bluuebunny/crossref_metadata_2025_split huggingface dataset:
A pilot prospective study of the vascular repair response following red cell transfusion in critically ill patients
Authors: Christou G. , Abou‐Nassar K. , Li Y. , Labonté L. , Tinmouth A. , McArdle T. , Watpool I. , McIntyre L. , Allan D. S. 
Published: March 2013

SummaryBackgroundRed blood cell transfusion has been associated with adverse outcomes including infection, delayed recovery and increased mortality in some patient populations. Circulating cells that yield endothelial‐like vascular progenitor cell (VPC) clusters are correlated with vascular repair and recovery after ischaemic injury. The impact of red cell transfusion on VPC clusters and vascular repair remains uncertain.Study designWe prospectively enrolled patients admitted to intensive care requiring red cell transfusion and subjects at low likelihood of requiring red cell transfusion. Levels of VPC clusters and plasma levels of angiogenic cytokines were compared. A total of 17 patients were recruited and had blood samples collected at time of enrolment and at 24–48 h, 48–72 h and 1 week following transfusion.ResultsWe could not discern differences in the number of VPC clusters between transfused patients (n = 6) and non‐transfused subjects (n = 11) at baseline or throughout the study period. VPC cluster levels demonstrated wide variance and were highest at 24‐h post‐enrolment in the entire cohort. Furthermore, levels of all 16 cytokines analysed were not significantly different between transfused and non‐transfused patients and we did not observe a correlation between cytokine concentrations and levels of circulating VPC‐cluster forming cells in the overall study population.ConclusionsOur data suggest that assessment of vascular repair responses after red blood cell transfusion in critically ill patients is challenging. Although our study did not allow us to discern an influence of red cell transfusion on VPC cluster levels or angiogenic cytokines, new methods evaluating vascular repair mechanisms may be required.
Embryo defective12 encodes the plastid initiation factor 3 and is essential for embryogenesis in maize
Authors: Shen Yun , Li Cuiling , McCarty Donald R. , Meeley Robert , Tan Bao‐Cai 
Published: March 2013

SummaryEmbryo‐specific mutants in maize define a unique class of genetic loci that affect embryogenesis without a significant deleterious impact on endosperm development. Here we report the characterization of an embryo specific12 (emb12) mutant in maize. Embryogenesis in the emb12 mutants is arrested at or before transition stage. The mutant embryo at an early stage exhibits abnormal cell structure with increased vacuoles and dramatically reduced internal membrane organelles. In contrast, the mutant endosperm appears normal in morphology, cell structure, starch, lipid and protein accumulation. The Emb12 locus was cloned by transposon tagging and predicts a protein with a high similarity to prokaryotic translation initiation factor 3 (IF3). EMB12–GFP fusion analysis indicates that EMB12 is localized in plastids. The RNA in situ hybridization and protein immunohistochemical analyses indicate that a high level of Emb12 expression localizes in the embryo proper at early developmental stages and in the embryo axis at later stages. Western analysis indicates that plastid protein synthesis is impaired. These results indicate that Emb12 encodes the plastid IF3 which is essential for embryogenesis but not for endosperm development in maize.
Commissioning of the Varian TrueBeam linear accelerator: A multi‐institutional study
Authors: Glide‐Hurst C. , Bellon M. , Foster R. , Altunbas C. , Speiser M. , Altman M. , Westerly D. , Wen N. , Zhao B. , Miften M. , Chetty I. J. , Solberg T. 
Published: March 2013

Purpose:Latest generation linear accelerators (linacs), i.e., TrueBeam (Varian Medical Systems, Palo Alto, CA) and its stereotactic counterpart, TrueBeam STx, have several unique features, including high‐dose‐rate flattening‐filter‐free (FFF) photon modes, reengineered electron modes with new scattering foil geometries, updated imaging hardware/software, and a novel control system. An evaluation of five TrueBeam linacs at three different institutions has been performed and this work reports on the commissioning experience.Methods:Acceptance and commissioning data were analyzed for five TrueBeam linacs equipped with 120 leaf (5 mm width) MLCs at three different institutions. Dosimetric data and mechanical parameters were compared. These included measurements of photon beam profiles (6X, 6XFFF, 10X, 10XFFF, 15X), photon and electron percent depth dose (PDD) curves (6, 9, 12 MeV), relative photon output factors (Scp), electron cone factors, mechanical isocenter accuracy, MLC transmission, and dosimetric leaf gap (DLG). End‐to‐end testing and IMRT commissioning were also conducted.Results:Gantry/collimator isocentricity measurements were similar (0.27–0.28 mm), with overall couch/gantry/collimator values of 0.46–0.68 mm across the three institutions. Dosimetric data showed good agreement between machines. The average MLC DLGs for 6, 10, and 15 MV photons were 1.33 ± 0.23, 1.57 ± 0.24, and 1.61 ± 0.26 mm, respectively. 6XFFF and 10XFFF modes had average DLGs of 1.16 ± 0.22 and 1.44 ± 0.30 mm, respectively. MLC transmission showed minimal variation across the three institutions, with the standard deviation <0.2% for all linacs. Photon and electron PDDs were comparable for all energies. 6, 10, and 15 MV photon beam quality, %dd(10)x varied less than 0.3% for all linacs. Output factors (Scp) and electron cone factors agreed within 0.27%, on average; largest variations were observed for small field sizes (1.2% coefficient of variation, 10 MV, 2 × 2 cm2) and small cone sizes (<1% coefficient of variation, 6 × 6 cm2 cone), respectively.Conclusions:Overall, excellent agreement was observed in TrueBeam commissioning data. This set of multi‐institutional data can provide comparison data to others embarking on TrueBeam commissioning, ultimately improving the safety and quality of beam commissioning.
Dependency of image quality on system configuration parameters in a stationary digital breast tomosynthesis system
Authors: Tucker Andrew W. , Lu Jianping , Zhou Otto 
Published: March 2013

Purpose:In principle, a stationary digital breast tomosynthesis (s‐DBT) system has better image quality when compared to continuous motion DBT systems due to zero motion blur of the source. The authors have developed a s‐DBT system by using a linear carbon nanotube x‐ray source array. The purpose of the current study was to quantitatively evaluate the performance of the s‐DBT system; and investigate the dependence of imaging quality on the system configuration parameters.Methods:Physical phantoms were used to assess the image quality of each configuration including inplane resolution as measured by the modulation transfer function (MTF), inplane contrast as measured by the signal difference to noise ratio (SdNR), and depth resolution as measured by the z‐axis artifact spread function. Five parameters were varied to create five groups of configurations: (1) total angular span; (2) total number of projection images; (3) distribution of exposure (mAs) across the projection images; (4) entrance dose; (5) detector pixel size.Results:It was found that the z‐axis depth resolution increased with the total angular span but was insensitive to the number of projection images, mAs distribution, entrance dose, and detector pixel size. The SdNR was not affected by the angular span or the number of projection images. A decrease in SdNR was observed when the mAs was not evenly distributed across the projection images. As expected, the SdNR increased with entrance dose and when larger pixel sizes were used. For a given detector pixel size, the inplane resolution was found to be insensitive to the total angular span, number of projection images, mAs distribution, and entrance dose. A 25% increase in the MTF was observed when the detector was operating in full resolution mode (70μm pixel size) compared to 2 × 2 binned mode (140 μm pixel size).Conclusions:The results suggest that the optimal imaging configuration for a s‐DBT system is a large angular span, an intermittent number of projection views, and a uniform mAs distribution over all views. With the detector operating at full resolution, a stationary DBT system can achieve an inplane resolution of 5.1 cycles per mm, which is significantly better than continuous motion DBT systems.
Monte Carlo investigation of I‐125 interseed attenuation for standard and thinner seeds in prostate brachytherapy with phantom validation using a MOSFET
Authors: Mason J. , Al‐Qaisieh B. , Bownes P. , Henry A. , Thwaites D. 
Published: March 2013

Purpose:In permanent seed implant prostate brachytherapy the actual dose delivered to the patient may be less than that calculated by TG‐43U1 due to interseed attenuation (ISA) and differences between prostate tissue composition and water. In this study the magnitude of the ISA effect is assessed in a phantom and in clinical prostate postimplant cases. Results are compared for seed models 6711 and 9011 with 0.8 and 0.5 mm diameters, respectively.Methods:A polymethyl methacrylate (PMMA) phantom was designed to perform ISA measurements in a simple eight‐seed arrangement and at the center of an implant of 36 seeds. Monte Carlo (MC) simulation and experimental measurements using a MOSFET dosimeter were used to measure dose rate and the ISA effect. MC simulations of 15 CT‐based postimplant prostate treatment plans were performed to compare the clinical impact of ISA on dose to prostate, urethra, rectum, and the volume enclosed by the 100% isodose, for 6711 and 9011 seed models.Results:In the phantom, ISA reduced the dose rate at the MOSFET position by 8.6%–18.3% (6711) and 7.8%–16.7% (9011) depending on the measurement configuration. MOSFET measured dose rates agreed with MC simulation predictions within the MOSFET measurement uncertainty, which ranged from 5.5% to 7.2% depending on the measurement configuration (k = 1, for the mean of four measurements). For 15 clinical implants, the mean ISA effect for 6711 was to reduce prostate D90 by 4.2 Gy (3%), prostate V100 by 0.5 cc (1.4%), urethra D10 by 11.3 Gy (4.4%), rectal D2cc by 5.5 Gy (4.6%), and the 100% isodose volume by 2.3 cc. For the 9011 seed the mean ISA effect reduced prostate D90 by 2.2 Gy (1.6%), prostate V100 by 0.3 cc (0.7%), urethra D10 by 8.0 Gy (3.2%), rectal D2cc by 3.1 Gy (2.7%), and the 100% isodose volume by 1.2 cc. Differences between the MC simulation and TG‐43U1 consensus data for the 6711 seed model had a similar impact, reducing mean prostate D90 by 6 Gy (4.2%) and V100 by 0.6 cc (1.8%).Conclusions:ISA causes the delivered dose in prostate seed implant brachytherapy to be lower than the dose calculated by TG‐43U1. MC simulation of phantom seed arrangements show that dose at a point can be reduced by up to 18% and this has been validated using a MOSFET dosimeter. Clinical simulations show that ISA reduces DVH parameter values, but the reduction is less for thinner seeds.
Automated x‐ray/light field congruence using the LINAC EPID panel
Authors: Polak Wojciech , O'Doherty Jim , Jones Matt 
Published: March 2013

Purpose:X‐ray/light field alignment is a test described in many guidelines for the routine quality control of clinical linear accelerators (LINAC). Currently, the gold standard method for measuring alignment is through utilization of radiographic film. However, many modern LINACs are equipped with an electronic portal imaging device (EPID) that may be used to perform this test and thus subsequently reducing overall cost, processing, and analysis time, removing operator dependency and the requirement to sustain the departmental film processor.Methods:This work describes a novel method of utilizing the EPID together with a custom inhouse designed jig and automatic image processing software allowing measurement of the light field size, x‐ray field size, and congruence between them. The authors present results of testing the method for aS1000 and aS500 Varian EPID detectors for six LINACs at a range of energies (6, 10, and 15 MV) in comparison with the results obtained from the use of radiographic film.Results:Reproducibility of the software in fully automatic operation under a range of operating conditions for a single image showed a congruence of 0.01 cm with a coefficient of variation of 0. Slight variation in congruence repeatability was noted through semiautomatic processing by four independent operators due to manual marking of positions on the jig. Testing of the methodology using the automatic method shows a high precision of 0.02 mm compared to a maximum of 0.06 mm determined by film processing. Intraindividual examination of operator measurements of congruence was shown to vary as much as 0.75 mm. Similar congruence measurements of 0.02 mm were also determined for a lower resolution EPID (aS500 model), after rescaling of the image to the aS1000 image size.Conclusions:The designed methodology was proven to be time efficient, cost effective, and at least as accurate as using the gold standard radiographic film. Additionally, congruence testing can be easily performed for all four cardinal gantry angles which can be difficult when using radiographic film. Therefore, the authors propose it can be used as an alternative to the radiographic film method allowing decommissioning of the film processor.
Characteristics of Extended-Spectrum β-Lactamase- and Carbapenemase-Producing Enterobacteriaceae Isolates from Rivers and Lakes in Switzerland
Authors: Zurfluh Katrin , Hächler Herbert , Nüesch-Inderbinen Magdalena , Stephan Roger 
Published: March 2013

ABSTRACT

One of the currently most relevant resistance mechanisms in
Enterobacteriaceae
is the production of enzymes that lead to modern expanded-spectrum cephalosporin and even carbapenem resistance, mainly extended-spectrum β-lactamases (ESBLs) and carbapenemases. A worrisome aspect is the spread of ESBL and carbapenemase producers into the environment. The aim of the present study was to assess the occurrence of ESBL- and carbapenemase-producing
Enterobacteriaceae
and to further characterize ESBL- and carbapenemase-producing
Enterobacteriaceae
in rivers and lakes in Switzerland. ESBL-producing
Enterobacteriaceae
were detected in 21 (36.2%) of the 58 bodies of water sampled. One river sample tested positive for a carbapenemase-producing
Klebsiella pneumoniae
subsp.
pneumoniae
strain. Seventy-four individual strains expressing an ESBL phenotype were isolated. Species identification revealed 60
Escherichia coli
strains, seven
Klebsiella pneumoniae
subsp.
pneumoniae
strains, five
Raoultella planticola
strains, one
Enterobacter cloacae
strain, and one
Enterobacter amnigenus
strain. Three strains were identified as SHV-12 ESBL producers, and 71 strains carried genes encoding CTX-M ESBLs. Of the 71 strains with CTX-M ESBL genes, 8 isolates expressed CTX-M-1, three produced CTX-M-3, 46 produced CTX-M-15, three produced CTX-M-55, one produced CTX-M-79, six produced CTX-M-14, and four produced CTX-M-27. Three of the four CTX-M-27 producers belonged to the multiresistant pandemic sequence type
E. coli
B2:ST131 that is strongly associated with potentially severe infections in humans and animals.
Autotrophic Growth of Bacterial and Archaeal Ammonia Oxidizers in Freshwater Sediment Microcosms Incubated at Different Temperatures
Authors: Wu Yucheng , Ke Xiubin , Hernández Marcela , Wang Baozhan , Dumont Marc G. , Jia Zhongjun , Conrad Ralf 
Published: March 2013

ABSTRACT

Both bacteria and archaea potentially contribute to ammonia oxidation, but their roles in freshwater sediments are still poorly understood. Seasonal differences in the relative activities of these groups might exist, since cultivated archaeal ammonia oxidizers have higher temperature optima than their bacterial counterparts. In this study, sediment collected from eutrophic freshwater Lake Taihu (China) was incubated at different temperatures (4°C, 15°C, 25°C, and 37°C) for up to 8 weeks. We examined the active bacterial and archaeal ammonia oxidizers in these sediment microcosms by using combined stable isotope probing (SIP) and molecular community analysis. The results showed that accumulation of nitrate in microcosms correlated negatively with temperature, although ammonium depletion was the same, which might have been related to enhanced activity of other nitrogen transformation processes. Incubation at different temperatures significantly changed the microbial community composition, as revealed by 454 pyrosequencing targeting bacterial 16S rRNA genes. After 8 weeks of incubation, [
13
C]bicarbonate labeling of bacterial
amoA
genes, which encode the ammonia monooxygenase subunit A, and an observed increase in copy numbers indicated the activity of ammonia-oxidizing bacteria in all microcosms.
Nitrosomonas
sp. strain Is79A3 and
Nitrosomonas communis
lineages dominated the heavy fraction of CsCl gradients at low and high temperatures, respectively, indicating a niche differentiation of active bacterial ammonia oxidizers along the temperature gradient. The
13
C labeling of ammonia-oxidizing archaea in microcosms incubated at 4 to 25°C was minor. In contrast, significant
13
C labeling of
Nitrososphaera
-like archaea and changes in the abundance and composition of archaeal
amoA
genes were observed at 37°C, implicating autotrophic growth of ammonia-oxidizing archaea under warmer conditions.
Positive Feedback Regulation of
stgR
Expression for Secondary Metabolism in Streptomyces coelicolor
Authors: Mao Xu-Ming , Sun Zhi-Hao , Liang Bi-Rong , Wang Zhi-Bin , Feng Wei-Hong , Huang Fang-Liang , Li Yong-Quan 
Published: March 2013

ABSTRACT

LysR-type transcriptional regulators (LTTRs) compose a large family and are responsible for various physiological functions in bacteria, while little is understood about their regulatory mechanism on secondary metabolism in
Streptomyces
. Here we reported that StgR, a typical LTTR in
Streptomyces coelicolor
, was a negative regulator of undecylprodigiosin (Red) and γ-actinorhodin (Act) production in the early developmental phase of secondary metabolism by suppressing the expression of two pathway-specific regulator genes,
redD
and
actII-orf4
, respectively. Meanwhile,
stgR
expression was downregulated during secondary metabolism to remove its repressive effects on antibiotic production. Moreover,
stgR
expression was positively autoregulated by direct binding of StgR to its own promoter (
stgRp
), and the binding site adjacent to translation start codon was determined by a DNase I footprinting assay. Furthermore, the StgR-
stgRp
interaction could be destroyed by the antibiotic γ-actinorhodin produced from
S. coelicolor
. Thus, our results suggested a positive feedback regulatory mechanism of
stgR
expression and antibiotic production for the rapid and irreversible development of secondary metabolism in
Streptomyces
.
6S-1 RNA Function Leads to a Delay in Sporulation in Bacillus subtilis
Authors: Cavanagh Amy T. , Wassarman Karen M. 
Published: March 2013

ABSTRACT

We have discovered that 6S-1 RNA (encoded by
bsrA
) is important for appropriate timing of sporulation in
Bacillus subtilis
in that cells lacking 6S-1 RNA sporulate earlier than wild-type cells. The time to generate a mature spore once the decision to sporulate has been made is unaffected by 6S-1 RNA, and, therefore, we propose that it is the timing of onset of sporulation that is altered. Interestingly, the presence of cells lacking 6S-1 RNA in coculture leads to all cell types exhibiting an early-sporulation phenotype. We propose that cells lacking 6S-1 RNA modify their environment in a manner that promotes early sporulation. In support of this model, resuspension of wild-type cells in conditioned medium from Δ
bsrA
cultures also resulted in early sporulation. Use of
Escherichia coli
growth as a reporter of the nutritional status of conditioned media suggested that
B. subtilis
cells lacking 6S-1 RNA reduce the nutrient content of their environment earlier than wild-type cells. Several pathways known to impact the timing of sporulation, such as the
skf
- and
sdp
-dependent cannibalism pathways, were eliminated as potential targets of 6S-1 RNA-mediated changes, suggesting that 6S-1 RNA activity defines a novel mechanism for altering the timing of onset of sporulation. In addition, 6S-2 RNA does not influence the timing of sporulation, providing further evidence of the independent influences of these two related RNAs on cell physiology.
The Major Outer Sheath Protein (Msp) of Treponema denticola Has a Bipartite Domain Architecture and Exists as Periplasmic and Outer Membrane-Spanning Conformers
Authors: Anand Arvind , Luthra Amit , Edmond Maxwell E. , Ledoyt Morgan , Caimano Melissa J. , Radolf Justin D. 
Published: March 2013

ABSTRACT

The major outer sheath protein (Msp) is a primary virulence determinant in
Treponema denticola
, as well as the parental ortholog for the
Treponema pallidum
repeat (Tpr) family in the syphilis spirochete. The Conserved Domain Database (CDD) server revealed that Msp contains two conserved domains, major outer sheath protein
N
(MOSP
N
) and MOSP
C
, spanning residues 77 to 286 and 332 to 543, respectively, within the N- and C-terminal regions of the protein. Circular dichroism (CD) spectroscopy, Triton X-114 (TX-114) phase partitioning, and liposome incorporation demonstrated that full-length, recombinant Msp (Msp
Fl
) and a recombinant protein containing MOSP
C
, but not MOSP
N
, form amphiphilic, β-sheet-rich structures with channel-forming activity. Immunofluorescence analysis of intact
T. denticola
revealed that only MOSP
C
contains surface-exposed epitopes. Data obtained using proteinase K accessibility, TX-114 phase partitioning, and cell fractionation revealed that Msp exists as distinct OM-integrated and periplasmic trimers. Msp
Fl
folded in Tris buffer contained slightly less β-sheet structure than detergent-folded Msp
Fl
; both forms, however, partitioned into the TX-114 detergent-enriched phase. CDD analysis of the nine Tpr paralogs predicted to be outer membrane proteins (OMPs) revealed that seven have an Msp-like bipartite structure; phylogenetic analysis revealed that the MOSP
N
and MOSP
C
domains of Msp are most closely related to those of TprK. Based upon our collective results, we propose a model whereby a newly exported, partially folded intermediate can be either processed for OM insertion by the β-barrel assembly machinery (BAM) or remain periplasmic, ultimately forming a stable, water-soluble trimer. Extrapolated to
T. pallidum
, our model enables us to explain how individual Tprs can localize to either the periplasmic (e.g., TprK) or OM (e.g., TprC) compartments.
The Stringent Response Controls Catalases in Pseudomonas aeruginosa and Is Required for Hydrogen Peroxide and Antibiotic Tolerance
Authors: Khakimova Malika , Ahlgren Heather G. , Harrison Joe J. , English Ann M. , Nguyen Dao 
Published: March 2013

ABSTRACT

Pseudomonas aeruginosa
, a human opportunistic pathogen, possesses a number of antioxidant defense enzymes under the control of multiple regulatory systems. We recently reported that inactivation of the
P. aeruginosa
stringent response (SR), a starvation stress response controlled by the alarmone (p)ppGpp, caused impaired antioxidant defenses and antibiotic tolerance. Since catalases are key antioxidant enzymes in
P. aeruginosa
, we compared the levels of H
2
O
2
susceptibility and catalase activity in
P. aeruginosa
wild-type and Δ
relA
Δ
spoT
(ΔSR) mutant cells. We found that the SR was required for optimal catalase activity and mediated H
2
O
2
tolerance during both planktonic and biofilm growth. Upon amino acid starvation, induction of the SR upregulated catalase activity. Full expression of
katA
and
katB
also required the SR, and this regulation occurred through both RpoS-independent and RpoS-dependent mechanisms. Furthermore, overexpression of
katA
was sufficient to restore H
2
O
2
tolerance and to partially rescue the antibiotic tolerance of ΔSR cells. All together, these results suggest that the SR regulates catalases and that this is an important mechanism in protecting nutrient-starved and biofilm bacteria from H
2
O
2
- and antibiotic-mediated killing.