bluuebunny/crossref_metadata_2025_split huggingface dataset:
Key Outcomes From the Inaugural AGU Board of Directors Meeting
Authors: McPhaden Michael J. 
Published: October 2010

The engagement and enthusiasm of Board members and senior staff were evident as we met for the first Board of Directors meeting on 20–21 September 2010 at AGU headquarters, and much was accomplished over the 1.5 days.The meeting kicked off with a look to the future. Board members and staff had been asked to submit imagined headlines for 2019, the year that AGU will celebrate its 100th anniversary. This was a question raised by Executive Director Chris McEntee as she interacted with AGU leaders over the past several months. Board members and staff replied with a wide variety of headlines that inspired us to think about what is possible for AGU as we move forward as an organization. The headlines are posted on the AGU Web site (http://www.agu.org/about/presidents_msg/), and we encourage you to submit your own headline to agu_execdirector@agu.org.
SciNetS Search : Inference Search over an Integrated Life-sciences Database Based on the Semantic Web
Authors: Toyoda Tetsuro , Kobayashi Norio , Ishii Manabu , Yoshida Yuko , Makita Yuko , Matsushima Akihiro , Mochizuki Yoshiki 
Published: October 2010

AbstractIntegration of various omics databases is a fundamental approach for comprehensive understanding of life phenomena. Scientists’ Networking System (SciNetS) is a Semantic Web-based data repository that realises database integration by collecting metadata of databases described as a set of triples consisting of two bio-items such as gene and ontology terms and a semantically defined relationship between these bio-items. These triples are curated from various life-sciences databases including gene-publication relationships manually curated from MEDLINE and gene-phenotype relationships extracted from published databases by computer programs. SciNetS internally forms a metadata network by maximally concatenating triples.SciNetS Search realizes a cross-search over the integrated databases by traversing the metadata network managed by SciNetS. SciNetS Search allows a user to discover bio-items included in the ontological category specified by the user. The results include bio-items not only having a user’s keyword but also semantically inferred from these bio-items using metadata relationships, and are ranked using statistical scores computed on the basis of the metadata network. SciNetS Search is available via a user’s web browser and provides search service against over 30 million bio-items of 100 thousand categories and 100 million relationships curated from over 100 public omics databases of various species including human, mouse, rice and Arabidopsis.
Gas phase hydration, bond dissociation enthalpies, and acidity of aldehydes: A CBS-Q//B3, G4MP2, and G4 theoretical study of substituent effects
Authors: Rayne Sierra , Forest Kaya 
Published: October 2010

AbstractCBS-Q//B3, G4MP2, and G4 composite method calculations were used to estimate gas phase standard state (298.15 K, 1 atm) free energies of hydration (Δ~hydr~G°~(g)~), hydration equilibrium constants (log K~hydr,(g)~), bond dissociation enthalpies (BDEs), and enthalpies (Δ~d~H°~(g)~) and free energies (Δ~d~G°~(g)~) of aldehydic proton acid dissociation for various substituted aldehydes with electron withdrawing and electron releasing groups. Good quality log K~hydr,(g)~ correlations with the Swain-Lupton resonance effect parameters R and R^+^ were found, allowing extension of the model to predict log K~hydr,(g)~ values for 487 substituted aldehydes having available R-values and 108 substituted aldehydes having available R^+^-values. Good correlations were also found between experimental aqueous phase hydration equilibrium constants (log K~hydr,(aq)~) and summative R/R^+^-values for peripheral substituents on a range of carbonyl derivatives (aldehydes, ketones, esters, and amides), suggesting the structure-reactivity modeling approach can be extended to include all possible combinations of R~1~C(O)R~2~ carbonyl substitution in both gas and aqueous systems. Computationally derived BDEs and Δ~d~H°~(g)~ / Δ~d~G°~(g)~ were in good agreement with the limited experimental and theoretical datasets. BDEs did not generally correlate with any of the Hammett substituent constants or Swain-Lupton parameters considered. Gas phase acidities exhibited high correlation coefficients with Hammett inductive substituent constants (σ~I~) and field effect parameters (F), allowing these to be employed as surrogates for estimating the gas phase aldehydic proton acidities of a larger potential compound range.
Automatic protein clustering as a basis of automatic annotation
Authors: Sato Naoki 
Published: October 2010

AbstractDevelopment of new generation sequencers enabled genome sequencing feasible for every organism in a laboratory. A typical data flow of de novo seuqencing includes (1) assembly of sequence reads, (2) estimation of open reading frames, (3) annotation of proteins, and (4) finding RNA genes. The annotation is normally performed by BLASTP searches against several different databases. However, it is usually hard to find a plausible annotation by just looking at the results of BLASTP searches.Here I propose a potentially automatic method of annotation that exploits automatic protein clustering using the software GCLUST, which estimates proper similarity threshold for each list of homologs using ‘entropy-optimized organism count’ method (Sato 2009). The software has been used to construct a homolog database including both prokaryotic and eukaryotic proteins ("http://gclust.c.u-tokyo.ac.jp/":http://gclust.c.u-tokyo.ac.jp/). For use in genome annotation, we need de novo clustering including many genomes of related organisms as well as genomes of representative organisms. Application of protein clustering in the annotation in Arthrospira platensis was the first successful case (Fujisawa et al. 2010). I present here results of protein clustering of total predicted proteins in two draft genomes of cyanobacteria along with total predicted proteins of 41 cyanobacteria available at NCBI. For each of the resultant protein clusters, an alignment and a phylogenetic tree were also prepared for assistance in functional annotation. The quality of alignments was evaluated by counting ill-aligned proteins (missing N- or C-terminus, or insertion/deletion), which was 4-13% of total predicted proteins in most cyanobacterial genomes. Annotation may be automated by extracting significant key words alreadly assigned for member proteins of clusters or by comparison with reference protein clusters.
Integral presentation of Experimental Results and Bioinformatic Analyses on Ciona intestinalis Proteins
Authors: Yonezawa Kouki , Ueno Keisuke , Mineta Katsuhiko , Endo Toshinori 
Published: October 2010

AbstractFor the aim of facilitating biologists to find new knowledge through the comprehensive proteomic and transcriptomic data of Ciona intestinalis, we have been developing an intuitive and integral view of experimental and bioinformatic results for each protein, which, unlike on human proteins, was incomplete for Ciona proteins. In the presentation, we integrated in a view the experimental results of 2D-PAGE analyses done at Shimoda Marine Research Center, University of Tsukuba, 3D-view of expressions (3DPL) done by Hotta et al., and cross-references with JGI version 1 and ENSEMBL. A total of 1,673 entries of 2D-PAGE and 57 of 3DPL are currently contained in CIPRO database. The information is summarized in a single page for a protein. Together with BLAST results, comparative genomics, expression profiles, domain search results, localization, phylogeny etc., we provide biologists the highly integrated view amongst the existing databases, which facilitates to understand the protein. For example, the 2D-PAGE and the microarray results of the same protein are sometimes different, which implies the spatial or temporal gaps of the expressions between the mRNA and the protein. Besides, two functionalities are implemented. One is an improved 2D-PAGE viewer, which provides the compact view of spots and experimental information, and another is peptide fragment mass search functionality as improved PerMS algorithm by Hozumi et al., by enabling detection of seven kinds of modifications and suspected contaminants.
The Data Sharing Challenge. Learning Community From Consortia
Authors: Hide Winston , Altshuler Gabriel , Hofmann Oliver , Begley Kimberly 
Published: October 2010

AbstractToday’s data generation and analysis environment is changing rapidly as the lure of technologies provide new opportunities to laboratory scientists. From physicians seeking rapid translation to the bedside, to environmentalists seeking new paradigms to understand the biome - large scale data generation is everywhere. How do we overcome the challenges of curation, management, interpretation and sharing of these data in the new multidisciplinary environment? One key approach is to leverage the expertise inherent in existing systems - bringing together tools and paradigms that work in subfields, and making them work together for the consortium. We will discuss the stem cell discovery engine. The approach brings together leading experts in stem cell biology, molecular profiles from stem cell systems, and seeks to combine data from diverse platforms under the unifying theme of common biology. We explore the use of gene lists and canonical pathways as a supervisor - and present pathway fingerprinting as a molecular approach to a broader problem. We explore how the community seeks to interact with its data - under the glare of reality.
Passive Participle Marking by African American English–Speaking Children Reared in Poverty
Authors: Pruitt Sonja L. , Oetting Janna B. , Hegarty Michael 
Published: October 2010

Purpose
In this study, the authors examined the linguistic profile of African American English (AAE)-speaking children reared in poverty by focusing on their marking of passive participles and by comparing the results with the authors' previous study of homophonous forms of past tense (S. Pruitt & J. Oetting, 2009).

Method
The data were from 45 five- to six-year-olds who spoke AAE and who participated in the authors' earlier study. Fifteen were classified as low-income (LSES); the others were classified as middle-income and served as either age- or language-matched controls. The data came from a probe that was designed by S. M. Redmond (2003), but it was modified to examine the morphological and phonological characteristics of AAE.

Results
Participle marking by all 3 groups was influenced by AAE phonology, but the LSES children marked the participles at lower rates than the controls. The LSES children’s rates of participle marking were also lower than their rates of marking for homophonous forms of past tense. Unlike the children’s rates of past-tense marking, their rates of participle marking were correlated to their vocabulary test scores.

Conclusions
AAE-speaking children reared in poverty present weaknesses in aspects of grammatical morphology that are related to their vocabulary weaknesses.
The Effects of Age and Infant Hearing Status on Maternal Use of Prosodic Cues for Clause Boundaries in Speech
Authors: Kondaurova Maria V. , Bergeson Tonya R. 
Published: October 2010

Purpose
The present study examined the effects of age and hearing status of a child on maternal use of pitch change, preboundary vowel lengthening, and pause duration, all of which are prosodic cues correlated with clause boundaries in infant-directed speech.

Method

Mothers' speech to infants with normal hearing (NH;
n
= 18), infants who are profoundly deaf with a cochlear implant (HI;
n
= 9), and an adult experimenter were recorded at 2 time periods separated by 6 months. NH infants were matched to HI infants by chronological age or hearing experience. Fundamental frequency of pre- and postboundary vowels, vowel duration, and pause duration between utterances was measured.

Results
Results demonstrated that mothers (a) exaggerated prosodic characteristics in infant-directed speech regardless of infants' hearing status; (b) tailored preboundary vowel lengthening to infants' hearing experience rather than to chronological age; and (c) decreased exaggeration of pause duration over time.

Conclusions
The results suggest that acoustic cues correlated with clause boundaries are available in maternal speech to HI infants. Their exaggeration relative to adult-directed speech suggests that mothers' use of infant-directed speech is a natural behavior regardless of infant hearing status. Finally, mothers modify speech prosody according to their children’s age and hearing experience.
Lung Volume Measured During Sequential Swallowing in Healthy Young Adults
Authors: Wheeler Hegland Karen , Huber Jessica E. , Pitts Teresa , Davenport Paul W. , Sapienza Christine M. 
Published: October 2010

Purpose
Outcomes from studying the coordinative relationship between respiratory and swallow subsystems are inconsistent for sequential swallows, and the lung volume at the initiation of sequential swallowing remains undefined. The first goal of this study was to quantify the lung volume at initiation of sequential swallowing ingestion cycles and to identify the respiratory pattern(s) surrounding each sequential swallow ingestion cycle. The second goal was to compare these results with existing data for single swallows.

Method

Twenty healthy young adults served as participants, 9 males and 11 females, between 19 and 28 years of age (
M
= 22 years of age). Participants completed 2 trials each of 100 mL of water self-delivered by cup and by straw. Calibrated respiratory inductance plethysmography, surface electromyography, and a contact throat microphone were used to detect respiratory parameters, identify swallow-related muscle contraction, and identify swallowing sounds, respectively.

Results
Significantly higher lung volume initiation for trials delivered by straw and more variable respiratory patterns surrounding cup and straw sequential swallowing ingestion cycles existed compared with single swallows.

Conclusions
Results show that as the physiologic demands of swallowing deviate from single, small bolus swallows, the integration of the swallowing and respiratory systems change. This may reflect obligate differences in airway protection strategy and prolonged competition for respiratory resources.
Examining Continuity of Early Expressive Vocabulary Development: The Generation R Study
Authors: Henrichs Jens , Rescorla Leslie , Schenk Jacqueline J. , Schmidt Henk G. , Jaddoe Vincent W. V. , Hofman Albert , Raat Hein , Verhulst Frank C. , Tiemeier Henning 
Published: October 2010

Purpose
The authors investigated continuity and discontinuity of vocabulary skills in a population-based cohort in the Netherlands.

Method
Mothers of 3,759 children completed the Dutch version of the MacArthur Short Form Vocabulary Checklist (Zink & Lejaegere, 2003) at 18 months and a Dutch translation of the Language Development Survey (Rescorla, 1989) at 30 months. At both ages, expressive vocabulary delay was defined as vocabulary scores <10th age- and gender-specific percentile.

Results
Of the children, 85.2% had normal vocabulary development at both ages, 6.2% were “late bloomers,” 6.0% had late onset expressive vocabulary delay, and 2.6% had persistent expressive vocabulary delay. Word production and comprehension at 18 months explained 11.5% of the variance in 30-month vocabulary scores, with low birth weight, child age, gender and ethnicity, maternal age and education, and parenting stress explaining an additional 6.2%. Multinomial logistic regression was used to identify biological, demographic, and psychological factors associated with each of the vocabulary delay outcome groups relative to the typically developing group.

Conclusions
Although multiple perinatal, demographic, and maternal psychosocial factors significantly predicted vocabulary skills at 30 months, positive predictive value and sensitivity were low. Future studies should address to what extent additional factors, such as brain maturation and genetic influences, can improve the prediction and understanding of continuity and discontinuity of language delay.
The Influence of Auditory Acuity on Acoustic Variability and the Use of Motor Equivalence During Adaptation to a Perturbation
Authors: Brunner Jana , Ghosh Satrajit , Hoole Philip , Matthies Melanie , Tiede Mark , Perkell Joseph 
Published: October 2010

Purpose
The aim of this study was to relate speakers' auditory acuity for the sibilant contrast, their use of motor equivalent trading relationships in producing the sibilant /ʃ/, and their produced acoustic distance between the sibilants /s/ and /ʃ/. Specifically, the study tested the hypotheses that during adaptation to a perturbation of vocal-tract shape, high-acuity speakers use motor equivalence strategies to a greater extent than do low-acuity speakers in order to reach their smaller phonemic goal regions, and that high-acuity speakers produce greater acoustic distance between 2 sibilant phonemes than do low-acuity speakers.

Method
Articulographic data from 7 German speakers adapting to a perturbation were analyzed for the use of motor equivalence. The speakers' produced acoustic distance between /s/ and /ʃ/ was calculated. Auditory acuity was assessed for the same speakers.

Results
High-acuity speakers used motor equivalence to a greater extent when adapting to a perturbation than did low-acuity speakers. Additionally, high-acuity speakers produced greater acoustic contrasts than did low-acuity-speakers. It was observed that speech rate had an influence on the use of motor equivalence: Slow speakers used motor equivalence to a lesser degree than did fast speakers.

Conclusion
These results provide support for the mutual interdependence of speech perception and production.
Fast Mapping and Word Learning by Preschoolers With Specific Language Impairment in a Supported Learning Context: Effect of Encoding Cues, Phonotactic Probability, and Object Familiarity
Authors: Gray Shelley , Brinkley Shara 
Published: October 2010

Purpose
To investigate whether phonological or semantic encoding cues improved the fast mapping or word learning performance of preschoolers with specific language impairment (SLI) or typical development (TD) and whether performance varied for words containing high- or low-frequency sublexical sequences that named familiar or unfamiliar objects.

Method
Forty-two preschoolers with SLI, 42 preschoolers with TD matched for age and gender to the children with SLI, and 41 preschoolers with TD matched for expressive vocabulary and gender to the children with SLI learned words in a supported learning context. Fast mapping, word learning, and post-task performance were assessed.

Results
Encoding cues had no effect on fast mapping performance for any group or on the number of words children learned to comprehend. Encoding cues appeared to be detrimental to word production for children with TD. Across groups, a clear learning advantage was observed for words with low-frequency sequences and, to a lesser extent, words associated with an unfamiliar object.

Conclusion
The results suggest that phonotactic probability and previous lexical knowledge affect word learning in similar ways for children with TD and SLI and that encoding cues were not beneficial for any group.
Rhythmic Versus Phonemic Interference in Delayed Auditory Feedback
Authors: Kaspar Kai , Rübeling Hartmut 
Published: October 2010

Purpose

Delayed auditory feedback (DAF) of a speaker’s voice disturbs normal speech production. Various traditional theories assume that the content of the delayed feedback signal interferes with the actual production of a particular speech unit (
phonemic content hypothesis
). The
displaced rhythm hypothesis
as an alternative explanation suggests that speech disturbances arise from a disruptive rhythm that is produced by the delayed speech signal. The present experimental study directly contrasted the role of rhythm and speech content in a DAF task using speech units as stimuli.

Method
One hundred fifty-one participants read aloud 4 different sequences of double syllables that varied in phonemic content and rhythm while auditory feedback was either nondelayed or delayed by 200 or 400 ms.

Results
In line with previous studies, the authors found a peak of disturbances at a delay of about 200 ms, independent of speech rate. More important, the present results clearly support the displaced rhythm hypothesis. A speech rate dependency of this effect was also found.

Conclusion
Rhythm seems to be a significant criterion of speech monitoring, and hence a mismatch between spoken words and auditory feedback realized by DAF induces obvious speech problems on rhythmic level regardless of phonemic discrepancy at the same time.
Phylogenetic analysis of primate MIC (PERB11) sequences suggests that the representation of the gene family differs in different primates: comparison of MIC (PERB11) and C4
Authors: Cattley S. K. , Longman N. , Dawkins R. L. , Gaudieri S. , Kulski J. K. , Leelayuwat C. 
Published: October 2010

Duplication of segments within the MHC has led to numerous multicopy families such as class I, class II, C4 and MIC (PERB11). Different copy numbers between haplotypes and species may be explained by the extent of duplication and subsequent deletion. There are at least five copies of MIC (PERB11) in humans, but MICA (PERB11.1) appears to have been deleted from the chimpanzee.By comparing the sequences of primates (chimpanzee, gorilla, gibbon, orang‐utan, pygmy chimpanzee, Patas monkey, Aethiops and baboon) we conclude that the gorilla has a copy of PERB11.1, whereas the baboon and Patas possess MICD (PERB11.4) and/or MICE (PERB11.5) rather than MICA (PERB11.1). These findings indicate that the primate MHC is more plastic than has been appreciated.
R/qtl: high-throughput multiple QTL mapping
Authors: Arends Danny , Prins Pjotr , Jansen Ritsert C. , Broman Karl W. 
Published: October 2010

AbstractMotivation: R/qtl is free and powerful software for mapping and exploring quantitative trait loci (QTL). R/qtl provides a fully comprehensive range of methods for a wide range of experimental cross types. We recently added multiple QTL mapping (MQM) to R/qtl. MQM adds higher statistical power to detect and disentangle the effects of multiple linked and unlinked QTL compared with many other methods. MQM for R/qtl adds many new features including improved handling of missing data, analysis of 10 000 s of molecular traits, permutation for determining significance thresholds for QTL and QTL hot spots, and visualizations for cis–trans and QTL interaction effects. MQM for R/qtl is the first free and open source implementation of MQM that is multi-platform, scalable and suitable for automated procedures and large genetical genomics datasets.Availability: R/qtl is free and open source multi-platform software for the statistical language R, and is made available under the GPLv3 license. R/qtl can be installed from http://www.rqtl.org/. R/qtl queries should be directed at the mailing list, see http://www.rqtl.org/list/.Contact: kbroman@biostat.wisc.edu