bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of Stimulus Bandwidth on the Imitation of English Fricatives by Normal-Hearing Children
Authors: Stelmachowicz Patricia G. , Nishi Kanae , Choi Sangsook , Lewis Dawna E. , Hoover Brenda M. , Dierking Darcia , Lotto Andrew 
Published: July 2008

Purpose
Recent studies from the authors' laboratory have suggested that reduced audibility in the high frequencies (because of the bandwidth of hearing instruments) may play a role in the delays in phonological development often exhibited by children with hearing impairment. The goal of the current study was to extend previous findings on the effect of bandwidth on fricatives/affricates to more complex stimuli.

Method
Nine fricatives/affricates embedded in 2-syllable nonsense words were filtered at 5 and 10 kHz and presented to normal-hearing 6- to 7-year-olds who repeated words exactly as heard. Responses were recorded for subsequent phonetic and acoustic analyses.

Results
Significant effects of talker gender and bandwidth were found, with better performance for the male talker and the wider bandwidth condition. In contrast to previous studies, relatively small (5%) mean bandwidth effects were observed for /s/ and /z/ spoken by the female talker. Acoustic analyses of stimuli used in the previous and the current studies failed to explain this discrepancy.

Conclusions
It appears likely that a combination of factors (i.e., dynamic cues, prior phonotactic knowledge, and perhaps other unidentified cues to fricative identity) may have facilitated the perception of these complex nonsense words in the current study.
Candidacy for Bilateral Hearing Aids: A Retrospective Multicenter Study
Authors: Boymans Monique , Goverts S. Theo , Kramer Sophia E. , Festen Joost M. , Dreschler Wouter A. 
Published: July 2008

PurposeThe goal of this study was to find factors for refining candidacy criteria for bilateral hearing aid fittings. Clinical files of 1,000 consecutive hearing aid fittings were analyzed.MethodCase history, audiometric, and rehabilitation data were collected from clinical files, and an extensive questionnaire on long-term outcome measures was conducted. After at least 2 years of hearing aid use, 505 questionnaires were returned. In order to compare differences in benefits between unilateral and bilateral fittings, two subgroups were composed in which most relevant variables (age, degree of hearing loss, and audiometric asymmetry) were matched for unilateral fittings (n= 212) and bilateral fittings (n= 477).ResultsThe bilateral group had significantly higher benefit scores than the unilateral group for detection, speech intelligibility in reverberation, and localization, but poorer scores for comfort of loud sounds. The benefit of bilateral hearing aids was not significantly related to the level of technology of the hearing aids.ConclusionThe analysis of the relation between objective parameters and the subjective outcome measures showed that candidacy for a successful bilateral fitting could not be predicted from age, maximum speech intelligibility, employment, exposure to background noise, or social activities.
Subjective and Objective Effects of Fast and Slow Compression on the Perception of Reverberant Speech in Listeners With Hearing Loss
Authors: Shi Lu-Feng , Doherty Karen A. 
Published: July 2008

PurposeThe purpose of the current study was to assess the effect of fast and slow attack/release times (ATs/RTs) on aided perception of reverberant speech in quiet.MethodThirty listeners with mild-to-moderate sensorineural hearing loss were tested monaurally with a commercial hearing aid programmed in 3 AT/RT settings: linear, fast (AT = 9 ms, RT = 90 ms), and slow (AT = 900 ms, RT = 1,500 ms). Stimuli consisted of 200 low-predictability Speech-Perception-in-Noise sentences, presented at 60 dB SPL at 4 reverberation levels (RT60= 0, 0.6, 1.2, and 3.6 s). Listeners were randomly presented with 12 listening conditions (3 AT/RT settings × 4 reverberation levels). Intelligibility scores and clarity ratings of the sentences were obtained.ResultsAided speech intelligibility and clarity significantly decreased as reverberation increased. Both fast and slow ATs/RTs resulted in significantly higher speech intelligibility than linear, but no significant difference was observed between fast and slow ATs/RTs. Clarity rating was similar across 3 settings; however, rating decreased the fastest with fast AT/RT as reverberation increased. Slow AT/RT resulted in significantly higher real-ear aided response than fast AT/RT and linear, despite the same programmed gain for all settings.ConclusionReverberation had a more significant effect on aided speech perception than AT/RT, but fast and slow AT/RT resulted in improved speech intelligibility over linear amplification.
Phylocom: software for the analysis of phylogenetic community structure and trait evolution
Authors: Webb Campbell O. , Ackerly David D. , Kembel Steven W. 
Published: August 2008

Abstract
Motivation: The increasing availability of phylogenetic and trait data for communities of co-occurring species has created a need for software that integrates ecological and evolutionary analyses.
Capabilities: Phylocom calculates numerous metrics of phylogenetic community structure and trait similarity within communities. Hypothesis testing is implemented using several null models. Within the same framework, it measures phylogenetic signal and correlated evolution for species traits. A range of utility functions allow community and phylogenetic data manipulation, tree and trait generation, and integration into scientific workflows.
Availability: Open source at: http://phylodiversity.net/phylocom/
Contact: cwebb@oeb.harvard.edu
VistaClara: an expression browser plug-in for Cytoscape
Authors: Kincaid Robert , Kuchinsky Allan , Creech Michael 
Published: August 2008

Abstract
Summary: VistaClara is a plug-in for Cytoscape which provides a more flexible means to visualize gene and protein expression within a network context. An extended attribute browser is provided in the form of a graphical and interactive permutation matrix that resembles the heat map displays popular in gene-expression analysis. This extended browser permits a variety of display options and interactions not currently available in Cytoscape.
Availability: http://chianti.ucsd.edu/cyto_web/plugins/index.php
Contact: robert_kincaid@agilent.com
Discovery of a SNP in exon 7 of thelipoprotein lipasegene and its association with fatness traits in native and Cherry Valley Peking ducks
Authors: Wu Y. , Zhang H. L. , Wang J. , Liu X. L. 
Published: July 2008

SummaryLipoprotein lipase (LPL) is a multifunctional protein, playing a major role in the hydrolysis of triglycerides in chylomicrons and very low‐density lipoproteins. This study was designed to investigate the effects of variants in exon 7 of theLPLgene on duck growth and fatness traits. Two populations (native and Cherry Valley Peking duck populations) were used in this study. Growth and fatness traits were measured in them. Primers for exon 7 of theLPLgene were designed from chicken genomic and cDNA sequences. Polymorphisms were detected by DNA sequencing, and a PCR–SSCP method was developed to genotype the two populations. The results showed one novel polymorphism: a synonymous alteration in exon 7 of theLPLgene (c.91C>T;EU834120andEU834121). It was associated with abdominal fat weight and percentage of abdominal fat weight of native Peking duck and with percentage of subcutaneous fat plus skin weight and abdominal fat weight of Cherry Valley Peking duck. The alteration in exon 7 ofLPLmay be linked with potential major loci or genes affecting some fatness traits.
Sodium nitrite promotes regional blood flow in patients with sickle cell disease: a phase I/II study
Authors: Mack A. Kyle , McGowan II Vicki R. , Tremonti Carole K. , Ackah Diana , Barnett Christopher , Machado Roberto F. , Gladwin Mark T. , Kato Gregory J. 
Published: July 2008

SummaryIn addition to vaso‐occlusion by sickled erythrocytes, the pathophysiology of sickle cell disease (SCD) is compounded by the diminished bioavailability of nitric oxide (NO), associated with vasoconstriction, endothelial activation and cell adhesion. We tested the ability of sodium nitrite, which can be converted to NO by deoxyhaemoglobin at acid pH and low oxygen tension, to improve blood flow in patients with SCD. In a phase I/II clinical trial, sodium nitroprusside, NG‐monomethyl‐L‐arginine, and sodium nitrite were infused sequentially into the brachial artery in 14 patients at steady state. In a dose‐dependent manner, sodium nitrite infusion rates of 0·4, 4 and 40 μmol/min into the brachial artery augmented mean venous plasma nitrite concentrations (P < 0·0001) and stimulated forearm blood flow up to 77 ± 11% above baseline (P < 0·0001), measured by venous occlusion strain gauge plethysmography. This nitrite response was blunted significantly compared to controls without SCD, as previously seen with other NO donors. Sodium nitrite infusions were well tolerated without hypotension, clinically significant methaemoglobinaemia or other untoward events. The unique pharmacological properties of nitrite as a hypoxia‐potentiated vasodilator and cytoprotective agent in the setting of ischaemia‐reperfusion injury make this anion a plausible NO donor for future clinical trials in SCD.
Rivaroxaban – an oral, direct Factor Xa inhibitor – has potential for the management of patients with heparin‐induced thrombocytopenia
Authors: Walenga Jeanine M. , Prechel Margaret , Jeske Walter P. , Hoppensteadt Debra , Maddineni Jyothi , Iqbal Omer , Messmore Harry L. , Bakhos Mamdouh 
Published: July 2008

SummaryRivaroxaban is an oral, direct activated Factor Xa (FXa) inhibitor in advanced clinical development for the prevention and treatment of thromboembolic disorders. Currently available anticoagulants include unfractionated heparin (UFH) and low molecular weight heparins (LMWHs); however, their use can be restricted by heparin‐induced thrombocytopenia (HIT). HIT is usually caused by the production of antibodies to a complex of heparin and platelet factor‐4 (PF4). This study was performed to evaluate, in vitro, the potential of rivaroxaban as an anticoagulant for the management of patients with HIT. UFH, the LMWH enoxaparin, fondaparinux and the direct thrombin inhibitor argatroban were tested to enable comparative analyses. Rivaroxaban did not cause platelet activation or aggregation in the presence of HIT antibodies, unlike UFH and enoxaparin, suggesting that rivaroxaban does not cross‐react with HIT antibodies. Furthermore, rivaroxaban did not cause the release of PF4 from platelets and did not interact with PF4, unlike UFH and enoxaparin. These findings suggest that rivaroxaban may be a suitable anticoagulant for the management of patients with HIT.
Road age and its importance in earthworm invasion of northern boreal forests
Authors: Cameron Erin K. , Bayne Erin M. 
Published: August 2008

SummaryRoads are an important conduit for the spread of invasive species. Road age is a key factor that could influence the susceptibility of roads to invasion as older roads are typically subject to higher cumulative levels of human disturbance and propagule pressure than younger roads. We investigated the effects of road age on the spread of non‐native earthworms, which act as ecosystem engineers.We sampled earthworms and habitat variables at 98 roads in the boreal forest of Alberta, Canada, to determine the influence of road age on non‐native earthworm occurrence at the landscape level. The extent and rate of local spread were also assessed at seven sites adjacent to old and young roads. Generalized estimating equations and zero‐inflated negative binomial regression were used to analyze landscape‐ and local‐level results, respectively. We used our models to create maps that predict the current and potential future extent of earthworms in north‐eastern Alberta.Probability of earthworm occurrence and extent of spread increased as road age increased. Areas closer to agriculture and towards the south and west of our study area were also significantly more likely to be invaded by earthworms.Our spread model indicated that approximately 9% of the boreal forest of north‐eastern Alberta is likely invaded by earthworms currently. This is projected to increase to 49% of suitable forest habitat over the next 50 years as human development intensifies in this region.Synthesis and applications. Although the effects of roads and linear features are commonly investigated in relation to native species, our results emphasize the importance of considering the impacts of linear feature creation on the spread of invasive species. We demonstrate that road age in particular can be an important factor affecting the spread of invasive species. In the boreal forest, reducing the number of roads being constructed, restricting traffic, and reclaiming temporary roads will be critical to reduce the future extent of earthworm invasions.
Polygynandry and sexual size dimorphism in the sea spiderAmmothea hilgendorfi(Pycnogonida: Ammotheidae), a marine arthropod with brood‐carrying males
Authors: BARRETO FELIPE S , AVISE JOHN C 
Published: August 2008

AbstractSpecies that exhibit uniparental postzygotic investment by males are potentially good systems for investigating the interplay of sexual selection, parental care and mating systems. In all species of sea spiders (Class Pycnogonida), males exclusively provide postzygotic care by carrying fertilized eggs until they hatch. However, the mating systems of sea spiders are poorly known. Here we describe the genetic mating system of the sea spiderAmmothea hilgendorfiby assaying nearly 1400 embryos from a total of 13 egg‐carrying males across four microsatellite markers. We also determine the extent of sexual dimorphism in trunk and leg size, and assess how reproductive success in males varies with these morphological traits. We detected instances of multiple mating by both sexes, indicating that this species has a polygynandrous mating system. Genotypic assays also showed that: males do not mix eggs from different females in the same clusters; eggs from the same female are often partitioned into several clusters along a male's oviger; and clusters are laid chronologically from proximal to distal along ovigers. Females were on average larger than males with respect to leg length and width and trunk length, whereas males had wider trunks. Among the genotyped egg‐carrying males, neither the number of eggs carried nor the number of mates was correlated with body‐size traits. Nevertheless, the high variance in mating success, genetically documented, suggests that males differ in their ability to acquire mates, so future studies are needed to determine what traits are the targets of sexual selection in this species. In addition to providing the first description of the mating system in a sea spider, our study illustrates the potential uses of this group for testing hypotheses from parental investment and sexual selection theories.
Dissecting individual steps of nitrogen transcription factor cooperation in the Aspergillus nidulans nitrate cluster
Authors: Berger Harald , Basheer Asjad , Böck Sandra , Reyes‐Dominguez Yazmid , Dalik Thomas , Altmann Friedrich , Strauss Joseph 
Published: July 2008

SummaryIn the ascomycete fungus Aspergillus nidulans, the transcriptional activation of nitrate assimilating genes (niiA, niaD) depends on the cooperativity between a general nitrogen status‐sensing regulator (the GATA factor AreA) and a pathway‐specific activator (the Zn‐cluster regulator NirA). Because nitrate assimilation leads to intracellular ammonium formation, it is difficult to determine the individual contributions of NirA and AreA in this complex activation/inactivation process. In an attempt to find a suitable marker for the nitrogen status sensed by AreA, we determined the intracellular free amino acid levels on different nitrogen growth conditions. We show that the amount of glutamine (Gln) inversely correlates with all known AreA activities. We find that AreA mediates chromatin remodelling by increasing histone H3 acetylation, a process triggered by transcriptional activation and, independently of transcription, by nitrogen starvation. NirA also participates in the chromatin opening process during nitrate induction but its function is not related to histone acetylation. This chromatin remodelling function of NirA is dispensable only in nitrogen‐starved cells, conditions that lead to elevated AreA chromatin occupancy and histone H3 hyperacetylation. Continuous nitrate assimilation leads to self‐nitrogen metabolite repression but nitrate‐activated NirA is partially compensating for lowered AreA activities under these conditions.
Metabolic adaptation in Cryptococcus neoformans during early murine pulmonary infection
Authors: Hu Guanggan , Cheng Po‐Yan , Sham Anita , Perfect John R. , Kronstad James W. 
Published: July 2008

SummaryThe pathogenic fungus Cryptococcus neoformans generally initiates infection in mammalian lung tissue and subsequently disseminates to the brain. We performed serial analysis of gene expression (SAGE) on C. neoformans cells recovered from the lungs of mice and found elevated expression of genes for central carbon metabolism including functions for acetyl‐CoA production and utilization. Deletion of the highly expressed ACS1 gene encoding acetyl‐CoA synthetase revealed a requirement for growth on acetate and for full virulence. Transcripts for transporters (e.g. for monosaccharides, iron, copper and acetate) and for stress‐response proteins were also elevated thus indicating a nutrient‐limited and hostile host environment. The pattern of regulation was reminiscent of the control of alternative carbon source utilization and stress response by the Snf1 protein kinase in Saccharomyces cerevisiae. A snf1 mutant of C. neoformans showed defects in alternative carbon source utilization, the response to nitrosative stress, melanin production and virulence. However, loss of Snf1 did not influence the expression of a set of genes for carbon metabolism that were elevated upon lung infection. Taken together, the results reveal specific metabolic adaptations of C. neoformans during pulmonary infection and indicate a role for ACS1 and SNF1 in virulence.
Hierarchal type III secretion of translocators and effectors from Escherichia coli O157:H7 requires the carboxy terminus of SepL that binds to Tir
Authors: Wang Dai , Roe Andrew J. , McAteer Sean , Shipston Michael. J. , Gally David L. 
Published: July 2008

SummaryType III secretion (T3S) from enteric bacteria is a co‐ordinated process with a hierarchy of secreted proteins. In enteropathogenic and enterohaemorrhagic Escherichia coli, SepL and SepD are essential for translocator but not effector protein export, but how they function to control this differential secretion is not known. This study has focused on the different activities of SepL including membrane localization, SepD binding, EspD export and Tir secretion regulation. Analyses of SepL truncates demonstrated that the different functions associated with SepL can be separated. In particular, SepL with a deletion of 11 amino acids from the C‐terminus was able to localize to the bacterial membrane, export translocon proteins but not regulate Tir or other effector protein secretion. From the repertoire of effector proteins only Tir was shown to bind directly to full‐length SepL and the C‐terminal 48 amino acids of SepL was sufficient to interact with Tir. By synchronizing induction of T3S, it was evident that the Tir‐binding capacity of SepL is important to delay the release of effector proteins while the EspADB translocon is secreted. The interaction between Tir and SepL is therefore a critical step that controls the timing of T3S in attaching and effacing pathogens.
tmRNA‐dependent trans‐translation is required for sporulation in Bacillus subtilis
Authors: Abe Teppei , Sakaki Kazutaka , Fujihara Ai , Ujiie Hiromi , Ushida Chisato , Himeno Hyouta , Sato Tsutomu , Muto Akira 
Published: July 2008

SummarySpore formation in Bacillus subtilis is significantly impaired by the deletion of the gene for tmRNA (ssrA), which facilitates the trans‐translation reaction that rescues stalled ribosomes and degrades incompletely synthesized peptides. Microscopic analysis revealed that the sporulation of most ΔssrA cells is blocked after forespore formation. Expression analysis of lacZ‐fused genes directed by several RNA polymerase σ factors showed that the synthesis of active σK, encoded by the sigK gene, is predominantly inhibited in ΔssrA cells. The defect in σK synthesis is attributable to a defect in the skin element excision, which generates the sigK gene, caused in turn by reduced expression of SpoIVCA (recombinase) in ΔssrA cells.
Depletion of thiol‐containing proteins in response to quinones in Bacillus subtilis
Authors: Liebeke Manuel , Pöther Dierk‐Christoph , Van Duy Nguyen , Albrecht Dirk , Becher Dörte , Hochgräfe Falko , Lalk Michael , Hecker Michael , Antelmann Haike 
Published: July 2008

SummaryQuinones are highly toxic naturally occurring thiol‐reactive compounds. We have previously described novel pathways for quinone detoxification in the Gram‐positive bacterium Bacillus subtilis. In this study, we have investigated the extent of irreversible and reversible thiol modifications caused in vivo by electrophilic quinones. Exposure to toxic benzoquinone (BQ) concentrations leads to depletion of numerous Cys‐rich cytoplasmic proteins in the proteome of B. subtilis. Mass spectrometry and immunoblot analyses demonstrated that these BQ‐depleted proteins represent irreversibly damaged BQ aggregates that escape the two‐dimensional gel separation. This enabled us to quantify the depletion of thiol‐containing proteins which are the in vivo targets for thiol‐(S)‐alkylation by toxic quinone compounds. Metabolomic approaches confirmed that protein depletion is accompanied by depletion of the low‐molecular‐weight (LMW) thiol cysteine. Finally, no increased formation of disulphide bonds was detected in the thiol‐redox proteome in response to sublethal quinone concentrations. The glyceraldehyde‐3‐phosphate dehydrogenase (GapA) was identified as the only new target for reversible thiol modifications after exposure to toxic quinones. Together our data show that the thiol‐(S)‐alkylation reaction with protein and non‐protein thiols is the in vivo mechanism for thiol depletion and quinone toxicity in B. subtilis and most likely also in other bacteria.
Rapid autocatalytic activation of the M4 metalloprotease aureolysin is controlled by a conserved N‐terminal fungalysin‐thermolysin‐propeptide domain
Authors: Nickerson Nicholas N. , Joag Vineet , McGavin Martin J. 
Published: July 2008

SummaryThe Staphylococcus aureus proteolytic cascade consists of a metalloprotease aureolysin (Aur), which activates a serine protease zymogen proSspA, which in turn activates the SspB cysteine protease. As with other M4 metalloproteases, including elastase of Pseudomonas aeruginosa, the propeptide of proAur contains an N‐terminal fungalysin‐thermolysin‐propeptide (FTP) domain. Autocatalytic activation of proAur was initiated by processing at T85↓L86 in the FTP domain. This differed from the mechanism described for proElastase, where the FTP domain has an RY motif in place of TL86, and processing occurred at the junction of the propeptide and metalloprotease domains, which remained as an inactive complex during passage across the outer membrane. When TL86 in the FTP domain was replaced with RY, an intact N‐terminal propeptide was secreted, but the M4 metalloprotease domain was degraded. Consequently, this segment of the FTP domain promotes intramolecular processing of proAur while bestowing a chaperone function, but discourages processing within the FTP domain of proElastase, where activation must be co‐ordinated with passage across a second membrane. We conclude that the FTP domain of proAur is adapted to facilitate a rapid autocatalytic activation mechanism, consistent with the role or proAur as initiator of the staphylococcal proteolytic cascade.