bluuebunny/crossref_metadata_2025 huggingface dataset:
Applications of fipronil (Adonis 3UL) and Metarhizium acridum for use against locusts have minimal effect on litter decomposition and microbial functional diversity in Australian arid grassland
Authors: Maute Kimberly , Story Paul , Hose Grant C. , Bull C. M. , French Kris
Published: September 2016

Litter and microbes are key drivers of nutrient cycles, particularly in arid ecosystems where decomposition rates are low. Locust control in arid regions represents a potentially important hazard to microbes, because local taxa are unlikely to have adapted to pesticide exposure and operations often occur during times of high microbial activity. We monitored the response of aboveground litter decomposition and soil bacteria functional diversity to aerial applications of fipronil (a chemical pesticide) barrier treatments and Metarhizium acridum (a fungal biopesticide) blanket treatments. Decomposition was monitored over 2 years (before and after treatments) using a replicated litter-bag experiment, whereas changes in bacteria functional diversity were measured over 1 month. Analysis of litter mass loss indicated there were no pesticide treatment effects relative to control. Less litter decomposed in small than large mesh bags, and less litter decomposed during the second year of the study. Litter had higher mean nitrogen (N) and carbon (C), and a lower C:N ratio, during the first year of the study. In contrast, within-treatment site analysis revealed a significant increase in litter mass remaining in bags at M. acridum-treated subsites. However, these values were only 4% different from control sites, suggesting that the effect detected may not be biologically significant. There appeared to be no pesticide treatment effect on bacterial community functional diversity and no significant temporal variation. The lack of large-scale pesticide treatment effects suggests that arid zone fungi and bacteria are resilient to such disturbances. Differences in decomposition was explained by differences in the activity of arthropods and in the shade provided by the two mesh sizes, and an annual decline could be attributed to lower litter C and N content and lower annual rainfall in Year 2. Results show the temporal variation possible in decomposition and microbe community measures in arid systems.
Dissolved organic nitrogen contributes significantly to leaching from furrow-irrigated cotton–wheat–maize rotations
Authors: Macdonald B. C. T. , Ringrose-Voase A. J. , Nadelko A. J. , Farrell M. , Tuomi S. , Nachimuthu G.
Published: September 2016

Leaching of nitrogen (N) in intensive irrigated agriculture can be a significant loss pathway. Though many studies have focussed on losses of mineral N, and in particular nitrate, dissolved organic N (DON) has received less coverage. In the present study, over a 5-year period (2008–2013), 740kgNha–1 fertiliser was applied to an irrigated cotton–wheat–maize rotation on a cracking clay (grey Vertosol). Deep drainage from the undisturbed soil profile at the site was measured at 2.1m below the soil surface using a variable tension lysimeter. In total, 108mm of drainage occurred during the 5 years and the majority of the drainage and the irrigations occurred during the cotton seasons. The majority of the N loss occurred during the first 3–4 irrigations and neither the N loss nor its composition were affected by the product or timing of the fertiliser application. The N in the drainage was composed of 12.8kgNOx-Nha–1, 8.7 DON-N and 0.1 NH4+-Nkgha–1, which shows that DON is an important component (40%) of the deep drainage N from irrigated Vertosol cotton production systems. Overall the total N flux lost via deep drainage represents 3% of the applied N fertiliser.
Harnessing adolescent values to motivate healthier eating
Authors: Bryan Christopher J. , Yeager David S. , Hinojosa Cintia P. , Chabot Aimee , Bergen Holly , Kawamura Mari , Steubing Fred
Published: September 2016

Significance

Behavioral science has rarely offered effective strategies for changing adolescent health behavior. One limitation of previous approaches may be an overemphasis on long-term health outcomes as the focal source of motivation. The present research uses a rigorous randomized trial to evaluate an approach that aligns healthy behavior with values about which adolescents already care: feeling like a socially conscious, autonomous person worthy of approval from one’s peers. It improved the health profile of snacks and drinks participants chose in an ostensibly unrelated context and did so because it caused adolescents to construe the healthy behavior as being aligned with prominent adolescent values. This suggests a route to an elusive result: effective motivation for adolescent behavior change.
How the accusative became the relative
Authors: Fortescue Michael
Published: September 2016

The Eskimo-Uralic hypothesis of a genetic link between Eskimo-Aleut and the Uralic languages is now reaching its second centenary. Two major problems with its advancement sinceBergsland’s (1959)summary of its status are addressed in this article. The first of these is the lack of an obvious correlate of the ubiquitous Eskimo-Aleut (EA) relative case marker -min Uralic; the other is the lack of anm-initial first person singular morpheme in EA to correlate with that of the Uralic languages. That the EA singular genitive/relative marker -m— as well as the instrumental/accusative singular -məkbased on it — might be cognate with Uralic singular accusative -mwas suggested already bySauvageot (1953), but no firm conclusion on the matter has since been reached. This has remained a tantalizing possibility, despite the conflicting semantics. However, the remarkable morphosyntactic parallels between Eskimo-Aleut and Samoyedic in particular have grown more apparent with recent publications. A solution is proposed, linking the emergence of ergativity in the Eskimo-Aleut family with a reanalysis of the original nominative-accusative case marking system.
Gothic evidence for the pronunciation of Greek in the fourth century AD
Authors: Leppänen Ville
Published: September 2016

The Gothic Bible offers valuable secondary evidence for the pronunciation of Greek in the fourth century AD. However, inferences based on such data may result in a vicious circle, as the interpretation of Gothic is, to a great extent, dependent on the historical details of contemporary Greek. I show that a circular argument can be avoided by using a novel method, which is based on the comparison of transcription correspondences of Greek loan words and biblical names occurring in the Greek original and the Gothic version. I test the method by applying it to three example cases. The first concerns the aspirated stops φ, θ, χ: Gothic evidence confirms the fricativization of these stops. The second case concerns the potential fricativization of voiced stops β, δ, γ: the results are inconclusive, which is an important finding, since this shows that Gothic cannot be used as evidence for the fricativization of these stops. The third case concerns front vowels: Gothic evidence confirms the coalescence of αι and ε on the one hand, and ει and ῑ on the other, while it also indicates that η was not (yet) pronounced as [iː] in the fourth century AD.
Plastic letters
Authors: Dickinson Jennifer A.
Published: September 2016

This article examines the complex intersection of language ideologies shaping alphabetic choices in Ukrainian outdoor advertising and shop signs, focusing on alphabet mixing through the insertion of Latin letters into Cyrillic texts and the juxtaposition of parallel or alternating texts using both of these writing systems. Drawing upon ethnographic data from work with graphic designers and consumers as well as analysis of language use in signs, I argue that while alphabet mixing is often characterized as “faddish” or “youth-oriented” these practices also reflect Soviet-era ideological stances towards both Latin typefaces, seen as “plastic” letters associated with Western capitalism, and Cyrillic typefaces, seen as “rigid” forms subject to strong central control by the Soviet state. The increasing availability of personal computers with word-processing and graphic design software in Ukraine has both increased access by individuals to print technology, and promoted a new typographic aesthetic through the dissemination of Cyrillic fonts based on Latin, not Soviet or pre-Soviet Cyrillic, models.
Typing your way to technical identity
Authors: Lange Patricia G.
Published: September 2016

Informal, online environments facilitate creative self-expression through typographic and orthographic stylistics. Yet, ideologies of writing may be invoked to discourage written forms that are purportedly difficult to read. This paper analyzes how members of an online, text-based, gaming community negotiate appropriate, written communications as expressions of technical identity. These encounters may reify communities of technologists who are associated with using or avoiding forms such as abbreviations, capital letters, and “leet speak.” Amid the technologizing of the word, the paper argues that those who do not conform to assumed norms may be indexed as less technical than those who do. By examining troubled encounters, the paper explores how metapragmatic negotiations affect creativity and technical identity performance online. The paper argues that contrary to discourses that online interactants pay little attention to written stylistics, the present participants closely attended to subtle and small forms. Further, it discusses how ideologies may be idiosyncratically applied to assist in forming asymmetrical, technical identities. Finally, it argues that technical affiliations are just as important to study as other variables such as gender, ethnicity, age, and class that have traditionally received attention in analyses of ideologies of writing and New Literacy Studies.
A corpus linguistics approach to the research and teaching of Chinese as a second language
Authors: Du Hang
Published: September 2016

This paper reports on the results of preliminary analyses of two corpora of learner Chinese that students produced during study abroad in China: A written corpus and a spoken corpus of longitudinal data. Several native language corpora were used as references. Results not only revealed that learners still underused the ba-construction, they also quantified the extent of the underuse. Additionally, findings from the longitudinal spoken corpus reveal that spending an entire year studying abroad in China can help students make progress in their production of the ba-construction. Pedagogically, it is suggested that teachers should consult native as well as learner corpora in developing teaching materials, and students should be encouraged to take learning into their own hands by consulting native corpora themselves, to engage in Data Driven Learning (DDL). This paper argues for the usefulness of corpus linguistics in the research and teaching of Chinese as a second language.
An ERP study of the processing of Mandarin classifiers
Authors: Qian Zhiying , Garnsey Susan
Published: September 2016

Comprehension of Mandarin classifier-noun sequences was examined by comparing event-related brain potential (ERP) responses to classifier-noun matches (一张纸; a sheet of paper) and mismatches (一张咖啡; a sheet of coffee). One goal was to determine which ERP components are sensitive to such matches, as a clue about the nature of the underlying combinatorial processes. Another goal was to examine effects of classifier constraint strength (a piece of … vs a sheet of …) on anticipation of the subsequent noun. Results showed that nouns evoked larger N400 in mismatching classifier-noun sequences, suggesting that combinatorial processing was primarily semantic. General classifiers evoked a larger sustained frontal negativity than specific classifiers, reflecting effects of constraint strength on anticipation of the upcoming noun. In addition, classifier presence was manipulated. The classifier-absent condition evoked a P600 in the first half of the experiment and an Anterior Negativity in the second half, suggesting that readers changed processing strategy over time.
Metalinguistic awareness and self-repair in Chinese language learning
Authors: Tao Liang
Published: September 2016

The importance of metalinguistic knowledge in foreign language learning is exemplified by beginning Chinese learners’ practice of self-initiated self-repairs. It demonstrates how such knowledge helps learners to enhance accurate L2 production. Repair constitutes an important part of the social organization of conversation for the interactional needs of human communication. Self-repair by native speakers illustrates their metalinguistic awareness of communicative needs at the subliminal level; whereas self-repair by beginning Chinese language learners reflects their conscious effort and self-monitoring of their utterances for accurate Chinese production. This study suggests that developing metalinguistic knowledge should help learners to suppress L1 influence, and linguistic research offers a vital role in fostering the development of learners’ metalinguistic knowledge.
Prosody and discourse functions of ranhou 然后
Authors: Wang Wei
Published: September 2016

This paper attempts to integrate linguistic research with language teaching, taking ranhou as a case study. It first explores the discourse functions of ranhou. Three functions have thus been identified, i.e. TCU extension, turn continuation and new topic initiation. Then, it examines the prosodic features associated with each discourse function, including duration, gap, and pitch. Finally, this paper discusses the ways in which the findings can be applied pedagogically and demonstrates the feasibility to teach discourse functions and prosody in the classroom.
Patterns of plural NP + dou (都) expressions in conversational discourse and their pedagogical implications
Authors: Wu Haiping , Tao Hongyin
Published: September 2016

As a common adverb, dou (都) ‘all, every, completely, even’ has received extensive attention from various theoretical approaches. However, most previous studies tend to focus on its semantic scope and quantification functions. In this paper, we take an interactional linguistics approach to explore one of the most commonly seen subtypes of dou expressions, Plural NP + dou, in conversational discourse. Our findings show that, in general, subjective use outnumbers objective use, contrary to what is implied in most earlier studies. On the basis of the discourse-based findings, we propose ways to integrate the research results in language teaching, with particular reference to material design, classroom activities, and assessment methods.
Pragmatic markers as constructions. The case of anyway
Authors: Aijmer Karin
Published: September 2016

The aim of the study is to explore the idea that discourse markers are oriented to properties of spoken language and the interaction and have special uses or tasks depending on formal and contextual factors. The empirical data comes from an analysis of anyway in informal conversation in several regional varieties of English. The British component of the ICE-corpus was selected as the home variety. Comparisons have been made with Canadian English (ICE-CAN), Philippine English (ICE-PHIL), and New Zealand English (ICE-NZ). Anyway has been analysed in a constructional approach as a combination of form and function. It does not have a fixed meaning but a meaning potential containing information about the position of anyway in the clause and the turn sequence, collocation, activity types and regional specialization. The analysis has shown that anyway can be regarded as distinct constructions (or meaning potentials) in the left and the right periphery or as a stand-alone marker. The meanings reflect the activities and tasks which have to be performed at interactionally sensitive transitions in the evolving discourse. While some varieties prefer anyway in the left periphery this may not be a general tendency when we look at more varieties.
Mirativity and rhetorical structure
Authors: Gentens Caroline , Kimps Ditte , Davidse Kristin , Jacobs Gilles , Van linden An , Brems Lieselotte
Published: September 2016

This paper studies from a synchronic-diachronic perspective the formal and semantic-discursive properties of adverbial expressions with a negative quantifier + wonder (henceforth ‘no’ wonder). They are used as mirative qualifiers which assess a proposition as ‘not surprising’, typically motivated by an explicit justification. As a result, the ‘no’ wonder adverbials function in a larger rhetorical structure, within which they convey the ‘causally justified expectedness’ of a state-of-affairs. We point out that in Present-day English, there are two types of ‘no’ wonder adverbials that are in different ways ‘outside of the clause’ they assess. On the one hand, there are disjunct uses of ‘no’ wonder, which in our data always occur in sentence-initial position, scoping over the following proposition, with the justification either preceding or following the miratively qualified proposition. On the other hand, there is the anaphoric adverbial ‘no’ wonder, which retrospectively qualifies a proposition in a preceding clause or sentence, but is itself part of a separate complex containing the justification. We argue that historically these two adverbial subtypes are related to different multi-clausal patterns involving clauses with be + no wonder: disjuncts to extraposition constructions and anaphoric adverbials to clauses that qualify a preceding clause. We also show that in Present-day spoken data the anaphoric mirative qualifier is prosodically more independent, while the disjunct uses tend to be prosodically integrated with the proposition.
From clause to adverb
Authors: López-Couso María José , Méndez-Naya Belén
Published: September 2016

This chapter is concerned with the origin and development of the English epistemic adverb maybe. Using various historical corpora, including the Helsinki Corpus and ARCHER as a baseline, we analyse a range of structures featuring the sequence (it) may be, paying special attention to those which may have contributed, in varying degrees, to the emergence of the adverb maybe. We argue that the development of maybe can be regarded as an instance of grammaticalization, whereby a matrix clause in a complementation structure (it may be (that)…) is downgraded to a parenthetical, thus losing its original clausal morpho-syntactic features, and eventually becoming an adverb. Therefore, the adverbialization of maybe seems to have followed a similar path of development to that of (quasi-)adverbs such as methinks and looks like. We also argue, however, that even though complement-taking-predicate clauses are the ultimate main source of the adverb, via an intermediate parenthetical stage, other constructions (e.g. it may be + phrasal constituent) may have played a role in its development.
The syntax of confirmationals
Authors: Wiltschko Martina , Heim Johannes
Published: September 2016

This paper explores the form, function and distribution of certain discourse markers which seem to occur outside traditional clause boundaries and are used to request confirmation. These ‘confirmationals’ differ according to what is expected to be confirmed. Some confirmationals trigger a response from the addressee to confirm that the proposition is true; others require a response to confirm that the addressee knows that the proposition is true. This variation is reminiscent of scope effects and suggests that confirmationals should be analysed in syntactic terms despite their peripheral position. For our analysis, we adopt the Universal Spine Hypothesis (Wiltschko 2014), which promotes a hierarchically organized series of core functional projections. We propose that the highest functional projection of a clause is dedicated to a ‘grounding’ layer, which in turn consists of a speaker-oriented and an addressee-oriented structure. The topmost layer is dedicated to regulate response and consists of a position that encodes the call on the addressee. Our analysis of speech act structure is an updated version of Ross’ (1970) performative hypothesis. We explore the predictions and implications of this hypothesis for the syntax-pragmatics interface.
Intensifying adverbs ‘outside the clause’
Authors: Haselow Alexander
Published: September 2016

This paper discusses utterance-final uses of intensifying adverbs (absolutely, definitely, really and totally), which are often ambiguous in terms of their syntactic status between postposed clausal constituents and extra-clausal units. These adverbs are analyzed as macrogrammatical elements serving different cognitive tasks arising at one particular point in the linear production of an utterance, namely its potential end, such as modifying illocutionary force and strengthening the display of alignment with the co-participant’s views. As part of macrogrammar, they accompany a microgrammatical unit, which is characterized by internal morphosyntactic dependency relations. Final intensifying adverbs are showcase examples of the piece-by-piece emergence of linguistic structure in on-line speech production and thus require an analytic approach based on the linearity of speaking in time.
Leaving-home transition and later parent–child relationships: proximity and contact in Italy
Authors: Tosi Marco
Published: September 2016

Previous research points out that early life-course transitions affect subsequent parent–child relationships. This study examines the association between the leaving-home transition and later parent–child relations in Italy, by taking into account different timings and reasons to move out of the parental home. Using pooled data from two waves (2003 and 2009) of the Family and Social Subject Survey, Ordered Logistic regression models were adopted to analyze residential proximity and face-to-face contact between parents and their adult children. The findings show that the longer the time adult children spent in their parents’ home, the higher the propensity to reside near, and maintain frequent interaction with parents in later life is. Spending longer time in the parental home seems to provide much less benefit for daughters than for sons. The positive association between co-residence duration and later parent–daughter relations decreases until disappearing in concomitance with the normative age for leaving home. Considering the reasons for leaving home, adult children moving out to get married tend to have more intense intergenerational ties. Marriage continues to be the normative occasion to leave the parental family, particularly among adult daughters, who are subject to greater cultural expectations about family ties.
Ecosystem ecology as a framework for organizing and advancing greenroof research
Authors: Starry O.S.
Published: September 2016

This paper explores the application of an ecosystem ecology framework to greenroof systems. It investigates how aspects of greenroof design or structure relate to functions such as rates of nutrient and energy cycling. Three main sections include energy budgets, cycling of nutrients and water, and ecosystem response to disturbance. Comparisons between greenroofs and other systems indicated that, functionally, greenroofs may be very different from ecosystem analogs. A further assessment of the greenroof energy budget called into question how food webs are supported. An evaluation of factors predicting system response to disturbance identified ways in which greenroofs may be less resilient to disturbance. One challenge with the ecosystem approach is a lack of sufficient data for fully holistic models, especially with respect to management practices. Ecosystem ecology is nevertheless shown to be a valuable framework for integrating existing greenroof research as well as targeting areas for future research and model development.
Integrating ecology into green roof research
Authors: Blaustein Leon , Kadas Gyongyver J. , Gurevitch Jessica
Published: September 2016

Green roofs can provide environmental benefits that include increased building insulation, mitigating urban heat islands, providing aesthetic value, reducing runoff and storm water flooding in urban environments, improving air quality by sequestering pollutants, cooling photovoltaic panels to improve their function, and providing habitat for fauna and flora. Until very recently, improvements of green-roof environmental services had been achieved largely by horticulturalists, engineers, and architects. In recent years, ecologists have increased their participation, implementing ecological theory for enhancing biodiversity, and selecting specific plant assemblages for other environmental services such as carbon sequestration and for providing cooler roofs. Moreover, ecologists can use green roofs as relatively novel habitats for testing and developing ecological theory. This special issue is devoted to fostering input from ecologists for advancing the environmental and ecosystem services of green roofs. A wide range of ecologists can explore the topic of the ecological aspects of green roof design and implementation including island biogeography theory, niche theory and null models, the role of environmental heterogeneity, invasion ecology, and plant selection. They can contribute ecological methodology and study design for strong inference.
Early epithelial signaling center governs tooth budding morphogenesis
Authors: Ahtiainen Laura , Uski Isa , Thesleff Irma , Mikkola Marja L.
Published: September 2016

During organogenesis, cell fate specification and patterning are regulated by signaling centers, specialized clusters of morphogen-expressing cells. In many organs, initiation of development is marked by bud formation, but the cellular mechanisms involved are ill defined. Here, we use the mouse incisor tooth as a model to study budding morphogenesis. We show that a group of nonproliferative epithelial cells emerges in the early tooth primordium and identify these cells as a signaling center. Confocal live imaging of tissue explants revealed that although these cells reorganize dynamically, they do not reenter the cell cycle or contribute to the growing tooth bud. Instead, budding is driven by proliferation of the neighboring cells. We demonstrate that the activity of the ectodysplasin/Edar/nuclear factor κB pathway is restricted to the signaling center, and its inactivation leads to fewer quiescent cells and a smaller bud. These data functionally link the signaling center size to organ size and imply that the early signaling center is a prerequisite for budding morphogenesis.
The soluble pattern recognition receptor PTX3 links humoral innate and adaptive immune responses by helping marginal zone B cells
Authors: Chorny Alejo , Casas-Recasens Sandra , Sintes Jordi , Shan Meimei , Polentarutti Nadia , García-Escudero Ramón , Walland A. Cooper , Yeiser John R. , Cassis Linda , Carrillo Jorge , Puga Irene , Cunha Cristina , Bastos Hélder , Rodrigues Fernando , Lacerda João F. , Morais António , Dieguez-Gonzalez Rebeca , Heeger Peter S. , Salvatori Giovanni , Carvalho Agostinho , Garcia-Sastre Adolfo , Blander J. Magarian , Mantovani Alberto , Garlanda Cecilia , Cerutti Andrea
Published: September 2016

Pentraxin 3 (PTX3) is a fluid-phase pattern recognition receptor of the humoral innate immune system with ancestral antibody-like properties but unknown antibody-inducing function. In this study, we found binding of PTX3 to splenic marginal zone (MZ) B cells, an innate-like subset of antibody-producing lymphocytes strategically positioned at the interface between the circulation and the adaptive immune system. PTX3 was released by a subset of neutrophils that surrounded the splenic MZ and expressed an immune activation–related gene signature distinct from that of circulating neutrophils. Binding of PTX3 promoted homeostatic production of IgM and class-switched IgG antibodies to microbial capsular polysaccharides, which decreased in PTX3-deficient mice and humans. In addition, PTX3 increased IgM and IgG production after infection with blood-borne encapsulated bacteria or immunization with bacterial carbohydrates. This immunogenic effect stemmed from the activation of MZ B cells through a neutrophil-regulated pathway that elicited class switching and plasmablast expansion via a combination of T cell–independent and T cell–dependent signals. Thus, PTX3 may bridge the humoral arms of the innate and adaptive immune systems by serving as an endogenous adjuvant for MZ B cells. This property could be harnessed to develop more effective vaccines against encapsulated pathogens.
Historical observations contributing insights on etiopathogenesis of rheumatoid arthritis and role of rheumatoid factor
Authors: Tan Eng M. , Smolen Josef S.
Published: September 2016

When studies on rheumatoid arthritis (RA) that were made many decades ago and could be considered “historical” in nature are analyzed in the context of recent observations, important insights on RA and on the function of rheumatoid factor (RF) become apparent. RF in the role of antibody to immune complexes (ICs) appears to be involved in activation of the complement system and in the production of chemotactic and inflammatory mediators, creating a condition that can be sustained and reinitiated. In the synovial cavity, a state of nonresolving inflammation is produced with the formation of citrullinated protein antigen–antibody complexes or other forms of ICs. This is followed by a second wave of IC production in the form of RF acting as antibody reactive with the initial ICs. Both of these processes are associated with complement consumption and production of inflammatory mediators. We present a model of an initiation phase of RA that might represent an example of repetitive formation of ICs and complement-mediated inflammation. Targeting therapy at this phase of RA to break the cycles of recurrent inflammation might be a novel approach to aid in further control of the disease.
Pore size matters for potassium channel conductance
Authors: Naranjo David , Moldenhauer Hans , Pincuntureo Matías , Díaz-Franulic Ignacio
Published: September 2016

Ion channels are membrane proteins that mediate efficient ion transport across the hydrophobic core of cell membranes, an unlikely process in their absence. K+ channels discriminate K+ over cations with similar radii with extraordinary selectivity and display a wide diversity of ion transport rates, covering differences of two orders of magnitude in unitary conductance. The pore domains of large- and small-conductance K+ channels share a general architectural design comprising a conserved narrow selectivity filter, which forms intimate interactions with permeant ions, flanked by two wider vestibules toward the internal and external openings. In large-conductance K+ channels, the inner vestibule is wide, whereas in small-conductance channels it is narrow. Here we raise the idea that the physical dimensions of the hydrophobic internal vestibule limit ion transport in K+ channels, accounting for their diversity in unitary conductance.
ImmuneDB: a system for the analysis and exploration of high-throughput adaptive immune receptor sequencing data
Authors: Rosenfeld Aaron M , Meng Wenzhao , Luning Prak Eline T , Hershberg Uri
Published: September 2016

As high-throughput sequencing of B cells becomes more common, the need for tools to analyze the large quantity of data also increases. This article introduces ImmuneDB, a system for analyzing vast amounts of heavy chain variable region sequences and exploring the resulting data. It can take as input raw FASTA/FASTQ data, identify genes, determine clones, construct lineages, as well as provide information such as selection pressure and mutation analysis. It uses an industry leading database, MySQL, to provide fast analysis and avoid the complexities of using error prone flat-files.

Availability and Implementation

ImmuneDB is freely available at http://immunedb.com

A demo of the ImmuneDB web interface is available at: http://immunedb.com/demo

Supplementary information

Supplementary data are available at Bioinformatics online.
Jianguo Hou: major reforms in China's S&T funding mechanisms
Authors: Poo Mu-ming , Wang Ling
Published: September 2016

In late June, the first batch of National Major R&D Projects was announced on the Public Service Platform of National Science and Technology Management Information System (http://service.most.gov.cn/index/). This signified a new round of major top-down reform of China's S&T program management reform, a reform generally considered to be unprecedented in both scope and depth. In line with rapid economic growth, China now produces more research articles than any other country except the USA, boasting the world's highest number of researchers (∼3.8 million). Yet, these impressive numbers are insufficient to meet the need for innovation in Chinese economy, which is still relying heavily on imported core technologies. The S&T program management has long been plagued by fragmentation, duplication and diffuseness, with widespread complaints by researchers on the lack of both openness and transparency in funding review processes. In a recent interview with NSR, the Vice Minister of Science and Technology Jianguo Hou elaborated upon the new reform of S&T program management that aims to address many of these problems, and new polices that impact on how research will be conducted in China.
Effect of Digestive Enzyme Treatment on Antioxidant Properties of Germinated Green Gram Fortified with Minerals
Authors: Oghbaei Morteza , Prakash Jamuna
Published: September 2016

The antioxidant activity (AA) of green gram germinated in mineral‐fortified water (with iron at 100 or 200 mg/100 mL or zinc at 50 or 100 mg/100 mL), cooked under pressure (PC), or microwaved and subjected to digestive enzyme treatment was determined by using three assay methods. Total AA showed that dehulled grains (DG) had higher AA than whole grains (WG). Cooking reduced the AA in both methods compared with raw grains with a lower percent retention of AA, although significant variations were not found between methods. The percent retention of AA in postdigestion samples was 22.68–51.39 (DG) and 15.67–44.0 (WG). Free radical scavenging activity indicated a different pattern, in which WG exhibited higher AA than DG and, among cooking methods, PC grains had higher activity. A reducing‐power assay showed similar results: DG had lower and PC samples had higher AA. Postdigestion AA of WG was higher for cooked than raw samples, although DG showed the opposite trend. In all cases, samples fortified with iron showed less AA because of prooxidant action of iron. In all assays, postdigestion samples had less activity than predigested extracts. In conclusion, germinated grains showed high AA, influenced by the presence of minerals, dehulling process, and cooking.
Early Detection of Airborne Inoculum of Magnaporthe oryzae in Turfgrass Fields Using a Quantitative LAMP Assay
Authors: Villari Caterina , Mahaffee Walter F. , Mitchell Thomas K. , Pedley Kerry F. , Pieck Michael L. , Hand Francesca Peduto
Published: September 2016

Gray leaf spot (GLS) is a destructive disease of perennial ryegrass caused by a host specific pathotype of the ascomycete Magnaporthe oryzae. Early diagnosis is crucial for effective disease management and the implementation of Integrated Pest Management practices. However, a rapid protocol for the detection of low levels of airborne inoculum is still missing. We developed a pathogen-specific quantitative loop-mediated isothermal amplification (qLAMP) assay coupled with a spore trap system for rapid detection and quantification of airborne inoculum of the M. oryzae perennial ryegrass pathotype, and tested its suitability for implementation in GLS-infected turfgrass fields. In summer 2015, two perennial ryegrass plots were artificially inoculated with the pathogen, with four continuously running custom impaction spore traps placed in each plot. Sampling units were replaced daily and tested with the developed qLAMP assay, while plots were monitored for symptom development. Results confirmed that the qLAMP assay-trap system was able to detect as few as 10 conidia up to 12 days before symptoms developed in the field. LAMP technology is particularly appropriate for field implementation by nontechnical users, and has the potential to be a powerful decision support tool to guide timing of fungicide applications for GLS management.
Phenomic Approaches and Tools for Phytopathologists
Authors: Simko Ivan , Jimenez-Berni Jose A. , Sirault Xavier R. R.
Published: September 2016

Plant phenomics approaches aim to measure traits such as growth, performance, and composition of plants using a suite of noninvasive technologies. The goal is to link phenotypic traits to the genetic information for particular genotypes, thus creating the bridge between the phenome and genome. Application of sensing technologies for detecting specific phenotypic reactions occurring during plant−pathogen interaction offers new opportunities for elucidating the physiological mechanisms that link pathogen infection and disease symptoms in the host, and also provides a faster approach in the selection of genetic material that is resistant to specific pathogens or strains. Appropriate phenomics methods and tools may also allow presymptomatic detection of disease-related changes in plants or to identify changes that are not visually apparent. This review focuses on the use of sensor-based phenomics tools in plant pathology such as those related to digital imaging, chlorophyll fluorescence imaging, spectral imaging, and thermal imaging. A brief introduction is provided for less used approaches like magnetic resonance, soft x-ray imaging, ultrasound, and detection of volatile compounds. We hope that this concise review will stimulate further development and use of tools for automatic, nondestructive, and high-throughput phenotyping of plant−pathogen interaction.
Further Characterization of Genetically Distinct Groups of Acidovorax citrulli Strains
Authors: Zivanovic M. , Walcott R. R.
Published: September 2016

Bacterial fruit blotch of cucurbits (BFB) is caused by the gram-negative bacterium Acidovorax citrulli, whose populations can be distinguished into two genetically distinct groups, I and II. Based on visual assessment of BFB severity on cucurbit seedlings and fruit after inoculation under greenhouse conditions, group I A. citrulli strains have been reported to be moderately to highly virulent on several cucurbit hosts, whereas group II strains have exhibited high virulence on watermelon but low virulence on other cucurbits. Additionally, group I strains are recovered from a range of cucurbit hosts, while group II strains are predominantly found on watermelon. The goal of this research was to develop tools to characterize and rapidly distinguish group I and II A. citrulli strains. We first sought to determine whether quantification of A. citrulli colonization of cucurbit seedling tissue reflects the differences between group I and II strains established by visual assessment of BFB symptom severity. Spray inoculation of melon seedlings with cell suspensions containing approximately 1 × 104 CFU/ml resulted in significantly higher (P = 0.01) population growth of M6 (group I; mean area under population growth curve [AUPGC] = 43.73) than that of AAC00-1 (group II; mean AUPGC = 39.33) by 10 days after inoculation. We also investigated the natural spread of bacterial cells and the resulting BFB incidence on watermelon and melon seedlings exposed to three group I and three group II A. citrulli strains under mist chamber conditions. After 5 days of exposure, the mean BFB incidence on melon seedlings exposed to representative group II A. citrulli strains was significantly lower (25 and 3.98% in experiments 1 and 2, respectively) than on melon seedlings exposed to representative group I strains (94.44 and 76.11% in experiments 1 and 2, respectively), and on watermelon seedlings exposed to representative group I and II strains (70 to 93.33%). Finally, we developed a polymerase chain reaction assay based on the putative type III secretion effector gene, Aave_2166, to rapidly distinguish group I and II A. citrulli strains. This assay will be important for future epidemiological studies on BFB.
The Role of Biomarkers in Diverticular Disease
Authors: Gallo Antonella , Ianiro Gianluca , Montalto Massimo , Cammarota Giovanni
Published: September 2016

Diverticulosis of the colon is a common condition in western countries. Acute diverticulitis may occur in 10% to 25% of the patients, sometimes associated with the presence of complications such as abscess, fistula, and perforation. Early diagnosis and accurate assessment of acute diverticulitis are necessary to start an efficacious treatment promptly, either conservatively or by surgery. The clinical picture may mimic other abdominal conditions; therefore, imaging techniques such as ultrasound or computed tomography are usually recommended, although they are expensive, examiner dependent, and potentially harmful. Recently, there has been increasing interest about the role of biological markers in diverticular disease as noninvasive, reliable, and inexpensive tools, conceivably able to support physicians in the diagnosis, the assessment of activity, and the monitoring of acute diverticulitis. By a MEDLINE search, most of the relevant data derived from C-reactive protein showed that it strongly supported the diagnosis of acute diverticulitis at values of >50 mg/L. It also represents a stronger marker compared with other serum biomarkers, able to correlate with the histologic severity in acute diverticulitis, the risk of perforation, and the response to therapy. Regarding fecal biomarkers, an interesting role has been reported for fecal calprotectin. It significantly correlates with inflammatory infiltrate. More relevantly, it correlates with the response to therapy and may predict the recurrence of colonic diverticulitis, as it is reliable in detecting subclinical intestinal inflammation, as reported already for inflammatory bowel disease. These represent encouraging results, but need to be confirmed in further larger studies.
Joint analysis of area and thickness as a replacement for the analysis of cortical volume
Authors: Winkler Anderson M. , Greve Douglas N. , Bjuland Knut J. , Nichols Thomas E. , Sabuncu Mert R. , Håberg Asta K. , Skranes Jon , Rimol Lars M.
Published: September 2016

Cortical surface area is an increasingly used brain morphology metric that is ontogenetically and phylogenetically distinct from cortical thickness and offers a separate index of neurodevelopment and disease. However, the various existing methods for assessment of cortical surface area from magnetic resonance images have never been systematically compared. We show that the surface area method implemented in FreeSurfer corresponds closely to the exact, but computationally more demanding, mass-conservative (pyc-nophylactic) method, provided that images are smoothed. Thus, the data produced by this method can be interpreted as estimates of cortical surface area, as opposed to areal expansion. In addition, focusing on the joint analysis of thickness and area, we compare an improved, analytic method for measuring cortical volume to a permutation based non-parametric combination (NPC) method. We use the methods to analyse area, thickness and volume in young adults born preterm with very low birth weight, and show that NPC analysis is a more sensitive option for studying joint effects on area and thickness, giving equal weight to variation in both of these two morphological features.
Metagenomic sequencing of dung beetle intestinal contents directly detects and identifies mammalian fauna
Authors: Gillett Conrad P.D.T. , Johnson Andrew J. , Barr Iain , Hulcr Jiri
Published: September 2016

Cost, time, and expertise constraints limit traditional observation-based comprehensive biodiversity assessment. Therefore, surrogate focal taxa representative of wider biodiversity are commonly used as an imperfect ‘proxy’. Contemporary biodiversity assessments are also increasingly benefiting from the combination of high-throughput sequencing and metagenomic methodologies that enable identification of environmental DNA samples. However, there is a need for empirical studies combining the use of surrogate taxa with metagenomic approaches, that promise rapid and efficient biodiversity assessment.

We here tested for the first time the possibility of using the intestinal contents of wild-collected dung beetles (Scarabaeidae) as a source of mammalian DNA, in a metagenomics proof-of-concept approach to directly detect and identify mammals from an area of savanna-scrub in southern Africa. Dung beetles have been purveyed as an indirect proxy measure of mammalian diversity, owing to their dependence upon vertebrate dung as a food source, and the ease with which they can be comprehensively sampled using simple and repeatable trapping protocols, achievable much faster than vertebrate surveys.

Following shotgun sequencing of gut content DNA extractions from ten dung beetle species, we usedin silicofilters to identify mammals by searching the resulting reads against known mammalian mitochondrial DNA from online sequence repositories, matching 546 paired reads to known mitogenomes held in GenBank, and 634 reads to known mammal barcode sequences held in BOLD. Identified mammalian sequences were consistent with wild and domesticated ungulates known from the sampling site, and included blue wildebeest, plains zebra, and domestic cattle and goat. Four dung beetle samples yielded sufficient sequence data to successfully assemble the near-complete mitogenome of blue wildebeest at up to 21 X mean coverage, despite low initial DNA concentrations, unambiguously corroborating identification.

It is conceptually and practically possible to rapidly and economically apply metagenomic techniques in dung beetle gut sequencing to detect the presence of mammals upon whose dung the beetles have fed. Since the approach can be readily scaled up, it may prove to be of practical use as a complement to traditional biodiversity assessment methods, and should be tested in usefulness for detecting rare, endangered or cryptic mammal species.
Consumers, Norwegian food and belonging: a qualitative study
Authors: Roos Gun Mikaela , Hansen Kai Victor , Skuland Aase Vorre
Published: September 2016

Purpose

The purpose of this paper is to provide an insight into considerations underlying consumers’ perceptions of Norwegian food and to examine what the concept of belonging can add to the understanding of national food.

Design/methodology/approach

Two-stage qualitative research design, where data were first collected by in-store interviews with 100 customers in 30 different food retail stores (supermarkets, low discount and specialty stores) in three areas in Norway (East, West and Mid). This was followed by four focus groups with consumers (n=34) in two areas (East and West).

Findings

The consumers perceived Norwegian food as having two main dimensions: foods grown and produced in Norway and dishes belonging to traditional cuisine. These two dimensions could coexist and foods that embodied both aspects were higher on a scale of national identity. Perceptions of Norwegian food reflected context, food category and consumer group. The findings support the use of the concept of belonging. Emotional belonging was mainly expressed by the consumers when talking about traditional dishes and Norwegian cuisine, whereas politics of belonging had to do with supporting domestic agriculture and especially produce that has been traditionally grown in Norway.

Research limitations/implications

The findings may have implications for product differentiation and marketing.

Originality/value

This study adds the concept of belonging to the existing literature on consumers, food and place.