bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tungsten anode spectral model using interpolating cubic splines: Unfiltered x‐ray spectra from 20 kV to 640 kV
Authors: Hernandez Andrew M. , Boone John M. 
Published: March 2014

Purpose:Monte Carlo methods were used to generate lightly filtered high resolution x‐ray spectra spanning from 20 kV to 640 kV.Methods:X‐ray spectra were simulated for a conventional tungsten anode. The Monte Carlo N‐Particle eXtended radiation transport code (MCNPX 2.6.0) was used to produce 35 spectra over the tube potential range from 20 kV to 640 kV, and cubic spline interpolation procedures were used to create piecewise polynomials characterizing the photon fluence per energy bin as a function of x‐ray tube potential. Using these basis spectra and the cubic spline interpolation, 621 spectra were generated at 1 kV intervals from 20 to 640 kV. The tungsten anode spectral model using interpolating cubic splines (TASMICS) produces minimally filtered (0.8 mm Be) x‐ray spectra with 1 keV energy resolution. The TASMICS spectra were compared mathematically with other, previously reported spectra.Results:Using pairedt‐test analyses, no statistically significant difference (i.e., p > 0.05) was observed between compared spectra over energy bins above 1% of peak bremsstrahlung fluence. For all energy bins, the correlation of determination (R2) demonstrated good correlation for all spectral comparisons. The mean overall difference (MOD) and mean absolute difference (MAD) were computed over energy bins (above 1% of peak bremsstrahlung fluence) and over all the kV permutations compared. MOD and MAD comparisons with previously reported spectra were 2.7% and 9.7%, respectively (TASMIP), 0.1% and 12.0%, respectively [R. Birch and M. Marshall, “Computation of bremsstrahlung x‐ray spectra and comparison with spectra measured with a Ge(Li) detector,” Phys. Med. Biol. 24, – (1979)], 0.4% and 8.1%, respectively (Poludniowski), and 0.4% and 8.1%, respectively (AAPM TG 195). The effective energy of TASMICS spectra with 2.5 mm of added Al filtration ranged from 17 keV (at 20 kV) to 138 keV (at 640 kV); with 0.2 mm of added Cu filtration the effective energy was 9 keV at 20 kV and 169 keV at 640 kV.Conclusions:Ranging from 20 kV to 640 kV, 621 x‐ray spectra were produced and are available at 1 kV tube potential intervals. The spectra are tabulated at 1 keV intervals. TASMICS spectra were shown to be largely equivalent to published spectral models and are available in spreadsheet format for interested users by emailing the corresponding author (JMB).
Measurements and simulations of focused beam for orthovoltage therapy
Authors: Abbas Hassan , Mahato Dip N. , Satti Jahangir , MacDonald C. A. 
Published: March 2014

Purpose:Megavoltage photon beams are typically used for therapy because of their skin‐sparing effect. However, a focused low‐energy x‐ray beam would also be skin sparing, and would have a higher dose concentration at the focal spot. Such a beam can be produced with polycapillary optics. MCNP5 was used to model dose profiles for a scanned focused beam, using measured beam parameters. The potential of low energy focused x‐ray beams for radiation therapy was assessed.Methods:A polycapillary optic was used to focus the x‐ray beam from a tungsten source. The optic was characterized and measurements were performed at 50 kV. PMMA blocks of varying thicknesses were placed between optic and the focal spot to observe any variation in the focusing of the beam after passing through the tissue‐equivalent material. The measured energy spectrum was used to model the focused beam in MCNP5. A source card (SDEF) in MCNP5 was used to simulate the converging x‐ray beam. Dose calculations were performed inside a breast tissue phantom.Results:The measured focal spot size for the polycapillary optic was 0.2 mm with a depth of field of 5 mm. The measured focal spot remained unchanged through 40 mm of phantom thickness. The calculated depth dose curve inside the breast tissue showed a dose peak several centimeters below the skin with a sharp dose fall off around the focus. The percent dose falls below 10% within 5 mm of the focus. It was shown that rotating the optic during scanning would preserve the skin‐sparing effect of the focused beam.Conclusions:Low energy focused x‐ray beams could be used to irradiate tumors inside soft tissue within 5 cm of the surface.
Transcriptional and Phenotypic Responses of Listeria monocytogenes to Chlorine Dioxide
Authors: Pleitner Aaron M. , Trinetta Valentina , Morgan Mark T. , Linton Richard L. , Oliver Haley F. 
Published: March 2014

ABSTRACTSignificant food-borne disease outbreaks have occurred from consumption of ready-to-eat foods, including produce, contaminated withListeria monocytogenes. Challenging food matrices (e.g., cantaloupe, sprouts) with limited processing steps postharvest to reduce pathogen loads have underscored a need for new mitigation strategies. Chlorine dioxide (ClO2) is increasingly being used in produce and other food systems to reduce food-borne pathogen levels. The goal of this study was to characterize the transcriptional response and survival ofL. monocytogenes10403S exposed to ClO2. The transcriptional profile of log-phase cells exposed to 300 mg/liter ClO2for 15 min was defined by whole-genome microarray. A total of 340 genes were significantly differentially expressed. Among the differentially expressed genes, 223 were upregulated (fold change ≥ 1.5; adjustedPvalue < 0.05) in role categories responsible for protein fate, cellular processes, and energy metabolism. There were 113 and 16 genes differentially expressed belonging to regulatory networks of σBand CtsR, respectively. We assessedL. monocytogenes10403S survival after exposure to 100, 300, and 500 mg/liter aqueous ClO2in brain heart infusion (BHI) broth; there was a significant difference between cells exposed to 500 mg/liter ClO2and those exposed to all other conditions over time (Pvalue < 0.05). Isogenic ΔsigBand ΔctsRmutants exposed to 300 mg/liter ClO2were more sensitive to ClO2than the wild type under the same conditions. These results provide an initial insight into the mechanisms thatL. monocytogenesemploys to survive sublethal ClO2and further our understanding of the inactivation mechanisms of this increasingly used sanitizer.
Nitrogen Utilization and Metabolism in Ruminococcus albus 8
Authors: Kim Jong Nam , Henriksen Emily DeCrescenzo , Cann Isaac K. O. , Mackie Roderick I. 
Published: March 2014

ABSTRACT

The model rumen
Firmicutes
organism
Ruminococcus albus
8 was grown using ammonia, urea, or peptides as the sole nitrogen source; growth was not observed with amino acids as the sole nitrogen source. Growth of
R. albus
8 on ammonia and urea showed the same growth rate (0.08 h
−1
) and similar maximum cell densities (for ammonia, the optical density at 600 nm [OD
600
] was 1.01; and for urea, the OD
600
was 0.99); however, growth on peptides resulted in a nearly identical growth rate (0.09 h
−1
) and a lower maximum cell density (OD
600
= 0.58). To identify differences in gene expression and enzyme activities, the transcript abundances of 10 different genes involved in nitrogen metabolism and specific enzyme activities were analyzed by harvesting mRNA and crude protein from cells at the mid- and late exponential phases of growth on the different N sources. Transcript abundances and enzyme activities varied according to nitrogen source, ammonia concentration, and growth phase. Growth of
R. albus
8 on ammonia and urea was similar, with the only observed difference being an increase in urease transcript abundance and enzyme activity in urea-grown cultures. Growth of
R. albus
8 on peptides showed a different nitrogen metabolism pattern, with higher gene transcript abundance levels of
gdhA
,
glnA
,
gltB
,
amtB
,
glnK
, and
ureC
, as well as higher activities of glutamate dehydrogenase and urease. These results demonstrate that ammonia, urea, and peptides can all serve as nitrogen sources for
R. albus
and that nitrogen metabolism genes and enzyme activities of
R. albus
8 are regulated by nitrogen source and the level of ammonia in the growth medium.
Genomic and Transcriptomic Analyses of the Facultative Methanotroph Methylocystis sp. Strain SB2 Grown on Methane or Ethanol
Authors: Vorobev Alexey , Jagadevan Sheeja , Jain Sunit , Anantharaman Karthik , Dick Gregory J. , Vuilleumier Stéphane , Semrau Jeremy D. 
Published: March 2014

ABSTRACT

A minority of methanotrophs are able to utilize multicarbon compounds as growth substrates in addition to methane. The pathways utilized by these microorganisms for assimilation of multicarbon compounds, however, have not been explicitly examined. Here, we report the draft genome of the facultative methanotroph
Methylocystis
sp. strain SB2 and perform a detailed transcriptomic analysis of cultures grown with either methane or ethanol. Evidence for use of the canonical methane oxidation pathway and the serine cycle for carbon assimilation from methane was obtained, as well as for operation of the complete tricarboxylic acid (TCA) cycle and the ethylmalonyl-coenzyme A (EMC) pathway. Experiments with
Methylocystis
sp. strain SB2 grown on methane revealed that genes responsible for the first step of methane oxidation, the conversion of methane to methanol, were expressed at a significantly higher level than those for downstream oxidative transformations, suggesting that this step may be rate limiting for growth of this strain with methane. Further, transcriptomic analyses of
Methylocystis
sp. strain SB2 grown with ethanol compared to methane revealed that on ethanol (i) expression of the pathway of methane oxidation and the serine cycle was significantly reduced, (ii) expression of the TCA cycle dramatically increased, and (iii) expression of the EMC pathway was similar. Based on these data, it appears that
Methylocystis
sp. strain SB2 converts ethanol to acetyl-coenzyme A, which is then funneled into the TCA cycle for energy generation or incorporated into biomass via the EMC pathway. This suggests that some methanotrophs have greater metabolic flexibility than previously thought and that operation of multiple pathways in these microorganisms is highly controlled and integrated.
Biochar Enhances Aspergillus niger Rock Phosphate Solubilization by Increasing Organic Acid Production and Alleviating Fluoride Toxicity
Authors: Mendes Gilberto de Oliveira , Zafra David Lopez , Vassilev Nikolay Bojkov , Silva Ivo Ribeiro , Ribeiro José Ivo , Costa Maurício Dutra 
Published: March 2014

ABSTRACT

During fungal rock phosphate (RP) solubilization, a significant quantity of fluoride (F
−
) is released together with phosphorus (P), strongly inhibiting the process. In the present study, the effect of two F
−
adsorbents [activated alumina (Al
2
O
3
) and biochar] on RP solubilization by
Aspergillus niger
was examined. Al
2
O
3
adsorbed part of the F
−
released but also adsorbed soluble P, which makes it inappropriate for microbial RP solubilization systems. In contrast, biochar adsorbed only F
−
while enhancing phosphate solubilization 3-fold, leading to the accumulation of up to 160 mg of P per liter. By comparing the values of F
−
measured in solution at the end of incubation and those from a predictive model, it was estimated that up to 19 mg of F
−
per liter can be removed from solution by biochar when added at 3 g liter
−1
to the culture medium. Thus, biochar acted as an F
−
sink during RP solubilization and led to an F
−
concentration in solution that was less inhibitory to the process. In the presence of biochar,
A. niger
produced larger amounts of citric, gluconic, and oxalic acids, whether RP was present or not. Our results show that biochar enhances RP solubilization through two interrelated processes: partial removal of the released F
−
and increased organic acid production. Given the importance of organic acids for P solubilization and that most of the RPs contain high concentrations of F
−
, the proposed solubilization system offers an important technological improvement for the microbial production of soluble P fertilizers from RP.
Microbiota of Human Breast Tissue
Authors: Urbaniak Camilla , Cummins Joanne , Brackstone Muriel , Macklaim Jean M. , Gloor Gregory B. , Baban Chwanrow K. , Scott Leslie , O'Hanlon Deidre M. , Burton Jeremy P. , Francis Kevin P. , Tangney Mark , Reid Gregor 
Published: March 2014

ABSTRACT

In recent years, a greater appreciation for the microbes inhabiting human body sites has emerged. In the female mammary gland, milk has been shown to contain bacterial species, ostensibly reaching the ducts from the skin. We decided to investigate whether there is a microbiome within the mammary tissue. Using 16S rRNA sequencing and culture, we analyzed breast tissue from 81 women with and without cancer in Canada and Ireland. A diverse population of bacteria was detected within tissue collected from sites all around the breast in women aged 18 to 90, not all of whom had a history of lactation. The principal phylum was
Proteobacteria
. The most abundant taxa in the Canadian samples were
Bacillus
(11.4%),
Acinetobacter
(10.0%),
Enterobacteriaceae
(8.3%),
Pseudomonas
(6.5%),
Staphylococcus
(6.5%),
Propionibacterium
(5.8%),
Comamonadaceae
(5.7%),
Gammaproteobacteria
(5.0%), and
Prevotella
(5.0%). In the Irish samples the most abundant taxa were
Enterobacteriaceae
(30.8%),
Staphylococcus
(12.7%),
Listeria welshimeri
(12.1%),
Propionibacterium
(10.1%), and
Pseudomonas
(5.3%). None of the subjects had signs or symptoms of infection, but the presence of viable bacteria was confirmed in some samples by culture. The extent to which these organisms play a role in health or disease remains to be determined.
In Vivo
Self-Assembly of Stable Green Fluorescent Protein Fusion Particles and Their Uses in Enzyme Immobilization
Authors: Venning-Slater Mark , Hooks David O. , Rehm Bernd H. A. 
Published: March 2014

ABSTRACT

Bacterial inclusion bodies are aggregations of mostly inactive and misfolded proteins. However, previously the
in vivo
self-assembly of green fluorescent protein (GFP) fusions into fluorescent particles which displayed specific binding sites suitable for applications in bioseparation and diagnostics was demonstrated. Here, the suitability of GFP particles for enzyme immobilization was assessed. The enzymes tested were a thermostable α-amylase from
Bacillus licheniformis
,
N
-acetyl-
d
-neuraminic acid aldolase (NanA) from
Escherichia coli
, and organophosphohydrolase (OpdA) from
Agrobacterium radiobacter
. Respective GFP particles were isolated and could be stably maintained outside the cell. These enzyme-bearing GFP particles exhibited considerable stability across a range of temperature, pH, and storage conditions and could be recycled. The α-amylase-bearing particles retained activity after treatments at 4 to 85°C and at pHs 4 to 10, were stable for 3 months at 4°C, and could be recycled up to three times. OpdA-bearing particles retained degradation activity after treatments at 4 to 45°C and at pHs 5 to 10 and were able to be recycled up to four times. In contrast, the performance of NanA-bearing particles rapidly declined (>50% loss) after each recycling step and 3 months storage at 4°C. However, they were still able to convert
N
-acetylmannosamine and pyruvate to
N
-acetylneuraminic acid after treatment at 4 to 85°C and at pHs 4 to 11. Fluorescent GFP fusion particles represent a novel method for the immobilization and display of enzymes. Potential applications include diagnostic assays, biomass conversion, pharmaceutical production, and bioremediation.
Soil Microbial Responses to Increased Moisture and Organic Resources along a Salinity Gradient in a Polar Desert
Authors: Van Horn David J. , Okie Jordan G. , Buelow Heather N. , Gooseff Michael N. , Barrett John E. , Takacs-Vesbach Cristina D. 
Published: March 2014

ABSTRACT

Microbial communities in extreme environments often have low diversity and specialized physiologies suggesting a limited resistance to change. The McMurdo Dry Valleys (MDV) are a microbially dominated, extreme ecosystem currently undergoing climate change-induced disturbances, including the melting of massive buried ice, cutting through of permafrost by streams, and warming events. These processes are increasing moisture across the landscape, altering conditions for soil communities by mobilizing nutrients and salts and stimulating autotrophic carbon inputs to soils. The goal of this study was to determine the effects of resource addition (water/organic matter) on the composition and function of microbial communities in the MDV along a natural salinity gradient representing an additional gradient of stress in an already extreme environment. Soil respiration and the activity of carbon-acquiring extracellular enzymes increased significantly (
P
< 0.05) with the addition of resources at the low- and moderate-salinity sites but not the high-salinity site. The bacterial community composition was altered, with an increase in
Proteobacteria
and
Firmicutes
with water and organic matter additions at the low- and moderate-salinity sites and a near dominance of
Firmicutes
at the high-salinity site. Principal coordinate analyses of all samples using a phylogenetically informed distance matrix (UniFrac) demonstrated discrete clustering among sites (analysis of similarity [ANOSIM],
P
< 0.05 and
R
> 0.40) and among most treatments within sites. The results from this experimental work suggest that microbial communities in this environment will undergo rapid change in response to the altered resources resulting from climate change impacts occurring in this region.
High-Resolution Melt Analysis for Rapid Comparison of Bacterial Community Compositions
Authors: Hjelmsø Mathis Hjort , Hansen Lars Hestbjerg , Bælum Jacob , Feld Louise , Holben William E. , Jacobsen Carsten Suhr 
Published: March 2014

ABSTRACT
In the study of bacterial community composition, 16S rRNA gene amplicon sequencing is today among the preferred methods of analysis. The cost of nucleotide sequence analysis, including requisite computational and bioinformatic steps, however, takes up a large part of many research budgets. High-resolution melt (HRM) analysis is the study of the melt behavior of specific PCR products. Here we describe a novel high-throughput approach in which we used HRM analysis targeting the 16S rRNA gene to rapidly screen multiple complex samples for differences in bacterial community composition. We hypothesized that HRM analysis of amplified 16S rRNA genes from a soil ecosystem could be used as a screening tool to identify changes in bacterial community structure. This hypothesis was tested using a soil microcosm setup exposed to a total of six treatments representing different combinations of pesticide and fertilization treatments. The HRM analysis identified a shift in the bacterial community composition in two of the treatments, both including the soil fumigant Basamid GR. These results were confirmed with both denaturing gradient gel electrophoresis (DGGE) analysis and 454-based 16S rRNA gene amplicon sequencing. HRM analysis was shown to be a fast, high-throughput technique that can serve as an effective alternative to gel-based screening methods to monitor microbial community composition.
Large-Scale Intersubspecific Recombination in the Plant-Pathogenic Bacterium Xylella fastidiosa Is Associated with the Host Shift to Mulberry
Authors: Nunney Leonard , Schuenzel Erin L. , Scally Mark , Bromley Robin E. , Stouthamer Richard 
Published: March 2014

ABSTRACT

Homologous recombination plays an important role in the structuring of genetic variation of many bacteria; however, its importance in adaptive evolution is not well established. We investigated the association of intersubspecific homologous recombination (IHR) with the shift to a novel host (mulberry) by the plant-pathogenic bacterium
Xylella fastidiosa
. Mulberry leaf scorch was identified about 25 years ago in native red mulberry in the eastern United States and has spread to introduced white mulberry in California. Comparing a sequence of 8 genes (4,706 bp) from 21 mulberry-type isolates to published data (352 isolates representing all subspecies), we confirmed previous indications that the mulberry isolates define a group distinct from the 4 subspecies, and we propose naming the taxon
X. fastidiosa
subsp.
morus
. The ancestry of its gene sequences was mixed, with 4 derived from
X. fastidiosa
subsp.
fastidiosa
(introduced from Central America), 3 from
X. fastidiosa
subsp.
multiplex
(considered native to the United States), and 1 chimeric, demonstrating that this group originated by large-scale IHR. The very low within-type genetic variation (0.08% site polymorphism), plus the apparent inability of native
X. fastidiosa
subsp.
multiplex
to infect mulberry, suggests that this host shift was achieved after strong selection acted on genetic variants created by IHR. Sequence data indicate that a single ancestral IHR event gave rise not only to
X. fastidiosa
subsp.
morus
but also to the
X. fastidiosa
subsp.
multiplex
recombinant group which infects several hosts but is the only type naturally infecting blueberry, thus implicating this IHR in the invasion of at least two novel native hosts, mulberry and blueberry.
Improved HF183 Quantitative Real-Time PCR Assay for Characterization of Human Fecal Pollution in Ambient Surface Water Samples
Authors: Green Hyatt C. , Haugland Richard A. , Varma Manju , Millen Hana T. , Borchardt Mark A. , Field Katharine G. , Walters William A. , Knight R. , Sivaganesan Mano , Kelty Catherine A. , Shanks Orin C. 
Published: March 2014

ABSTRACT

Quantitative real-time PCR (qPCR) assays that target the human-associated HF183 bacterial cluster within members of the genus
Bacteroides
are among the most widely used methods for the characterization of human fecal pollution in ambient surface waters. In this study, we show that a current TaqMan HF183 qPCR assay (HF183/BFDrev) routinely forms nonspecific amplification products and introduce a modified TaqMan assay (HF183/BacR287) that alleviates this problem. The performance of each qPCR assay was compared in head-to-head experiments investigating limits of detection, analytical precision, predicted hybridization to 16S rRNA gene sequences from a reference database, and relative marker concentrations in fecal and sewage samples. The performance of the modified HF183/BacR287 assay is equal to or improves upon that of the original HF183/BFDrev assay. In addition, a qPCR chemistry designed to combat amplification inhibition and a multiplexed internal amplification control are included. In light of the expanding use of PCR-based methods that rely on the detection of extremely low concentrations of DNA template, such as qPCR and digital PCR, the new TaqMan HF183/BacR287 assay should provide more accurate estimations of human-derived fecal contaminants in ambient surface waters.