bluuebunny/crossref_metadata_2025_split huggingface dataset:
Volatile fragrances associated with flowers mediate host plant alternation of a polyphagous mirid bug
Authors: Pan Hongsheng , Lu Yanhui , Xiu Chunli , Geng Huihui , Cai Xiaoming , Sun Xiaoling , Zhang Yongjun , Williams III Livy , Wyckhuys Kris A. G. , Wu Kongming 
Published: October 2015

AbstractApolygus lucorum(Hemiptera: Miridae) is an important insect pest of cotton and fruit trees in China. The adults prefer host plants at the flowering stage and their populations track flowering plants both spatially and temporally. In this study, we examine whether flower preference of its adults is mediated by plant volatiles and which volatile compositions play an important role in attracting them. In olfactometer tests with 18 key host species, the adults preferred flowering plants over non-flowering plants of each species. Coupled gas chromatography-electroantennography revealed the presence of seven electrophysiologically active compounds from flowering plants. Although the adults responded to all seven synthetic plant volatiles in electroantennography tests, only four (m-xylene, butyl acrylate, butyl propionate and butyl butyrate) elicited positive behavioral responses in Y-tube olfactometer bioassays. The adults were strongly attracted to these four active volatiles in multi-year laboratory and field trials. Our results suggest that these four fragrant volatiles, which are emitted in greater amounts once plants begin to flower, mediateA. lucorum’s preference to flowering host plants. We proved that the use of commonly occurring plant volatiles to recognize a large range of plant species can facilitate host selection and preference of polyphagous insect herbivore.
Chronic aerobic swimming exercise promotes functional and morphological changes in rat ileum
Authors: da Cunha Araujo Layanne Cabral , de Souza Iara Leão Luna , Vasconcelos Luiz Henrique César , de Freitas Brito Aline , Queiroga Fernando Ramos , Silva Alexandre Sérgio , da Silva Patrícia Mirella , de Andrade Cavalcante Fabiana , da Silva Bagnólia Araújo 
Published: October 2015

Several studies have reported the gastrointestinal (GI) effects promoted by the physical exercise. Thus, we aimed to evaluate the influence of swimming exercise on the contractile reactivity, lipid peroxidation and morphology of rat ileum. Wistar rats were divided into sedentary (SED) and groups exercised for two (EX2), four (EX4), six (EX6) or eight (EX8) weeks, 5 days/week. Animals were killed; the ileum was removed and suspended in organ baths where the isotonic contractions were recorded. Lipid peroxidation was evaluated by MDA (malondialdehyde) measurement with TBARS (thiobarbituric acid reactive substances) assay and morphology by histological staining. Cumulative concentration-response curves to KCl were attenuated, as the Emax values were changed from 100% (SED) to 63.1±3.9 (EX2), 48.8±3.8 (EX4), 19.4±1.8 (EX6) and 59.4±2.8% (EX8). Similarly, cumulative concentration-response curves to carbamylcholine hydrochloride (CCh) were attenuated, as the Emax values were changed from 100% (SED) to 74.1±5.4 (EX2), 75.9±5.2 (EX4) and 62.9±4.6 (EX6), but not in the EX8 (89.7±3.4%). However, CCh potency was increased in this latter, as the EC50 was altered from 1.0±0.1×10−6 (SED) to 2.1±0.4×10−7 (EX8). MDA concentration was altered only in EX4 (44.3±4.4) compared with SED (20.6±3.6 μmol/l). Circular layer was reduced in SED when compared with the exercised groups. Conversely, longitudinal layer was increased. In conclusion, chronic swimming exercise reduces the ileum contraction, equilibrates the oxidative damage and promotes changes in tissue size to establish an adaptation to the exercise.
Exploring Expressive Vocabulary Variability in Two-Year-Olds: The Role of Working Memory
Authors: Newbury Jayne , Klee Thomas , Stokes Stephanie F. , Moran Catherine 
Published: October 2015

Purpose
This study explored whether measures of working memory ability contribute to the wide variation in 2-year-olds' expressive vocabulary skills.

Method
Seventy-nine children (aged 24–30 months) were assessed by using standardized tests of vocabulary and visual cognition, a processing speed measure, and behavioral measures of verbal working memory and phonological short-term memory.

Results
Strong correlations were observed between phonological short-term memory, verbal working memory, and expressive vocabulary. Speed of spoken word recognition showed a moderate significant correlation with expressive vocabulary. In a multivariate regression model for expressive vocabulary, the most powerful predictor was a measure of phonological short-term memory (accounting for 66% unique variance), followed by verbal working memory (6%), sex (2%), and age (1%). Processing speed did not add significant unique variance.

Conclusions
These findings confirm previous research positing a strong role for phonological short-term memory in early expressive vocabulary acquisition. They also extend previous research in two ways. First, a unique association between verbal working memory and expressive vocabulary in 2-year-olds was observed. Second, processing speed was not a unique predictor of variance in expressive vocabulary when included alongside measures of working memory.
Fractional Fourier transform‐based unassisted tracking method for Global Navigation Satellite System signal carrier with high dynamics
Authors: Xia Xuan , Zhao Jiankang , Long Haihui , Yang Guang , Sun Jun , Yang Wenbo 
Published: October 2015

This study proposes a novel tracking method for Global Navigation Satellite System (GNSS) signal carrier, based on fractional Fourier transform. This method not only overcomes the limitations caused by the tripartite trade‐off between tracking accuracy, loop bandwidth and dynamic stress, but also needs no auxiliary devices such as inertial measurement units (IMUs). Through a time–frequency analysis of high dynamic carrier signal, the authors show that an acceleration estimator can replace the function of IMU, and a high dynamic frequency discriminator can track the carrier Doppler frequency. Since the tracking accuracy (frequency resolution) and loop bandwidth (time resolution) are not affected by dynamics in the authors’ method, the upper bound of dynamic stress is improved significantly. Furthermore, due to the cancellation of IMU calibration and initial alignment, their method improves the rapid reaction capability of vehicles, reduces the possibility of external interference, and simplifies the tracking loop design. Simulation results show that their method has the ability to track GNSS signal under at least 200 g dynamic stress.
X-ray microtomography using correlation of near-field speckles for material characterization
Authors: Zanette Irene , Zdora Marie-Christine , Zhou Tunhe , Burvall Anna , Larsson Daniel H. , Thibault Pierre , Hertz Hans M. , Pfeiffer Franz 
Published: October 2015

Significance
We present X-ray speckle tracking tomography, a simple, robust, and versatile method to obtain simultaneously phase and absorption tomograms of the sample at the micrometer scale with a laboratory X-ray source. The method is based on correlation of near-field speckles and yields quantitative measurements of the full X-ray refractive index of the object with high sensitivity. X-ray speckle tracking tomography broadens the capabilities of X-ray imaging at laboratory sources with strong potential in materials and life sciences.
Fibonacci family of dynamical universality classes
Authors: Popkov Vladislav , Schadschneider Andreas , Schmidt Johannes , Schütz Gunter M. 
Published: October 2015

Significance
Universality is a well-established central concept of equilibrium physics. It asserts that, especially near phase transitions, the properties of a physical system do not depend on its details such as the precise form of interactions. Far from equilibrium, such universality has also been observed, but, in contrast to equilibrium, a deeper understanding of its underlying principles is still lacking. We show that the two best-known examples of nonequilibrium universality classes, the diffusive and Kardar−Parisi−Zhang classes, are only part of an infinite discrete family. The members of this family can be identified by their dynamical exponent, which, surprisingly, can be expressed by a Kepler ratio of Fibonacci numbers. This strongly indicates the existence of a simpler underlying mechanism that determines the different classes.
A bilingual child’s multimodal path into negation
Authors: Benazzo Sandra , Morgenstern Aliyah 
Published: October 2015

The study of the expression of negation in longitudinal adult-child data is a privileged locus for a multimodal approach to language acquisition. In the case of bilingual language acquisition, the necessity to enter two languages at once might have an influence on the management of the visual-gestural and the auditory modalities. In order to tackle these issues, we analyze the longitudinal data of Antoine, a bilingual French/Italian child recorded separately once a month for an hour with his Italian mother and with his French father between the ages of 1;5 and 3;5.
Our analyses of all his multimodal utterances with negations show that Antoine has created efficient transitional systems during his developmental path both by combining modalities and by mixing his two native languages. The visual-gestural modality is a stable resource to rely on in all the types of linguistic environments Antoine experiences. His bilingual environment could be connected to the creation of his mixed verbal productions also addressed to both French speaking and Italian speaking interlocutors. Those two transitory creative systems are efficient elements of his communicative repertoire during an important period of his language development. Gesture might therefore have a compensatory function for that little boy. It is a wonderful resource to communicate efficiently in his specific environment during his multimodal, multilingual entry into language.
Unconfirmed peers and spinelessness
Authors: Sherman Ben 
Published: September 2015

AbstractThe Equal Weight View holds that, when we discover we disagree with an epistemic peer, we should give our peer’s judgment as much weight as our own. But how should we respond when we cannot tell whether those who disagree with us are our epistemic peers? I argue for a position I will call the Earn-a-Spine View. According to this view, parties to a disagreement can remain confident, at least in some situations, by finding justifiable reasons to think their opponents are less credible than themselves, even if those reasons are justifiable only because they lack information about their opponents.
Experiences with bilingual publishing: surveys of authors and editors
Authors: BARTHOLOMÄUS Elke , GOLDBECK‐WOOD Sandy , SEWERING Meike , BAETHGE Christopher 
Published: September 2015

ABSTRACTBilingual publishing has become a strategy employed by journals from the non‐Anglophone world to gain wider recognition. Beyond anecdotal evidence, however, there are no published accounts of the experiences of editors and authors of bilingual journals with the process of bilingual publication. It is also unclear how authors writing in bilingual journals judge the quality of the translations and whether they consider this sort of publishing as beneficial for their aims. Consequently, we carried out two surveys: one among editors of bilingual journals and one anonymous survey among authors and translators of articles published in Deutsches Ärzteblatt International, the bilingual journal of the German Medical Association. Eight of nine journals as well as 233 of 353 authors and 4 of 6 translators took part. Most journals reported that bilingual publication helped in becoming indexed in important databases (e.g. Medline), receiving or improving an Impact Factor, and in attracting authors. All journals plan to continue publishing bilingually. Authors were ‘satisfied’ (40.8%) or ‘very satisfied’ (57.8%) with translations. Almost all (96.7%) were in favour of bilingual publication of their work. They did not view an English translation as an obstacle to another related English language paper. Translators highlighted challenges relating to specialized terminology and to terms specific to the regional healthcare system.
ANARCI: antigen receptor numbering and receptor classification
Authors: Dunbar James , Deane Charlotte M. 
Published: October 2015

Abstract
Motivation: Antibody amino-acid sequences can be numbered to identify equivalent positions. Such annotations are valuable for antibody sequence comparison, protein structure modelling and engineering. Multiple different numbering schemes exist, they vary in the nomenclature they use to annotate residue positions, their definitions of position equivalence and their popularity within different scientific disciplines. However, currently no publicly available software exists that can apply all the most widely used schemes or for which an executable can be obtained under an open license.
Results: ANARCI is a tool to classify and number antibody and T-cell receptor amino-acid variable domain sequences. It can annotate sequences with the five most popular numbering schemes: Kabat, Chothia, Enhanced Chothia, IMGT and AHo.
Availability and implementation: ANARCI is available for download under GPLv3 license at opig.stats.ox.ac.uk/webapps/anarci. A web-interface to the program is available at the same address.
Contact: deane@stats.ox.ac.uk
Warpgroup: increased precision of metabolomic data processing by consensus integration bound analysis
Authors: Mahieu Nathaniel G. , Spalding Jonathan L. , Patti Gary J. 
Published: October 2015

Abstract
Motivation: Current informatic techniques for processing raw chromatography/mass spectrometry data break down under several common, non-ideal conditions. Importantly, hydrophilic liquid interaction chromatography (a key separation technology for metabolomics) produces data which are especially challenging to process. We identify three critical points of failure in current informatic workflows: compound specific drift, integration region variance, and naive missing value imputation. We implement the Warpgroup algorithm to address these challenges.
Results: Warpgroup adds peak subregion detection, consensus integration bound detection, and intelligent missing value imputation steps to the conventional informatic workflow. When compared with the conventional workflow, Warpgroup made major improvements to the processed data. The coefficient of variation for peaks detected in replicate injections of a complex Escherichia Coli extract were halved (a reduction of 19%). Integration regions across samples were much more robust. Additionally, many signals lost by the conventional workflow were ‘rescued’ by the Warpgroup refinement, thereby resulting in greater analyte coverage in the processed data.
Availability and i mplementation: Warpgroup is an open source R package available on GitHub at github.com/nathaniel-mahieu/warpgroup. The package includes example data and XCMS compatibility wrappers for ease of use.
Supplementary information: Supplementary data are available at Bioinformatics online.
Contact: nathaniel.mahieu@wustl.edu or gjpattij@wustl.edu
Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data
Authors: Okonechnikov Konstantin , Conesa Ana , García-Alcalde Fernando 
Published: October 2015

Abstract
Motivation: Detection of random errors and systematic biases is a crucial step of a robust pipeline for processing high-throughput sequencing (HTS) data. Bioinformatics software tools capable of performing this task are available, either for general analysis of HTS data or targeted to a specific sequencing technology. However, most of the existing QC instruments only allow processing of one sample at a time.
Results: Qualimap 2 represents a next step in the QC analysis of HTS data. Along with comprehensive single-sample analysis of alignment data, it includes new modes that allow simultaneous processing and comparison of multiple samples. As with the first version, the new features are available via both graphical and command line interface. Additionally, it includes a large number of improvements proposed by the user community.
Availability and implementation: The implementation of the software along with documentation is freely available at http://www.qualimap.org.
Contact: meyer@mpiib-berlin.mpg.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Child Abuse Mimic
Authors: Deutsch Stephanie Anne , Long Christopher J. , Srinivasan Arun K. , Wood Joanne N. 
Published: October 2015

Abstract
Sexual abuse of children is prevalent in today's society. In 2012, approximately 686,000 children (9.2 per 1000) in the United States were determined to be victims of substantiated child abuse and neglect, according to national data compiled by child protective service agencies; victimization rates were highest for children younger than 1 year. Nearly 9.3% of maltreated children were victims of sexual abuse, this finding was reported by US Department of Health and Human Services (http://www.acf.hhs.gov/programs/cb/research-data-technology/statistics-research/child-maltreatment). Previous research has shown that as many as 1 in 3 girls and 1 in 7 boys will be sexually abused during childhood (Child Abuse Negl. 2003;27:1205–1222). Although sexual abuse seems to be less common in boys than girls, this may be partly due to underdiagnosis and underreporting of sexual abuse in boys (Arch Dis Child. 2007;92:328–331). Clinicians should therefore consider the possibility of sexual abuse when boys present with genital injuries, because failing to recognize and diagnose sexual abuse can pose an ongoing safety risk to a child. However, an erroneous diagnosis of sexual abuse can have equally hazardous repercussions, including removal of a child from their caregivers or prosecution of an innocent individual. A number of medical conditions can mimic child sexual abuse injuries, including anal fissures, failure of midline fusion, perianal streptococcal dermatitis, and straddle injury (J Pediatr Health Care. 2009;23:283–288 and Acta Paediatr. 2011;100:590–593). The following case involves a 5-week-old male infant who presented to the pediatric emergency department with an avulsion injury to his penis concerning for sexual abuse. He was ultimately diagnosed with a relatively rare anatomic variant of the genitalia and determined to have sustained an accidental injury whose appearance mimicked abuse.
TRPA1 tunes mosquito thermotaxis to host temperatures
Authors: Corfas Román A. , Vosshall Leslie B. 
Published: October 2015

SUMMARYWhile most ectotherms thermotax only to regulate their temperature, female mosquitoes are attracted to human body heat during pursuit of a blood meal. Here we elucidate the basic rules ofAedes aegyptithermotaxis and test the function of candidate thermoreceptors in this important behavior. We show that host-seeking mosquitoes are maximally attracted to thermal stimuli approximating host body temperatures, seeking relative warmth while avoiding both relative cooling and stimuli exceeding host body temperature. We found that the cation channelTRPA1,in addition to playing a conserved role in thermoregulation and chemosensation, is required for this specialized host-selective thermotaxis in mosquitoes. During host-seeking,AaegTRPA1-/-mutants failed to avoid stimuli exceeding host temperature, and were unable to discriminate between host-temperature and high-temperature stimuli.TRPA1-dependent tuning of thermotaxis is likely critical for mosquitoes host-seeking in a complex thermal environment in which humans are warmer than ambient air, but cooler than surrounding sun-warmed surfaces.
Modelling the role of immunity in reversion of viral antigenic sites
Authors: Chan Carmen H. S. , Sanders Lloyd P. , Tanaka Mark M. 
Published: October 2015

AbstractAntigenic sites in viral pathogens exhibit distinctive evolutionary dynamics due to their role in evading recognition by host immunity. Antigenic selection is known to drive higher rates of non-synonymous substitution; less well understood is why differences are observed between viruses in their propensity to mutate to a novel or previously encountered amino acid. Here, we present a model to explain patterns of antigenic reversion and forward substitution in terms of the epidemiological and molecular processes of the viral population. We develop an analytical three-strain model and extend the analysis to a multi-site model to predict characteristics of observed sequence samples. Our model provides insight into how the balance between selection to escape immunity and to maintain viability is affected by the rate of mutational input. We also show that while low probabilities of reversion may be due to either a low cost of immune escape or slowly decaying host immunity, these two scenarios can be differentiated by the frequency patterns at antigenic sites. Comparison between frequency patterns of human influenza A (H3N2) and human RSV-A suggests that the increased rates of antigenic reversion in RSV-A is due to faster decaying immunity and not higher costs of escape.
Improving the use of physical manipulatives in teaching science concepts through lesson study
Authors: Tan Rolando M. 
Published: October 2015

Purpose
– The purpose of this paper is to present how lesson study can be instrumental in improving the use of physical manipulatives that are used in teaching elementary science topics.

Design/methodology/approach
– Objectives are achieved through the following means: first, planning a research lesson in the workshop; second, presentation and critiquing in a seminar workshop; third, implementing the research lesson with observation of co-teachers and knowledgeable other; fourth, post lesson discussion; and fifth, revising the research lesson.

Findings
– The research lesson improved significantly after the first post lesson discussion as the concrete to abstract approach was used and the defect of the physical manipulative (eardrum model) was addressed to avoid possible misconceptions from pupils during discussions as part of the formative assessment portion of the lesson.

Research limitations/implications
– The lesson study process was not further extended to the third and fourth implementation to see other problems in the use of their physical manipulative (eardrum) model.

Practical implications
– The need for teachers to use the physical manipulative as an analogical model in teaching science concepts.

Originality/value
– The paper shows the effectiveness of lesson study in the development of manipulative models in instruction.