bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic and Environmental Effects on Vocal Symptoms and Their Intercorrelations
Authors: Nybacka Ida , Simberg Susanna , Santtila Pekka , Sala Eeva , Sandnabba N. Kenneth
Published: December 2011

Purpose

Recently, Simberg et al. (2009) found genetic effectson a composite variable consisting of 6 vocal symptom items measuring dysphonia. The purpose of the present study was to determine genetic and environmental effects on the individual vocal symptoms in a population-based sample of Finnish twins.

Method

The sample comprised 1,728 twins (125 monozygotic and 108 dizygotic twin pairs) born between 1961 and 1989, who completed a questionnaire concerning 6 vocal symptoms. Values for additive genetic, dominant genetic, shared environmental, and nonshared environmental components were computed separately for all symptoms. Multivariate analyses to determine genetic and environmental associations between the vocal symptoms were also performed.

Results

Variance was explained by significant additive genetic effects (27%) in only one of the vocal symptoms, namely,voice gets low or hoarse,whereas the variance of one of the vocal symptoms,voice gets strained or tires,could be explained by nonshared environmental influence alone. Multivariate analyses showed that the correlations for most of the symptom combinations were significant.

Conclusions

Both genetic and environmental components influence vocal symptoms. Genetic and environmental influences seem to be differently balanced in different vocal symptoms. Genetic effects are moderate, whereas environmental effects seem to be the most important factor contributing to the presence of vocal symptoms.
Phonology and Language Development in Italian Children: An Analysis of Production and Accuracy
Authors: Zanobini Mirella , Viterbori Paola , Saraceno Francesca
Published: December 2011

Purpose

The principal aims of this study were to detect phonetic measures (consonant inventory, intelligibility, frequency, and types of phonological errors) associated with lexical and morphosyntactic ability and to analyze the types of phonological processes in children with different language skills.

Method

The sample was composed of 30 children between the ages of 36 and 42 months. Two tests were administered, one investigating phonological ability and one investigating general linguistic ability.

Results

A strong relationship between phonetic measures and language performance was found. The proportion of unintelligible productions and simplified words correlated with all the linguistic measures considered. A comparison of the phonological processes used by children with low, average, and high linguistic performance showed that phonotactic structure errors discriminated better than did system errors between the three groups. In particular, the less competent talkers were more likely to delete weak syllables, omit consonants and vowels, reduce diphthongs, and make consonant harmony errors.

Conclusions

The results emphasize the importance of phonetic measures in explaining differences in language performance and suggest the possibility of identifying children with low linguistic competence on the basis of phonetic measures, such as the level of intelligibility and the type of errors committed.
Relationship Between Consonant Recognition in Noise and Hearing Threshold
Authors: Yoon Yang-soo , Allen Jont B. , Gooler David M.
Published: December 2011

Purpose

Although poorer understanding of speech in noise by listeners who are hearing-impaired (HI) is known not to be directly related to audiometric hearing threshold,
HT
(f), grouping HI listeners with
HT
(f) is widely practiced. In this article, the relationship between consonant recognition and
HT
(f) is considered over a range of signal-to-noise ratios (SNRs).

Method

Confusion matrices (CMs) from 25 HI ears were generated in response to 16 consonant-vowel syllables presented at 6 different SNRs. Individual differences scaling (INDSCAL) was applied to both feature-based matrices and CMs in order to evaluate the relationship between
HT
(f) and consonant recognition among HI listeners.

Results

The results showed no predictive relationship between the percent error scores (
Pe
) and
HT
(f) across SNRs. The multiple regression models showed that the
HT
(f) accounted for 39% of the total variance of the slopes of the
Pe
. Feature-based INDSCAL analysis showed consistent grouping of listeners across SNRs, but not in terms of
HT
(f). Systematic relationship between measures was also not defined by CM-based INDSCAL analysis across SNRs.

Conclusions

HT
(f) did not account for the majority of the variance (39%) in consonant recognition in noise when the complete body of the CM was considered.
Is Tongue Strength an Important Influence on Rate of Articulation in Diadochokinetic and Reading Tasks?
Authors: Neel Amy T. , Palmer Phyllis M.
Published: December 2011

Purpose

The purpose of this study was to assess the relationship between tongue strength and rate of articulation in 2 speech tasks, diadochokinetic rates and reading aloud, in healthy men and women between 20 and 78 years of age.

Method

Diadochokinetic rates were measured for the syllables /pʌ/, /tʌ/, /kʌ/, and /pʌtəkə/, and articulation rates were calculated for a reading of the Rainbow Passage for 57 adult volunteers. The Iowa Oral Performance Instrument (LLC Northwest) was used to obtain maximum tongue pressure, tongue pressure exerted during production of /tʌ/, and tongue endurance. Correlation analyses were performed to determine the relation among articulation rate and tongue pressure and endurance measures.

Results

Maximum tongue pressure, the pressure used to produce /tʌ/, the proportion of maximum pressure used to produce /tʌ/, and tongue endurance were poor predictors of diadochokinetic rates and articulation rate in reading for healthy speakers.

Discussion

Focus must remain on factors beyond strength, such as movement precision and coordination, to improve researchers' understanding of normal and disordered speech production in adults.
Are Syllabification and Resyllabification Strategies Phonotactically Directed in French Children With Dyslexia? A Preliminary Report
Authors: Maïonchi-Pino Norbert , de Cara Bruno , écalle Jean , Magnan Annie
Published: December 2011

Purpose

In this study, the authors queried whether French-speaking children with dyslexia were sensitive to consonant sonority and position within syllable boundaries to influence a phonological syllable-based segmentation in silent reading.

Method

Participants included 15 French-speaking children with dyslexia, compared with 30 chronological age–matched and reading level–matched controls. Children were tested with an audiovisual recognition task. A target pseudoword (TOLPUDE) was simultaneously presented visually and auditorily and then was compared with a printed test pseudoword that either was identical or differed after the coda deletion (TOPUDE) or the onset deletion (TOLUDE). The intervocalic consonant sequences had either a
sonorant coda–sonorant onset
(TOR.LADE),
sonorant coda–obstruent onset
(TOL.PUDE),
obstruent coda–sonorant onset
(DOT.LIRE), or
obstruent coda–obstruent onset
(BIC.TADE) sonority profile.

Results

All children processed identity better than they processed deletion, especially with the optimal sonorant coda–obstruent onset sonority profile. However, children preserved syllabification (coda deletion; TO.PUDE) rather than resyllabification (onset deletion; TO.LUDE) with intervocalic consonant sequence reductions, especially when sonorant codas were deleted but the optimal intersyllable contact was respected.

Conclusions

It was surprising to find that although children with dyslexia generally exhibit phonological and acoustic–phonetic impairments (voicing), they showed sensitivity to the optimal sonority profile and a preference for preserved syllabification. The authors proposed a sonority-modulated explanation to account for phonological syllable-based processing. Educational implications are discussed.
Bilingual Listeners' Perception of Temporally Manipulated English Passages
Authors: Shi Lu-Feng , Farooq Nadia
Published: December 2011

Purpose

The current study measured, objectively and subjectively, how changes in speech rate affect recognition of English passages in bilingual listeners.

Method

Ten native monolingual, 20 English-dominant bilingual, and 20 non-English-dominant bilingual listeners repeated target words in English passages at five speech rates (unprocessed, two expanded, and two compressed), in quiet and in noise. For noise conditions, performance was measured at a signal-to-noise ratio that was determined through an adaptive procedure to avoid ceiling and floor effects. Listeners also made subjective judgments of speech rate, speech clarity, and performance confidence.

Results

In noise, stepwise improvement was observed as rate slowed down. A similar effect was not found in quiet. This pattern in performance was largely comparable across listener groups but was most robust in English-dominant listeners. Changes in speech rate and presence of noise significantly affected listeners' subjective ratings; however, no intergroup differences were observed for any of the subjective ratings.

Conclusions

Bilingual listeners benefited from slow speech rates, more evidently so in noise than in quiet. Their performance, however, did not reach a monolingual level, even at the most favorable rate. Nonetheless, all listeners reported comparable confidence when processing temporally manipulated English passages.
Speech Recognition and Acoustic Features in Combined Electric and Acoustic Stimulation
Authors: Yoon Yang-soo , Li Yongxin , Fu Qian-Jie
Published: December 2011

Purpose

In this study, the authors aimed to identify speech information processed by a hearing aid (HA) that is additive to information processed by a cochlear implant (CI) as a function of signal-to-noise ratio (SNR).

Method

Speech recognition was measured with CI alone, HA alone, and CI + HA. Ten participants were separated into 2 groups; good (aided pure-tone average [PTA] < 55 dB) and poor (aided PTA ≥ 55 dB) at audiometric frequencies ≤ 1 kHz in HA.

Results

Results showed that the good-aided PTA group derived a clear bimodal benefit (performance difference between CI + HA and CI alone) for vowel and sentence recognition in noise, whereas the poor-aided PTA group received little benefit across speech tests and SNRs. Results also showed that a better aided PTA helped in processing cues embedded in both low and high frequencies; none of these cues was significantly perceived by the poor-aided PTA group.

Conclusions

The aided PTA is an important indicator for bimodal advantage in speech perception. The lack of bimodal benefits in the poor group may be attributed to the nonoptimal HA fitting. Bimodal listening provides a synergistic effect for cues in both low- and high-frequency components in speech.
Perception of Speech Features by French-Speaking Children With Cochlear Implants
Authors: Bouton Sophie , Serniclaes Willy , Bertoncini Josiane , Colé Pascale
Published: December 2011

Purpose

The present study investigates the perception of phonological features in French-speaking children with cochlear implants (CIs) compared with normal-hearing (NH) children matched for listening age.

Method

Scores for discrimination and identification of minimal pairs for all features defining consonants (e.g., place, voicing, manner, nasality) and vowels (e.g., frontness, nasality, aperture) were measured in each listener.

Results

The results indicated no differences in “categorical perception,” specified as a similar difference between discrimination and identification between CI children and controls. However, CI children demonstrated a lower level of “categorical precision,” that is, lesser accuracy in both feature identification and discrimination, than NH children, with the magnitude of the deficit depending on the feature.

Conclusions

If sensitive periods of language development extend well beyond the moment of implantation, the consequences of hearing deprivation for the acquisition of categorical perception should be fairly important in comparison to categorical precision because categorical precision develops more slowly than categorical perception in NH children. These results do not support the idea that the sensitive period for development of categorical perception is restricted to the first 1–2 years of life. The sensitive period may be significantly longer. Differences in precision may reflect the acoustic limitations of the cochlear implant, such as coding for temporal fine structure and frequency resolution.
Perceptual Learning of Dysarthric Speech: A Review of Experimental Studies
Authors: Borrie Stephanie A. , McAuliffe Megan J. , Liss Julie M.
Published: December 2011

Purpose

This review article provides a theoretical overview of the characteristics of perceptual learning, reviews perceptual learning studies that pertain to dysarthric populations, and identifies directions for future research that consider the application of perceptual learning to the management of dysarthria.

Method

A critical review of the literature was conducted that summarized and synthesized previously published research in the area of perceptual learning with atypical speech. Literature related to perceptual learning of neurologically degraded speech was emphasized with the aim of identifying key directions for future research with this population.

Conclusions

Familiarization with unfamiliar or ambiguous speech signals can facilitate perceptual learning of that same speech signal. There is a small but growing body of evidence that perceptual learning also occurs for listeners familiarized with dysarthric speech. Perceptual learning of the dysarthric signal is both theoretically and clinically significant. In order to establish the efficacy of exploiting perceptual learning paradigms for rehabilitative gain in dysarthria management, research is required to build on existing empirical evidence and develop a theoretical framework for learning to better recognize neurologically degraded speech.
How Children With Autism Extend New Words
Authors: McGregor Karla K. , Bean Allison
Published: December 2011

Purpose

How do children with autism spectrum disorders (ASD) extend a noun to the category of objects it labels? Given their tendency to perceive locally, their extensions might be too narrow. Given their social-communicative deficits and a context in which the knowledge of a social-communicative partner promotes narrow extensions, their extensions might be too broad.

Method

We tested these predictions by comparing 25 high-functioning school-aged children with ASD to 29 age-matched peers with typical development (TD) in a task that required extraction of commonalities of object referents and use of social-communicative context to support the category inference.

Results

The children with ASD readily extended a given noun to multiple exemplars, thereby demonstrating tacit knowledge that words label categories and the ability to override local perceptual biases they might have. However, unlike their peers with TD, those who had concomitant weaknesses in semantic and syntactic language ability formed broad categories when their social partner’s behavior suggested narrow categories.

Conclusions

Some, but not all, people with ASD fail to use social context to support inferences about word extension. The direction of any causal relationship between failure to use social contextual cues and language deficits awaits determination.
Transport-mechanism analysis of the reverse leakage current in GaInN light-emitting diodes
Authors: Shan Qifeng , Meyaard David S. , Dai Qi , Cho Jaehee , Fred Schubert E. , Kon Son Joong , Sone Cheolsoo
Published: December 2011

The reverse leakage current of a GaInN light-emitting diode (LED) is analyzed by temperature dependent current–voltage measurements. At low temperature, the leakage current is attributed to variable-range-hopping conduction. At high temperature, the leakage current is explained by a thermally assisted multi-step tunneling model. The thermal activation energies (95–162 meV), extracted from the Arrhenius plot in the high-temperature range, indicate a thermally activated tunneling process. Additional room temperature capacitance–voltage measurements are performed to obtain information on the depletion width and doping concentration of the LED.
Acoustic trapping of particle by a periodically structured stiff plate
Authors: Cai Feiyan , He Zhaojian , Liu Zhengyou , Meng Long , Cheng Xin , Zheng Hairong
Published: December 2011

We present a study on the acoustic radiation forces exerted on a cylindrical particle near the surface of a periodically structured brass plate. When resonance of the structured plate occurs, this configuration shows an interesting trapping effect, which essentially arises from the gradient force induced by gradient vortex velocity field near the surface. This artificial structure for providing a geometrically modulated trapping force may be of interest for acoustic manipulation and sorting in various complex mechanical systems.
Controlling split-ring resonators with light
Authors: Kapitanova Polina V. , Maslovski Stanislav I. , Shadrivov Ilya V. , Voroshilov Pavel M. , Filonov Dmitry S. , Belov Pavel A. , Kivshar Yuri S.
Published: December 2011

We propose an original approach for creating tunable electromagnetic metamaterials. We demonstrate experimentally that magnetic resonance of a split-ring resonator (“meta-atom” of a composite material) with a photodiode operated in photovoltaic mode can be tuned by changing the intensity of an external light source. Moreover, for two coupled resonators, we show that we can achieve light-induced switching between dark- and bright-mode responses.
Fast large-scale clustering of protein structures using Gauss integrals
Authors: Harder Tim , Borg Mikael , Boomsma Wouter , Røgen Peter , Hamelryck Thomas
Published: December 2011

Motivation: Clustering protein structures is an important task in structural bioinformatics. De novo structure prediction, for example, often involves a clustering step for finding the best prediction. Other applications include assigning proteins to fold families and analyzing molecular dynamics trajectories.

Results: We present Pleiades, a novel approach to clustering protein structures with a rigorous mathematical underpinning. The method approximates clustering based on the root mean square deviation by first mapping structures to Gauss integral vectors—which were introduced by Røgen and co-workers—and subsequently performing K-means clustering.

Conclusions: Compared to current methods, Pleiades dramatically improves on the time needed to perform clustering, and can cluster a significantly larger number of structures, while providing state-of-the-art results. The number of low energy structures generated in a typical folding study, which is in the order of 50 000 structures, can be clustered within seconds to minutes.

Contact:  thamelry@binf.ku.dk; harder@binf.ku.dk

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Modeling mechanistic biological networks: An advanced Boolean approach
Authors: Handorf T. , Klipp E.
Published: December 2011

Motivation: The understanding of the molecular sources for diseases like cancer can be significantly improved by computational models. Recently, Boolean networks have become very popular for modeling signaling and regulatory networks. However, such models rely on a set of Boolean functions that are in general not known. Unfortunately, while detailed information on the molecular interactions becomes available in large scale through electronic databases, the information on the Boolean functions does not become available simultaneously and has to be included manually into the models, if at all known.

Results: We propose a new Boolean approach which can directly utilize the mechanistic network information available through modern databases. The Boolean function is implicitly defined by the reaction mechanisms. Special care has been taken for the treatment of kinetic features like inhibition. The method has been applied to a signaling model combining the Wnt and MAPK pathway.

Availability: A sample C++ implementation of the proposed method is available for Linux and compatible systems through http://code.google.com/p/libscopes/wiki/Paper2011

Contact:  handorf@physik.hu-berlin.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
MeQA: a pipeline for MeDIP-seq data quality assessment and analysis
Authors: Huang J. , Renault V. , Sengenès J. , Touleimat N. , Michel S. , Lathrop M. , Tost J.
Published: December 2011

Motivation: We present a pipeline for the pre-processing, quality assessment, read distribution and methylation estimation for methylated DNA immunoprecipitation (MeDIP)-sequence datasets. This is the first MeDIP-seq-specific analytic pipeline that starts at the output of the sequencers. This pipeline will reduce the data analysis load on staff and allows the easy and straightforward analysis of sequencing data for DNA methylation. The pipeline integrates customized scripting and several existing tools, which can deal with both paired and single end data.

Availability: The package and extensive documentation, and comparison to public data is available at http://life.tongji.edu.cn/meqa/

Contact:  jhuang@cephb.fr
Dietary Supplement Intake by 6‐month‐old Taiwanese Infants
Authors: Chuang Chao‐Hua , Yang Shwu‐Huey , Chang Pei‐Jen , Chen Pau‐Chung , Chen Yi Chun
Published: December 2011

Objectives:

The objective of the present study was to investigate the types of dietary supplements administered to healthy 6‐month‐old infants and to identify the factors influencing the use of such supplements.

Subjects and Methods:

The present study was based on the Taiwan Birth Cohort Study database. Questionnaires were used to collect information on the use of dietary supplements from birth, infant feeding practices, and other covariates at 6 months of age. We excluded low‐birth‐weight, preterm babies, and those whose caregivers returned incomplete questionnaires, leaving a sample size of 18,658. Multiple logistic regression was used to determine the characteristics capable of predicting the use of supplements in this population. A total of 34.9% of infants were fed dietary supplements from birth.

Results:

The most common types of supplements administered to infants were probiotics, calcium, and multivitamin/mineral supplements. Formula feeding, earlier weaning, and earlier complementary feeding were positively related to the use of several supplements.

Conclusions:

The present study demonstrates that the use of pediatric dietary supplements is relatively common among infants in Taiwan, even in the earliest stages of life. For infants whose diet is adequate, no need exists for dietary supplements, and excessive intake can adversely influence health. Communication between health professionals and child caregivers should be promoted to increase understanding of infant feeding, as well as the safety and efficacy of dietary supplements.
STAT3 Genotypic Variation and Cellular STAT3 Activation and Colon Leukocyte Recruitment in Pediatric Crohn Disease
Authors: Willson Tara A. , Kuhn Benjamin R. , Jurickova Ingrid , Gerad Shaina , Moon David , Bonkowski Erin , Carey Rebecca , Collins Margaret H. , Xu Huan , Jegga Anil G. , Guthery Stephen L. , Denson Lee A.
Published: December 2011

Objectives:

Genotypic variation in signal transducer and activator of transcription 3 (STAT3) increases risk for inflammatory bowel disease (IBD), and STAT3‐dependent inflammatory networks are induced in the colon in these patients. We hypothesized that STAT3 “A” risk allele carriage would be associated with increased cellular STAT3 activation and colon leukocyte recruitment.

Methods:

Colonic expression of genes regulating STAT3 signaling and leukocyte recruitment and function was measured in pediatric patients with Crohn disease (CD) stratified by STAT3 genotype. The frequency of colonic pSTAT3+ and CXCR2+ neutrophils was determined using immunohistochemistry. STAT3 tyrosine phosphorylation (pSTAT3) was measured in circulating leukocytes by flow cytometry, and mechanisms regulating STAT3 activation were tested in IBD Epstein‐Barr virus (EBV)–transformed lymphocytes (EBL).

Results:

Colonic expression of interleukin 6 (IL‐6), the STAT3 target gene SOCS3, the neutrophil chemoattractants IL‐8, CXCL1, and CXCL3, and the neutrophil products S100A8, S100A9, and S100A12 were increased in patients carrying the STAT3 “A” risk allele. The frequency of neutrophils expressing the cognate receptor for IL‐8, CXCR2, was increased in colonic biopsies from patients carrying the risk allele, and the frequency of pSTAT3+ or CXCR2+ neutrophils correlated with histologic severity. The frequency of CD4+ lymphocytes and granulocytes expressing pSTAT3 was increased in patients carrying the STAT3 “A” risk allele. EBLs from patients carrying the STAT3 “A” risk allele exhibited increased basal and IL‐6–stimulated STAT3 tyrosine phosphorylation, increased transcription of STAT3 and SOCS3 after IL‐6 stimulation, and increased membrane localization of the IL‐6 receptor, GP130, and Janus‐associated kinase 2.

Conclusions:

The STAT3 “A” risk allele is associated with increased cellular STAT3 activation and upregulation of pathways that promote recruitment of CXCR2+ neutrophils to the gut.
Correlation Between IgA Tissue Transglutaminase Antibody Ratio and Histological Finding in Celiac Disease
Authors: Alessio Maria G. , Tonutti Elio , Brusca Ignazio , Radice Antonella , Licini Lisa , Sonzogni Aurelio , Florena Ada , Schiaffino Eugenio , Marus Wally , Sulfaro Sandro , Villalta Danilo ,   Study Group on Autoimmune Diseases of the Italian Society of Laboratory Medicine
Published: December 2011

Objectives:

Positivity of both immumoglobulin A anti‐tissue transglutaminase (TTG) and anti‐endomysium antibodies (EMA) has a positive predictive value of nearly 100% for celiac disease (CD). The objective of the present study was to evaluate whether patients of any age, with high pretest probability of CD and high titre of anti‐TTG and EMA positivity, have a high probability of intestinal damage and may not require the biopsy for final diagnosis.

Methods:

A retrospective analysis of 412 consecutively referred patients, age range 10 months to 72 years, who underwent small‐bowel biopsy for suspicion of CD and positivity to both anti‐TTG and EMA, was performed at 4 Italian centers. Biopsies were evaluated independently by 2 pathologists using Marsh modified classification; in cases of dissimilar results, a third pathologist examined the biopsy. The final histological finding diagnosis was expressed as the prevalent or highest score assigned by the pathologist board.

Results:

Three hundred ninety‐six patients (96.1%) had histological findings consistent with CD (grade 2 and 3a, 3b, or 3c of modified Marsh classification). An anti‐TTG ratio ≥7 was able to identify with the 3 assays used (Celikey, anti‐TTG immumoglobulin A, EuTTG) all of the patients with significant mucosal damage (Marsh ≥2) independent of age and sex; specificity and positive predictive value were 100%. An anti‐TTG ratio >20 was more specific (99.8%) for identification of patients with villous atrophy (Marsh 3 a, b, or c).

Conclusions:

Patients with positivity of anti‐TTG ≥7‐fold cutoff, confirmed by positivity to EMA, have a high‐degree probability of duodenal damage. In selected conditions, a duodenal biopsy may be avoided and a confirmed greatly positive anti‐TTG result could be the basis to prescribe a gluten‐free diet.
Diagnostic Value of Anti‐deamidated Gliadin Peptide IgG Antibodies for Celiac Disease in Children and IgA‐deficient Patients
Authors: Mozo Lourdes , Gómez Jesús , Escanlar Esther , Bousoño Carlos , Gutiérrez Carmen
Published: December 2011

Objectives:

The aim of the study was to analyze the diagnostic performance of anti‐deamidated gliadin peptide (dGp) immunoglobulin (Ig) G and IgA regarding the age at celiac disease (CD) diagnosis and the anti‐dGp IgG usefulness for diagnosing CD IgA‐deficient patients.

Methods:

Anti‐dGp IgG and IgA and anti‐native gliadin (nGlia) IgA were determined by enzyme fluoroimmunoassay in 100 newly diagnosed anti‐tissue transglutaminase (tTG) IgA‐positive pediatric and adult patients with CD and in 100 age‐matched patients with other digestive pathologies. Anti‐dGp IgG was evaluated in 6 CD IgA‐deficient patients.

Results:

When analyzing all of the patients, the anti‐dGp IgG assay showed higher diagnostic accuracy (area under receiver operating characteristic curve), specificity, and positive predictive value than anti‐dGp IgA and anti‐nGlia IgA. All of the diagnostic parameters corresponding to anti‐dGp IgG reached the same values as anti‐tTG IgA in children 7 years or younger. In older patients, both anti‐dGp isotypes showed an inverse behavior, IgG having a higher specificity and positive predictive value but a lower sensitivity and negative predictive value than IgA. Anti‐dGp levels were associated with the severity of intestinal lesions, and an inverse association was found regarding age at diagnosis. Both anti‐dGp IgG and IgA were found to be positive in the 9 patients with minimal intestinal changes included in the study. All of the patients with CD with IgA deficiency were positive for anti‐dGp IgG.

Conclusions:

The diagnostic performance of anti‐dGp depends on the antibody isotype and on the age at CD diagnosis, anti‐dGp IgG being a serological marker at least as useful as anti‐tTG IgA for detecting CD in children ages 7 years or younger. Our data also indicate that anti‐dGp IgG can improve the diagnosis of IgA‐deficient patients.
Taste Perception and Food Choices
Authors: Negri Rossella , Di Feola Mariarosaria , Di Domenico Simone , Scala M. Giuseppa , Artesi Ginevra , Valente Serena , Smarrazzo Andrea , Turco Francesca , Morini Gabriella , Greco Luigi
Published: December 2011

Objectives:

The extent to which variation in taste perception influences food preferences is, to date, controversial. Bitterness in food triggers an innate aversion that is responsible for dietary restriction in children. We investigated the association among genetic variations in bitter receptor TAS2R38 and food choices in healthy children in the Mediterranean area, to develop appropriate tools to evaluate the relation among genetic predisposition, dietary habits, and feeding disorders. The aims of the study were to get a first baseline picture of taste sensitivity in healthy adults and their children and to explore taste sensitivity in a preliminary sample of obese children and in samples affected by functional gastrointestinal diseases.

Methods:

Individuals (98 children, 87 parents, 120 adults) were recruited from the general population in southern Italy. Bitterness sensitivity was assessed by means of a suprathreshold method with 6‐propyl‐2‐thiouracil. Genomic DNA from saliva was used to genotype individuals for 3 polymorphisms of TAS2R38 receptor, A49P, A262 V, and V296I. Food intake was assessed by a food frequency questionnaire.

Results:

Children's taste sensation differed from that of adults: we observed a higher frequency of supertasters among children even in the mother–child dyads with the same diplotypes. Among adults, supertaster status was related with proline‐alanine‐valine (taster allele) homozygous haplotype, whereas supertaster children were mainly heterozygous. Regarding the food choices, we found that a higher percentage of taster children avoided bitter vegetables or greens altogether compared with taster adults. Taster status was also associated with body mass index in boys.

Conclusions:

Greater sensitivity to 6‐propyl‐2‐thiouracil predicts lower preferences for vegetables in children, showing an appreciable effect of the genetic predisposition on food choices. None of the obese boys was a supertaster.
Parenteral Plant Sterols and Intestinal Failure–associated Liver Disease in Neonates
Authors: Kurvinen Annika , Nissinen Markku J. , Andersson Sture , Korhonen Päivi , Ruuska Tarja , Taimisto Mari , Kalliomäki Marko , Lehtonen Liisa , Sankilampi Ulla , Arikoski Pekka , Saarela Timo , Miettinen Tatu A. , Gylling Helena , Pakarinen Mikko P.
Published: December 2011

Objectives:

We prospectively evaluated incidence of prolonged (>28 days) parenteral nutrition (PN), associated complications, and significance of parenteral plant sterols (PS) in neonatal intestinal failure–associated liver disease (IFALD) compared with children.

Methods:

We recruited 28 neonates (mean age 50 days, range 28–126) and 11 children (6.9 y, 2.1–16.6) in all of Finland. Patients underwent repeated measurements of serum cholesterol, noncholesterol sterols, including PS, cholestanol and cholesterol precursors, and liver biochemistry during and 1 month after discontinuation of PN. Healthy matched neonates (n = 10) and children (n = 22) served as controls.

Results:

IFALD occurred more frequently among neonates (63%) than children (27%; P < 0.05). Ratios of serum PS, including stigmasterol, sitosterol, avenasterol, and campesterol, and total PS were increased among neonates compared with healthy controls and children on PN by 2‐ to 22‐ and 2‐ to 5‐fold (P < 0.005), respectively. Neonates with IFALD had significantly higher ratios of serum PS and cholestanol compared with neonates without IFALD (P < 0.05). Total duration of PN associated with serum cholestanol, stigmasterol, avenasterol, alanine aminotransferase, and aspartate aminotransferase (r = 0.472–0.636, P < 0.05). Cholestanol and individual serum PS, excluding campesterol, reflected direct bilirubin (r = 0.529–0.688, P < 0.05). IFALD persisted after discontinuation of PN in 25% of neonates with 4.2‐ and 2.2‐times higher ratios of serum stigmasterol and cholestanol compared with neonates without IFALD (P < 0.05).

Conclusions:

Frequent occurrence of IFALD among neonates on PN displays an association to duration of PN and markedly increased serum PS, especially stigmasterol, in comparison to healthy neonates and children on PN. Striking accumulation of parenteral PS may contribute to IFALD among neonates.
Flavobacterium ummariense sp. nov., isolated from hexachlorocyclohexane-contaminated soil, and emended description of

Flavobacterium ceti

Vela et al. 2007
Authors: Lata Pushp , Lal Devi , Lal Rup
Published: December 2011

A Gram-negative, strictly aerobic, yellow bacterial strain, designated DS-12T, was isolated from hexachlorocyclohexane-contaminated soil in Lucknow, Uttar Pradesh, India. Strain DS-12T showed the highest 16S rRNA gene sequence similarity with

Flavobacterium ceti

454-2T (94.2 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DS-12T belonged to the genus

Flavobacterium

. Strain DS-12T produced flexirubin-type pigments. Gliding motility was not observed. The major fatty acids of strain DS-12T were iso-C15 : 0 (48.0 %), summed feature 9 (comprising iso-C17 : 1ω9c and/or C16 : 0 10-methyl; 19.3 %), iso-C17 : 0 3-OH (8.5 %) and summed feature 3 (comprising one or more of C16 : 1ω7c, C16 : 1ω6c and iso-C15 : 0 2-OH; 7.2 %). The only respiratory quinone was menaquinone-6 and the major polyamine was homospermidine. Strain DS-12T contained phosphatidyldimethylethanolamine, phosphatidylserine, phosphatidylethanolamine, one unknown phospholipid and one unknown aminolipid. The DNA G+C content was 37.4 mol%. Phylogenetic inference and phenotypic properties indicated that strain DS-12T represents a novel species of the genus

Flavobacterium

, for which the name Flavobacterium ummariense sp. nov. is proposed. The type strain is DS-12T ( = CCM 7847T  = MTCC 10766T). An emended description of

Flavobacterium ceti

is also given.
Isolates belonging to CDC group II-i belong predominantly to Sphingobacterium mizutaii Yabuuchi et al. 1983: emended descriptions of S. mizutaii and of the genus Sphingobacterium
Authors: Wauters Georges , Janssens Michèle , De Baere Thierry , Vaneechoutte Mario , Deschaght Pieter
Published: December 2011

Two clinical strains, NF 296 and NF 931, present in our collection, were identified biochemically as members of CDC group II-i. Determination of the 16S rRNA gene sequence revealed highest similarity with strains ofSphingobacterium mizutaii. Because these strains produced indole, whereasS. mizutaiihas been described as indole-negative, we also investigated the type strain and a reference strain ofS. mizutaii, LMG 8340T( = CCUG 15907T) and LMG 8341 ( = CCUG 15908), and found both strains also to be positive for indole production. These data warrant inclusion of some of the CDC group II-i strains intoS. mizutaiiand emended descriptions ofSphingobacterium mizutaiias indole-production-positive and of the genusSphingobacteriumas variable for indole production.
Polaromonas

glacialis sp. nov. and Polaromonas cryoconiti sp. nov., isolated from alpine glacier cryoconite
Authors: Margesin Rosa , Spröer Cathrin , Zhang De-Chao , Busse Hans-Jürgen
Published: December 2011

The taxonomic positions of two Gram-staining-negative, psychrophilic bacteria, which were isolated from alpine glacier cryoconite and designated strains Cr4-12T and Cr4-35T, were investigated using a polyphasic approach. Both novel strains contained ubiquinone Q-8 as the sole quinone, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0 as the dominant cellular fatty acids, putrescine and 2-hydroxyputrescine as the major polyamines, and diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as the major polar lipids. The genomic DNA G+C contents of strains Cr4-12T and Cr4-35T were 61.3 mol% and 60.7 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the two strains belonged to the genus

Polaromonas

. Although the 16S rRNA gene sequences of strains Cr4-12T and Cr4-35T were very similar (98.7 % sequence similarity), hybridizations indicated a DNA–DNA relatedness value of only 26.9 % between the two novel strains. In pairwise comparisons with the type strains of recognized

Polaromonas

species, strains Cr4-12T and Cr4-35T showed 16S rRNA gene sequence similarities of 96.4–98.5 % and 96.5–98.4 %, respectively. Based on the phenotypic and phylogenetic evidence and DNA–DNA relatedness data, strains Cr4-12T and Cr4-35T represent two novel species within the genus

Polaromonas

, for which the names Polaromonas glacialis sp. nov. and Polaromonas cryoconiti sp. nov., respectively, are proposed. The type strain of Polaromonas glacialis sp. nov. is Cr4-12T ( = DSM 24062T  = LMG 26049T  = KACC 15089T) and that of Polaromonas cryoconiti sp. nov. is Cr4-35T ( = DSM 24248T  = LMG 26050T  = KACC 15090T).
Pseudomonas zeshuii sp. nov., isolated from herbicide-contaminated soil
Authors: Feng Zhaozhong , Zhang Jun , Huang Xing , Zhang Jing , Chen Minggen , Li Shunpeng
Published: December 2011

A Gram-stain-negative, rod-shaped, non-motile, non-spore-forming bacterium, designated strain BY-1T, was isolated from a soil sample from the city of Qiqihar in Heilongjiang Province, PR China. Strain BY-1Tgrew optimally at pH 7.0 and 30–35 °C in the presence of 0.5 % (w/v) NaCl. Analysis of 16S rRNA gene sequences revealed that strain BY-1Tfell within the radiation of the genusPseudomonas, and showed highest 16S rRNA gene sequence similarities toPseudomonas luteolaIAM 13000T(99.5 %) andPseudomonas duriflavaHR2T(97.3 %); the levels of sequence similarity with respect to other recognized species of the genusPseudomonaswere <96.7 %. Strain BY-1Tshowed low DNA–DNA relatedness values withPseudomonas luteolaIAM 13000T(29±3.1 %) andPseudomonas duriflavaHR2T(21±1.5 %). The G+C content of the genomic DNA of strain BY-1Twas 55.3 mol%. The major fatty acids were C18 : 1, C16 : 0and summed feature 3 (C16 : 1ω6cand/or C16 : 1ω7c). Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, and the major ubiquinone was Q-9. Data obtained in this study indicated that this isolate represents a novel species of the genusPseudomonas, for which the namePseudomonas zeshuiisp. nov. is proposed. The type strain is BY-1T( = KACC 15471T = ACCC 05688T).
Amycolatopsis dongchuanensis sp. nov., an actinobacterium isolated from soil
Authors: Nie Guo-Xing , Ming Hong , Li Shuai , Zhou En-Min , Cheng Juan , Tang Xia , Feng Hui-Gen , Tang Shu-Kun , Li Wen-Jun
Published: December 2011

A novel actinomycete strain, designated YIM 75904T, was isolated from a soil sample that had been collected from a dry and hot river valley in Dongchuan county, Yunnan province, south-western China. The taxonomic position of the novel strain was investigated by a polyphasic approach. In phylogenetic analyses based on 16S rRNA gene sequences, strain YIM 75904T formed a distinct clade within the genus

Amycolatopsis

and appeared to be closely related to

Amycolatopsis sacchari

K24T (99.3 % sequence similarity). Strain YIM 75904T had a type-IV cell wall, with no detectable mycolic acids, and had MK-9(H4) as its predominant menaquonine. Its cell wall contained meso-diaminopimelic acid, galactose, glucose and arabinose, and its major cellular fatty acids were iso-C16 : 0, iso-C15 : 0, anteiso-C17 : 0 and anteiso-C15 : 0. The genomic DNA G+C content of the novel strain was 68.5 mol%. Based on the results of physiological and biochemical tests and DNA–DNA hybridizations, strain YIM 75904T represents a novel species of the genus

Amycolatopsis

for which the name Amycolatopsis dongchuanensis sp. nov. is proposed. The type strain is YIM 75904T ( = CCTCC AA 2011016T  = JCM 18054T).
Alkalitalea saponilacus gen. nov., sp. nov., an obligately anaerobic, alkaliphilic, xylanolytic bacterium from a meromictic soda lake
Authors: Zhao Baisuo , Chen Shulin
Published: December 2011

A Gram-positive, obligately anaerobic, motile, slender, flexible rod, designated SC/BZ-SP2T, was isolated from mixed alkaline water and sediment of Soap Lake, Washington State, USA. Strain SC/BZ-SP2T formed salmon to pink colonies and was alkaliphilic. The isolate grew at pH35 °C 7.5–10.5 (optimum pH35 °C 9.7), at 8–40 °C (optimum 35–37 °C) and with 0.35–1.38 M Na+ (optimum 0.44–0.69 M Na+). The isolate utilized l-arabinose, d-ribose, d-xylose, d-fructose, d-mannose, d-galactose, cellobiose, maltose, sucrose, trehalose, sorbitol, xylan, malate and yeast extract as carbon and energy sources; best growth was observed with l-arabinose, cellobiose, maltose and trehalose. The major fermentation products from beechwood xylan were propionate and acetate. The dominant fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 0 3-OH, C17 : 0 3-OH and C15 : 0 3-OH. The cell-wall sugars were ribose, xylose, galactose and glucose. Thiosulfate and sulfite could be reduced to sulfide. The genomic DNA G+C content was 39.5±0.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SC/BZ-SP2T belonged to the family

Marinilabiliaceae

of the order

Bacteroidales

, class

Bacteroidia

. The most closely related strains were

Alkaliflexus imshenetskii

Z-7010T (91.8 % 16S rRNA gene sequence similarity),

Marinilabilia salmonicolor

Cy s1T (91.0 %) and

Anaerophaga thermohalophila

Fru22T (90.4 %). On the basis of phenotypic, chemotaxonomic and phylogenetic features, strain SC/BZ-SP2T represents a novel species in a new genus of the family

Marinilabiliaceae

, for which the name Alkalitalea saponilacus gen. nov., sp. nov. is proposed. The type strain of Alkalitalea saponilacus is SC/BZ-SP2T ( = ATCC BAA-2172T  = DSM 24412T).
Imtechella halotolerans gen. nov., sp. nov., a member of the family

Flavobacteriaceae

isolated from estuarine water
Authors: Surendra Vikram , Bhawana Pant , Suresh Korpole , Srinivas T. N. R. , Anil Kumar Pinnaka
Published: December 2011

A novel Gram-negative, rod-shaped, non-motile, non-sporulating bacterium, designated strain K1T, was isolated from an estuarine water sample collected from Kochi, Kerala, India. Colonies on marine agar were circular, 2.0–2.5 mm in diameter, shiny, yellow, translucent and convex with entire margins. Strain K1T was negative for ornithine decarboxylase, lysine decarboxylase, nitrate reduction and H2S production. The fatty acids were dominated by iso-branched components with a high abundance of iso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH; MK-6 (64 %) and MK-7 (34 %) were found as major respiratory quinones; and phosphatidylethanolamine, two unidentified aminolipids, four unidentified phospholipids and two unidentified lipids were major polar lipids. The DNA G+C content of strain K1T was 46.1 mol%. 16S rRNA gene sequence analysis indicated that strain K1T was related most closely to the type strain of

Zhouia amylolytica

(pairwise sequence similarity of 93.0 %). Phylogenetic analysis showed that strain K1T formed a distinct branch within the family

Flavobacteriaceae

and clustered with the clade comprising species of the genera

Zhouia

,

Coenonia

and

Capnocytophaga

, being phylogenetically most closely related to the type strain of

Zhouia amylolytica

at a distance of 9.2 % (90.8 % similarity). Other species of the genera within the same clade were related to strain K1T at distances of 15.0–23.1 %. Based on phenotypic and chemotaxonomic characteristics and on phylogenetic inference, strain K1T is considered to represent a novel species of a new genus in the family

Flavobacteriaceae

, for which the name Imtechella halotolerans gen. nov., sp. nov. is proposed. The type strain of Imtechella halotolerans is K1T ( = MTCC 11055T = JCM 17677T).
Reclassification of

Xylanibacter oryzae

Ueki et al. 2006 as Prevotella oryzae comb. nov., with an emended description of the genus

Prevotella
Authors: Sakamoto Mitsuo , Ohkuma Moriya
Published: December 2011

16S rRNA gene sequence information has indicated that

Xylanibacter oryzae

has a close relationship with the genus

Prevotella

. To clarify the taxonomic position of

X. oryzae

, we determined the sequence of hsp60 as it represents an alternative phylogenetic marker for identification and classification of Gram-negative anaerobic rods. On the basis of hsp60 sequences,

X. oryzae

was located within the genus

Prevotella

, indicating that the species does not represent a distinct taxon at the genus level. Statistical tests (the Shimodaira–Hasegawa test and the approximately unbiased test) supported the finding that

X. oryzae

is monophyletic with members of the genus

Prevotella

and thus belongs to the genus. On the basis of the phylogenetic findings, we propose that

X. oryzae

should be reclassified as Prevotella oryzae comb. nov.; the type strain is KB3T ( = JCM 13648T  = DSM 17970T). An emended description of the genus

Prevotella

is also provided.
Parent-of-Origin Effects on Gene Expression and DNA Methylation in the Maize Endosperm
Authors: Waters Amanda J. , Makarevitch Irina , Eichten Steve R. , Swanson-Wagner Ruth A. , Yeh Cheng-Ting , Xu Wayne , Schnable Patrick S. , Vaughn Matthew W. , Gehring Mary , Springer Nathan M.
Published: December 2011

Imprinting describes the differential expression of alleles based on their parent of origin. Deep sequencing of RNAs from maize (Zea mays) endosperm and embryo tissue 14 d after pollination was used to identify imprinted genes among a set of ~12,000 genes that were expressed and contained sequence polymorphisms between the B73 and Mo17 genotypes. The analysis of parent-of-origin patterns of expression resulted in the identification of 100 putative imprinted genes in maize endosperm, including 54 maternally expressed genes (MEGs) and 46 paternally expressed genes (PEGs). Three of these genes have been previously identified as imprinted, while the remaining 97 genes represent novel imprinted maize genes. A genome-wide analysis of DNA methylation identified regions with reduced endosperm DNA methylation in, or near, 19 of the 100 imprinted genes. The reduced levels of DNA methylation in endosperm are caused by hypomethylation of the maternal allele for both MEGs and PEGs in all cases tested. Many of the imprinted genes with reduced DNA methylation levels also show endosperm-specific expression patterns. The imprinted maize genes were compared with imprinted genes identified in genome-wide screens of rice (Oryza sativa) and Arabidopsis thaliana, and at least 10 examples of conserved imprinting between maize and each of the other species were identified.