits (β and γ) that are expressed in different tissues. We examined the molecular and biophysical mechanisms underlying the effects of brain-derived PIP2 on human Slo1 BK channel complexes with different subunit compositions that were heterologously expressed in human embryonic kidney cells. PIP2 inhibited macroscopic currents through Slo1 channels without auxiliary subunits and through Slo1 + γ1 complexes. In contrast, PIP2 markedly increased macroscopic currents through Slo1 + β1 and Slo1 + β4 channel complexes and failed to alter macroscopic currents through Slo1 + β2 and Slo1 + β2 Δ2–19 channel complexes. Results obtained at various membrane potentials and divalent cation concentrations suggest that PIP2 promotes opening of the ion conduction gate in all channel types, regardless of the specific subunit composition. However, in the absence of β subunits positioned near the voltage-sensor domains (VSDs), as in Slo1 and probably Slo1 + γ1, PIP2 augments the negative surface charge on the cytoplasmic side of the membrane, thereby shifting the voltage dependence of VSD-mediated activation in the positive direction. When β1 or β4 subunits occupy the space surrounding the VSDs, only the stimulatory effect of PIP2 is evident. The subunit compositions of native Slo1 BK channels differ in various cell types; thus, PIP2 may exert distinct tissue- and divalent cation–dependent modulatory influences.
bio-samtools 2: a package for analysis and visualization of sequence and alignment data with SAMtools in Ruby
Authors: Etherington Graham J. , Ramirez-Gonzalez Ricardo H. , MacLean Dan
Published: March 2015

Motivation: bio-samtools is a Ruby language interface to SAMtools, the highly popular library that provides utilities for manipulating high-throughput sequence alignments in the Sequence Alignment/Map format. Advances in Ruby, now allow us to improve the analysis capabilities and increase bio-samtools utility, allowing users to accomplish a large amount of analysis using a very small amount of code. bio-samtools can also be easily developed to include additional SAMtools methods and hence stay current with the latest SAMtools releases.

Results: We have added new Ruby classes for the MPileup and Variant Call Format (VCF) data formats emitted by SAMtools and introduced more analysis methods for variant analysis, including alternative allele calculation and allele frequency calling for SNPs. Our new implementation of bio-samtools also ensures that all the functionality of the SAMtools library is now supported and that bio-samtools can be easily extended to include future changes in SAMtools. bio-samtools 2 also provides methods that allow the user to directly produce visualization of alignment data.

Availability and implementation: bio-samtools is available as a BioGem from http://www.biogems.info or as source code from https://github.com/helios/bioruby-samtools under the MIT License.

Contact:  dan.maclean@tsl.ac.uk
Global optimization-based inference of chemogenomic features from drug–target interactions
Authors: Zu Songpeng , Chen Ting , Li Shao
Published: March 2015

Motivation: Gaining insight into chemogenomic drug–target interactions, such as those involving the substructures of synthetic drugs and protein domains, is important in fragment-based drug discovery and drug repositioning. Previous studies evaluated the interactions locally, thereby ignoring the competitive effects of different substructures or domains, but this could lead to high false-positive estimation, calling for a computational method that presents more predictive power.

Results: A statistical model, termed Global optimization-based InFerence of chemogenomic features from drug–Target interactions, or GIFT, is proposed herein to evaluate substructure-domain interactions globally such that all substructure-domain contributions to drug–target interaction are analyzed simultaneously. Combinations of different chemical substructures were included since they may function as one unit. When compared to previous methods, GIFT showed better interpretive performance, and performance for the recovery of drug–target interactions was good. Among 53 known drug–domain interactions, 81% were accurately predicted by GIFT. Eighteen of the top 100 predicted combined substructure-domain interactions had corresponding drug–target structures in the Protein Data Bank database, and 15 out of the 18 had been proved. GIFT was then implemented to predict substructure-domain interactions based on drug repositioning. For example, the anticancer activities of tazarotene, adapalene, acitretin and raloxifene were identified. In summary, GIFT is a global chemogenomic inference approach and offers fresh insight into drug–target interactions.

Availability and implementation: The source codes can be found at http://bioinfo.au.tsinghua.edu.cn/software/GIFT.

Contact:  shaoli@mail.tsinghua.edu.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA
Authors: Kelly Brendan J. , Gross Robert , Bittinger Kyle , Sherrill-Mix Scott , Lewis James D. , Collman Ronald G. , Bushman Frederic D. , Li Hongzhe
Published: March 2015

Motivation: The variation in community composition between microbiome samples, termed beta diversity, can be measured by pairwise distance based on either presence–absence or quantitative species abundance data. PERMANOVA, a permutation-based extension of multivariate analysis of variance to a matrix of pairwise distances, partitions within-group and between-group distances to permit assessment of the effect of an exposure or intervention (grouping factor) upon the sampled microbiome. Within-group distance and exposure/intervention effect size must be accurately modeled to estimate statistical power for a microbiome study that will be analyzed with pairwise distances and PERMANOVA.

Results: We present a framework for PERMANOVA power estimation tailored to marker-gene microbiome studies that will be analyzed by pairwise distances, which includes: (i) a novel method for distance matrix simulation that permits modeling of within-group pairwise distances according to pre-specified population parameters; (ii) a method to incorporate effects of different sizes within the simulated distance matrix; (iii) a simulation-based method for estimating PERMANOVA power from simulated distance matrices; and (iv) an R statistical software package that implements the above. Matrices of pairwise distances can be efficiently simulated to satisfy the triangle inequality and incorporate group-level effects, which are quantified by the adjusted coefficient of determination, omega-squared (ω2). From simulated distance matrices, available PERMANOVA power or necessary sample size can be estimated for a planned microbiome study.

Availability and implementation:  http://github.com/brendankelly/micropower.

Contact:  brendank@mail.med.upenn.edu or hongzhe@upenn.edu
ExaML version 3: a tool for phylogenomic analyses on supercomputers
Authors: Kozlov Alexey M. , Aberer Andre J. , Stamatakis Alexandros
Published: March 2015

Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Because of the next generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. We present ExaML version 3, a dedicated production-level code for inferring phylogenies on whole-transcriptome and whole-genome alignments using supercomputers.

Results: We introduce several improvements and extensions to ExaML: Extensions of substitution models and supported data types, the integration of a novel load balance algorithm as well as a parallel I/O optimization that significantly improve parallel efficiency, and a production-level implementation for Intel MIC-based hardware platforms.

Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/ExaML.

Contact:  Alexandros.Stamatakis@h-its.org

Supplementary information:  Supplementary data are available at Bioinformatics online.
Fortification of Wheat Dough with Calcium and Magnesium Ions Affects Empirical Rheological Properties
Authors: Sehn Georgia Ane Raquel , Nogueira Amanda de Cássia , Almeida Eveline Lopes , Chang Yoon Kil , Steel Caroline Joy
Published: March 2015

This study evaluated the influence of calcium and magnesium ions on the empirical rheological properties of wheat flour to verify possible effects of these ions on processing because, in addition to their nutritional importance, they are also responsible for water hardness. Calcium (0–1.30 g/100 g) and magnesium (0–0.34 g/100 g) ions from sulfate salts were added to wheat flour, according to a central composite rotatable design. The farinograph and extensigraph properties of wheat flour and its mixtures were evaluated. The results were analyzed by response surface methodology. Calcium ions stood out for increasing water absorption, decreasing mixing stability, and producing a delayed effect on dough extensibility (reduced at 135 min). Magnesium ions influenced most flour rheological properties in a similar manner to oxidizing agents (increased dough stability, increased resistance to extension, and reduced extensibility), thus proving to be a possible replacement agent for these additives. An interaction effect of the combined calcium and magnesium ions was observed on dough development time. The results showed that effects on processing can occur when wheat flour fortification is made, and adaptations on wheat flour specifications, product formulation, and processing parameters may be required.
Impact of Wheat Fiber on Frozen Dough Shelf Life and Bread Quality
Authors: Adams Vivian , Ragaee Sanaa , Abdel‐Aal El‐Sayed M.
Published: March 2015

Freezing and prolonged frozen storage of dough results in constant deterioration in the overall quality of the final product. In this study the effect of wheat bran and wheat aleurone as sources of arabinoxylan (AX) on the quality of bread baked from yeasted frozen dough was investigated. Wheat fiber sources were milled to pass through a 0.5 mm screen, prehydrated for 15 min, and incorporated into refined wheat flour at 15% replacement level. Dough products were prepared from refined flour (control A), whole wheat flour (control B), aleurone composite flour (composite flour A), and bran composite flour (composite flour B) and stored at –18°C for 28 weeks. Dough samples were evaluated for breadmaking quality at zero time, 14 weeks, and 28 weeks of storage. Quality parameters evaluated were loaf weight, loaf specific volume, and crumb firmness. Composite flour bread samples showed the most resistance to freeze damage (less reduction in the overall product quality), indicating a possible role of some fiber components (e.g., AX) in minimizing water redistribution in the dough system and therefore lessening adverse modifications to the gluten structure. The data suggest that the shelf life of frozen dough and quality of obtained bread can be improved with the addition of an AX source.
Phytochemical Profile and Antiproliferative Activity of Dough and Bread Fractions Made from Refined and Whole Wheat Flours
Authors: Lu Yingjian , Fuerst E. Patrick , Lv Junli , Morris Craig F. , Yu Lu , Fletcher Arnetta , Kiszonas Alecia M. , Yu Liangli , Luthria Devanand
Published: March 2015

Phytochemical profile (phenolic acids, carotenoids, and tocopherols) and antiproliferative properties of bread processing fractions, including the dough, crumb, and upper crust made from refined wheat and whole wheat flours were analyzed for two wheat cultivars. Ferulic acid, lutein, and α‐tocopherol were the predominant phenolic acid, carotenoid, and tocopherol, respectively, extracted from all fractions. The levels of all phytochemicals in whole wheat samples were over eightfold higher than their corresponding refined wheat samples. The concentrations of total phenolic acids (soluble and insoluble bound) were higher in the upper crust of refined (∼60–90%) and whole wheat (∼15–40%) breads than their corresponding dough fractions. However, the dough of whole wheat had higher levels of tocopherols and carotenoids compared with the crumb and upper crust, suggesting that phenolic acids were relatively stable during baking, whereas tocopherols (∼25–80%) and carotenoids (∼20–80%), were partially degraded. The antiproliferative activity of whole wheat bread extracts against HT‐29 cancer cells was weakly correlated with total phenolic acids but showed no correlations with total carotenoid and total tocopherol contents.
Effect of Water Flooding on Survival of Leptosphaeria biglobosa ‘brassicae’ in Stubble of Oilseed Rape (Brassica napus) in Central China
Authors: Cai Xiang , Zhang Jing , Wu Mingde , Jiang Daohong , Li Guoqing , Yang Long
Published: March 2015

Blackleg (Phoma stem canker) caused by Leptosphaeria maculans and L. biglobosa is an economically important disease on oilseed rape and many cruciferous vegetables. Oilseed rape–rice rotation is a routine cultivation practice in central China. This study was conducted to assess the effect of flooding on survival of L. biglobosa ‘brassicae’ in the stubble of winter oilseed rape (Brassica napus). Basal stems with typical blackleg symptoms were collected and cut into small pieces (2 cm) that were either submerged in water at 16 and 20, 20 and 28, 28 and 33, and 33 and 40°C (12 and 12 h) or kept dry at room temperature (control). Moreover, in a field experiment, the stem pieces were placed on the soil surface in a rice field or in a cotton field and either flooded in water or not flooded, respectively. After 1, 2, 4, 6, and 8 weeks, the stem pieces were sampled for retrieval of L. biglobosa ‘brassicae’ on V8-juice agar and for determination of dry weight. Selected L. biglobosa ‘brassicae’ isolates from the stem pieces were identified by polymerase chain reaction (PCR). Results from the two experiments showed that, compared with the controls, flooding for 1 to 2 weeks substantially reduced recovery of L. biglobosa ‘brassicae’ and flooding for 4 weeks resulted in negligible recovery of L. biglobosa ‘brassicae’. All of the 99 selected isolates produced a 444-bp DNA fragment in the PCR, confirming that they belong to L. biglobosa ‘brassicae’. Results also indicated that flooding caused rapid decomposition of the stem pieces. After flooding for 8 weeks, the dry weight of the stem pieces was reduced by 28 to 42% in the laboratory experiment and by 26 to 36% in the field experiment. These results suggest that oilseed rape–rice rotation is probably an efficient way to reduce longevity of L. biglobosa ‘brassicae’ in stubble of winter oilseed rape in central China.
Fungicide Sensitivity of Sclerotinia sclerotiorum: A Thorough Assessment Using Discriminatory Dose, EC50, High-Resolution Melting analysis, and Description of New Point Mutation Associated with Thiophanate-Methyl Resistance
Authors: Lehner M. S. , Paula Júnior T. J. , Silva R. A. , Vieira R. F. , Carneiro J. E. S. , Schnabel G. , Mizubuti E. S. G.
Published: March 2015

Thiophanate-methyl (TM), fluazinam, and procymidone are fungicides extensively used for white mold control of common bean in Brazil. We assessed the sensitivity of Brazilian isolates of Sclerotinia sclerotiorum to these three fungicides using discriminatory doses and concentration that results in 50% mycelial growth inhibition (EC50) values. In total, 282 isolates from the most important production areas were screened and none was resistant to fluazinam or procymidone. The EC50 values varied from 0.003 to 0.007 and from 0.11 to 0.72 μg/ml for fluazinam and procymidone, respectively. One isolate was resistant to TM. The EC50 of the TM-resistant isolate was greater than 100 μg/ml, whereas the EC50 of the sensitive isolates varied from 0.38 to 2.23 μg/ml. The TM-resistant isolate had a L240F mutation in the β-tubulin gene. This is the first report of mutation at codon 240 causing resistance to a benzimidazole fungicide in S. sclerotiorum. The high-resolution melting analysis allowed the distinction of TM-sensitive and -resistant isolates by specific melting peaks and curves. The TM-resistant isolate had mycelial growth, sclerotia production, and aggressiveness comparable with that of the sensitive isolates, indicating that this genotype will likely compete well against sensitive isolates in the field. This study demonstrates that resistance to TM, fluazinam, and procymidone is nonexistent or rare. Resistance management practices should be implemented, however, to delay the spread of TM-resistant genotypes.
Winter Conditions Correlate withPhytophthora alniSubspecies Distribution in Southern Sweden
Authors: Redondo Miguel A. , Boberg Johanna , Olsson Christer H. B. , Oliva Jonàs
Published: March 2015

During the last century, the number of forest pathogen invasions has increased substantially. Environmental variables can play a crucial role in determining the establishment of invasive species. The objective of the present work was to determine the correlation between winter climatic conditions and distribution of two subspecies of the invasive forest pathogen Phytophthora alni: P. alni subspp. alni and uniformis killing black alder (Alnus glutinosa) in southern Sweden. It is known from laboratory experiments that P. alni subsp. alni is more pathogenic than P. alni subsp. uniformis, and that P. alni subsp. alni is sensitive to low temperatures and long frost periods. By studying the distribution of these two subspecies at the northern limit of the host species, we could investigate whether winter conditions can affect the geographical distribution of P. alni subsp. alni spreading northward. Sixteen major river systems of southern Sweden were systematically surveyed and isolations were performed from active cankers. The distribution of the two studied subspecies was highly correlated with winter temperature and duration of periods with heavy frost. While P. alni subsp. uniformis covered the whole range of temperatures of the host, P. alni subsp. alni was recovered in areas subjected to milder winter temperatures and shorter frost periods. Our observations suggest that winter conditions can play an important role in limiting P. alni subsp. alni establishment in cold locations, thus affecting the distribution of the different subspecies of P. alni in boreal regions.
Predicting Cereal Root Disease in Western Australia Using Soil DNA and Environmental Parameters
Authors: Poole Grant J. , Harries Martin , Hüberli D. , Miyan S. , MacLeod W. J. , Lawes Roger , McKay A.
Published: March 2015

Root diseases have long been prevalent in Australian grain-growing regions, and most management decisions to reduce the risk of yield loss need to be implemented before the crop is sown. The levels of pathogens that cause the major root diseases can be measured using DNA-based services such as PreDicta B. Although these pathogens are often studied individually, in the field they often occur as mixed populations and their combined effect on crop production is likely to vary across diverse cropping environments. A 3-year survey was conducted covering most cropping regions in Western Australia, utilizing PreDicta B to determine soilborne pathogen levels and visual assessments to score root health and incidence of individual crop root diseases caused by the major root pathogens, including Rhizoctonia solani (anastomosis group [AG]-8), Gaeumannomyces graminis var. tritici (take-all), Fusarium pseudograminearum, and Pratylenchus spp. (root-lesion nematodes) on wheat roots for 115, 50, and 94 fields during 2010, 2011, and 2012, respectively. A predictive model was developed for root health utilizing autumn and summer rainfall and soil temperature parameters. The model showed that pathogen DNA explained 16, 5, and 2% of the variation in root health whereas environmental parameters explained 22, 11, and 1% of the variation in 2010, 2011, and 2012, respectively. Results showed that R. solani AG-8 soil pathogen DNA, environmental soil temperature, and rainfall parameters explained most of the variation in the root health. This research shows that interactions between environment and pathogen levels before seeding can be utilized in predictive models to improve assessment of risk from root diseases to assist growers to plan more profitable cropping programs.
Population Structure, Pathogenicity, and Mating Type Distribution of Magnaporthe oryzae Isolates from East Africa
Authors: Onaga Geoffrey , Wydra Kerstin , Koopmann Birger , Séré Yakouba , von Tiedemann Andreas
Published: March 2015

Rice blast, caused by Magnaporthe oryzae, is one of the emergent threats to rice production in East Africa (EA), where little is known about the population genetics and pathogenicity of this pathogen. We investigated the genetic diversity and mating type (MAT) distribution of 88 isolates of M. oryzae from EA and representative isolates from West Africa (WA) and the Philippines (Asia) using amplified fragment length polymorphism markers and mating-type-specific primer sets. In addition, the aggressiveness of each isolate was evaluated by inoculating on the susceptible Oryza sativa indica ‘Co39’, scoring the disease severity and calculating the disease progress. Hierarchical analysis of molecular variance revealed a low level of genetic differentiation at two levels (FST 0.12 and FCT 0.11). No evidence of population structure was found among the 65 isolates from EA, and gene flow among EA populations was high. Moreover, pairwise population differentiation (GST) in EA populations ranged from 0.03 to 0.04, suggesting that >96% of genetic variation is derived from within populations. However, the populations from Asia and WA were moderately differentiated from EA ones. The spatial analysis of principal coordinates and STRUCTURE revealed overlapping between individual M. oryzae isolates from EA, with limited distinctness according to the geographic origin. All the populations were clonal, given the positive and significant index of association (IA) and standardized index of association (rd), which indicates a significant (P < 0.001) departure from panmixia (IA and rd = 0). Both MAT1-1 and MAT1-2 were detected. However, MAT1-1 was more prevalent than MAT1-2. Pathogenicity analysis revealed variability in aggressiveness, suggesting a potential existence of different races. Our data suggest that either M. oryzae populations from EA could be distributed as a single genetic population or gene flow is exerting a significant influence, effectively swamping the action of selection. This is the first study of genetic differentiation of rice-infecting M. oryzae strains from EA, and may guide further studies on the pathogen as well as resistance breeding efforts.
Genomes of ‘Candidatus Liberibacter solanacearum’ Haplotype A from New Zealand and the United States Suggest Significant Genome Plasticity in the Species
Authors: Thompson Sarah M. , Johnson Chris P. , Lu Ashley Y. , Frampton Rebekah A. , Sullivan Kerry L. , Fiers Mark W. E. J. , Crowhurst Ross N. , Pitman Andrew R. , Scott Ian A. W. , Wen Aimin , Gudmestad Neil C. , Smith Grant R.
Published: March 2015

‘Candidatus Liberibacter solanacearum’ contains two solanaceous crop-infecting haplotypes, A and B. Two haplotype A draft genomes were assembled and compared with ZC1 (haplotype B), revealing inversion and relocation genomic rearrangements, numerous single-nucleotide polymorphisms, and differences in phage-related regions. Differences in prophage location and sequence were seen both within and between haplotype comparisons. OrthoMCL and BLAST analyses identified 46 putative coding sequences present in haplotype A that were not present in haplotype B. Thirty-eight of these loci were not found in sequences from other Liberibacter spp. Quantitative polymerase chain reaction (qPCR) assays designed to amplify sequences from 15 of these loci were screened against a panel of ‘Ca. L. solanacearum’-positive samples to investigate genetic diversity. Seven of the assays demonstrated within-haplotype diversity; five failed to amplify loci in at least one haplotype A sample while three assays produced amplicons from some haplotype B samples. Eight of the loci assays showed consistent A–B differentiation. Differences in genome arrangements, prophage, and qPCR results suggesting locus diversity within the haplotypes provide more evidence for genetic complexity in this emerging bacterial species.