bluuebunny/crossref_metadata_2025 huggingface dataset:
Noise source identification: A comparison of seven different techniques
Authors: Marroquin Marc
Published: October 2013

One of the most powerful tools that can be used in modern acoustics labs today is noise source identification. By identifying where the noise source(s) may be located, it becomes much easier then to try and reduce/remove/modify the overall dB level of a product. This is typically the end result of a noise reduction program, which is the typical goal of all NVH programs. Over the years many different techniques have become available as technology moves forward. In the beginning it was simple sound-pressure mapping techniques, then sound intensity added a new dimension to the art and science of NSI (noise source identification); last, multichannel applications such as acoustic holography and beamforming have given us tools that far exceed our capabilities of even 10 years ago. As with any advance in technology, each technique has strengths and weaknesses which must be understood to ensure proper measurement and analysis. This paper will offer an overview of seven commonly used NSI techniques along with a comparison of the strengths and weaknesses associated with each technique.
A theoretical elucidation for the experimentally observed backward displacement of waves reflected from an interface having superimposed periodicity
Authors: Declercq Nico F. , Degrieck Joris , Briers Rudy , Leroy Oswald
Published: October 2013

It has been shown experimentally by Breazeale and Torbet [M. A. Breazeale and M. A. Torbett, Appl. Phys. Lett. 29(8), 456–458 (1976)] that a backward beam displacement can occur when a beam is reflected from an interface having superimposed periodicity. The angle at which the phenomenon occurs was predicted by Bertoni and Tamir [H. L. Bertoni and T. Tamir, Appl. Phys. 2, 157–172 (1973)] with a classical approach dated before the inhomogeneous waves era. However, during that era it has been shown by many scientists that the ultimate theory to describe critical phenomena, such as the generation of surface waves or the existence of a beam displacement, is the inhomogeneous wave theory. In the present research, one applies the inhomogeneous wave theory and shows that the theory predicts extremely well the phenomenon of backward displacement when a bounded beam reflects from a periodically rough surface. The agreement reaches far beyond a prediction of the angle of occurrence. One is able to simulate the entire physical phenomenon as it happens in the experiments of Breazeale and Torbet. [Work supported by The Flemish Institute for the Encouragement of the Scientific and Technological Research in Industry (I.W.T.).]
An articulatory and acoustic study of Pima coronals
Authors: Avelino Heriberto , Kim Sahyang
Published: October 2013

The obstruents of Pima, a Uto-Aztecan language spoken in Arizona, have been impressionistically described as involving a contrast between dental and retroflex sounds (Saxton, Saxton, and Enos, 1983; Saxton, 1963). The current study aimed to refine the description of these sounds by investigating palatographic and linguographic data with a concurrent acoustic analysis of recordings from 6 Pima speakers. The results from articulatory data demonstrated that the traditionally so-called retroflex sounds are produced with the apex of the tongue in the alveolar region while the dentals are produced with the blade of the tongue. This evidence suggests that Pima retroflex sounds are not similar to the corresponding sounds in languages such as Hindi or Toda, which are articulated as apical post-alveolars or sub-apical palatal, respectively (Ladefoged and Bhaskararao, 1983; Shalev, Ladefoged, and Bhaskararao, 1994; Ladefoged and Maddieson, 1996). Rather, the Pima retroflexes are more similar to the corresponding sounds of Papago (Dart, 1993). The acoustic analysis showed that the apico-alveolar sounds in contrast to laminal-dentals present a lowering of higher formants (F3, F4), an effect produced by a larger sublingual cavity. The results indicate that in Pima, retroflex sounds are better characterized as apico-alveolar, and the dental as laminal.
Criteria for acoustic discomfort from major internal noises in residential and office spaces
Authors: Jeon Jin Yong
Published: October 2013

Although acoustic discomfort is difficult to qualify (in association with the acoustical characteristics of building spaces), there are some cases where noise limits related to activity disturbance can be clearly defined. In the experiment, the limits of perceptual loudness of noise were investigated in designed rooms similar to residential and office environment. As a result of the floor impact noise evaluations, the limit of lightweight impact noise was around 60 dBA, whereas the limit of heavyweight impact noise was lower. It was revealed that the subjects perceived the loudness of noise from a vacuum cleaner as not irritating. Noises implicated with humans, e.g., walking or talking sounds, are the most annoying in office environment. This paper also presents some definable parameters in the psychoacoustical sense such as Zwicker parameters and ACF/IACF factors along with subjective evaluation.
A novel beamformer array design for noise source location from intermediate measurement distances
Authors: Hald Jorgen , Christensen Jacob J.
Published: October 2013

Very regular beamformer array geometries will have grating lobes in their directivity pattern when applied above a certain frequency. The grating lobes can be suppressed by removing periodicities, typically by the use of random arrays or spiral arrays. Large irregular arrays are, however, difficult to build due to their complicated support structure and cabling. The present paper describes a novel array design, which maintains the low grating lobe level of irregular arrays, but which has a regularity that allows a much simpler support structure and cabling. The performance is compared with that of comparable regular and irregular arrays, and verified through practical measurements. Examples of application to the localization of source of wind noise and high-frequency engine noise will be presented.
Remote sensing and communications in random media
Authors: Papanicolaou George
Published: October 2013

Reliable, high-capacity communications in scattering media can be effectively established with some basic remote sensing techniques involving time reversal. I will formulate these problems and discuss the various mathematical approaches that can be used for analysis. It turns out that stochastic analysis plays an important role and, in some cases, gives very satisfactory results. One such result is the spectacular increase in communications capacity in a richly scattering environment. I will end with a discussion of applications and computational issues that arise in the realistic simulation of communication systems.
Two reasons not to bring your children to cocktail parties
Authors: Nittrouer Susan , Wilhelmsen Melanie , Shapley Kathy , Bodily Kathi , Creutz Tom
Published: October 2013

Two kinds of noise can affect speech perception at cocktail parties: others’ speech (sloping spectrum) and the environment (level spectrum). Recognition scores for phonetically balanced monosyllabic words in level noise at five SNRs for adults and children (4 to 8 years) were collected, and compared to those of Nittrouer and Boothroyd for speech-shaped noise [J. Acoust. Soc. Am. 87, 2705–2715 (1990)]. All listeners showed similar effects of level noise, and children’s results matched those for speech-shaped noise. However, adults showed a 22% advantage for speech-shaped over level noise, suggesting they use high-frequency speech elements not masked by the sloping long-term spectrum of speech. Next labeling of words differing in syllable-final voicing (using vocalic duration and offset transitions, neither high-frequency cues) was examined for children and adults in quiet and in level noise. All listeners performed similarly in quiet. Adults’ results for quiet and noise matched, but children showed a decreased weighting of transitions in noise compared to quiet, suggesting enhanced masking of this information. Thus children’s speech perception in noise is impaired both because they fail to use high-frequency cues available against the background of others’ speech and they experience enhanced masking of formant transitions, their preferred source of information. [Work supported by NIDCD Grant No. DC-00633.]
An approach to real-time magnetic resonance imaging for speech production
Authors: Narayanan Shrikanth , Nayak Krishna , Byrd Dani , Lee Sungbok
Published: October 2013

Magnetic resonance imaging has served as a valuable tool for studying primarily static postures in speech production. Now, recent improvements in imaging techniques, particularly in temporal resolution, are making it possible to examine the dynamics of vocal tract shaping during speech. Examples include Mady et al. (2001, 2002) (8 images/second, T1 fast gradient echo) and Demolin et al. (2000) (4–5 images/second, ultra fast turbo spin echo sequence). The present study uses a non 2D-FFT acquisition strategy (spiral k-space trajectory) on a GE Signa 1.5T CV/i scanner with a low-flip angle spiral gradient echo originally developed for cardiac imaging [Kerr et al. (1997), Nayak et al. (2001)] with reconstruction rates of 8–10 images/second. The experimental stimuli included English sentences varying the syllable position of /n, r, l/ (spoken by 2 subjects) and Tamil sentences varying among five liquids (spoken by one subject). The imaging parameters were the following: 15 deg flip angle, 20-interleaves, 6.7 ms TR, 1.88 mm resolution over a 20 cm FOV, 5 mm slice thickness, and 2.4 ms spiral readouts. Data show clear real-time movements of the lips, tongue and velum. Sample movies and data analysis strategies will be presented. Segmental durations, positions, and inter-articulator timing can all be quantitatively evaluated. [Work supported by NIH.]
Auditory and visual distance perception: The proximity-image effect revisited
Authors: Zahorik Pavel
Published: October 2013

The proximity-image effect [M. B. Gardner, J. Acoust. Soc. Am. 43, 163 (1968)] describes a phenomenon in which the apparent distance of an auditory target is determined by the distance of the nearest plausible visual target rather than by acoustic distance cues. Here this effect is examined using a single visual target (an un-energized loudspeaker) and invisible virtual sound sources. These sources were synthesized from binaural impulse-response measurements at distances ranging from 1 to 5 m (0.25-m steps) in the semi-reverberant room (7.7 m×4.2 m×2.7 m) in which the experiment was conducted. Listeners (n=11) were asked whether or not the auditory target appeared to be at the same distance as the visual target. Within a block of trials, the visual target was placed at a fixed distance of 1.5, 3, or 4.5 m, and the auditory target varied randomly from trial-to-trial over the sample of measurement distances. The resulting psychometric functions are consistent with the proximity-image effect, and can be predicted using a simple model of sensory integration and decision in which perceived auditory space is both compressed in distance and has lower resolution than perceived visual space. [Work supported by NIH-NEI.]
Perturbation analysis of acoustic cues for sound source identification
Authors: Lutfi Robert A.
Published: October 2013

Perturbation analysis has enjoyed recent success in vision as a means of revealing decision processes underlying object identification [J. Vision 2, 1–131 (2002)]. Here it is applied to auditory identification of elementary sound sources and their attributes. The analysis proceeds in two stages: First, listener decision strategy is determined from regression weights relating listener judgments to lawful perturbations in acoustic parameters from theoretical acoustics. Second, limits in processing are identified by comparing the obtained weights to those of a hypothetical observer who bases decisions on acoustic information intrinsic to the source attribute(s) being judged. The approach represents a significant advance over past methods that infer decision strategy from performance accuracy or from the effect of placing acoustic cues in unlawful opposition. Initial studies are reviewed revealing a complex pattern of results in which decision strategy is based on intrinsic acoustic information in some conditions but not in others, and in which there are sometimes individual differences in decision strategy that yield the same level of identification performance. [Work supported by NIDCD.]
Decay of Fecal Indicator Bacterial Populations and Bovine-Associated Source-Tracking Markers in Freshly Deposited Cow Pats
Authors: Oladeinde Adelumola , Bohrmann Thomas , Wong Kelvin , Purucker S. T. , Bradshaw Ken , Brown Reid , Snyder Blake , Molina Marirosa
Published: October 2013

Understanding the survival of fecal indicator bacteria (FIB) and microbial source-tracking (MST) markers is critical to developing pathogen fate and transport models. Although pathogen survival in water microcosms and manure-amended soils is well documented, little is known about their survival in intact cow pats deposited on pastures. We conducted a study to determine decay rates of fecal indicator bacteria (
Escherichia coli
and enterococci) and bovine-associated MST markers (CowM3, Rum-2-bac, and GenBac) in 18 freshly deposited cattle feces from three farms in northern Georgia. Samples were randomly assigned to shaded or unshaded treatment in order to determine the effects of sunlight, moisture, and temperature on decay rates. A general linear model (GLM) framework was used to determine decay rates. Shading significantly decreased the decay rate of the
E. coli
population (
P
< 0.0001), with a rate of −0.176 day
−1
for the shaded treatment and −0.297 day
−1
for the unshaded treatment. Shading had no significant effect on decay rates of enterococci, CowM3, Rum-2-bac, and GenBac (
P
> 0.05). In addition,
E. coli
populations showed a significant growth rate (0.881 day
−1
) in the unshaded samples during the first 5 days after deposition. UV-B was the most important parameter explaining the decay rate of
E. coli
populations. A comparison of the decay behaviors among all markers indicated that enterococcus concentrations exhibit a better correlation with the MST markers than
E. coli
concentrations. Our results indicate that bovine-associated MST markers can survive in cow pats for at least 1 month after excretion, and although their decay dynamic differs from the decay dynamic of
E. coli
populations, they seem to be reliable markers to use in combination with enterococci to monitor fecal pollution from pasture lands.
Extracellular Electron Transport-Mediated Fe(III) Reduction by a Community of Alkaliphilic Bacteria That Use Flavins as Electron Shuttles
Authors: Fuller Samuel J. , McMillan Duncan G. G. , Renz Marc B. , Schmidt Martin , Burke Ian T. , Stewart Douglas I.
Published: October 2013

The biochemical and molecular mechanisms used by alkaliphilic bacterial communities to reduce metals in the environment are currently unknown. We demonstrate that an alkaliphilic (pH > 9) consortium dominated by
Tissierella
,
Clostridium
, and
Alkaliphilus
spp. is capable of using iron (Fe
3+
) as a final electron acceptor under anaerobic conditions. Iron reduction is associated with the production of a freely diffusible species that, upon rudimentary purification and subsequent spectroscopic, high-performance liquid chromatography, and electrochemical analysis, has been identified as a flavin species displaying properties indistinguishable from those of riboflavin. Due to the link between iron reduction and the onset of flavin production, it is likely that riboflavin has an import role in extracellular metal reduction by this alkaliphilic community.
Single-Cell Analyses Revealed Transfer Ranges of IncP-1, IncP-7, and IncP-9 Plasmids in a Soil Bacterial Community
Authors: Shintani Masaki , Matsui Kazuhiro , Inoue Jun-ichi , Hosoyama Akira , Ohji Shoko , Yamazoe Atsushi , Nojiri Hideaki , Kimbara Kazuhide , Ohkuma Moriya
Published: October 2013

The conjugative transfer ranges of three different plasmids of the incompatibility groups IncP-1 (pBP136), IncP-7 (pCAR1), and IncP-9 (NAH7) were investigated in soil bacterial communities by culture-dependent and culture-independent methods.
Pseudomonas putida
, a donor of each plasmid, was mated with soil bacteria, and green fluorescent protein (GFP), encoded on the plasmid, was used as a reporter protein for successful transfer. GFP-expressing transconjugants were detected and separated at the single-cell level by flow cytometry. Each cell was then analyzed by PCR and sequencing of its 16S rRNA gene following either whole-genome amplification or cultivation. A large number of bacteria within the phylum
Proteobacteria
was identified as transconjugants for pBP136 by both culture-dependent and culture-independent methods. Transconjugants belonging to the phyla
Actinobacteria
,
Bacteroidetes
, and
Firmicutes
were detected only by the culture-independent method. Members of the genus
Pseudomonas
(class
Gammaproteobacteria
) were identified as major transconjugants of pCAR1 and NAH7 by both methods, whereas
Delftia
species (class
Betaproteobacteria
) were detected only by the culture-independent method. The transconjugants represented a minority of the soil bacteria. Although pCAR1-containing
Delftia
strains could not be cultivated after a one-to-one filter mating assay between the donor and cultivable
Delftia
strains as recipients, fluorescence
in situ
hybridization detected pCAR1-containing
Delftia
cells, suggesting that
Delftia
was a “transient” host of pCAR1.
Transferable Denitrification Capability of Thermus thermophilus
Authors: Alvarez Laura , Bricio Carlos , Blesa Alba , Hidalgo Aurelio , Berenguer José
Published: October 2013

Laboratory-adapted strains of
Thermus
spp. have been shown to require oxygen for growth, including the model strains
T. thermophilus
HB27 and HB8. In contrast, many isolates of this species that have not been intensively grown under laboratory conditions keep the capability to grow anaerobically with one or more electron acceptors. The use of nitrogen oxides, especially nitrate, as electron acceptors is one of the most widespread capabilities among these facultative strains. In this process, nitrate is reduced to nitrite by a reductase (Nar) that also functions as electron transporter toward nitrite and nitric oxide reductases when nitrate is scarce, effectively replacing respiratory complex III. In many
T. thermophilus
denitrificant strains, most electrons for Nar are provided by a new class of NADH dehydrogenase (Nrc). The ability to reduce nitrite to NO and subsequently to N
2
O by the corresponding Nir and Nor reductases is also strain specific. The genes encoding the capabilities for nitrate (
nar
) and nitrite (
nir
and
nor
) respiration are easily transferred between
T. thermophilus
strains by natural competence or by a conjugation-like process and may be easily lost upon continuous growth under aerobic conditions. The reason for this instability is apparently related to the fact that these metabolic capabilities are encoded in gene cluster islands, which are delimited by insertion sequences and integrated within highly variable regions of easily transferable extrachromosomal elements. Together with the chromosomal genes, these plasmid-associated genetic islands constitute the extended pangenome of
T. thermophilus
that provides this species with an enhanced capability to adapt to changing environments.
Estimating the Prevalence of Potential Enteropathogenic Escherichia coli and Intimin Gene Diversity in a Human Community by Monitoring Sanitary Sewage
Authors: Yang Kun , Pagaling Eulyn , Yan Tao
Published: October 2013

Presently, the understanding of bacterial enteric diseases in the community and their virulence factors relies almost exclusively on clinical disease reporting and examination of clinical pathogen isolates. This study aimed to investigate the feasibility of an alternative approach that monitors potential enteropathogenic
Escherichia coli
(EPEC) and enterohemorrhagic
E. coli
(EHEC) prevalence and intimin gene (
eae
) diversity in a community by directly quantifying and characterizing target virulence genes in the sanitary sewage. The quantitative PCR (qPCR) quantification of the
eae
,
stx
1
, and
stx
2
genes in sanitary sewage samples collected over a 13-month period detected
eae
in all 13 monthly sewage samples at significantly higher abundance (93 to 7,240 calibrator cell equivalents [CCE]/100 ml) than
stx
1
and
stx
2
, which were detected sporadically. The prevalence level of potential EPEC in the sanitary sewage was estimated by calculating the ratio of
eae
to
uidA
, which averaged 1.0% (σ = 0.4%) over the 13-month period. Cloning and sequencing of the
eae
gene directly from the sewage samples covered the majority of the
eae
diversity in the sewage and detected 17 unique
eae
alleles belonging to 14 subtypes. Among them,
eae
-β2 was identified to be the most prevalent subtype in the sewage, with the highest detection frequency in the clone libraries (41.2%) and within the different sampling months (85.7%). Additionally, sewage and environmental
E. coli
isolates were also obtained and used to determine the detection frequencies of the virulence genes as well as
eae
genetic diversity for comparison.
Evaluating Gulls as Potential Vehicles of Salmonella enterica Serotype Newport (JJPX01.0061) Contamination of Tomatoes Grown on the Eastern Shore of Virginia
Authors: Gruszynski Karen , Pao Steven , Kim Chyer , Toney Denise M. , Wright Kim , Colón Ana , Engelmeyer T. , Levine Seth J.
Published: October 2013

Salmonella enterica
serovar Newport pattern JJPX01.0061 has been identified as causing several multistate outbreaks in the last 10 years, primarily due to contamination of tomatoes grown in Virginia. The goal of this study was to evaluate gulls as a potential vehicle of
S
. Newport pattern 61 contamination for tomatoes grown on the Eastern Shore of Virginia. Gull fecal samples were collected at four sites in eastern Virginia for 3 months (May to July) in 2012, resulting in 360 samples, among which
Salmonella
was isolated from 62 samples. Twenty-two serotypes and 26 pulsed-field gel electrophoresis DNA fingerprint patterns, including
S
. Newport pattern 61, were identified. All of the patterns that were isolated multiple times, with the exception of
S
. Newport patterns JJPX01.0030 and JJPX01.0061, were clustered in time and geographical location. These results strongly suggest that both patterns of
S
. Newport are endemic to sites on the Eastern Shore where gulls were sampled. This study provides additional information regarding the epidemiology of
S
. Newport pattern 61 in Virginia and how tomatoes sold interstate may become contaminated in the field.
The Ability of Bifidobacteria To Degrade Arabinoxylan Oligosaccharide Constituents and Derived Oligosaccharides Is Strain Dependent
Authors: Rivière Audrey , Moens Frédéric , Selak Marija , Maes Dominique , Weckx Stefan , De Vuyst Luc
Published: October 2013

Arabinoxylan oligosaccharides (AXOS) are prebiotic carbohydrates with promising health-promoting properties that stimulate the activity of specific colon bacteria, in particular bifidobacteria. However, the mechanisms by which bifidobacterial strains break down these compounds in the colon is still unknown. This study investigates AXOS consumption of a large number of bifidobacterial strains (36), belonging to 11 different species, systematically. To determine their degradation mechanisms, all strains were grown on a mixture of arabinose and xylose, xylo-oligosaccharides, and complex AXOS molecules as the sole added energy sources. Based on principal component and cluster analyses of their different arabinose substituent and/or xylose backbone consumption patterns, five clusters that were species independent could be distinguished among the bifidobacterial strains tested. In parallel, the strains were screened for the presence of genes encoding several putative AXOS-degrading enzymes, but no clear-cut correlation could be made with the different degradation mechanisms. The intra- and interspecies differences in the consumption patterns of AXOS indicate that bifidobacterial strains could avoid competition among each other or even could cooperate jointly to degrade these complex prebiotics. The knowledge gained on the AXOS degradation mechanisms in bifidobacteria can be of importance in the rational design of prebiotics with tailor-made composition and thus increased specificity in the colon.
Host Specificity and Source of Enterocytozoon bieneusi Genotypes in a Drinking Source Watershed
Authors: Guo Yaqiong , Alderisio Kerri A. , Yang Wenli , Cama Vitaliano , Feng Yaoyu , Xiao Lihua
Published: October 2013

To assess the host specificity of
Enterocytozoon bieneusi
and to track the sources of
E. bieneusi
contamination, we genotyped
E. bieneusi
in wildlife and stormwater from the watershed of New York City's source water, using ribosomal internal transcribed spacer (ITS)-based PCR and sequence analyses. A total of 255 specimens from 23 species of wild mammals and 67 samples from stormwater were analyzed. Seventy-four (29.0%) of the wildlife specimens and 39 (58.2%) of the stormwater samples from streams were PCR positive. Altogether, 20
E. bieneusi
genotypes were found, including 8 known genotypes and 12 new ones. Sixteen and five of the genotypes were seen in animals and stormwater from the watershed, respectively, with WL4 being the most common genotype in both animals (35 samples) and stormwater (23 samples). The 20
E. bieneusi
genotypes belonged to five genogroups (groups 1, 3, 4, and 7 and an outlier), with only 23/113 (20.4%)
E. bieneusi
-positive samples belonging to zoonotic genogroup 1 and 3/20 genotypes ever being detected in humans. The two genogroups previously considered host specific, groups 3 and 4, were both detected in multiple groups of mammals. Thus, with the exception of the type IV, Peru11, and D genotypes, which were detected in only 7, 5, and 2 animals, respectively, most
E. bieneusi
strains in most wildlife samples and all stormwater samples in the watershed had no known public health significance, as these types have not previously been detected in humans. The role of different species of wild mammals in the contribution of
E. bieneusi
contamination in stormwater was supported by determinations of host-adapted
Cryptosporidium
species/genotypes in the same water samples. Data from this study indicate that the host specificity of
E. bieneusi
group 3 is broader than originally thought, and wildlife is the main source of
E. bieneusi
in stormwater in the watershed.
Impact of Substratum Surface on Microbial Community Structure and Treatment Performance in Biological Aerated Filters
Authors: Kim Lavane , Pagaling Eulyn , Zuo Yi Y. , Yan Tao
Published: October 2013

The impact of substratum surface property change on biofilm community structure was investigated using laboratory biological aerated filter (BAF) reactors and molecular microbial community analysis. Two substratum surfaces that differed in surface properties were created via surface coating and used to develop biofilms in test (modified surface) and control (original surface) BAF reactors. Microbial community analysis by 16S rRNA gene-based PCR-denaturing gradient gel electrophoresis (DGGE) showed that the surface property change consistently resulted in distinct profiles of microbial populations during replicate reactor start-ups. Pyrosequencing of the bar-coded 16S rRNA gene amplicons surveyed more than 90% of the microbial diversity in the microbial communities and identified 72 unique bacterial species within 19 bacterial orders. Among the 19 orders of bacteria detected,
Burkholderiales
and
Rhodocyclales
of the
Betaproteobacteria
class were numerically dominant and accounted for 90.5 to 97.4% of the sequence reads, and their relative abundances in the test and control BAF reactors were different in consistent patterns during the two reactor start-ups. Three of the five dominant bacterial species also showed consistent relative abundance changes between the test and control BAF reactors. The different biofilm microbial communities led to different treatment efficiencies, with consistently higher total organic carbon (TOC) removal in the test reactor than in the control reactor. Further understanding of how surface properties affect biofilm microbial communities and functional performance would enable the rational design of new generations of substrata for the improvement of biofilm-based biological treatment processes.
Novel Characteristics of Succinate Coenzyme A (Succinate-CoA) Ligases: Conversion of Malate to Malyl-CoA and CoA-Thioester Formation of Succinate Analogues
In Vitro
Authors: Nolte Johannes Christoph , Schürmann Marc , Schepers Catherine-Louise , Vogel Elvira , Wübbeler Jan Hendrik , Steinbüchel Alexander
Published: October 2013

Three succinate coenzyme A (succinate-CoA) ligases (SucCD) from
Escherichia coli
,
Advenella mimigardefordensis
DPN7
T
, and
Alcanivorax borkumensis
SK2 were characterized regarding their substrate specificity concerning succinate analogues. Previous studies had suggested that SucCD enzymes might be promiscuous toward succinate analogues, such as itaconate and 3-sulfinopropionate (3SP). The latter is an intermediate of the degradation pathway of 3,3′-dithiodipropionate (DTDP), a precursor for the biotechnical production of polythioesters (PTEs) in bacteria. The
sucCD
genes were expressed in
E. coli
BL21(DE3)/pLysS. The SucCD enzymes of
E. coli
and
A. mimigardefordensis
DPN7
T
were purified in the native state using stepwise purification protocols, while SucCD from
A. borkumensis
SK2 was equipped with a C-terminal hexahistidine tag at the SucD subunit. Besides the preference for the physiological substrates succinate, itaconate, ATP, and CoA, high enzyme activity was additionally determined for both enantiomeric forms of malate, amounting to 10 to 21% of the activity with succinate.

K
m

values ranged from 2.5 to 3.6 mM for
l
-malate and from 3.6 to 4.2 mM for
d
-malate for the SucCD enzymes investigated in this study. As
l
-malate-CoA ligase is present in the serine cycle for assimilation of C
1
compounds in methylotrophs, structural comparison of these two enzymes as members of the same subsubclass suggested a strong resemblance of SucCD to
l
-malate-CoA ligase and gave rise to the speculation that malate-CoA ligases and succinate-CoA ligases have the same evolutionary origin. Although enzyme activities were very low for the additional substrates investigated, liquid chromatography/electrospray ionization-mass spectrometry analyses proved the ability of SucCD enzymes to form CoA-thioesters of adipate, glutarate, and fumarate. Since all SucCD enzymes were able to activate 3SP to 3SP-CoA, we consequently demonstrated that the activation of 3SP is not a unique characteristic of the SucCD from
A. mimigardefordensis
DPN7
T
. The essential role of
sucCD
in the activation of 3SP
in vivo
was proved by genetic complementation.
Nonclinical and Clinical Enterococcus faecium Strains, but Not Enterococcus faecalis Strains, Have Distinct Structural and Functional Genomic Features
Authors: Kim Eun Bae , Marco Maria L.
Published: October 2013

Certain strains of
Enterococcus faecium
and
Enterococcus faecalis
contribute beneficially to animal health and food production, while others are associated with nosocomial infections. To determine whether there are structural and functional genomic features that are distinct between nonclinical (NC) and clinical (CL) strains of those species, we analyzed the genomes of 31
E. faecium
and 38
E. faecalis
strains. Hierarchical clustering of 7,017 orthologs found in the
E. faecium
pangenome revealed that NC strains clustered into two clades and are distinct from CL strains. NC
E. faecium
genomes are significantly smaller than CL genomes, and this difference was partly explained by significantly fewer mobile genetic elements (ME), virulence factors (VF), and antibiotic resistance (AR) genes.
E. faecium
ortholog comparisons identified 68 and 153 genes that are enriched for NC and CL strains, respectively. Proximity analysis showed that CL-enriched loci, and not NC-enriched loci, are more frequently colocalized on the genome with ME. In CL genomes, AR genes are also colocalized with ME, and VF are more frequently associated with CL-enriched loci. Genes in 23 functional groups are also differentially enriched between NC and CL
E. faecium
genomes. In contrast, differences were not observed between NC and CL
E. faecalis
genomes despite their having larger genomes than
E. faecium
. Our findings show that unlike
E. faecalis
, NC and CL
E. faecium
strains are equipped with distinct structural and functional genomic features indicative of adaptation to different environments.
Characterization of Two Mitochondrial Flavin Adenine Dinucleotide-Dependent Glycerol-3-Phosphate Dehydrogenases in Trypanosoma brucei
Authors: Škodová Ingrid , Verner Zdeněk , Bringaud Fréderic , Fabian Peter , Lukeš Julius , Horváth Anton
Published: October 2013

Glycerol-3-phosphate dehydrogenases (G3PDHs) constitute a shuttle that serves for regeneration of NAD
+
reduced during glycolysis. This NAD-dependent enzyme is employed in glycolysis and produces glycerol-3-phosphate from dihydroxyacetone phosphate, while its flavin adenine dinucleotide (FAD)-dependent homologue catalyzes a reverse reaction coupled to the respiratory chain.
Trypanosoma brucei
possesses two FAD-dependent G3PDHs. While one of them (mitochondrial G3PDH [mtG3PDH]) has been attributed to the mitochondrion and seems to be directly involved in G3PDH shuttle reactions, the function of the other enzyme (putative G3PDH [putG3PDH]) remains unknown. In this work, we used RNA interference and protein overexpression and tagging to shed light on the relative contributions of both FAD-G3PDHs to overall cellular metabolism. Our results indicate that mtG3PDH is essential for the bloodstream stage of
T. brucei
, while in the procyclic stage the enzyme is dispensable. Expressed putG3PDH-V5 was localized to the mitochondrion, and the data obtained by digitonin permeabilization, Western blot analysis, and immunofluorescence indicate that putG3PDH is located within the mitochondrion.
Binding and Transcriptional Regulation by 14-3-3 (Bmh) Proteins Requires Residues Outside of the Canonical Motif
Authors: Parua Pabitra K. , Young Elton T.
Published: October 2013

Evolutionarily conserved 14-3-3 proteins have important functions as dimers in numerous cellular signaling processes, including regulation of transcription. Yeast 14-3-3 proteins, known as Bmh, inhibit a post-DNA binding step in transcription activation by Adr1, a glucose-regulated transcription factor, by binding to its regulatory domain, residues 226 to 240. The domain was originally defined by regulatory mutations,
ADR1

c

alleles that alter activator-dependent gene expression. Here, we report that
ADR1

c

alleles and other mutations in the regulatory domain impair Bmh binding and abolish Bmh-dependent regulation both directly and indirectly. The indirect effect is caused by mutations that inhibit phosphorylation of Ser230 and thus inhibit Bmh binding, which requires phosphorylated Ser230. However, several mutations inhibit Bmh binding without inhibiting phosphorylation and thus define residues that provide important interaction sites between Adr1 and Bmh. Our proposed model of the Adr1 regulatory domain bound to Bmh suggests that residues Ser238 and Tyr239 could provide cross-dimer contacts to stabilize the complex and that this might explain the failure of a dimerization-deficient Bmh mutant to bind Adr1 and to inhibit its activity. A bioinformatics analysis of Bmh-interacting proteins suggests that residues outside the canonical 14-3-3 motif might be a general property of Bmh target proteins and might help explain the ability of 14-3-3 to distinguish target and nontarget proteins. Bmh binding to the Adr1 regulatory domain, and its failure to bind when mutations are present, explains at a molecular level the transcriptional phenotype of
ADR1

c

mutants.
Problems Caused by Heterogeneity in Meta-Analysis: A Case Study of Acupuncture Trials
Authors: Prady Stephanie L , Burch Jane , Crouch Simon , MacPherson Hugh
Published: October 2013

Objectives

To illustrate the pitfalls of using meta-analysis to combine estimates of effect in trials that are highly varied and have a high potential for bias.

Methods

We used a random-effects meta-analysis to pool the results of 51 sham-controlled acupuncture trials of chronic pain published in English before 2008 and explored the heterogeneity using meta-regression. We repeated the process on a subset of these trials that used a visually credible non-penetrating sham device as control (N = 12).

Results

In both analyses there were high levels of heterogeneity and many studies were at risk from potential bias. The heterogeneity was not explained by meta-regression.

Conclusions

Trials of interventions that have high potential for bias, such as many in the acupuncture literature, do not meet the assumptions of the statistical procedure that underlie random-effects meta-analysis. Even in the absence of bias, heterogeneity in meta-analyses is not accounted for by the CIs around the pooled estimate.
Adrenal ganglioneuroma in a patient with polycystic ovarian disease (PCOD): a rare association
Authors: Kumar Arvind , Singh Vishwajeet , Sankhwar Satyanarayan , Babu Suresh
Published: October 2013

Adrenal ganglioneuromas are rare, benign incidentalomas of a neural crest origin. A majority of these tumours are clinically silent and discovered on imaging for unrelated reasons. Polycystic ovarian disease (PCOD) is an endocrine disorder characterised by bilateral polycystic ovaries, anovulation leading to infertility, irregular menstrual cycles and features of androgen hormone excess. Herein we report a rare case of adrenal ganglioneuroma in a 14-year-old girl with PCOD. She was referred to us by the gynaecologist after incidental detection of adrenal mass on ultrasonography. Except for raised 24 h urinary metanephrines, rest of the hormones measured were in normal range. Transperitoneal adrenalectomy was performed and histopathology was suggestive of ganglioneuroma. Postoperative recovery was excellent and she is doing well. To our knowledge it is the first such type of case to be reported.
Multicomponent intervention to reduce daily sedentary time: a randomised controlled trial
Authors: Carr Lucas J , Karvinen Kristina , Peavler Mallory , Smith Rebecca , Cangelosi Kayla
Published: October 2013

Objectives

To test the efficacy of a multicomponent technology intervention for reducing daily sedentary time and improving cardiometabolic disease risk among sedentary, overweight university employees.

Design

Blinded, randomised controlled trial.

Setting

A large south-eastern university in the USA.

Participants

49 middle-aged, primarily female, sedentary and overweight adults working in sedentary jobs enrolled in the study. A total of 40 participants completed the study.

Interventions

Participants were randomised to either: (1) an intervention group (N=23; 47.6+9.9 years; 94.1% female; 33.2+4.5 kg/m2); (2) or wait-list control group (N=17; 42.6+8.9 years; 86.9% female; 31.7+4.9 kg/m2). The intervention group received a theory-based, internet-delivered programme, a portable pedal machine at work and a pedometer for 12 weeks. The wait-list control group maintained their behaviours for 12 weeks.

Outcome measures

Primary (sedentary and physical activity behaviour measured objectively through StepWatch) and secondary (heart rate, blood pressure, height, weight, waist circumference, per cent body fat, cardiorespiratory fitness, fasting lipids) outcomes were measured at baseline and postintervention (12 weeks). Exploratory outcomes including intervention compliance and process evaluation measures were also assessed postintervention.

Results

Compared to controls, the intervention group reduced daily sedentary time (mean change (95%CI): −58.7 min/day (−118.4 to 0.99; p<0.01)) after adjusting for baseline values and monitor wear time. Intervention participants logged on to the website 71.3% of all intervention days, used the pedal machine 37.7% of all working intervention days and pedalled an average of 31.1 min/day.

Conclusions

These findings suggest that the intervention was engaging and resulted in reductions in daily sedentary time among full-time sedentary employees. These findings hold public health significance due to the growing number of sedentary jobs and the potential of these technologies in large-scale worksite programmes.

Trial Registration

ClinicalTrials.gov #NCT01371084.
Continuation rates of oral hormonal contraceptives in a cohort of first-time users: a population-based registry study, Sweden 2005–2010
Authors: Josefsson Ann , Wiréhn Ann-Britt , Lindberg Malou , Foldemo Anniqa , Brynhildsen Jan
Published: October 2013

Objective

To investigate if continuation rates in first-time users of oral hormonal contraceptives differed between different formulations and to measure if the rates were related to the prescribing categories, that is, physicians and midwives.

Design

A longitudinal national population-based registry study.

Setting

The Swedish prescribed drug register.

Participants

All women born between 1977 and 1994 defined as first-time users of hormonal contraceptives from 2007 to 2009 (n=226 211).

Main outcome measures

A tendency to switch the type of hormonal contraceptive within 6 months use and repeated dispensation identical to the first were estimated as percentages and relative risks (RRs). Physicians’ and midwives’ prescription patterns concerning the women's continuation rates of oral hormonal contraceptive type.

Results

In Sweden, there were 782 375 women born between 1977 and 1994 at the time of the study. Of these, 226 211 women were identified as first-time users of hormonal contraceptives. Ethinylestradiol+levonorgestrel, desogestrel-only and ethinylestradiol+drospirenone were the hormonal contraceptives most commonly dispensed to first-time users at rates of 43.3%, 24.4% and 11.1%, respectively. The overall rate of switching contraceptive types in the first 6 months was 11.3%, which was highest for desogestrel-only (14.3%) and lowest for ethinylestradiol+drospirenone (6.6%). The switching rate for all three products was highest in the 16-year to 19-year age group. Having a repeated dispensation identical to the initial dispensation was highest for users of ethinylestradiol either combined with levonorgestrel or drospirenone, 81.4% and 81.2%, respectively, whereas this rate for the initial desogestrel-only users was 71.5%. The RR of switching of contraceptive type within the first 6 months was 1.35 (95% CI 1.32 to 1.39) for desogestrel-only and 0.63 (0.59 to 0.66) for ethinylestradiol+drospirenone compared with ethinylestradiol+levonorgestrel as the reference category. There were no differences in the women's continuation rates depending on the prescriber categories.

Conclusions

Desogestrel-only users conferred the highest switcher rate to another hormonal contraceptive within a 6-month period. Users of ethinylestradiol+levonorgestrel were more prone to switch to another product within 6 months than women using ethinylestradiol+drospirenone. These findings may be of clinical importance when tailoring hormonal contraceptives on an individual basis.
Matrix-assisted laser desorption ionisation time-of-flight mass spectrometry for identification of clinically significant bacteria that are difficult to identify in clinical laboratories
Authors: Lau Susanna K P , Tang Bone S F , Teng Jade L L , Chan Tsz-Ming , Curreem Shirly O T , Fan Rachel Y Y , Ng Ricky H Y , Chan Jasper F W , Yuen Kwok-Yung , Woo Patrick C Y
Published: October 2013

Aims

Although the revolutionary matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS) has been evaluated for identification of various groups of bacteria, its application in bacteria that are ‘difficult-to-identify’ by phenotypic tests has been less well studied. We aim to evaluate the usefulness of MALDI-TOF MS for identification of ‘difficult-to-identify’ bacterial isolates.

Methods

We evaluated the performance of the Bruker MALDI-TOF MS system for a collection of 67 diverse clinically important bacterial isolates that were less commonly encountered, possessed ambiguous biochemical profiles or belonged to newly discovered species. The results were compared with 16S rRNA gene sequencing as a reference method for species identification.

Results

Using 16S rRNA gene sequencing as the reference method, 30 (45%) isolates were identified correctly to species level (score ≥2.0), 20 (30%) were only identified to genus level (score ≥1.7), four (6%) were misidentified (incorrect species with score ≥2.0 or incorrect genus with score ≥1.7) and 13 (19%) showed ‘no identification’ (score <1.7). Aerobic Gram-positive bacteria showed the highest percentage of correct species identification, followed by aerobic Gram-negative, anaerobic Gram-positive and anaerobic Gram-negative bacteria. Sixteen isolates identified to genus level actually showed the correct species but with scores below the threshold for species identification. Most isolates which showed ‘no identification’ were due to the absence of the corresponding species in the Bruker database.

Conclusions

Expansion of commercial databases to include reference spectra of less commonly encountered and newly discovered species and to increase available spectra for each species is required to improve the accuracy of MALDI-TOF MS for identifying ‘difficult-to-identify’ bacteria.
Evaluation of MR safety for a new liquid embolic device
Authors: Audet-Griffin Annabelle J , Pakbaz Sean , Shellock Frank G
Published: October 2013

Background

As an alternative to conventional treatments, a new liquid embolic device (Neucrylate) may be used to treat aneurysms or arteriovenous malformation (AVMs). Because this device contains metal for opacification, an investigation was performed to evaluate MRI issues for this liquid embolic device.

Methods

The liquid embolic device was evaluated for magnetic field interactions (translational attraction and torque) at 3 T, MRI-related heating at 1.5 T/64 MHz and 3 T/128 MHz and artifacts at 3 T using standardized techniques. In each case, MRI-related heating was assessed with the liquid embolic device in a gelled saline-filled phantom and MRI was performed using relatively high levels of radiofrequency energy. Artifacts were characterized using T1-weighted spin echo and gradient echo pulse sequences. Additionally, conductivity (ie, electrical resistance) measurements were recorded.

Results

The liquid embolic device exhibited no magnetic field interactions. Heating was at the same level as background temperature rises (ie, the temperatures recorded without the liquid embolic device present in the phantom) under 1.5 T/64 MHz (highest temperature change 1.4°C) and 3 T/128 MHz (highest temperature change 1.8°C) MRI conditions. Artifacts were small in relation to the size and shape of the liquid embolic device. The device was found to pose no risks with regard to the conductivity of the material.

Conclusions

These findings demonstrate that it is acceptable for a patient with this new liquid embolic device to undergo MRI at ≤3 T. Notably, the associated artifacts are unlikely to create issues for diagnostic MRI examinations.