bluuebunny/crossref_metadata_2025_split huggingface dataset:
Experimental validation of a kilovoltage x‐ray source model for computing imaging dose
Authors: Poirier Yannick , Kouznetsov Alexei , Koger Brandon , Tambasco Mauro 
Published: March 2014

Purpose:To introduce and validate a kilovoltage (kV) x‐ray source model and characterization method to compute absorbed dose accrued from kV x‐rays.Methods:The authors propose a simplified virtual point source model and characterization method for a kV x‐ray source. The source is modeled by: (1) characterizing the spatial spectral and fluence distributions of the photons at a plane at the isocenter, and (2) creating a virtual point source from which photons are generated to yield the derived spatial spectral and fluence distribution at isocenter of an imaging system. The spatial photon distribution is determined by in‐air relative dose measurements along the transverse (x) and radial (y) directions. The spectrum is characterized using transverse axis half‐value layer measurements and the nominal peak potential (kVp). This source modeling approach is used to characterize a Varian® on‐board‐imager (OBI®) for four default cone‐beam CT beam qualities: beams using a half bowtie filter (HBT) with 110 and 125 kVp, and a full bowtie filter (FBT) with 100 and 125 kVp. The source model and characterization method was validated by comparing dose computed by the authors’ inhouse software (kVDoseCalc) to relative dose measurements in a homogeneous and a heterogeneous block phantom comprised of tissue, bone, and lung‐equivalent materials.Results:The characterized beam qualities and spatial photon distributions are comparable to reported values in the literature. Agreement between computed and measured percent depth‐dose curves is ⩽2% in the homogeneous block phantom and ⩽2.5% in the heterogeneous block phantom. Transverse axis profiles taken at depths of 2 and 6 cm in the homogeneous block phantom show an agreement within 4%. All transverse axis dose profiles in water, in bone, and lung‐equivalent materials for beams using a HBT, have an agreement within 5%. Measured profiles of FBT beams in bone and lung‐equivalent materials were higher than their computed counterparts resulting in an agreement within 2.5%, 5%, and 8% within solid water, bone, and lung, respectively.Conclusions:The proposed virtual point source model and characterization method can be used to compute absorbed dose in both the homogeneous and heterogeneous block phantoms within of 2%–8% of measured values, depending on the phantom and the beam quality. The authors’ results also provide experimental validation for their kV dose computation software, kVDoseCalc.
Deriving adaptive MRF coefficients from previous normal‐dose CT scan for low‐dose image reconstruction via penalized weighted least‐squares minimization
Authors: Zhang Hao , Han Hao , Wang Jing , Ma Jianhua , Liu Yan , Moore William , Liang Zhengrong 
Published: March 2014

Purpose:Repeated computed tomography (CT) scans are required for some clinical applications such as image‐guided interventions. To optimize radiation dose utility, a normal‐dose scan is often first performed to set up reference, followed by a series of low‐dose scans for intervention. One common strategy to achieve the low‐dose scan is to lower the x‐ray tube current and exposure time (mAs) or tube voltage (kVp) setting in the scanning protocol, but the resulted image quality by the conventional filtered back‐projection (FBP) method may be severely degraded due to the excessive noise. Penalized weighted least‐squares (PWLS) image reconstruction has shown the potential to significantly improve the image quality from low‐mAs acquisitions, where the penalty plays an important role. In this work, the authorsˈ explore an adaptive Markov random field (MRF)‐based penalty term by utilizing previous normal‐dose scan to improve the subsequent low‐dose scans image reconstruction.Methods:In this work, the authors employ the widely‐used quadratic‐form MRF as the penalty model and explore a novel idea of using the previous normal‐dose scan to obtain the MRF coefficients for adaptive reconstruction of the low‐dose images. In the coefficients determination, the authors further explore another novel idea of using the normal‐dose scan to obtain a scale map, which describes an optimal neighborhood for the coefficients determination such that a local uniform region has a small spread of frequency spectrum and, therefore, a small MRF window, andvice versa. The proposed penalty term is incorporated into the PWLS image reconstruction framework, and the low‐dose images are reconstructed via the PWLS minimization.Results:The presented adaptive MRF based PWLS algorithm was validated by physical phantom and patient data. The experimental results demonstrated that the presented algorithm is superior to the PWLS reconstruction using the conventional Gaussian MRF penalty or the edge‐preserving Huber penalty and the conventional FBP method, in terms of image noise reduction and edge/detail/contrast preservation.Conclusions:This study demonstrated the feasibility and efficacy of the proposed scheme in utilizing previous normal‐dose CT scan to improve the subsequent low‐dose scans.
Tumor detection in automated breast ultrasound images using quantitative tissue clustering
Authors: Moon Woo Kyung , Lo Chung‐Ming , Chen Rong‐Tai , Shen Yi‐Wei , Chang Jung Min , Huang Chiun‐Sheng , Chen Jeon‐Hor , Hsu Wei‐Wen , Chang Ruey‐Feng 
Published: March 2014

Purpose:A computer‐aided detection (CADe) system based on quantitative tissue clustering algorithm was proposed to identify potential tumors in automated breast ultrasound (ABUS) images.Methods:Our three‐dimensional (3D) ABUS images database included 148 biopsy‐verified lesions (size 0.4–7.9 cm; mean 1.76 cm). An ABUS volume was comprised of 229–282 slices of two‐dimensional (2D) images. For tumor detection, the fast 3D mean shift method was used to remove the speckle noise and the segment tissues with similar properties. The hypoechogenic regions, i.e., the tumor candidates, were extracted using fuzzy c‐means clustering. Seven features related to echogenicity and morphology were quantified and used to predict the likelihood of identifying a tumor and filtering out the false‐positive (FP) regions.Results:The sensitivity of the proposed CADe system achieved 89.19% (132/148) with 2.00 FPs per volume. For the volumes without lesion, the FP rate was 1.27. The sensitivity was 92.50% (74/80) for malignant tumors and 85.29% (58/68) for benign tumors.Conclusions:The proposed CADe system provides an automatic and quantitative procedure for tumor detection in ABUS images. Further studies are needed to reduce the FP rate of the CADe algorithm.
Computerized segmentation of pulmonary nodules depicted in CT examinations using freehand sketches
Authors: Qiang Yongqian , Wang Qiuping , Xu Guiping , Ma Hongxia , Deng Lei , Zhang Lei , Pu Jiantao , Guo Youmin 
Published: March 2014

Purpose:To aid a consistent segmentation of pulmonary nodules, the authors describe a novel computerized scheme that utilizes a freehand sketching technique and an improved break‐and‐repair strategy.Methods:This developed scheme consists of two primary parts. The first part is freehand sketch analysis, where the freehand sketching not only serves a natural way of specifying the location of a nodule, but also provides a mechanism for inferring adaptive information (e.g., the mass center, the density, and the size) in regard to the nodule. The second part is an improved break‐and‐repair strategy. The improvement avoids the time‐consuming ray‐triangle intersections using spherical bins and replaces the original global implicit surface reconstruction with a local implicit surface fitting and blending scheme. The performance of this scheme, including accuracy and consistence, was assessed using 50 CT examinations in the Lung Image Database Consortium (LIDC). For each of these examinations, a single nodule was selected under the aid of a publically available tool to assure these nodules were diverse in size, location, and density. Two radiologists were asked to use the developed tool to segment these nodules twice at different times (at least three months apart). A Hausdorff distance based method was used to assess the discrepancies (agreements) between the computerized results and the results by the four radiologists in the LIDC as well as the inter‐ and intrareader agreements in freehand sketching.Results:The maximum and mean discrepancies in boundary outlines between the computerized scheme and the radiologists were 2.73 ± 1.32 mm and 1.01 ± 0.47 mm, respectively. When the nodules were classified (binned) into different size ranges, the maximum errors ranged from 1.91 to 4.13 mm; but smaller nodules had larger percentage discrepancies in term of size. Under the aid of the developed scheme, the inter‐ and intrareader variability in averaged maximum discrepancy across all types of pulmonary nodules were consistently smaller than 0.15 ± 0.07 mm. The computational cost in time of segmenting a pulmonary nodule ranged from 0.4 to 2.3 s with an average of 1.1 s for a typical desktop computer.Conclusions:The experiments showed that this scheme could achieve a reasonable performance in nodule segmentation and demonstrated the merits of incorporating freehand sketching into pulmonary nodule segmentation.
Microbial Community Stratification Linked to Utilization of Carbohydrates and Phosphorus Limitation in a Boreal Peatland at Marcell Experimental Forest, Minnesota, USA
Authors: Lin Xueju , Tfaily Malak M. , Steinweg J. Megan , Chanton Patrick , Esson Kaitlin , Yang Zamin K. , Chanton Jeffrey P. , Cooper William , Schadt Christopher W. , Kostka Joel E. 
Published: March 2014

ABSTRACT

This study investigated the abundance, distribution, and composition of microbial communities at the watershed scale in a boreal peatland within the Marcell Experimental Forest (MEF), Minnesota, USA. Through a close coupling of next-generation sequencing, biogeochemistry, and advanced analytical chemistry, a biogeochemical hot spot was revealed in the mesotelm (30- to 50-cm depth) as a pronounced shift in microbial community composition in parallel with elevated peat decomposition. The relative abundance of
Acidobacteria
and the
Syntrophobacteraceae
, including known hydrocarbon-utilizing genera, was positively correlated with carbohydrate and organic acid content, showing a maximum in the mesotelm. The abundance of
Archaea
(primarily crenarchaeal groups 1.1c and 1.3) increased with depth, reaching up to 60% of total small-subunit (SSU) rRNA gene sequences in the deep peat below the 75-cm depth. Stable isotope geochemistry and potential rates of methane production paralleled vertical changes in methanogen community composition to indicate a predominance of acetoclastic methanogenesis mediated by the
Methanosarcinales
in the mesotelm, while hydrogen-utilizing methanogens predominated in the deeper catotelm. RNA-derived pyrosequence libraries corroborated DNA sequence data to indicate that the above-mentioned microbial groups are metabolically active in the mid-depth zone. Fungi showed a maximum in rRNA gene abundance above the 30-cm depth, which comprised only an average of 0.1% of total bacterial and archaeal rRNA gene abundance, indicating prokaryotic dominance. Ratios of C to P enzyme activities approached 0.5 at the acrotelm and catotelm, indicating phosphorus limitation. In contrast, P limitation pressure appeared to be relieved in the mesotelm, likely due to P solubilization by microbial production of organic acids and C-P lyases. Based on path analysis and the modeling of community spatial turnover, we hypothesize that P limitation outweighs N limitation at MEF, and microbial communities are structured by the dominant shrub,
Chamaedaphne calyculata
, which may act as a carbon source for major consumers in the peatland.
Development of a Homologous Expression System for and Systematic Site-Directed Mutagenesis Analysis of Thurincin H, a Bacteriocin Produced by Bacillus thuringiensis SF361
Authors: Wang Gaoyan , Manns David C. , Churey John J. , Worobo Randy W. 
Published: March 2014

ABSTRACT

Thurincin H is an antimicrobial peptide produced by
Bacillus thuringiensis
SF361. With a helical back bone, the 31 amino acids of thurincin H form a hairpin structure maintained by four pairs of very unique sulfur-to-α-carbon thioether bonds. The production of thurincin H depends on a putative gene cluster containing 10 open reading frames. The gene cluster includes three tandem structural genes (
thnA1
,
thnA2
, and
thnA3
) encoding three identical 40-amino-acid thurincin H prepeptides and seven other genes putatively responsible for prepeptide processing, regulation, modification, exportation, and self-immunity. A homologous thurincin H expression system was developed by transforming a thurincin H-deficient host with a novel expression vector, pGW133. The host, designated
B. thuringiensis
SF361 Δ
thnA1
Δ
thnA2
Δ
thnA3
, was constructed by deletion of the three tandem structural genes from the chromosome of the natural thurincin H producer. The thurincin H expression vector pGW133 was constructed by cloning the thurincin H native promoter,
thnA1
, and a Cry protein terminator into the
Escherichia coli
-
B. thuringiensis
shuttle vector pHT315. Thirty-three different pGW133 variants, each containing a different point mutation in the
thnA1
gene, were generated and separately transformed into
B. thuringiensis
SF361 Δ
thnA1
Δ
thnA2
Δ
thnA3
. Those site-directed mutants contained either a single radical or conservative amino acid substitution on the thioether linkage-forming positions or a radical substitution on all other nonalanine amino acids. The bacteriocin activities of
B. thuringiensis
SF361 Δ
thnA1
Δ
thnA2
Δ
thnA3
carrying different pGW133 variants against three different indicator strains were subsequently compared.
Directed Evolution of Unspecific Peroxygenase from Agrocybe aegerita
Authors: Molina-Espeja Patricia , Garcia-Ruiz Eva , Gonzalez-Perez David , Ullrich René , Hofrichter Martin , Alcalde Miguel 
Published: March 2014

ABSTRACT

Unspecific peroxygenase (UPO) represents a new type of heme-thiolate enzyme with self-sufficient mono(per)oxygenase activity and many potential applications in organic synthesis. With a view to taking advantage of these properties, we subjected the
Agrocybe aegerita
UPO1-encoding gene to directed evolution in
Saccharomyces cerevisiae
. To promote functional expression, several different signal peptides were fused to the mature protein, and the resulting products were tested. Over 9,000 clones were screened using an
ad hoc
dual-colorimetric assay that assessed both peroxidative and oxygen transfer activities. After 5 generations of directed evolution combined with hybrid approaches, 9 mutations were introduced that resulted in a 3,250-fold total activity improvement with no alteration in protein stability. A breakdown between secretion and catalytic activity was performed by replacing the native signal peptide of the original parental type with that of the evolved mutant; the evolved leader increased functional expression 27-fold, whereas an 18-fold improvement in the
k
cat
/

K
m

value for oxygen transfer activity was obtained. The evolved UPO1 was active and highly stable in the presence of organic cosolvents. Mutations in the hydrophobic core of the signal peptide contributed to enhance functional expression up to 8 mg/liter, while catalytic efficiencies for peroxidative and oxygen transfer reactions were increased by several mutations in the vicinity of the heme access channel. Overall, the directed-evolution platform described is a valuable point of departure for the development of customized UPOs with improved features and for the study of structure-function relationships.
Raman Spectroscopy of Microbial Pigments
Authors: Jehlička Jan , Edwards Howell G. M. , Oren Aharon 
Published: March 2014

ABSTRACTRaman spectroscopy is a rapid nondestructive technique providing spectroscopic and structural information on both organic and inorganic molecular compounds. Extensive applications for the method in the characterization of pigments have been found. Due to the high sensitivity of Raman spectroscopy for the detection of chlorophylls, carotenoids, scytonemin, and a range of other pigments found in the microbial world, it is an excellent technique to monitor the presence of such pigments, both in pure cultures and in environmental samples. Miniaturized portable handheld instruments are available; these instruments can be used to detect pigments in microbiological samples of different types and origins under field conditions.
Spontaneously Induced Prophages in Lactobacillus gasseri Contribute to Horizontal Gene Transfer
Authors: Baugher J. L. , Durmaz E. , Klaenhammer T. R. 
Published: March 2014

ABSTRACT

Lactobacillus gasseri
is an endogenous species of the human gastrointestinal tract and vagina. With recent advances in microbial taxonomy, phylogenetics, and genomics,
L. gasseri
is recognized as an important commensal and is increasingly being used in probiotic formulations.
L. gasseri
strain ADH is lysogenic and harbors two inducible prophages. In this study, prophage ϕadh was found to spontaneously induce in broth cultures to populations of ∼10
7
PFU/ml by stationary phase. The ϕadh prophage-cured ADH derivative NCK102 was found to harbor a new, second inducible phage, vB_Lga_jlb1 (jlb1). Phage jlb1 was sequenced and found to be highly similar to the closely related phage LgaI, which resides as two tandem prophages in the neotype strain
L. gasseri
ATCC 33323. The common occurrence of multiple prophages in
L. gasseri
genomes, their propensity for spontaneous induction, and the high degree of homology among phages within multiple species of
Lactobacillus
suggest that temperate bacteriophages likely contribute to horizontal gene transfer (HGT) in commensal lactobacilli. In this study, the host ranges of phages ϕadh and jlb1 were determined against 16
L. gasseri
strains. The transduction range and the rate of spontaneous transduction were investigated in coculture experiments to ascertain the degree to which prophages can promote HGT among a variety of commensal and probiotic lactobacilli. Both ϕadh and jlb1 particles were confirmed to mediate plasmid transfer. As many as ∼10
3
spontaneous transductants/ml were obtained. HGT by transducing phages of commensal lactobacilli may have a significant impact on the evolution of bacteria within the human microbiota.
Genes of the
N
-Methylglutamate Pathway Are Essential for Growth of Methylobacterium extorquens DM4 with Monomethylamine
Authors: Gruffaz Christelle , Muller Emilie E. L. , Louhichi-Jelail Yousra , Nelli Yella R. , Guichard Gilles , Bringel Françoise 
Published: March 2014

ABSTRACT

Monomethylamine (MMA, CH
3
NH
2
) can be used as a carbon and nitrogen source by many methylotrophic bacteria.
Methylobacterium extorquens
DM4 lacks the MMA dehydrogenase encoded by
mau
genes, which in
M. extorquens
AM1 is essential for growth on MMA. Identification and characterization of minitransposon mutants with an MMA-dependent phenotype showed that strain DM4 grows with MMA as the sole source of carbon, energy, and nitrogen by the
N
-methylglutamate (NMG) pathway. Independent mutations were found in a chromosomal region containing the genes
gmaS
,
mgsABC
, and
mgdABCD
for the three enzymes of the pathway, γ-glutamylmethylamide (GMA) synthetase, NMG synthase, and NMG dehydrogenase, respectively. Reverse transcription-PCR confirmed the operonic structure of the two divergent gene clusters
mgsABC-gmaS
and
mgdABCD
and their induction during growth with MMA. The genes
mgdABCD
and
mgsABC
were found to be essential for utilization of MMA as a carbon and nitrogen source. The gene
gmaS
was essential for MMA utilization as a carbon source, but residual growth of mutant DM4
gmaS
growing with succinate and MMA as a nitrogen source was observed. Plasmid copies of
gmaS
and the
gmaS
homolog METDI4690, which encodes a protein 39% identical to GMA synthetase, fully restored the ability of mutants DM4
gmaS
and DM4
gmaS
Δmetdi4690 to use MMA as a carbon and nitrogen source. Similarly, chemically synthesized GMA, the product of GMA synthetase, could be used as a nitrogen source for growth in the wild-type strain, as well as in DM4
gmaS
and DM4
gmaS
Δmetdi4690 mutants. The NADH:ubiquinone oxidoreductase respiratory complex component NuoG was also found to be essential for growth with MMA as a carbon source.
Utility of the Clostridial Site-Specific Recombinase TnpX To Clone Toxic-Product-Encoding Genes and Selectively Remove Genomic DNA Fragments
Authors: Adams Vicki , Bantwal Radhika , Stevenson Lauren , Cheung Jackie K. , Awad Milena M. , Nicholson Joel , Carter Glen P. , Mackin Kate E. , Rood Julian I. , Lyras Dena 
Published: March 2014

ABSTRACT

TnpX is a site-specific recombinase responsible for the excision and insertion of the transposons Tn
4451
and Tn
4453
in
Clostridium perfringens
and
Clostridium difficile
, respectively. Here, we exploit phenotypic features of TnpX to facilitate genetic mutagenesis and complementation studies. Genetic manipulation of bacteria often relies on the use of antibiotic resistance genes; however, a limited number are available for use in the clostridia. The ability of TnpX to recognize and excise specific DNA fragments was exploited here as the basis of an antibiotic resistance marker recycling system, specifically to remove antibiotic resistance genes from plasmids in
Escherichia coli
and from marked chromosomal
C. perfringens
mutants. This methodology enabled the construction of a
C. perfringens
plc virR
double mutant by allowing the removal and subsequent reuse of the same resistance gene to construct a second mutation. Genetic complementation can be challenging when the gene of interest encodes a product toxic to
E. coli
. We show that TnpX represses expression from its own promoter, P

attCI

, which can be exploited to facilitate the cloning of recalcitrant genes in
E. coli
for subsequent expression in the heterologous host
C. perfringens
. Importantly, this technology expands the repertoire of tools available for the genetic manipulation of the clostridia.
Depletion of the Trypanosome Pumilio Domain Protein PUF2 or of Some Other Essential Proteins Causes Transcriptome Changes Related to Coding Region Length
Authors: Jha Bhaskar Anand , Fadda Abeer , Merce Clementine , Mugo Elisha , Droll Dorothea , Clayton Christine 
Published: March 2014

ABSTRACT

Pumilio domain RNA-binding proteins are known mainly as posttranscriptional repressors of gene expression that reduce mRNA translation and stability.
Trypanosoma brucei
has 11 PUF proteins. We show here that PUF2 is in the cytosol, with roughly the same number of molecules per cell as there are mRNAs. Although PUF2 exhibits a low level of
in vivo
RNA binding, it is not associated with polysomes. PUF2 also decreased reporter mRNA levels in a tethering assay, consistent with a repressive role. Depletion of PUF2 inhibited growth of bloodstream-form trypanosomes, causing selective loss of mRNAs with long open reading frames and increases in mRNAs with shorter open reading frames. Reexamination of published RNASeq data revealed the same trend in cells depleted of some other proteins. We speculate that these length effects could be caused by inhibition of the elongation phase of transcription or by an influence of translation status or polysomal conformation on mRNA decay.