bluuebunny/crossref_metadata_2025 huggingface dataset:
Residual Elimination Algorithm Enhancements to Improve Foot Motion Tracking During Forward Dynamic Simulations of Gait
Authors: Jackson Jennifer N. , Hass Chris J. , Fregly Benjamin J.
Published: August 2015

Patient-specific gait optimizations capable of predicting post-treatment changes in joint motions and loads could improve treatment design for gait-related disorders. To maximize potential clinical utility, such optimizations should utilize full-body three-dimensional patient-specific musculoskeletal models, generate dynamically consistent gait motions that reproduce pretreatment marker measurements closely, and achieve accurate foot motion tracking to permit deformable foot-ground contact modeling. This study enhances an existing residual elimination algorithm (REA) Remy, C. D., and Thelen, D. G., 2009, “Optimal Estimation of Dynamically Consistent Kinematics and Kinetics for Forward Dynamic Simulation of Gait,” ASME J. Biomech. Eng., 131(3), p. 031005) to achieve all three requirements within a single gait optimization framework. We investigated four primary enhancements to the original REA: (1) manual modification of tracked marker weights, (2) automatic modification of tracked joint acceleration curves, (3) automatic modification of algorithm feedback gains, and (4) automatic calibration of model joint and inertial parameter values. We evaluated the enhanced REA using a full-body three-dimensional dynamic skeletal model and movement data collected from a subject who performed four distinct gait patterns: walking, marching, running, and bounding. When all four enhancements were implemented together, the enhanced REA achieved dynamic consistency with lower marker tracking errors for all segments, especially the feet (mean root-mean-square (RMS) errors of 3.1 versus 18.4 mm), compared to the original REA. When the enhancements were implemented separately and in combinations, the most important one was automatic modification of tracked joint acceleration curves, while the least important enhancement was automatic modification of algorithm feedback gains. The enhanced REA provides a framework for future gait optimization studies that seek to predict subject-specific post-treatment gait patterns involving large changes in foot-ground contact patterns made possible through deformable foot-ground contact models.
Analysis and Prediction of Shock-Induced Vortex Circulation in Transonic Compressors
Authors: Clark Kenneth P. , Gorrell Steven E.
Published: August 2015

Multiple high-fidelity time-accurate computational fluid dynamics simulations were performed to investigate the effects of upstream stator loading and rotor shock strength on vortex shedding characteristics in a single-stage transonic compressor. Three loadings on the upstream stator row of decreased, nominal, and increased loading in conjunction with three axial spacings of close, mid, and far were studied for this analysis. The time-accurate urans code turbo was used to generate periodic, quarter annulus simulations of the blade row interaction (BRI) compressor rig. It was observed that vortex shedding was synchronized to the passing of a rotor bow shock. Results show that vortex strength increases linearly with stator loading and rotor bow shock strength. “Normal” and “large” shock-induced vortices formed on the stator trailing edge (TE) immediately after the shock passing, but the large vortices were strengthened at the TE due to a low-velocity region on the suction surface. This low-velocity region was generated upstream on the suction surface from a shock-induced thickening of the boundary layer or separation bubble. The circulation of the large vortices was greater than the normal vortices by a factor of 1.7, 1.83, and 2.04 for decreased, nominal, and increased deswirler loadings. At decreased loading, only 24% of the measured vortices were considered large, while at nominal loading 58% were large. A model was developed to predict shock-induced vortex circulation from a known rotor bow shock strength, stator diffusion factor, and near-wake parameters. The model predicts the average vortex circulation very well, with 5% difference between predicted and measured values. An understanding of the unsteady interactions associated with blade loading and rotor shock strength in transonic stages will help compressor designers account for unsteady flow physics at design and off-design operating conditions.
Heat Transfer and Entropy Generation Analysis of Bingham Plastic Fluids in Circular Microchannels
Authors: Mohammadi Mohammad-Reza , Moghadam Ali Jabari
Published: August 2015

The thermal characteristics of Bingham plastic fluid flows are analyzed in circular microchannels under uniform wall heat flux condition. The analytic approach presented here reveals that the governing parameters are Bingham number, dimensionless radius of the plug flow region, and Brinkman number. The results demonstrate that there is a strong influence of viscous dissipation on heat transfer and entropy generation for Brinkman numbers greater than a specific value. With increasing the Brinkman number and dimensionless radius of the plug flow region, entropy generation is increased, while the Nusselt number is decreased. The influence of these parameters on the entropy generation from heat transfer is strongly higher than the entropy generation from fluid friction. The average dimensionless total entropy shows that the Bingham plastic fluids generate entropy more than Newtonian fluids; also, an increase in the dimensionless radius of the plug flow region results in increasing the average dimensionless total entropy generation. By letting the dimensionless radius of the plug flow region equal to zero, the generalized expressions and results will be simplified to Newtonian fluids.
The Kronig-Penney model extended to arbitrary potentials via numerical matrix mechanics
Authors: Pavelich R. L. , Marsiglio F.
Published: August 2015

The Kronig-Penney model is a common starting point for studying the quantum mechanics of electrons in a confining periodic potential. This model uses a square-well potential; the energies and eigenstates can be obtained analytically for a single well, and then Bloch's theorem allows one to extend these solutions to the periodically repeating potential. In this work, we describe how to obtain simple numerical solutions for the eigenvalues and eigenstates for any confining one-dimensional potential within a unit cell and then extend this procedure, with virtually no extra effort, to the case of arbitrary periodically repeating potentials. In this way, one can study the band structure effects that arise from differently shaped potentials. One of these effects is the electron-hole mass asymmetry; more realistic unit cell potentials generally give rise to higher electron-hole mass asymmetries.
Simple and synergistic ways to understand the Boltzmann distribution function
Authors: Engelhardt Larry , Lopez del Puerto Marie , Chonacky Norman
Published: August 2015

This paper presents three approaches to providing undergraduate students with a conceptual understanding of the Boltzmann distribution: (1) a simple logical argument for why it is described by an exponential function, (2) a computational experiment to demonstrate and validate this result, and (3) a computer simulation of a laboratory experiment that allows this result to be observed. Together, these three perspectives complement one another to broaden students' understanding and prepare them for more formal, complete treatments. These examples illustrate how the convergence of theoretical, computational, and experimental approaches, applied to a single physical problem, contribute to a deeper and more unified understanding of statistical systems than could otherwise be had using any one of the methods alone.
Geometric reasoning about damped and forced harmonic motion in the complex plane
Authors: Close Hunter G.
Published: August 2015

Complex-valued functions are commonly used to solve differential equations for one-dimensional motion of a harmonic oscillator with linear damping, a sinusoidal driving force, or both. However, the usual approach treats complex functions as an algebraic shortcut, neglecting geometrical representations of those functions and discarding imaginary parts. This article emphasizes the benefit of using diagrams in the complex plane for such systems, in order to build intuition about harmonic motion and promote spatial reasoning and the use of varied representations. Examples include the analysis of exact time sequences of various kinematic events in damped harmonic motion, sense-making about the phase difference between a driving force and the resulting motion, and understanding the discrepancy between the resonant frequency and the natural undamped frequency for forced, damped harmonic motion. The approach is suitable for supporting instruction in undergraduate upper-division classical mechanics.
Wave physics of the graphene lattice emulated in a ripple tank
Authors: Rössler J. , Rössler C. , Märki P. , Ensslin K. , Ihn T.
Published: August 2015

Using the example of graphene, we have extended the classic ripple tank experiment to illustrate the behavior of waves in periodic lattices. A loudspeaker driving air through a periodically perforated plate onto the tank's water surface creates wave patterns that are in agreement with numerical simulations and are explained in terms of solid state theory. From an educational point of view, the experiment provides an illustrative example of the concepts of reciprocal space and symmetry.
Artificial halos
Authors: Selmke Markus
Published: August 2015

Judged by their frequency and beauty, ice halos easily rival rainbows as a prominent atmospheric optics phenomenon. This article presents experimental halo demonstrations of varying complexity. Using a single commercially available hexagonal glass prism, a variety of artificial halos can be simulated. The experiments include laser beam path analysis, a modified classic spinning prism experiment, and a novel Monte-Carlo machine for three-dimensional rotations. Each of these experiments emulates different conditions of certain halo displays, and in combination, they allow a thorough understanding of these striking phenomena.
The spiderwheel: A new apparatus to demonstrate energy conservation and moment of inertia
Authors: Mears Matthew
Published: August 2015

A new rolling apparatus known as the spiderwheel is described, which allows for large changes in mass distribution (and hence moment of inertia) without anything being added to or removed from the body. A quantitative analysis of the rolling spiderwheel motion allows students to determine its moment of inertia and compare it with model systems such as a rotating point mass, a solid cylinder, and a thin rigid hoop. Despite the spiderwheel's complex geometry and multiple components, a simple point-mass model provides an excellent approximation.
“On Second Thoughts…”: Changes of Mind as an Indication of Competing Knowledge Structures
Authors: Wilson Kate F. , Low David J.
Published: August 2015

A review of student answers to diagnostic questions concerned with Newton's Laws showed a tendency for some students to change their answer to a question when the following question caused them to think more about the situation. We investigate this behavior and interpret it in the framework of the resource model; in particular, a weak Newton's Third Law structure being dominated by an inconsistent Newton's Second Law (or “Net Force”) structure, in the absence of a strong, consistent Newtonian structure. This observation highlights the hidden problem in instruction where the implicit use of Newton's Third Law is dominated by the explicit conceptual and mathematical application of Newton's Second Law, both within individual courses and across a degree program. To facilitate students' development of a consistent Newtonian knowledge structure, it is important that instructors highlight the interrelated nature of Newton's Laws in problem solving.
Hierarchical Ni-Mo-S nanosheets on carbon fiber cloth: A flexible electrode for efficient hydrogen generation in neutral electrolyte
Authors: Miao Jianwei , Xiao Fang-Xing , Yang Hong Bin , Khoo Si Yun , Chen Jiazang , Fan Zhanxi , Hsu Ying-Ya , Chen Hao Ming , Zhang Hua , Liu Bin
Published: August 2015

A flexible cloth-like electrode, which can efficiently split water to produce H
2
at neutral pH, is successfully demonstrated.
“Newton’s cradle” proton relay with amide–imidic acid tautomerization in inverting cellulase visualized by neutron crystallography
Authors: Nakamura Akihiko , Ishida Takuya , Kusaka Katsuhiro , Yamada Taro , Fushinobu Shinya , Tanaka Ichiro , Kaneko Satoshi , Ohta Kazunori , Tanaka Hiroaki , Inaka Koji , Higuchi Yoshiki , Niimura Nobuo , Samejima Masahiro , Igarashi Kiyohiko
Published: August 2015

A study of the visualization of proton relay in cellulase by neutron crystallography.
Control of coupled oscillator networks with application to microgrid technologies
Authors: Skardal Per Sebastian , Arenas Alex
Published: August 2015

Nonlinear control is applied to coupled oscillator networks to attain full synchronization.
Nanodiamonds: The intersection of nanotechnology, drug development, and personalized medicine
Authors: Ho Dean , Wang Chung-Huei Katherine , Chow Edward Kai-Hua
Published: August 2015

A method of developing new cancer therapies with nanodiamonds.
Abrupt recent trend changes in atmospheric nitrogen dioxide over the Middle East
Authors: Lelieveld Jos , Beirle Steffen , Hörmann Christoph , Stenchikov Georgiy , Wagner Thomas
Published: August 2015

Space observations of the Middle East show that geopolitics and armed conflict have drastically altered air pollution emissions.
Unified understanding of superconductivity and Mott transition in alkali-doped fullerides from first principles
Authors: Nomura Yusuke , Sakai Shiro , Capone Massimo , Arita Ryotaro
Published: August 2015

A quantitative theory unveils unique synergy of phonons and electron correlations behind exotic pairing next to the Mott phase.
The Ocean as a Global Reservoir of Antibiotic Resistance Genes
Authors: Hatosy Stephen M. , Martiny Adam C.
Published: August 2015

Recent studies of natural environments have revealed vast genetic reservoirs of antibiotic resistance (AR) genes. Soil bacteria and human pathogens share AR genes, and AR genes have been discovered in a variety of habitats. However, there is little knowledge about the presence and diversity of AR genes in marine environments and which organisms host AR genes. To address this, we identified the diversity of genes conferring resistance to ampicillin, tetracycline, nitrofurantoin, and sulfadimethoxine in diverse marine environments using functional metagenomics (the cloning and screening of random DNA fragments). Marine environments were host to a diversity of AR-conferring genes. Antibiotic-resistant clones were found at all sites, with 28% of the genes identified as known AR genes (encoding beta-lactamases, bicyclomycin resistance pumps, etc.). However, the majority of AR genes were not previously classified as such but had products similar to proteins such as transport pumps, oxidoreductases, and hydrolases. Furthermore, 44% of the genes conferring antibiotic resistance were found in abundant marine taxa (e.g.,
Pelagibacter
,
Prochlorococcus
, and
Vibrio
). Therefore, we uncovered a previously unknown diversity of genes that conferred an AR phenotype among marine environments, which makes the ocean a global reservoir of both clinically relevant and potentially novel AR genes.
Stability of Secondary and Tertiary Structures of Virus-Like Particles Representing Noroviruses: Effects of pH, Ionic Strength, and Temperature and Implications for Adhesion to Surfaces
Authors: Samandoulgou Idrissa , Hammami Riadh , Morales Rayas Rocio , Fliss Ismail , Jean Julie
Published: August 2015

Loss of ordered molecular structure in proteins is known to increase their adhesion to surfaces. The aim of this work was to study the stability of norovirus secondary and tertiary structures and its implications for viral adhesion to fresh foods and agrifood surfaces. The pH, ionic strength, and temperature conditions studied correspond to those prevalent in the principal vehicles of viral transmission (vomit and feces) and in the food processing and handling environment (pasteurization and refrigeration). The structures of virus-like particles representing GI.1, GII.4, and feline calicivirus (FCV) were studied using circular dichroism and intrinsic UV fluorescence. The particles were remarkably stable under most of the conditions. However, heating to 65°C caused losses of β-strand structure, notably in GI.1 and FCV, while at 75°C the α-helix content of GII.4 and FCV decreased and tertiary structures unfolded in all three cases. Combining temperature with pH or ionic strength caused variable losses of structure depending on the particle type. Regardless of pH, heating to pasteurization temperatures or higher would be required to increase GII.4 and FCV adhesion, while either low or high temperatures would favor GI.1 adhesion. Regardless of temperature, increased ionic strength would increase GII.4 adhesion but would decrease GI.1 adhesion. FCV adsorption would be greater at refrigeration, pasteurization, or high temperature combined with a low salt concentration or at a higher NaCl concentration regardless of temperature. Norovirus adhesion mediated by hydrophobic interaction may depend on hydrophobic residues normally exposed on the capsid surface at pH 3, pH 8, physiological ionic strength, and low temperature, while at pasteurization temperatures it may rely more on buried hydrophobic residues exposed upon structural rearrangement.
Pseudomonas aeruginosa and Achromobacter sp. Clonal Selection Leads to Successive Waves of Contamination of Water in Dental Care Units
Authors: Abdouchakour Fatima , Dupont Chloé , Grau Delphine , Aujoulat Fabien , Mournetas Patricia , Marchandin Hélène , Parer Sylvie , Gibert Philippe , Valcarcel Jean , Jumas-Bilak Estelle
Published: August 2015

Dental care unit waterlines (DCUWs) consist of complex networks of thin tubes that facilitate the formation of microbial biofilms. Due to the predilection toward a wet environment, strong adhesion, biofilm formation, and resistance to biocides,
Pseudomonas aeruginosa
, a major human opportunistic pathogen, is adapted to DCUW colonization. Other nonfermentative Gram-negative bacilli, such as members of the genus
Achromobacter
, are emerging pathogens found in water networks. We reported the 6.5-year dynamics of bacterial contamination of waterlines in a dental health care center with 61 dental care units (DCUs) connected to the same water supply system. The conditions allowed the selection and the emergence of clones of
Achromobacter
sp. and
P. aeruginosa
characterized by multilocus sequence typing, multiplex repetitive elements-based PCR, and restriction fragment length polymorphism in pulsed-field gel electrophoresis, biofilm formation, and antimicrobial susceptibility. One clone of
P. aeruginosa
and 2 clones of
Achromobacter
sp. colonized successively all of the DCUWs: the last colonization by
P. aeruginosa
ST309 led to the closing of the dental care center. Successive dominance of species and clones was linked to biocide treatments.
Achromobacter
strains were weak biofilm producers compared to
P. aeruginosa
ST309, but the coculture of
P. aeruginosa
and
Achromobacter
enhanced
P. aeruginosa
ST309 biofilm formation. Intraclonal genomic microevolution was observed in the isolates of
P. aeruginosa
ST309 collected chronologically and in
Achromobacter
sp. clone A. The contamination control was achieved by a complete reorganization of the dental health care center by removing the connecting tubes between DCUs.
Housefly Larva Vermicomposting Efficiently Attenuates Antibiotic Resistance Genes in Swine Manure, with Concomitant Bacterial Population Changes
Authors: Wang Hang , Li Hongyi , Gilbert Jack A. , Li Haibo , Wu Longhua , Liu Meng , Wang Liling , Zhou Qiansheng , Yuan Junxiang , Zhang Zhijian
Published: August 2015

Manure from swine treated with antimicrobials as feed additives is a major source for the expansion of the antibiotic resistance gene (ARG) reservoir in the environment. Vermicomposting via housefly larvae (
Musca domestica
) can be efficiently used to treat manure and regenerate biofertilizer, but few studies have investigated its effect on ARG attenuation. Here, we tracked the abundances of 9 ARGs and the composition and structure of the bacterial communities in manure samples across 6 days of full-scale manure vermicomposting. On day 6, the abundances of genes encoding tetracycline resistance [
tet
(M),
tet
(O),
tet
(Q), and
tet
(W)] were reduced (
P
< 0.05), while those of genes encoding sulfonamide resistance (
sul1
and
sul2
) were increased (
P
< 0.05) when normalized to 16S rRNA. The abundances of tetracycline resistance genes were correlated (
P
< 0.05) with the changing concentrations of tetracyclines in the manure. The overall diversity and richness of the bacteria significantly decreased during vermicomposting, accompanied by a 100 times increase in the relative abundance of
Flavobacteriaceae
spp. Variations in the abundances of ARGs were correlated with the changing microbial community structure and the relative abundances of the family
Ruminococcaceae
, class
Bacilli
, or phylum
Proteobacteria
. Vermicomposting, as a waste management practice, can reduce the overall abundance of ARGs. More research is warranted to assess the use of this waste management practice as a measure to attenuate the dissemination of antimicrobial residues and ARGs from livestock production before vermicompost can be safely used as biofertilizer in agroecosystems.
Evolutionary Aspects of Emerging Lyme Disease in Canada
Authors: Ogden N. H. , Feil E. J. , Leighton P. A. , Lindsay L. R. , Margos G. , Mechai S. , Michel P. , Moriarty T. J.
Published: August 2015

In North America, Lyme disease (LD) is a tick-borne zoonosis caused by the spirochete bacterium
Borrelia burgdorferi
sensu stricto
, which is maintained by wildlife. Tick vectors and bacteria are currently spreading into Canada and causing increasing numbers of cases of LD in humans and raising a pressing need for public health responses. There is no vaccine, and LD prevention depends on knowing who is at risk and informing them how to protect themselves from infection. Recently, it was found in the United States that some strains of
B. burgdorferi
sensu stricto
cause severe disease, whereas others cause mild, self-limiting disease. While many strains occurring in the United States also occur in Canada, strains in some parts of Canada are different from those in the United States. We therefore recognize a need to identify which strains specific to Canada can cause severe disease and to characterize their geographic distribution to determine which Canadians are particularly at risk. In this review, we summarize the history of emergence of LD in North America, our current knowledge of
B. burgdorferi
sensu stricto
diversity, its intriguing origins in the ecology and evolution of the bacterium, and its importance for the epidemiology and clinical and laboratory diagnosis of LD. We propose methods for investigating associations between
B. burgdorferi
sensu stricto
diversity, ecology, and pathogenicity and for developing predictive tools to guide public health interventions. We also highlight the emergence of
B. burgdorferi
sensu stricto
in Canada as a unique opportunity for exploring the evolutionary aspects of tick-borne pathogen emergence.
Experimental Evolution of Enhanced Growth by Bacillus subtilis at Low Atmospheric Pressure: Genomic Changes Revealed by Whole-Genome Sequencing
Authors: Waters Samantha M. , Zeigler Daniel R. , Nicholson Wayne L.
Published: August 2015

Knowledge of how microorganisms respond and adapt to low-pressure (LP) environments is limited. Previously,
Bacillus subtilis
strain WN624 was grown at the near-inhibitory LP of 5 kPa for 1,000 generations and strain WN1106, which exhibited increased relative fitness at 5 kPa, was isolated. Genomic sequence differences between ancestral strain WN624 and LP-evolved strain WN1106 were identified using whole-genome sequencing. LP-evolved strain WN1106 carried amino acid-altering mutations in the coding sequences of only seven genes (
fliI
,
parC
,
ytoI
,
bacD
,
resD
,
walK
, and
yvlD
) and a single 9-nucleotide in-frame deletion in the
rnjB
gene that encodes RNase J2, a component of the RNA degradosome. By using a collection of frozen stocks of the LP-evolved culture taken at 50-generation intervals, it was determined that (i) the fitness increase at LP occurred rapidly, while (ii) mutation acquisition exhibited complex kinetics. A knockout mutant of
rnjB
was shown to increase the competitive fitness of
B. subtilis
at both LP and standard atmospheric pressure.
FleQ Coordinates Flagellum-Dependent and -Independent Motilities in Pseudomonas syringae pv. tomato DC3000
Authors: Nogales Joaquina , Vargas Paola , Farias Gabriela A. , Olmedilla Adela , Sanjuán Juan , Gallegos María-Trinidad
Published: August 2015

Motility plays an essential role in bacterial fitness and colonization in the plant environment, since it favors nutrient acquisition and avoidance of toxic substances, successful competition with other microorganisms, the ability to locate the preferred hosts, access to optimal sites within them, and dispersal in the environment during the course of transmission. In this work, we have observed that the mutation of the flagellar master regulatory gene,
fleQ
, alters bacterial surface motility and biosurfactant production, uncovering a new type of motility for
Pseudomonas syringae
pv. tomato DC3000 on semisolid surfaces. We present evidence that
P. syringae
pv. tomato DC3000 moves over semisolid surfaces by using at least two different types of motility, namely, swarming, which depends on the presence of flagella and syringafactin, a biosurfactant produced by this strain, and a flagellum-independent surface spreading or sliding, which also requires syringafactin. We also show that FleQ activates flagellum synthesis and negatively regulates syringafactin production in
P. syringae
pv. tomato DC3000. Finally, it was surprising to observe that mutants lacking flagella or syringafactin were as virulent as the wild type, and only the simultaneous loss of both flagella and syringafactin impairs the ability of
P. syringae
pv. tomato DC3000 to colonize tomato host plants and cause disease.
Mucosa-Associated Faecalibacterium prausnitzii Phylotype Richness Is Reduced in Patients with Inflammatory Bowel Disease
Authors: Lopez-Siles Mireia , Martinez-Medina Margarita , Abellà Carles , Busquets David , Sabat-Mir Miriam , Duncan Sylvia H. , Aldeguer Xavier , Flint Harry J. , Garcia-Gil L. Jesús
Published: August 2015

Faecalibacterium prausnitzii
depletion in intestinal diseases has been extensively reported, but little is known about intraspecies variability. This work aims to determine if subjects with gastrointestinal disease host mucosa-associated
F. prausnitzii
populations different from those hosted by healthy individuals. A new species-specific PCR-denaturing gradient gel electrophoresis (PCR-DGGE) method targeting the 16S rRNA gene was developed to fingerprint
F. prausnitzii
populations in biopsy specimens from 31 healthy control (H) subjects and 36 Crohn's disease (CD), 23 ulcerative colitis (UC), 6 irritable bowel syndrome (IBS), and 22 colorectal cancer (CRC) patients. The richness of
F. prausnitzii
subtypes was lower in inflammatory bowel disease (IBD) patients than in H subjects. The most prevalent operational taxonomic units (OTUs) consisted of four phylotypes (OTUs with a 99% 16S rRNA gene sequence similarity [OTU99]), which were shared by all groups of patients. Their distribution and the presence of some disease-specific
F. prausnitzii
phylotypes allowed us to differentiate the populations in IBD and CRC patients from that in H subjects. At the level of a minimum similarity of 97% (OTU97), two phylogroups accounted for 98% of the sequences. Phylogroup I was found in 87% of H subjects but in under 50% of IBD patients (
P
= 0.003). In contrast, phylogroup II was detected in >75% of IBD patients and in only 52% of H subjects (
P
= 0.005). This study reveals that even though the main members of the
F. prausnitzii
population are present in both H subjects and individuals with gut diseases, richness is reduced in the latter and an altered phylotype distribution exists between diseases. This approach may serve as a basis for addressing the suitability of
F. prausnitzii
phylotypes to be quantified as a putative biomarker of disease and depicting the importance of the loss of these subtypes in disease pathogenesis.
Light-Dependent Sulfide Oxidation in the Anoxic Zone of the Chesapeake Bay Can Be Explained by Small Populations of Phototrophic Bacteria
Authors: Findlay Alyssa J. , Bennett Alexa J. , Hanson Thomas E. , Luther George W.
Published: August 2015

Microbial sulfide oxidation in aquatic environments is an important ecosystem process, as sulfide is potently toxic to aerobic organisms. Sulfide oxidation in anoxic waters can prevent the efflux of sulfide to aerobic water masses, thus mitigating toxicity. The contribution of phototrophic sulfide-oxidizing bacteria to anaerobic sulfide oxidation in the Chesapeake Bay and the redox chemistry of the stratified water column were investigated in the summers of 2011 to 2014. In 2011 and 2013, phototrophic sulfide-oxidizing bacteria closely related to
Prosthecochloris
species of the phylum
Chlorobi
were cultivated from waters sampled at and below the oxic-anoxic interface, where measured light penetration was sufficient to support populations of low-light-adapted photosynthetic bacteria. In 2012, 2013, and 2014, light-dependent sulfide loss was observed in freshly collected water column samples. In these samples, extremely low light levels caused 2- to 10-fold increases in the sulfide uptake rate over the sulfide uptake rate under dark conditions. An enrichment, CB11, dominated by
Prosthecochloris
species, oxidized sulfide with a

K
s

value of 11 μM and a
V
max
value of 51 μM min
−1
(mg protein
−1
). Using these kinetic values with
in situ
sulfide concentrations and light fluxes, we calculated that a small population of
Chlorobi
similar to those in enrichment CB11 can account for the observed anaerobic light-dependent sulfide consumption activity in natural water samples. We conclude that
Chlorobi
play a far larger role in the Chesapeake Bay than currently appreciated. This result has potential implications for coastal anoxic waters and expanding oxygen-minimum zones as they begin to impinge on the photic zone.
Quantitative Microbial Ecology through Stable Isotope Probing
Authors: Hungate Bruce A. , Mau Rebecca L. , Schwartz Egbert , Caporaso J. Gregory , Dijkstra Paul , van Gestel Natasja , Koch Benjamin J. , Liu Cindy M. , McHugh Theresa A. , Marks Jane C. , Morrissey Ember M. , Price Lance B.
Published: August 2015

Bacteria grow and transform elements at different rates, and as yet, quantifying this variation in the environment is difficult. Determining isotope enrichment with fine taxonomic resolution after exposure to isotope tracers could help, but there are few suitable techniques. We propose a modification to
s
table
i
sotope
p
robing (SIP) that enables the isotopic composition of DNA from individual bacterial taxa after exposure to isotope tracers to be determined. In our modification, after isopycnic centrifugation, DNA is collected in multiple density fractions, and each fraction is sequenced separately. Taxon-specific density curves are produced for labeled and nonlabeled treatments, from which the shift in density for each individual taxon in response to isotope labeling is calculated. Expressing each taxon's density shift relative to that taxon's density measured without isotope enrichment accounts for the influence of nucleic acid composition on density and isolates the influence of isotope tracer assimilation. The shift in density translates quantitatively to isotopic enrichment. Because this revision to SIP allows quantitative measurements of isotope enrichment, we propose to call it quantitative stable isotope probing (qSIP). We demonstrated qSIP using soil incubations, in which soil bacteria exhibited strong taxonomic variations in
18
O and
13
C composition after exposure to [
18
O]water or [
13
C]glucose. The addition of glucose increased the assimilation of
18
O into DNA from [
18
O]water. However, the increase in
18
O assimilation was greater than expected based on utilization of glucose-derived carbon alone, because the addition of glucose indirectly stimulated bacteria to utilize other substrates for growth. This example illustrates the benefit of a quantitative approach to stable isotope probing.
Cerium Regulates Expression of Alternative Methanol Dehydrogenases in Methylosinus trichosporium OB3b
Authors: Farhan Ul Haque Muhammad , Kalidass Bhagyalakshmi , Bandow Nathan , Turpin Erick A. , DiSpirito Alan A. , Semrau Jeremy D.
Published: August 2015

Methanotrophs have multiple methane monooxygenases that are well known to be regulated by copper, i.e., a “copper switch.” At low copper/biomass ratios the soluble methane monooxygenase (sMMO) is expressed while expression and activity of the particulate methane monooxygenase (pMMO) increases with increasing availability of copper. In many methanotrophs there are also multiple methanol dehydrogenases (MeDHs), one based on Mxa and another based on Xox. Mxa-MeDH is known to have calcium in its active site, while Xox-MeDHs have been shown to have rare earth elements in their active site. We show here that the expression levels of Mxa-MeDH and Xox-MeDH in
Methylosinus trichosporium
OB3b significantly decreased and increased, respectively, when grown in the presence of cerium but the absence of copper compared to the absence of both metals. Expression of sMMO and pMMO was not affected. In the presence of copper, the effect of cerium on gene expression was less significant, i.e., expression of Mxa-MeDH in the presence of copper and cerium was slightly lower than in the presence of copper alone, but Xox-MeDH was again found to increase significantly. As expected, the addition of copper caused sMMO and pMMO expression levels to significantly decrease and increase, respectively, but the simultaneous addition of cerium had no discernible effect on MMO expression. As a result, it appears Mxa-MeDH can be uncoupled from methane oxidation by sMMO in
M. trichosporium
OB3b but not from pMMO.
MIG1Regulates Resistance of Candida albicans against the Fungistatic Effect of Weak Organic Acids
Authors: Cottier Fabien , Tan Alrina Shin Min , Xu Xiaoli , Wang Yue , Pavelka Norman
Published: August 2015

Candida albicansis the leading cause of fungal infections; but it is also a member of the human microbiome, an ecosystem of thousands of microbial species potentially influencing the outcome of host-fungal interactions. Accordingly, antibacterial therapy raises the risk of candidiasis, yet the underlying mechanism is currently not fully understood. We hypothesize the existence of bacterial metabolites that normally controlC. albicansgrowth and of fungal resistance mechanisms against these metabolites. Among the most abundant microbiota-derived metabolites found on human mucosal surfaces are weak organic acids (WOAs), such as acetic, propionic, butyric, and lactic acid. Here, we used quantitative growth assays to investigate the dose-dependent fungistatic properties of WOAs onC. albicansgrowth and found inhibition of growth to occur at physiologically relevant concentrations and pH values. This effect was conserved across distantly related fungal species both inside and outside the CTG clade. We next screened a library of transcription factor mutants and identified several genes required for the resistance ofC. albicansto one or more WOAs. A single gene,MIG1, previously known for its role in glucose repression, conferred resistance against all four acids tested. Consistent with glucose being an upstream activator of Mig1p, the presence of this carbon source was required for WOA resistance in wild-typeC. albicans. Conversely, aMIG1-complemented strain completely restored the glucose-dependent resistance against WOAs. We conclude that Mig1p plays a central role in orchestrating a transcriptional program to fight against the fungistatic effect of this class of highly abundant metabolites produced by the gastrointestinal tract microbiota.
Head injury from falls in children younger than 6 years of age
Authors: Burrows P , Trefan L , Houston R , Hughes J , Pearson G , Edwards R J , Hyde P , Maconochie I , Parslow R C , Kemp A M
Published: August 2015

The risk of serious head injury (HI) from a fall in a young child is ill defined. The relationship between the object fallen from and prevalence of intracranial injury (ICI) or skull fracture is described.

Method

Cross-sectional study of HIs from falls in children (<6 years) admitted to UK hospitals, analysed according to the object fallen from and associated Glasgow Coma Score (GCS) or alert, voice, pain, unresponsive (AVPU) and CT scan results.

Results

Of 1775 cases ascertained (median age 18 months, 54.7% boys), 87% (1552) had a GCS=15/AVPU=alert. 19.3% (342) had a CT scan: 32% (110/342) were abnormal; equivalent to 5.9% of the overall population, 16.9% (58) had isolated skull fractures and 13.7% (47) had ICI (49% (23/47) had an associated skull fracture). The prevalence of ICI increased with neurological compromise; however, 12% of children with a GCS=15/AVPU=alert had ICI. When compared to falls from standing, falls from a person's arms (233 children (mean age 1 year)) had a significant relative OR for a skull fracture/ICI of 6.94 (95% CI 3.54 to 13.6), falls from a building (eg, window or attic) (mean age 3 years) OR 6.84 (95% CI 2.65 to 17.6) and from an infant or child product (mean age 21 months) OR 2.75 (95% CI 1.36 to 5.65).

Conclusions

Most HIs from a fall in these children admitted to hospital were minor. Infants, dropped from a carer's arms, those who fell from infant products, a window, wall or from an attic had the greatest chance of ICI or skull fracture. These data inform prevention and the assessment of the likelihood of serious injury when the object fallen from is known.
Should children with overweight or obesity be excluded from height references?
Authors: Júlíusson Pétur B , Brannsether Bente , Kristiansen Hege , Hoppenbrouwers Karel , Bjerknes Robert , Roelants Mathieu
Published: August 2015

Background and objectives

Growth reference charts are usually based on measurements of children free from a medical condition that affects growth. However, samples collected during the past decades often contain a large proportion of overweight or obese children. Because obesity increases linear growth, the question arises to what extent the percentiles curves for length/height are affected by the presence of children with overweight or obesity.

Methods

Data from two cross-sectional samples of 2-year-old to 18-year-old children were analysed: 12 252 Belgian children, measured in 2002–2004, and 6159 Norwegian children, measured in 2003–2006. The LMS method was used to estimate height-for-age curves with and without children considered overweight or obese according to the International Obesity Task Force thresholds.

Results

The prevalence of overweight (including obesity) and obesity was 13.0% and 2.8% in the Belgian and 13.8% and 2.3% in the Norwegian sample. Children were taller when overweight (+0.49 and 0.43 SD, in the Belgian and Norwegian sample, respectively) or obese (+0.73 and 0.72 SD in the Belgian and Norwegian sample, respectively). Effect sizes were smaller in younger and older children, which points to an advanced age of maturation as a possible cause. Excluding overweight and obese children had only a minor impact on the growth curves with largest difference in mean height SD scores −0.09 in the Belgian and −0.12 in the Norwegian sample with a corresponding increase of up to 0.5% and 1.2% in number of children >+2 SD.

Conclusions

Current Belgian and Norwegian growth references for length/height were found to be largely unaffected by the current proportion of overweight and obese children. There is, therefore, no need for revised height charts that exclude overweight or obese children.
Presentation of childhood cancers to a paediatric shared care unit
Authors: Roskin Jeremy , Diviney James , Nanduri Vasanta
Published: August 2015

Objective

To describe the pathways by which children with cancer present to a shared care oncology unit.

Design

A population-based retrospective cohort study of children diagnosed with cancer between the years 2004 and 2014.

Setting

District General Hospital with a level 2 Paediatric Oncology Shared Care Unit.

Patients

93 children aged 0–15 years.

Outcome measures

Time to presentation (TTP) was defined as time from initial symptoms to time seen by secondary paediatrics. Time to diagnosis (TTD) was defined as time from initial symptoms to diagnosis at a Principal Treatment Centre. Patient pathways to diagnosis were mapped and routes for different cancers were compared.

Results

Only 2/93 cases (2.1%) in 10 years were referred via the 2-week pathway. Most presentations were acute via immediate general practitioner (GP) referral or self-referral to the emergency department 62/93 (67%). Leukaemia presented acutely and via the GP more often than via self-presentation to the emergency department 21/28 (75% vs 25%), while solid tumours were self-referred to the emergency department 21/34 (62% vs 38%) more often than via the GP. TTP and TTD were calculated for 87 patients. Wilms’ tumour demonstrated the shortest median TTP of 7 days and TTD of 16 days. Lymphoma had the longest TTD, with TTP 107 days and TTD 120 days. Pathways to diagnosis via other specialties were longer.

Conclusion

The majority of children diagnosed with cancer present via acute services, with the route varying between tumour types. Only two cases in 10 years were referred via the 2-week pathway, thus challenging its relevance in the paediatric population.
A Meckel's diverticulum presenting as pyogenic liver abscesses
Authors: Field Patrick , Umer Affan , Mecca-Monahan Mary Ann , Tandon Rajnish
Published: August 2015

Meckel's diverticula are the most common congenital malformation of the small intestine. The condition is rarely symptomatic and is usually an incidental finding during surgery. Bleeding in children and obstruction in adults are the most common symptomatic presentations. Our case involves a 50-year-old man with multiple pyogenic liver abscesses due to a Meckel's diverticulum. The abscesses were percutaneously drained and the diverticulum was eventually resected. Pyogenic liver abscess is a very rare presentation of a Meckel's diverticulum. The diverticulum in our case appeared to have a thickened wall on imaging but no signs of acute inflammation were present on the CT scan or noticed intraoperatively. It was presumed to be the possible source as all other possibilities were ruled out. Ultimately, the surgical pathology revealed acute inflammation and focal abscess. We propose that elective resection of a Meckel's diverticulum should be considered in the setting of pyogenic liver abscess with no other identifiable source.
Risk factors for under-5 mortality: evidence from Bangladesh Demographic and Health Survey, 2004–2011
Authors: Abir Tanvir , Agho Kingsley Emwinyore , Page Andrew Nicolas , Milton Abul Hasnat , Dibley Michael John
Published: August 2015

Objective

The aim of this study was to identify factors associated with mortality in children under 5 years of age using a nationally representative sample of singleton births for the period of 2004–2011.

Design, setting and participants

Pooled 2004, 2007 and 2011 cross-sectional data sets of the Bangladesh Demographic and Health Surveys were analysed. The surveys used a stratified two-stage cluster sample of 16 722 singleton live-born infants of the most recent birth of a mother within a 3-year period.

Main outcome measures

Outcome measures were neonatal mortality (0–30 days), postneonatal mortality (1–11 months), infant mortality (0–11 months), child mortality (1–4 years) and under-5 mortality (0–4 years).

Results

Survival information for 16 722 singleton live-born infants and 522 deaths of children <5 years of age included: 310 neonatal deaths, 154 postneonatal deaths, 464 infant deaths, 58 child deaths and 522 under-5 deaths. Multiple variable analysis showed that, over a 7-year period, mortality reduced significantly by 48% for postneonatal deaths, 33% for infant deaths and 29% for under-5 deaths, but there was no significant reduction in neonatal deaths (adjusted OR (AOR)=0.79, 95% CI 0.59 to 1.06) or child deaths (AOR=1.00, 95% CI 0.51 to 1.94). The odds of neonatal, postneonatal, infant, child and under-5 deaths decreased significantly among mothers who used contraceptive and mothers who had other children aged 3 years or older. The risk of neonatal, postneonatal, infant, child and under-5 deaths was significantly higher in mothers who reported a previous death of a sibling.

Conclusions

Our study suggests that family planning is needed to further reduce the overall rate of under-5 deaths in Bangladesh. To reduce childhood mortality, public health interventions that focus on child spacing and contraceptive use by mothers may be most effective.
The impact of distance and duration of travel on participation rates and participants’ satisfaction: results from a pilot study at one study centre in Pretest 2 of the German National Cohort
Authors: Schweitzer Aparna , Akmatov Manas K , Kindler Florentina , Kemmling Yvonne , Kreienbrock Lothar , Krause Gérard , Pessler Frank
Published: August 2015

Objectives

In this pilot study within the Pretest 2 phase of the German National Cohort, we aimed to (1) test the hypothesis that distance and duration of travel to a study centre may affect participation rates and participants’ satisfaction and (2) to obtain data that would help to select recruitment areas around the study centre Hannover with the greatest projected participation rate for the main study.

Setting

Mixed urban/suburban environment in Northern Germany with approximately 600 000 inhabitants. 4 recruitment areas with divergent estimated mean distances (range, 7–40 km) and duration of travel to the study centre Hannover were selected.

Participants

1050 men and women (ratio, 1:1), aged 20–69 years, were randomly selected from the population registries of the 4 recruitment areas and invited by mail to participate in the Pretest 2 study programme at the study centre Hannover, covering a variety of questionnaire-based and physical assessments. 166 individuals participated (16%).

Interventions

All 166 participants completed a travel questionnaire containing 5 items relating to travel duration and satisfaction, amounting to a participation rate of 100% in the questionnaire-based part of the study.

Results

Participation rates in the Pretest 2 programme at the study centre Hannover by area ranged from 11% (area farthest from the study centre, estimated median distance 38 km) to 18% (nearest area, 2 km). The odds of non-participation were highest in the area farthest from the study centre (adjusted OR 2.06; p=0.01; CI 1.28 to 3.32). Nonetheless, 97% of participants were satisfied with travel duration.

Conclusions

Increasing distance was associated with a lower participation rate. However, acceptance of duration of travel was high, irrespective of distance or duration. Thus, recruiting in farther away locations may select individuals with a greater frustration tolerance for travel to the study centre, perhaps due to a greater interest in participating in health-oriented studies and thus different health-related behaviour.