bluuebunny/crossref_metadata_2025 huggingface dataset:
Computational Study of Hemodynamic Effects of Abnormal E/A Ratio on Left Ventricular Filling
Authors: Zheng Xudong , Xue Qian , Mittal Rajat
Published: March 2014

Three-dimensional numerical simulations are employed to investigate the hemodynamic effects of abnormal E/A ratios on left ventricular filling. The simulations are performed in a simplified geometric model of the left ventricle (LV) in conjunction with a specified endocardial motion. The model has been carefully designed to match the important geometric and flow parameters under the physiological conditions. A wide range of E/A ratios from 0 to infinity is employed with the aim to cover all the possible stages of left ventricle diastolic dysfunction (DD). The effects of abnormal E/A ratios on vortex dynamics, flow propagation velocity, energy consumption as well as flow transport and mixing are extensively discussed. Our results are able to confirm some common findings reported by the previous studies, and also uncover some interesting new features.
Bipolar Electrosurgical Vessel-Sealing Device With Compressive Force Monitoring
Authors: Chen Roland K. , Chastagner Matthew W. , Geiger James D. , Shih Albert J.
Published: March 2014

Bipolar electrosurgical vessel sealing is commonly used in surgery to perform hemostasis. The electrode compressive force is demonstrably an important factor affecting the vessel seal burst pressure, an index of the seal quality. Using a piezoresistive force sensor attached to the handle of a laparoscopic surgical device, applied handle force was measured and used to predict the electrosurgical vessel compressive force and the pressure at the electrode. The sensor enables the monitoring of vessel compressive force during surgery. Four levels of compressive force were applied to seal three types of porcine vessels (carotid artery, femoral artery, and jugular vein). The burst pressure of the vessel seal was tested to evaluate the seal quality. Compressive pressure was found to be a statistically significant factor affecting burst pressure for femoral arteries and jugular veins. Vessels sealed with low compressive pressure (<300 kPa) have a higher failure rate (burst pressure < 100 mm Hg) than vessels sealed with high compressive pressure. An adequate compressive force is required to generate the compressive pressure needed to form a seal with high burst pressure. A laparoscopic surgical device with compressive force monitoring capability can help ensure adequate compressive pressure, vessel burst pressure, and quality of seal.
Analysis of Aluminum and Steel Pistons—Comparison of Friction, Piston Temperature, and Combustion
Authors: Schreer Kai , Roth Ingo , Schneider Simon , Ehnis Holger
Published: March 2014

While steel pistons have been in use for a long time in commercial vehicle diesel engines, the first series production applications for passenger car diesel engines are currently imminent. The main reason for the use of steel pistons in high speed diesel engines is not, as maybe initially hypothesized, the increasing requirements on the component strength due to increasing mechanical loads, but rather challenges based on the actual CO2-legislation. The increasing requirements to reduce the fuel consumption necessitate new innovative technologies. The imminent penalties for exceeding the prescribed CO2 emissions seem to make the steel piston a viable alternative today, despite its higher manufacturing costs. So far, the CO2-benefits using steel pistons were mainly ascribed to the reduced friction between piston and cylinder liner due to no thermal interference.
Gray-Box Modeling for Performance Control of an HCCI Engine With Blended Fuels
Authors: Bidarvatan M. , Shahbakhti M.
Published: March 2014

High fidelity models that balance accuracy and computation load are essential for real-time model-based control of homogeneous charge compression ignition (HCCI) engines. Gray-box modeling offers an effective technique to obtain desirable HCCI control models. In this paper, a physical HCCI engine model is combined with two feed-forward artificial neural network models to form a serial architecture gray-box model. The resulting model can predict three major HCCI engine control outputs, including combustion phasing, indicated mean effective pressure (IMEP), and exhaust gas temperature (Texh). The gray-box model is trained and validated with the steady-state and transient experimental data for a large range of HCCI operating conditions. The results indicate that the gray-box model significantly improves the predictions from the physical model. For 234 HCCI conditions tested, the gray-box model predicts combustion phasing, IMEP, and Texh with an average error of less than 1 crank angle degree, 0.2 bar, and 6 °C, respectively. The gray-box model is computationally efficient and it can be used for real-time control application of HCCI engines.
Integrated HCCI Engine Control Based on a Performance Index
Authors: Bidarvatan M. , Shahbakhti M.
Published: March 2014

The integrated control of a homogenous charge compression ignition (HCCI) combustion phasing, load, and exhaust aftertreatment system is essential for realizing high-efficient HCCI engines, while maintaining low hydrocarbon (HC) and carbon monoxide (CO) emissions. This paper introduces a new approach for integrated HCCI engine control by defining a novel performance index to characterize different HCCI operating regions. The experimental data from a single cylinder engine at 214 operating conditions is used to determine the performance index for a blended fuel HCCI engine. The new performance index is then used to design an optimum reference trajectory for a multi-input multi-output HCCI controller. The optimum trajectory is designed for control of the combustion phasing and indicated mean effective pressure (IMEP), while meeting catalyst light-off requirements for the exhaust aftertreatment system. The designed controller is tested on a previously validated physical HCCI engine model. The simulation results illustrate the successful application of the new approach for controller design of HCCI engines.
Computationally Efficient Simulation of Multicomponent Fuel Combustion Using a Sparse Analytical Jacobian Chemistry Solver and High-Dimensional Clustering
Authors: Perini Federico , Krishnasamy Anand , Ra Youngchul , Reitz Rolf D.
Published: March 2014

The need for more efficient and environmentally sustainable internal combustion engines is driving research towards the need to consider more realistic models for both fuel physics and chemistry. As far as compression ignition engines are concerned, phenomenological or lumped fuel models are unreliable to capture spray and combustion strategies outside of their validation domains—typically, high-pressure injection and high-temperature combustion. Furthermore, the development of variable-reactivity combustion strategies also creates the need to model comprehensively different hydrocarbon families even in single fuel surrogates. From the computational point of view, challenges to achieving practical simulation times arise from the dimensions of the reaction mechanism, which can be of hundreds species even if hydrocarbon families are lumped into representative compounds and, thus, modeled with nonelementary, skeletal reaction pathways. In this case, it is also impossible to pursue further mechanism reductions to lower dimensions. central processing unit (CPU) times for integrating chemical kinetics in internal combustion engine simulations ultimately scale with the number of cells in the grid and with the cube number of species in the reaction mechanism. In the present work, two approaches to reduce the demands of engine simulations with detailed chemistry are presented. The first one addresses the demands due to the solution of the chemistry ordinary differential equation (ODE) system, and features the adoption of SpeedCHEM, a newly developed chemistry package that solves chemical kinetics using sparse analytical Jacobians. The second one aims to reduce the number of chemistry calculations by binning the computational fluid dynamics (CFD) cells of the engine grid into a subset of clusters, where chemistry is solved and then mapped back to the original domain. In particular, a high-dimensional representation of the chemical state space is adopted for keeping track of the different fuel components, and a newly developed bounding-box- constrained k-means algorithm is used to subdivide the cells into reactively homogeneous clusters. The approaches have been tested on a number of simulations featuring multicomponent diesel fuel surrogates and different engine grids. The results show that significant CPU time reductions, of about 1 order of magnitude, can be achieved without loss of accuracy in both engine performance and emissions predictions, prompting for their applicability to more refined or full-sized engine grids.
Design and Validation of a Compatible 3-Degrees of Freedom Shoulder Exoskeleton With an Adaptive Center of Rotation
Authors: Yan Hua , Yang Canjun , Zhang Yansong , Wang Yiqi
Published: March 2014

This paper outlines an experimentally based design method for a compatible 3-DOF shoulder exoskeleton with an adaptive center of rotation (CoR) by matching the mechanical CoR with the anatomical CoR to reduce human–machine interaction forces and improve comfort during dynamic humeral motion. The spatial–temporal description for anatomical CoR motion is obtained via a specific experimental task conducted on six healthy subjects. The task is comprised of a static section and a dynamic section, both of which are recorded with an infrared motion capture system using body-attached markers. To reduce the influence of human soft tissues, a custom-made four-marker group block was placed on the upper arm instead of using discrete markers. In the static section, the position of anatomical CoR is kept stationary and calculated using a well-known functional method. Based on the static results, the dynamic section determines the statistical relationship between the dynamic CoR position and the humeral orientation using an optimization method when subjects move their upper arm freely in the sagittal and coronal planes. Based on the resolved anatomical CoR motion, a new mechanical CoR model derived from a traditional ball-and-socket joint is applied to match the experimental results as closely as possible. In this mechanical model, the CoR motion in three-dimensional space is adjusted by translating two of the three intersecting joint axes, including the shoulder abduction/adduction and flexion/extension. A set of optimal translation parameters is obtained through proper matching criterion for the two CoRs. Based on the translation parameters, a compatible shoulder exoskeleton was manufactured and compared with a traditional shoulder exoskeleton with a fixed CoR. An experimental test was conducted to validate the CoR motion adaptation ability by measuring the human–machine interaction force during passive shoulder joint motion. The results provide a promising direction for future anthropomorphic shoulder exoskeleton design.
Evaluation of smartphone sound measurement applications
Authors: Kardous Chucri A. , Shaw Peter B.
Published: March 2014

This study reports on the accuracy of smartphone sound measurement applications (apps) and whether they can be appropriately employed for occupational noise measurements. A representative sample of smartphones and tablets on various platforms were acquired, more than 130 iOS apps were evaluated but only 10 apps met our selection criteria. Only 4 out of 62 Android apps were tested. The results showed two apps with mean differences of 0.07 dB (unweighted) and −0.52 dB (A-weighted) from the reference values. Two other apps had mean differences within ±2 dB. The study suggests that certain apps may be appropriate for use in occupational noise measurements.
Refining a model of hearing impairment using speech psychophysics
Authors: Jepsen Morten L. , Dau Torsten , Ghitza Oded
Published: March 2014

The premise of this study is that models of hearing, in general, and of individual hearing impairment, in particular, can be improved by using speech test results as an integral part of the modeling process. A conceptual iterative procedure is presented which, for an individual, considers measures of sensitivity, cochlear compression, and phonetic confusions using the Diagnostic Rhyme Test (DRT) framework. The suggested approach is exemplified by presenting data from three hearing-impaired listeners and results obtained with models of the hearing impairment of the individuals. The work reveals that the DRT data provide valuable information of the damaged periphery and that the non-speech and speech data are complementary in obtaining the best model for an individual.
Draft Genome Comparison of Representatives of the Three Dominant Genotype Groups of Dairy Bacillus licheniformis Strains
Authors: Dhakal Rajat , Seale R. Brent , Deeth Hilton C. , Craven Heather , Turner Mark S.
Published: March 2014

The spore-forming bacterium
Bacillus licheniformis
is a common contaminant of milk and milk products. Strains of this species isolated from dairy products can be differentiated into three major groups, namely, G, F1, and F2, using random amplification of polymorphic DNA (RAPD) analysis; however, little is known about the genomic differences between these groups and the identity of the fragments that make up their RAPD profiles. In this work we obtained high-quality draft genomes of representative strains from each of the three RAPD groups (designated strain G-1, strain F1-1, and strain F2-1) and compared them to each other and to
B. licheniformis
ATCC 14580 and
Bacillus subtilis
168. Whole-genome comparison and multilocus sequence typing revealed that strain G-1 contains significant sequence variability and belongs to a lineage distinct from the group F strains. Strain G-1 was found to contain genes coding for a type I restriction modification system, urease production, and bacitracin synthesis, as well as the 8-kbp plasmid pFL7, and these genes were not present in strains F1-1 and F2-1. In agreement with this, all isolates of group G, but no group F isolates, were found to possess urease activity and antimicrobial activity against
Micrococcus
. Identification of RAPD band sequences revealed that differences in the RAPD profiles were due to differences in gene lengths, 3′ ends of predicted primer binding sites, or gene presence or absence. This work provides a greater understanding of the phylogenetic and phenotypic differences observed within the
B. licheniformis
species.
Sinorhizobium meliloti Chemoreceptor McpU Mediates Chemotaxis toward Host Plant Exudates through Direct Proline Sensing
Authors: Webb Benjamin A. , Hildreth Sherry , Helm Richard F. , Scharf Birgit E.
Published: March 2014

Bacterial chemotaxis is an important attribute that aids in establishing symbiosis between rhizobia and their legume hosts. Plant roots and seeds exude a spectrum of molecules into the soil to attract their bacterial symbionts. The alfalfa symbiont
Sinorhizobium meliloti
possesses eight chemoreceptors to sense its environment and mediate chemotaxis toward its host. The methyl accepting chemotaxis protein McpU is one of the more abundant
S. meliloti
chemoreceptors and an important sensor for the potent attractant proline. We established a dominant role of McpU in sensing molecules exuded by alfalfa seeds. Mass spectrometry analysis determined that a single germinating seed exudes 3.72 nmol of proline, producing a millimolar concentration near the seed surface which can be detected by the chemosensory system of
S. meliloti
. Complementation analysis of the
mcpU
deletion strain verified McpU as the key proline sensor. A structure-based homology search identified tandem Cache (
ca
lcium channels and
che
motaxis receptors) domains in the periplasmic region of McpU. Conserved residues Asp-155 and Asp-182 of the N-terminal Cache domain were determined to be important for proline sensing by evaluating mutant strains in capillary and swim plate assays. Differential scanning fluorimetry revealed interaction of the isolated periplasmic region of McpU (McpU
40-284
) with proline and the importance of Asp-182 in this interaction. Using isothermal titration calorimetry, we determined that proline binds with a

K
d

(dissociation constant) of 104 μM to McpU
40-284
, while binding was abolished when Asp-182 was substituted by Glu. Our results show that McpU is mediating chemotaxis toward host plants by direct proline sensing.
Uptake of Dissolved Organic Carbon by Gammaproteobacterial Subgroups in Coastal Waters of the West Antarctic Peninsula
Authors: Nikrad Mrinalini P. , Cottrell Matthew T. , Kirchman David L.
Published: March 2014

Heterotrophic bacteria are well known to be key players in the turnover of dissolved organic material (DOM) in the oceans, but the relationship between DOM uptake and bacterial clades is still not well understood. Here we explore the turnover and single-cell use of glucose, an amino acid mixture,
N
-acetylglucosamine (NAG), and protein by gammaproteobacterial clades in coastal waters of the West Antarctic Peninsula in summer and fall. More than 60% of the cells within two closely related gammaproteobacterial clades, Ant4D3 and Arctic96B-16, were active in using the amino acid mixture, protein, and NAG. In contrast, an average of only 7% of all SAR86 cells used amino acids and protein even in summer when DOM use was high. In addition to DOM uptake within a group, we explored the contribution of the three gammaproteobacterial groups to total community uptake of a compound. SAR86 contributed 5- to 10-fold less than the other gammaproteobacterial subgroups to the uptake of all compounds. We found that the overall contribution of the Ant4D3 clade to DOM uptake was highest, whereas the SAR86 clade contributed the least to DOM turnover in West Antarctic Peninsula waters. Our results suggest that the low growth activity of a bacterial clade leads to low abundance, fewer active cells and a low contribution to the turnover of DOM components.
Distribution of Burkholderia pseudomallei in Northern Australia, a Land of Diversity
Authors: McRobb Evan , Kaestli Mirjam , Price Erin P. , Sarovich Derek S. , Mayo Mark , Warner Jeffrey , Spratt Brian G. , Currie Bart J.
Published: March 2014

Burkholderia pseudomallei
is a Gram-negative soil bacillus that is the etiological agent of melioidosis and a biothreat agent. Little is known about the biogeography of this bacterium in Australia, despite its hyperendemicity in the northern region of this continent. The population structure of 953 Australian
B. pseudomallei
strains representing 779 and 174 isolates of clinical and environmental origins, respectively, was analyzed using multilocus sequence typing (MLST). Bayesian population structure and network SplitsTree analyses were performed on concatenated MLST loci, and sequence type (ST) diversity and evenness were examined using Simpson's and Pielou's indices and a multivariate dissimilarity matrix. Bayesian analysis found two
B. pseudomallei
populations in Australia that were geographically distinct; isolates from the Northern Territory were grouped mainly into the first population, whereas the majority of isolates from Queensland were grouped in a second population. Differences in ST evenness were observed between sampling areas, confirming that
B. pseudomallei
is widespread and established across northern Australia, with a large number of fragmented habitats. ST analysis showed that
B. pseudomallei
populations diversified as the sampling area increased. This observation was in contrast to smaller sampling areas where a few STs predominated, suggesting that
B. pseudomallei
populations are ecologically established and not frequently dispersed. Interestingly, there was no identifiable ST bias between clinical and environmental isolates, suggesting the potential for all culturable
B. pseudomallei
isolates to cause disease. Our findings have important implications for understanding the ecology of
B. pseudomallei
in Australia and for potential source attribution of this bacterium in the event of unexpected cases of melioidosis.
Chromosomal Insertions in the Lactobacillus casei
upp
Gene That Are Useful for Vaccine Expression
Authors: Song Bai-fen , Ju Long-zhu , Li Yi-jing , Tang Li-jie
Published: March 2014

To develop a stable and marker-free
Lactobacillus
strain useful for the expression of vaccines, we developed a temperature-sensitive suicide plasmid with expression cassettes containing an HCE promoter, a PgsA anchor, the alpha-toxin gene, and an
rrnB
T1T2 terminator (PPαT) that uses a 5-fluorouracil (5-FU) counterselectable marker for
Lactobacillus casei
. Three strains containing the correct PPαT expression cassettes were produced via the selective pressure of 5-FU screening. We confirmed that the
upp
gene was deleted and that the PPαT expression cassettes were inserted into the
upp
site of
L. casei
ATCC 393 by genomic PCR amplification and sequencing. 5-FU resistance in recombinant bacteria could be stably inherited for as long as 40 generations following insertion. However, bacteria containing the integrated DNA grew more slowly than wild-type
L. casei
. An indirect enzyme-linked immunosorbent assay (ELISA) analysis demonstrated that the alpha-toxin gene was expressed. Also, we visualized expression of the protein on the surface of
L. casei
cells using laser confocal microscopy. These results taken together demonstrate that these recombinant bacteria should provide a safe tool for effective vaccine production.
Reconstruction of an Acetogenic 2,3-Butanediol Pathway Involving a Novel NADPH-Dependent Primary-Secondary Alcohol Dehydrogenase
Authors: Köpke Michael , Gerth Monica L. , Maddock Danielle J. , Mueller Alexander P. , Liew FungMin , Simpson Séan D. , Patrick Wayne M.
Published: March 2014

Acetogenic bacteria use CO and/or CO
2
plus H
2
as their sole carbon and energy sources. Fermentation processes with these organisms hold promise for producing chemicals and biofuels from abundant waste gas feedstocks while simultaneously reducing industrial greenhouse gas emissions. The acetogen
Clostridium autoethanogenum
is known to synthesize the pyruvate-derived metabolites lactate and 2,3-butanediol during gas fermentation. Industrially, 2,3-butanediol is valuable for chemical production. Here we identify and characterize the
C. autoethanogenum
enzymes for lactate and 2,3-butanediol biosynthesis. The putative
C. autoethanogenum
lactate dehydrogenase was active when expressed in
Escherichia coli
. The 2,3-butanediol pathway was reconstituted in
E. coli
by cloning and expressing the candidate genes for acetolactate synthase, acetolactate decarboxylase, and 2,3-butanediol dehydrogenase. Under anaerobic conditions, the resulting
E. coli
strain produced 1.1 ± 0.2 mM 2
R
,3
R
-butanediol (23 μM h
−1
optical density unit
−1
), which is comparable to the level produced by
C. autoethanogenum
during growth on CO-containing waste gases. In addition to the 2,3-butanediol dehydrogenase, we identified a strictly NADPH-dependent primary-secondary alcohol dehydrogenase (CaADH) that could reduce acetoin to 2,3-butanediol. Detailed kinetic analysis revealed that CaADH accepts a range of 2-, 3-, and 4-carbon substrates, including the nonphysiological ketones acetone and butanone. The high activity of CaADH toward acetone led us to predict, and confirm experimentally, that
C. autoethanogenum
can act as a whole-cell biocatalyst for converting exogenous acetone to isopropanol. Together, our results functionally validate the 2,3-butanediol pathway from
C. autoethanogenum
, identify CaADH as a target for further engineering, and demonstrate the potential of
C. autoethanogenum
as a platform for sustainable chemical production.
Salivary Microbiota and Metabolome Associated with Celiac Disease
Authors: Francavilla Ruggiero , Ercolini Danilo , Piccolo Maria , Vannini Lucia , Siragusa Sonya , De Filippis Francesca , De Pasquale Ilaria , Di Cagno Raffaella , Di Toma Michele , Gozzi Giorgia , Serrazanetti Diana I. , De Angelis Maria , Gobbetti Marco
Published: March 2014

This study aimed to investigate the salivary microbiota and metabolome of 13 children with celiac disease (CD) under a gluten-free diet (treated celiac disease [T-CD]). The same number of healthy children (HC) was used as controls. The salivary microbiota was analyzed by an integrated approach using culture-dependent and -independent methods. Metabolome analysis was carried out by gas chromatography-mass spectrometry–solid-phase microextraction. Compared to HC, the number of some cultivable bacterial groups (e.g., total anaerobes) significantly (
P
< 0.05) differed in the saliva samples of the T-CD children. As shown by community-level catabolic profiles, the highest Shannon's diversity and substrate richness were found in HC. Pyrosequencing data showed the highest richness estimator and diversity index values for HC. Levels of
Lachnospiraceae
,
Gemellaceae
, and
Streptococcus sanguinis
were highest for the T-CD children.
Streptococcus thermophilus
levels were markedly decreased in T-CD children. The saliva of T-CD children showed the largest amount of
Bacteroidetes
(e.g.,
Porphyromonas
sp.,
Porphyromonas endodontalis
, and
Prevotella nanceiensis
), together with the smallest amount of
Actinobacteria
. T-CD children were also characterized by decreased levels of some
Actinomyces
species,
Atopobium
species, and
Corynebacterium durum
.
Rothia mucilaginosa
was the only
Actinobacteria
species found at the highest level in T-CD children. As shown by multivariate statistical analyses, the levels of organic volatile compounds markedly differentiated T-CD children. Some compounds (e.g., ethyl-acetate, nonanal, and 2-hexanone) were found to be associated with T-CD children. Correlations (false discovery rate [FDR], <0.05) were found between the relative abundances of bacteria and some volatile organic compounds (VOCs). The findings of this study indicated that CD is associated with oral dysbiosis that could affect the oral metabolome.
Analysis of Hydroxycinnamic Acid Degradation in Agrobacterium fabrum Reveals a Coenzyme A-Dependent, Beta-Oxidative Deacetylation Pathway
Authors: Campillo Tony , Renoud Sébastien , Kerzaon Isabelle , Vial Ludovic , Baude Jessica , Gaillard Vincent , Bellvert Floriant , Chamignon Cécile , Comte Gilles , Nesme Xavier , Lavire Céline , Hommais Florence
Published: March 2014

The soil- and rhizosphere-inhabiting bacterium
Agrobacterium fabrum
(genomospecies G8 of the
Agrobacterium tumefaciens
species complex) is known to have species-specific genes involved in ferulic acid degradation. Here, we characterized, by genetic and analytical means, intermediates of degradation as feruloyl coenzyme A (feruloyl-CoA), 4-hydroxy-3-methoxyphenyl-β-hydroxypropionyl–CoA, 4-hydroxy-3-methoxyphenyl-β-ketopropionyl–CoA, vanillic acid, and protocatechuic acid. The genes
atu1416
,
atu1417
, and
atu1420
have been experimentally shown to be necessary for the degradation of ferulic acid. Moreover, the genes
atu1415
and
atu1421
have been experimentally demonstrated to be essential for this degradation and are proposed to encode a phenylhydroxypropionyl-CoA dehydrogenase and a 4-hydroxy-3-methoxyphenyl-β-ketopropionic acid (HMPKP)–CoA β-keto-thiolase, respectively. We thus demonstrated that the
A. fabrum
hydroxycinnamic degradation pathway is an original coenzyme A-dependent β-oxidative deacetylation that could also transform
p
-coumaric and caffeic acids. Finally, we showed that this pathway enables the metabolism of toxic compounds from plants and their use for growth, likely providing the species an ecological advantage in hydroxycinnamic-rich environments, such as plant roots or decaying plant materials.
Anoxic Androgen Degradation by the Denitrifying Bacterium Sterolibacterium denitrificans via the 2,3-seco Pathway
Authors: Wang Po-Hsiang , Yu Chang-Ping , Lee Tzong-Huei , Lin Ching-Wen , Ismail Wael , Wey Shiaw-Pyng , Kuo An-Ti , Chiang Yin-Ru
Published: March 2014

The biodegradation of steroids is a crucial biochemical process mediated exclusively by bacteria. So far, information concerning the anoxic catabolic pathways of androgens is largely unknown, which has prevented many environmental investigations. In this work, we show that
Sterolibacterium denitrificans
DSMZ 13999 can anaerobically mineralize testosterone and some C
19
androgens. By using a
13
C-metabolomics approach and monitoring the sequential appearance of the intermediates, we demonstrated that
S. denitrificans
uses the 2,3-
seco
pathway to degrade testosterone under anoxic conditions. Furthermore, based on the identification of a C
17
intermediate, we propose that the A-ring cleavage may be followed by the removal of a C
2
side chain at C-5 of 17-hydroxy-1-oxo-2,3-
seco
-androstan-3-oic acid (the A-ring cleavage product) via retro-aldol reaction. The androgenic activities of the bacterial culture and the identified intermediates were assessed using the
lacZ
-based yeast androgen assay. The androgenic activity in the testosterone-grown
S. denitrificans
culture decreased significantly over time, indicating its ability to eliminate androgens. The A-ring cleavage intermediate (≤500 μM) did not exhibit androgenic activity, whereas the sterane-containing intermediates did. So far, only two androgen-degrading anaerobes (
Sterolibacterium denitrificans
DSMZ 13999 [a betaproteobacterium] and
Steroidobacter denitrificans
DSMZ 18526 [a gammaproteobacterium]) have been isolated and characterized, and both of them use the 2,3-
seco
pathway to anaerobically degrade androgens. The key intermediate 2,3-
seco
-androstan-3-oic acid can be used as a signature intermediate for culture-independent environmental investigations of anaerobic degradation of C
19
androgens.
Enzyme Treatment Reverse Transcription-PCR To Differentiate Infectious and Inactivated F-Specific RNA Phages
Authors: Yang Yongheng , Griffiths Mansel W.
Published: March 2014

F-specific (F+) RNA phages are recommended as indicators of fecal contamination and the presence of enteric viruses and as viral surrogates to elucidate the resistance of viruses to adverse conditions or to assess the effectiveness of inactivating processes. Reverse transcription (RT)-PCR methods have been used to detect, quantify, or identify subgroups of F+ RNA phages. However, these methods may overestimate the infectivity of F+ RNA phages in test samples, since the presence of both infectious and inactivated phages (or naked RNA) can lead to positive RT-PCR signals. In this study, we evaluated the ability of an enzyme treatment (ET) with proteinase K and RNase A prior to RNA extraction, followed by RT-PCR, to differentiate infectious and inactivated F+ RNA phages. The results indicated that ET RT-PCR reduced, but did not completely eliminate, false-positive signals encountered with RT-PCR alone. The two-step ET RT-PCR, in which the enzymes were added sequentially, was more effective at reducing false-positive signals than the one-step ET RT-PCR, which involved addition of both enzymes together. Despite its inability to completely eliminate false-positive signals, ET RT-PCR gave more reliable information on the infectivity of F+ RNA phages. Thus, the method is better than RT-PCR alone for detecting F+ RNA phages as indicators to assess the risk of fecal contamination by enteric pathogens or to evaluate the effectiveness of virus-inactivating processes.
Gene Transfer Potential of Outer Membrane Vesicles of Acinetobacter baylyi and Effects of Stress on Vesiculation
Authors: Fulsundar Shweta , Harms Klaus , Flaten Gøril E. , Johnsen Pål J. , Chopade Balu Ananda , Nielsen Kaare M.
Published: March 2014

Outer membrane vesicles (OMVs) are continually released from a range of bacterial species. Numerous functions of OMVs, including the facilitation of horizontal gene transfer (HGT) processes, have been proposed. In this study, we investigated whether OMVs contribute to the transfer of plasmids between bacterial cells and species using Gram-negative
Acinetobacter baylyi
as a model system. OMVs were extracted from bacterial cultures and tested for the ability to vector gene transfer into populations of
Escherichia coli
and
A. baylyi
, including naturally transformation-deficient mutants of
A. baylyi
. Anti-double-stranded DNA (anti-dsDNA) antibodies were used to determine the movement of DNA into OMVs. We also determined how stress affected the level of vesiculation and the amount of DNA in vesicles. OMVs were further characterized by measuring particle size distribution (PSD) and zeta potential. Transmission electron microscopy (TEM) and immunogold labeling were performed using anti-fluorescein isothiocyanate (anti-FITC)-conjugated antibodies and anti-dsDNA antibodies to track the movement of FITC-labeled and DNA-containing OMVs. Exposure to OMVs isolated from plasmid-containing donor cells resulted in HGT to
A. baylyi
and
E. coli
at transfer frequencies ranging from 10
−6
to 10
−8
, with transfer efficiencies of approximately 10
3
and 10
2
per μg of vesicular DNA, respectively. Antibiotic stress was shown to affect the DNA content of OMVs as well as their hydrodynamic diameter and zeta potential. Morphological observations suggest that OMVs from
A. baylyi
interact with recipient cells in different ways, depending on the recipient species. Interestingly, the PSD measurements suggest that distinct size ranges of OMVs are released from
A. baylyi
.
The Salmonella enterica Serovar Typhi LeuO Global Regulator Forms Tetramers: Residues Involved in Oligomerization, DNA Binding, and Transcriptional Regulation
Authors: Guadarrama Carmen , Medrano-López Abraham , Oropeza Ricardo , Hernández-Lucas Ismael , Calva Edmundo
Published: March 2014

LeuO is a LysR-type transcriptional regulator (LTTR) that has been described to be a global regulator in
Escherichia coli
and
Salmonella enterica
, since it positively and negatively regulates the expression of genes involved in multiple biological processes. LeuO is comprised of an N-terminal DNA-binding domain (DBD) with a winged helix-turn-helix (wHTH) motif and of a long linker helix (LH) involved in dimerization that connects the DBD with the C-terminal effector-binding domain (EBD) or regulatory domain (RD; which comprises subdomains RD-I and RD-II). Here we show that the oligomeric structure of LeuO is a tetramer that binds with high affinity to DNA. A collection of single amino acid substitutions in the LeuO DBD indicated that this region is involved in oligomerization, in positive and negative regulation, as well as in DNA binding. Mutants with point mutations in the central and C-terminal regions of RD-I were affected in transcriptional activation. Deletion of the RD-II and RD-I C-terminal subdomains affected not only oligomerization but also DNA interaction, showing that they are involved in positive and negative regulation. Together, these data demonstrate that not only the C terminus but also the DBD of LeuO is involved in oligomer formation; therefore, each LeuO domain appears to act synergistically to maintain its regulatory functions in
Salmonella enterica
serovar Typhi.
Spontaneous retroperitoneal haemorrhage in a young adult
Authors: Baksi Aditya , Gupta Shahana , Ray Udipta , Ghosh Shibajyoti
Published: March 2014

We report a rare case of a primary adrenal cortical malignancy presenting with spontaneous retroperitoneal haemorrhage in a young adult. To the best of our knowledge, this is the thirteenth such case to be reported in the English literature.
Paediatric benign cystic monodermal testicular teratoma
Authors: Patel Ramnik V , Marshall David , Gannon Caroline
Published: March 2014

We present a case of a painless progressively increasing mass in the left upper testis in a 5-year-old boy, which was detected by his father performing testicular examination after observing asymmetry of the scrotum. Clinical examination, tumour markers, ultrasound scan including colour Doppler studies, and finally inguinal exploration and histopathology were helpful in establishing the diagnosis of benign cystic monodermal testicular teratoma. Testicular teratoma should be considered in the differential diagnosis of any child presenting with non-traumatic painless progressive scrotal swelling. Inguinal radical orchiectomy is the traditional gold standard treatment for benign testicular teratoma in children. Testis-sparing surgery should be reserved for smaller testicular tumours known to be benign.
Infected total elbow arthroplasty treated by cemented arthrodesis
Authors: Lui Tun Hing
Published: March 2014

A lady had suffered from deep infection of the GSB III prosthesis of her right elbow. The infection could not be controlled by repeated debridement. Finally, cemented arthrodesis was performed and the infection was eradicated.
Stercoral perforation in a child: a rare complication of NSAID use
Authors: Al Omran Yasser , Al Hindi Saeed , Alarayedh Sharif , Hawash Aamenah
Published: March 2014

The adverse effects of non-steroidal anti-inflammatory drugs (NSAIDs) on the gastrointestinal (GI) tract are well known. However, NSAID use rarely leads to a stercoral perforation, an extremely rare but life-threatening cause of acute abdomen. We present a case of stercoral sigmoid colon perforation in a 2-year-old girl, secondary to unintentional NSAID overdose, developing as a result of miscommunication between the general practitioner (GP) and the mother. To the best of our knowledge, stercoral perforation has never before been reported in a child.
The foot core system: a new paradigm for understanding intrinsic foot muscle function
Authors: McKeon Patrick O , Hertel Jay , Bramble Dennis , Davis Irene
Published: March 2014

The foot is a complex structure with many articulations and multiple degrees of freedom that play an important role in static posture and dynamic activities. The evolutionary development of the arch of the foot was coincident with the greater demands placed on the foot as humans began to run. The movement and stability of the arch is controlled by intrinsic and extrinsic muscles. However, the intrinsic muscles are largely ignored by clinicians and researchers. As such, these muscles are seldom addressed in rehabilitation programmes. Interventions for foot-related problems are more often directed at externally supporting the foot rather than training these muscles to function as they are designed. In this paper, we propose a novel paradigm for understanding the function of the foot. We begin with an overview of the evolution of the human foot with a focus on the development of the arch. This is followed by a description of the foot intrinsic muscles and their relationship to the extrinsic muscles. We draw the parallels between the small muscles of the trunk region that make up the lumbopelvic core and the intrinsic foot muscles, introducing the concept of the foot core. We then integrate the concept of the foot core into the assessment and treatment of the foot. Finally, we call for an increased awareness of the importance of the foot core stability to normal foot and lower extremity function.
Hip chondropathy at arthroscopy: prevalence and relationship to labral pathology, femoroacetabular impingement and patient-reported outcomes
Authors: Kemp Joanne L , Makdissi Michael , Schache Anthony G , Pritchard Michael G , Pollard Thomas C B , Crossley Kay M
Published: March 2014

Background

This study aimed to describe chondropathy prevalence in adults who had undergone hip arthroscopy for hip pain. The relationships between chondropathy severity and (1) participant characteristics; and (2) patient-reported outcomes (PROs) at initial assessment (∼18 months postsurgery) and over a further 12 months (∼30 months postsurgery) were evaluated. Finally, the relationships between chondropathy and coexisting femoroacetabular impingement (FAI) and labral pathology at the time of surgery were evaluated.

Methods

100 consecutive patients (36±12 years) who underwent hip arthroscopy 18 months previously participated. Hip Osteoarthritis and Disability Outcome Score (HOOS) and International Hip Outcome Tool (iHOT-33) data were collected prospectively at 18 months postsurgery and at 30 months postsurgery. Surgical data were collected retrospectively. Participants were grouped: Outerbridge grade 0, no chondropathy; Outerbridge grade I–II, mild chondropathy; Outerbridge III–IV, severe chondropathy. The presence of FAI or labral pathology was noted.

Results

The prevalence of chondropathy (≥grade I) at hip arthroscopy was 72%. Participants with severe chondropathy were significantly worse for all HOOS subscales and the iHOT-33 at 18 months postsurgery (HOOS-symptoms (p=0.017); HOOS-pain (p=0.024); HOOS-activity (p=0.009); HOOS-sport (p=0.004); HOOS-quality-of-life (p=0.006); iHOT-33 (p=0.013)) than those with no chondropathy. At 12-month follow-up, HOOS-quality-of-life in those without chondropathy was the only PRO that improved. Relative risk of coexisting chondropathy with labral pathology or FAI was 40%.

Conclusions

Chondropathy was prevalent, and associated with increasing age, coexisting labral pathology or FAI. Severe chondropathy was associated with worse pain and function at 18 months postsurgery. Little improvements were observed in participants over a further 12 months, regardless of chondropathy status.
Standardised criteria improve accuracy of ECG interpretation in competitive athletes: a randomised controlled trial
Authors: Exeter Daniel J , Elley C Raina , Fulcher Mark L , Lee Arier C , Drezner Jonathan A , Asif Irfan M
Published: March 2014

Background

Screening to prevent sudden cardiac death remains a contentious topic in sport and exercise medicine. The aim of this study was to assess whether the use of a standardised criteria tool improves the accuracy of ECG interpretation by physicians screening athletes.

Methods

Design: Randomised control trial. Study population: General practitioners with an interest in sports medicine, sports physicians, sports medicine registrars and cardiologists from Australia and New Zealand were eligible to participate. Outcome measures: Accuracy, sensitivity, specificity and false-positive rates of screening ECG interpretation of athletes. Intervention: A two-page standardised ECG criteria tool was provided to intervention participants. Control participants undertook ‘usual’ interpretation.

Results

62 physicians, with a mean duration of practice of 16 years, were randomised to intervention and control. 10 baseline and 30 postrandomisation athlete ECGs were interpreted by the participants. Intervention participants were more likely to be correct: OR 1.72 (95% CI 1.31 to 2.27, p<0.001). Correct ECG interpretation was higher in the intervention group, 88.4% (95% CI 85.7% to 91.2%), than in the control group, 82.2% (95% CI 78.8% to 85.5%; p=0.005). Sensitivity was 95% in the intervention group and 92% in the control group (p=0.4), with specificity of 86% and 78%, respectively (p=0.006). There were 36% fewer false positives in the intervention group (p=0.006).

Conclusions

ECG interpretation in athletes can be improved by using a standardised ECG criteria tool. Use of the tool results in lower false-positive rates; this may have implications for screening recommendations.

Trial Registration number:

ACTRN12612000641897.
Epidemiology of concussion in men's elite Rugby-7s (Sevens World Series) and Rugby-15s (Rugby World Cup, Junior World Championship and Rugby Trophy, Pacific Nations Cup and English Premiership)
Authors: Fuller Colin W , Taylor Aileen , Raftery Martin
Published: March 2014

Objective

To determine the incidence, nature and causes of concussions sustained during men's elite professional Rugby-7s and Rugby-15s.

Design

A prospective cohort study recording injuries classified as a time-loss concussion.

Population

Players competing in the following tournaments: Rugby 15s—English Premiership (2007/2008 to 2010/2011), Rugby World Cup (2007, 2011), Pacific Nations Cup (2012, 2013), Junior World Championship (2008, 2010–2013), Junior World Rugby Trophy (2008, 2010–2013); Rugby 7s—Sevens World Series (2008/2009, 2010/2011 to 2012/2013).

Method

The study was implemented according to the international consensus statement for epidemiological studies in rugby union; the main outcome measures included the number, incidence (number of concussions/1000 player-match-hours), mean and median severity (days absence) and cause of concussion.

Results

The incidence of concussion in Rugby-7s was significantly higher than that in Rugby-15s (risk ratio=1.84; p<0.001). The severity of concussions were significantly higher in Rugby-7s than Rugby-15s (mean—Rugby-7s: 19.2, Rugby-15s: 10.1; median—Rugby 7s: 20, Rugby-15s: 7; p<0.001). The main causes of concussion were tackling (44.1%) in Rugby-7s and collisions (43.6%) in Rugby-15s. Significantly more (risk ratio=1.49; p=0.004) concussed players were removed immediately from the game in Rugby-7s (69.7%) compared to Rugby-15s (46.7%).

Conclusions

Six actions were identified to improve the management of concussion in rugby: implement a pitch-side concussion assessment protocol; improve compliance with return-to-play protocols; work with referees to review the nature and consequences of collisions; improve players’ tackle technique; investigate the forces involved in tackles and collisions; and evaluate reasons for the higher incidence of concussions in Rugby-7s.
Monitoring of biological markers indicative of doping: the athlete biological passport
Authors: Saugy Martial , Lundby Carsten , Robinson Neil
Published: March 2014

The athlete biological passport (ABP) was recently implemented in anti-doping work and is based on the individual and longitudinal monitoring of haematological or urine markers. These may be influenced by illicit procedures performed by some athletes with the intent to improve exercise performance. Hence the ABP is a valuable tool in the fight against doping. Actually, the passport has been defined as an individual and longitudinal observation of markers. These markers need to belong to the biological cascade influenced by the application of forbidden hormones or more generally, affected by biological manipulations which can improve the performance of the athlete. So far, the haematological and steroid profile modules of the ABP have been implemented in major sport organisations, and a further module is under development. The individual and longitudinal monitoring of some blood and urine markers are of interest, because the intraindividual variability is lower than the corresponding interindividual variability. Among the key prerequisites for the implementation of the ABP is its prospect to resist to the legal and scientific challenges. The ABP should be implemented in the most transparent way and with the necessary independence between planning, interpretation and result management of the passport. To ensure this, the Athlete Passport Management Unit (APMU) was developed and the WADA implemented different technical documents associated to the passport. This was carried out to ensure the correct implementation of a profile which can also stand the challenge of any scientific or legal criticism. This goal can be reached only by following strictly important steps in the chain of production of the results and in the management of the interpretation of the passport. Various technical documents have been then associated to the guidelines which correspond to the requirements for passport operation. The ABP has been completed very recently by the steroid profile module. As for the haematological module, individual and longitudinal monitoring have been applied and the interpretation cascade is also managed by a specific APMU in a similar way as applied in the haematological module. Thus, after exclusion of any possible pathology, specific variation from the individual norms will be then considered as a potential misuse of hormones or other modulators to enhance performance.