bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcription of nitrification genes by the methane-oxidizing bacterium, Methylococcus capsulatus strain Bath
Authors: Poret-Peterson Amisha T , Graham James E , Gulledge Jay , Klotz Martin G 
Published: July 2008

Abstract
Methylococcus capsulatus strain Bath, a methane-oxidizing bacterium, and ammonia-oxidizing bacteria (AOB) carry out the first step of nitrification, the oxidation of ammonia to nitrite, through the intermediate hydroxylamine. AOB use hydroxylamine oxidoreductase (HAO) to produce nitrite. M. capsulatus Bath was thought to oxidize hydroxylamine with cytochrome P460 (cytL), until the recent discovery of an hao gene in its genome. We used quantitative PCR analyses of cDNA from M. capsulatus Bath incubated with CH4 or CH4 plus 5 mm (NH4)2SO4 to determine whether cytL and hao transcript levels change in response to ammonia. While mRNA levels for cytL were not affected by ammonia, hao mRNA levels increased by 14.5- and 31-fold in duplicate samples when a promoter proximal region of the transcript was analyzed, and by sixfold when a region at the distal end of the transcript was analyzed. A conserved open reading frame, orf2, located 3′ of hao in all known AOB genomes and in M. capsulatus Bath, was cotranscribed with hao and showed increased mRNA levels in the presence of ammonia. These data led to designating this gene pair as haoAB, with the role of haoB still undefined. We also determined mRNA levels for additional genes that encode proteins involved in N-oxide detoxification: cytochrome c′-β (CytS) and nitric oxide (NO) reductase (NorCB). Whereas cytS mRNA levels increased in duplicate samples by 28.5- and 40-fold in response to ammonia, the cotranscribed norC-norB mRNA did not increase. Our results strongly suggest that M. capsulatus Bath possesses a functional, ammonia-responsive HAO involved in nitrification.
Differences in Age-Related Alterations in Muscle Contraction Properties in Rat Tongue and Hindlimb
Authors: Connor Nadine P. , Ota Fumikazu , Nagai Hiromi , Russell John A. , Leverson Glen 
Published: July 2008

Purpose
Because of differences in muscle architecture and biomechanics, the purpose of this study was to determine whether muscle contractile properties of rat hindlimb and tongue were differentially affected by aging.

Method
Deep peroneal and hypoglossal nerves were stimulated in 6 young and 7 old Fischer 344-Brown Norway rats to allow recording of muscle contractile properties of tongue and extensor digitorum longus (EDL) muscle in the hindlimb. In the same animals, the following measurements were made: (a) twitch contraction time (CT; in milliseconds), (b) half decay time (HDT; in milliseconds), (c) maximum twitch force (in grams), (d) tetanic force, and (e) fatigue index determined from repetitive stimulation of the muscles.

Results

No significant differences were observed in young versus old groups in retrusive tongue forces, whereas a significant (
p
< .05) decrement in EDL tetanic forces was found in old rats. Slower CT in old rats was observed only in the tongue. Old and young groups were not significantly different in fatigue index or HDT for tongue or EDL.

Conclusions
Old animals generated equivalent maximum tongue forces with stimulation, but they were slower in achieving these forces than young animals. Limb and cranial muscles were not affected equally by aging. As such, information derived from limb muscle studies may not easily generalize to the cranial motor system.
Phonotactic Probability Effects in Children Who Stutter
Authors: Anderson Julie D. , Byrd Courtney T. 
Published: July 2008

Purpose

The purpose of this study was to examine the influence of
phonotactic probability,
which is the frequency of different sound segments and segment sequences, on the overall fluency with which words are produced by preschool children who stutter (CWS) as well as to determine whether it has an effect on the type of stuttered disfluency produced.

Method
A 500+ word language sample was obtained from 19 CWS. Each stuttered word was randomly paired with a fluently produced word that closely matched it in grammatical class, word length, familiarity, word and neighborhood frequency, and neighborhood density. Phonotactic probability values were obtained for the stuttered and fluent words from an online database.

Results
Phonotactic probability did not have a significant influence on the overall susceptibility of words to stuttering, but it did impact the type of stuttered disfluency produced. In specific, single-syllable word repetitions were significantly lower in phonotactic probability than fluently produced words, part-word repetitions, and sound prolongations.

Conclusions
In general, the differential impact of phonotactic probability on the type of stuttering-like disfluency produced by young CWS provides some support for the notion that different disfluency types may originate in the disruption of different levels of processing.
The Effect of Frequency Altered Feedback on Stuttering Duration and Type
Authors: Stuart Andrew , Frazier Carmen L. , Kalinowski Joseph , Vos Paul W. 
Published: July 2008

Purpose
The effect of frequency altered feedback (FAF) on stuttering type (i.e., prolongation, repetition, or silent block) and stuttering duration (i.e., average duration of stuttering event and total stuttering time) was examined.

Method

Retrospective analyses of previously collected data from 12 adult persons who stutter who participated in an
ABA
time-series design while reading orally was undertaken. It was hypothesized that stuttering duration would decrease and there would be a differential reduction in the type of stuttering during FAF, concurrent with previously confirmed reduction of stuttering episodes. A total of 2,971 stuttered syllables were analyzed.

Results

The total stuttering duration (s/min) was significantly reduced by approximately 50% irrespective of stuttering type (
p
= .0014). Although significant differences in the average duration(s) of the 3 stuttering types (
p
= .0064) existed, FAF significantly reduced each type of stuttering by approximately 20% (
p
= .0055). There was no differential effect on the reduction of proportion of stuttering type during FAF (
p
= .36).

Conclusions
FAF positively affects the speech of persons who stutter by reducing the proportion of stuttered events with a concomitant decrease in duration of residual stuttering and total stuttering time during oral reading.
An Evaluation of the Aurora System as a Flesh-Point Tracking Tool for Speech Production Research
Authors: Kröger Bernd J. , Pouplier Marianne , Tiede Mark K. 
Published: July 2008

Purpose
Northern Digital Instruments (NDI; Waterloo, Ontario, Canada) manufactures a commercially available magnetometer device called Aurora that features real-time display of sensor position tracked in 3 dimensions. To test its potential for speech production research, data were collected to assess the measurement accuracy and reliability of the system.

Method
First, sensors affixed at a known distance on a rigid ruler were moved systematically through the measurement space. Second, sensors attached to the speech articulators of a human participant were tracked during various speech tasks.

Results
In the ruler task, results showed mean distance errors of less than 1 mm, with some sensitivity to location within the measurement field. In the speech tasks, Euclidean distance between jaw-mounted sensors showed comparable accuracy; however, a high incidence of missing samples was observed, positively correlated with sensor velocity.

Conclusions
The real-time positional feedback provided by the system makes it potentially useful in speech therapy applications. The overall missing data rate observed during speech tasks makes use of the system in its current form problematic for the quantitative measurement of speech articulator movements; however, NDI is actively working to improve the Aurora system for use in this context.
Language-Specific Effects of Task Demands on the Manifestation of Specific Language Impairment: A Comparison of English and Icelandic
Authors: Thordardottir Elin 
Published: July 2008

Purpose
Previous research has indicated that the manifestation of specific language impairment (SLI) varies according to factors such as language, age, and task. This study examined the effect of task demands on language production in children with SLI cross-linguistically.

Method

Icelandic- and English-speaking school-age children with SLI and normal language (NL) peers (
n
= 42) were administered measures of verbal working memory. Spontaneous language samples were collected in contexts that vary in task demands: conversation, narration, and expository discourse. The effect of the context-related task demands on the accuracy of grammatical inflections was examined.

Results
Children with SLI in both language groups scored significantly lower than their NL peers in verbal working memory. Nonword repetition scores correlated with morphological accuracy. In both languages, mean length of utterance (MLU) varied systematically across sampling contexts. Context exerted a significant effect on the accuracy of grammatical inflection in English only. Error rates were higher overall in English than in Icelandic, but whether the difference was significant depended on the sampling context. Errors in Icelandic involved verb and noun phrase inflection to a similar extent.

Conclusions
The production of grammatical morphology appears to be more taxing for children with SLI who speak English than for those who speak Icelandic. Thus, whereas children with SLI in both language groups evidence deficits in language processing, cross-linguistic differences are seen in which linguistic structures are vulnerable when processing load is increased. Future research should carefully consider the effect of context on children’s language performance.
Cortical Mechanisms of Speech Perception in Noise
Authors: Wong Patrick C. M. , Uppunda Ajith K. , Parrish Todd B. , Dhar Sumitrajit 
Published: July 2008

Purpose
The present study examines the brain basis of listening to spoken words in noise, which is a ubiquitous characteristic of communication, with the focus on the dorsal auditory pathway.

Method
English-speaking young adults identified single words in 3 listening conditions while their hemodynamic response was measured using fMRI: speech in quiet, speech in moderately loud noise (signal-to-noise ratio [SNR] 20 dB), and in loud noise (SNR −5 dB).

Results
Behaviorally, participants’ performance (both accuracy and reaction time) did not differ between the quiet and SNR 20 dB condition, whereas they were less accurate and responded slower in the SNR −5 dB condition compared with the other 2 conditions. In the superior temporal gyrus (STG), both left and right auditory cortex showed increased activation in the noise conditions relative to quiet, including the middle portion of STG (mSTG). Although the right posterior STG (pSTG) showed similar activation for the 2 noise conditions, the left pSTG showed increased activation in the SNR −5 dB condition relative to the SNR 20 dB condition.

Conclusion
We found cortical task-independent and noise-dependent effects concerning speech perception in noise involving bilateral mSTG and left pSTG. These results likely reflect demands in acoustic analysis, auditory–motor integration, and phonological memory, as well as auditory attention.
Enriched random forests
Authors: Amaratunga Dhammika , Cabrera Javier , Lee Yung-Seop 
Published: July 2008

Abstract
Although the random forest classification procedure works well in datasets with many features, when the number of features is huge and the percentage of truly informative features is small, such as with DNA microarray data, its performance tends to decline significantly. In such instances, the procedure can be improved by reducing the contribution of trees whose nodes are populated by non-informative features. To some extent, this can be achieved by prefiltering, but we propose a novel, yet simple, adjustment that has demonstrably superior performance: choose the eligible subsets at each node by weighted random sampling instead of simple random sampling, with the weights tilted in favor of the informative features. This results in an ‘enriched random forest’. We illustrate the superior performance of this procedure in several actual microarray datasets.
Contact: damaratu@prdus.jnj.com
GenoSNP: a variational Bayes within-sample SNP genotyping algorithm that does not require a reference population
Authors: Giannoulatou Eleni , Yau Christopher , Colella Stefano , Ragoussis Jiannis , Holmes Christopher C. 
Published: July 2008

AbstractSummary: Current genotyping algorithms typically call genotypes by clustering allele-specific intensity data on a single nucleotide polymorphism (SNP) by SNP basis. This approach assumes the availability of a large number of control samples that have been sampled on the same array and platform. We have developed a SNP genotyping algorithm for the Illumina Infinium SNP genotyping assay that is entirely within-sample and does not require the need for a population of control samples nor parameters derived from such a population. Our algorithm exhibits high concordance with current methods and &gt;99% call accuracy on HapMap samples. The ability to call genotypes using only within-sample information makes the method computationally light and practical for studies involving small sample sizes and provides a valuable independent quality control metric for other population-based approaches.Availability: http://www.stats.ox.ac.uk/~giannoul/GenoSNP/Contact: cholmes@stats.ox.ac.uk
Genome-Wide Analysis of Transposon Insertion Polymorphisms Reveals Intraspecific Variation in Cultivated Rice
Authors: Huang Xuehui , Lu Guojun , Zhao Qiang , Liu Xiaohui , Han Bin 
Published: July 2008

AbstractInsertions and precise eliminations of transposable elements generated numerous transposon insertion polymorphisms (TIPs) in rice (Oryza sativa). We observed that TIPs represent more than 50% of large insertions and deletions (&gt;100 bp) in the rice genome. Using a comparative genomic approach, we identified 2,041 TIPs between the genomes of two cultivars, japonica Nipponbare and indica 93-11. We also identified 691 TIPs between Nipponbare and indica Guangluai 4 in the 23-Mb collinear regions of chromosome 4. Among them, retrotransposon-based insertion polymorphisms were used to reveal the evolutionary relationships of these three cultivars. Our conservative estimates suggest that the TIPs generated approximately 14% of the genomic DNA sequence differences between subspecies indica and japonica. It was also found that more than 10% of TIPs were located in expressed gene regions, representing an important source of genetic variation. Transcript evidence implies that these TIPs induced a series of genetic differences between two subspecies, including interrupting host genes, creating different expression forms, drastically changing intron length, and affecting expression levels of adjacent genes. These analyses provide genome-wide insights into evolutionary history and genetic variation of rice.
Pharmacokinetic interaction of flecainide and paroxetine in relation to the CYP2D6*10 allele in healthy Korean subjects
Authors: Lim Kyoung Soo , Cho Joo‐Youn , Jang In‐Jin , Kim Bo‐Hyung , Kim JaeWoo , Jeon Ji‐Young , Tae Yu‐Mi , Yi SoJeong , Eum SoYoung , Shin Sang‐Goo , Yu Kyung‐Sang 
Published: July 2008

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT • The only existing study of CYP2D6*10‐associated alterations in flecainide pharmacokinetics was retrospective.• Paroxetine has been known as a strong inhibitor of CYP2D6. WHAT THIS STUDY ADDS • This study reports that the extent of drug interaction between flecainide and paroxetine is influenced by the CYP2D6*10 allele in healthy subjects, which is frequent in Asians.AIMSThe objectives were to evaluate the effect of CYP2D6 genetic polymorphism on the pharmacokinetics of flecainide, and also on the extent of drug interaction with paroxetine as a CYP2D6 inhibitor after a single oral administration in healthy subjects.METHODSAn open‐label, two‐period, single‐sequence, cross‐over study was performed in 21 healthy Korean male volunteers (seven for CYP2D6*1/*1 or *1/*2, group 1; seven for CYP2D6*1/*10, group 2; seven for CYP2D6*10/*10 or *10/*36, group 3). Subjects were administered 200 mg of flecainide on day 1. After a 7‐day wash‐out period, subjects were administered 20 mg of paroxetine from day 8 to 14, and 200 mg of flecainide on day 15. Blood sampling was performed up to 72 h after flecainide administration.RESULTSTerminal elimination half‐life and mean residence time (MRT) were significantly different among three genotype groups after a single oral administration of flecainide (P = 0.021, 0.011, respectively). Area under the concentration–time curve, terminal elimination half‐life and MRT increased significantly after paroxetine co‐administration only in groups 1 and 2.CONCLUSIONSThis study reports that the extent of drug interaction between flecainide and paroxetine is influenced by the CYP2D6*10 allele in healthy subjects, which is frequent in Asians.
New diagnostic reporting format for endometrial cytology based on cytoarchitectural criteria
Authors: Yanoh K. , Norimatsu Y. , Hirai Y. , Takeshima N. , Kamimori A. , Nakamura Y. , Shimizu K. , Kobayashi T. K. , Murata T. , Shiraishi T. 
Published: July 2008

Objective:  The aim of this study was to develop a new reporting format for endometrial cytology that would standardize the diagnostic criteria and the terminology used for reporting.Methods:  In previous studies, cytoarchitectural criteria were found to be useful for the cytological assessment of endometrial lesions. To apply these criteria, an appropriate cytological specimen is imperative. In this article, the requirements of an adequate endometrial cytological specimen for the new diagnostic criteria are first discussed. Then, the diagnostic criteria, standardized on a combination of conventional and cytoarchitectural criteria, are presented. Third, terminology that could be used, not only for reporting the histopathological diagnosis, but also for providing better guidance for the gynaecologist to determine further clinical action, is introduced. The proposed reporting format was investigated using endometrial cytology of 58 cases that were cytologically underestimated or overestimated compared to the histopathological diagnosis made on the subsequent endometrial biopsy or surgical specimens.Results:  Of the 58 cases, 12 were reassessed as being unsatisfactory for evaluation. Among the remaining 46 cases, 25 of the 27 cases, which had been underestimated and subsequently diagnosed as having endometrial carcinoma or a precursor stage on histopathological examination,were reassessed as recommended for endometrial biopsy. On the other hand, 19 cases overestimated by cytology were all reassessed as not requiring biopsy.Conclusions:  The reporting format for endometrial cytology proposed in this article may improve diagnostic accuracy and reduce the number of patients managed inappropriately.
Control of stream insect assemblages: roles of spatial configuration and local environmental factors
Authors: HEINO JANI , MYKRÄ HEIKKI 
Published: July 2008

Abstract1. Current views in ecology emphasise that community structure is the sum of multiple processes, with imprints of both regional and local drivers. However, the degree to which stream insect assemblages are structured by spatial configuration (complying with the dispersal‐based neutral hypothesis) and local environmental features (complying with the niche‐based species sorting hypothesis) has not been rigorously examined based on surveys in multiple years.2. Stream sites in a boreal drainage system were surveyed during three consecutive years and the relative contribution of spatial configuration and local environmental variables to aquatic insect assemblage structure (characterised by both abundance and presence–absence data) was assessed. Separate analyses were conducted for mayflies (Ephemeroptera), stoneflies (Plecoptera), caddisflies (Trichoptera), and non‐biting midges (Diptera: Chironomidae) in each year.3. There were no relationships between the spatial location and local environmental features of streams in Mantel tests, facilitating exploration of their independent effects on assemblage structure. The study found virtually no effects of spatial location on stream insect assemblages across the study drainage system, as evidenced by Mantel tests and canonical correspondence analyses (CCA). The environmental variables were also rather weakly associated with assemblage structure, with the total amount of explained variation ranging from 9.8% to 31.7% in the CCAs. There were no appreciable differences in the amount of environment‐related explained variation in assemblage structure between mayflies, stoneflies, caddisflies, and midges, but some between‐year differences were noticeable in most insect groups. The environmental variables that were significantly related to assemblage structure exhibited some between‐group and between‐year variability. In general, patterns shown by abundance and presence–absence data were highly similar.4. It appears that stream insect assemblages comply with the niche‐based species sorting hypothesis in the context of metacommunity ecology. In contrast, the absence of spatial structuring suggests that stream insect assemblages do not comply with the neutral hypothesis, being not strongly dispersal limited at the within‐drainage basin scale.
Polyphagy, flightlessness, and reproductive output of females: a case study with bagworms (Lepidoptera: Psychidae)
Authors: RHAINDS MARC , LEATHER SIMON R. , SADOF CLIFFORD 
Published: July 2008

Abstract 1. We evaluated the relation between plant‐mediated larval traits and the fitness of female bagworms, Thyridopteryx ephemeraeformis Haworth (Lepidoptera: Psychidae) by sampling 29 populations of bagworms on five plant genera (Thuja, Pinus, Picea, Juniperus, and Gleditsia).2. Compared with those on other genera of plants, female larvae on Thuja attained a larger size at pupation and developed faster. The superior quality of Thuja as a larval food plant resulted in a higher potential fitness of females, as indicated by a low level of pupal mortality and high fecundity.3. The fecundity of females increased with pupal size on different plant genera, and the effect of host plant genus was negligible compared with pupal size.4. The mating success of females varied among different populations (0–37% unmated females), but neither host plant, emergence time, nor the size of females had a significant influence on the proportion of mated females.5. The conversion of adult biomass into reproductive tissue, measured as the ratio between the biomass of eggs divided by the biomass of calling females, increased with the pupal size of females and approached 90% for large females. The high rate of egg conversion in bagworms may be related to the neoteny of short‐lived females that invest little in somatic tissue.