bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigating cardiac energetics in heart failure
Authors: Lygate Craig A. , Schneider Jürgen E. , Neubauer Stefan 
Published: September 2012

New Findings
What is the topic of this review?This report reviews the current literature on non‐invasive in vivo methodologies for the assessment of cardiac energetics in the mouse.
What advances does it highlight?Example applications of magnetic resonance spectroscopy are discussed, including suggestions for how this approach can be advanced.
The energetic requirements of the heart are, weight for weight, higher than for any other organ. The heart provides non‐stop function for a lifetime, while maintaining energy in reserve in order to respond to increased demand. This demand is met by continuously recycling a relatively small pool of ATP, with the creatine kinase (CK) system acting as a spatial and temporal buffer. In the failing heart, key components of this system are downregulated, but whether these energetic changes are biomarkers or drivers of dysfunction and whether they represent therapeutic targets are the subjects of ongoing research. Key methodologies are now becoming available in vivo to help address these questions in mouse models, such as 31P magnetic resonance spectroscopy to detect high‐energy phosphates and 1H magnetic resonance spectroscopy to detect total creatine. This report briefly discusses the challenges involved in using these technologies, the application and pitfalls of murine surgical models of heart failure, and how this has contributed to our understanding of pathophysiology in recent years.
Voluntary scheduled exercise alters diurnal rhythms of behaviour, physiology and gene expression in wild‐type and vasoactive intestinal peptide‐deficient mice
Authors: Schroeder Analyne M. , Truong Danny , Loh Dawn H. , Jordan Maria C. , Roos Kenneth P. , Colwell Christopher S. 
Published: September 2012

Key points
The circadian system drives rhythms of behaviour, physiology and gene expression in alignment to a light–dark cycle, and misalignment of the internal clock with the external environment can lead to disease.
We sought to determine whether scheduled exercise could alter rhythmic properties in mice while subjected to the strong entrainment effects of light and whether we could improve diurnal deficits observed in the vasointestinal polypeptide (VIP)‐deficient mouse.
Scheduled exercise altered daily rhythms of activity, physiology and gene expression in wild‐type and VIP‐deficient mice.
Scheduled exercise during the late night improved many of the rhythmic deficits observed in VIP‐deficient mice, including changes in gene expression within the suprachiasmatic nucleus, the site of circadian rhythm generation.
The results raise the possibility that scheduled exercise could be a tool to drive and improve daily rhythms in humans to mitigate the negative consequences of circadian misalignment.
Abstract  The circadian system co‐ordinates the temporal patterning of behaviour and many underlying biological processes. In some cases, the regulated outputs of the circadian system, such as activity, may be able to feed back to alter core clock processes. In our studies, we used four wheel‐access conditions (no access; free access; early night; and late night) to manipulate the duration and timing of activity while under the influence of a light–dark cycle. In wild‐type mice, scheduled wheel access was able to increase ambulatory activity, inducing a level of exercise driven at various phases of the light–dark cycle. Scheduled exercise also manipulated the magnitude and phasing of the circadian‐regulated outputs of heart rate and body temperature. At a molecular level, the phasing and amplitude of PER2::LUCIFERASE (PER2::LUC) expression rhythms in the SCN and peripheral tissues of Per2::Luc knockin mice were altered by scheduled exercise. We then tested whether scheduled wheel access could improve deficits observed in vasointestinal polypeptide‐deficient mice under the influence of a light–dark cycle. We found that scheduled wheel access during the late night improved many of the behavioural, physiological and molecular deficits previously described in vasointestinal polypeptide‐deficient mice. Our results raise the possibility that scheduled exercise could be used as a tool to modulate daily rhythms and, when applied, may counteract some of the negative impacts of ageing and disease on the circadian system.
Tissue characterization using a phantom to validate four‐dimensional tissue deformation
Authors: Szegedi Martin , Rassiah‐Szegedi Prema , Sarkar Vikren , Hinkle Jacob , Wang Brian , Huang Yu‐Huei , Zhao Hui , Joshi Sarang , Salter B. J. 
Published: September 2012

Purpose:This project proposes using a real tissue phantom for 4D tissue deformation reconstruction (4DTDR) and 4D deformable image registration (DIR) validation, which allows for the complete verification of the motion path rather than limited end‐point to end‐point of motion.Methods:Three electro‐magnetic‐tracking (EMT) fiducials were implanted into fresh porcine liver that was subsequently animated in a clinically realistic phantom. The animation was previously shown to be similar to organ motion, including hysteresis, when driven using a real patientˈs breathing pattern. For this experiment, 4DCTs and EMT traces were acquired when the phantom was animated using both sinusoidal and recorded patient‐breathing traces. Fiducial were masked prior to 4DTDR for reconstruction. The original 4DCT data (with fiducials) were sampled into 20 CT phase sets and fiducials’ coordinates were recorded, resulting in time‐resolved fiducial motion paths. Measured values of fiducial location were compared to EMT measured traces and the result calculated by 4DTDR.Results:For the sinusoidal breathing trace, 95% of EMT measured locations were within 1.2 mm of the measured 4DCT motion path, allowing for repeatable accurate motion characterization. The 4DTDR traces matched 95% of the EMT trace within 1.6 mm. Using the more irregular (in amplitude and frequency) patient trace, 95% of the EMT trace points fitted both 4DCT and 4DTDR motion path within 4.5 mm. The average match of the 4DTDR estimation of the tissue hysteresis over all CT phases was 0.9 mm using a sinusoidal signal for animation and 1.0 mm using the patient trace.Conclusions:The real tissue phantom is a tool which can be used to accurately characterize tissue deformation, helping to validate or evaluate a DIR or 4DTDR algorithm over a complete motion path. The phantom is capable of validating, evaluating, and quantifying tissue hysteresis, thereby allowing for full motion path validation.
Traceable micro‐CT scaling accuracy phantom for applications requiring exact measurement of distances or volumes
Authors: Waring Christopher S. R. , Bax Jeffrey S. , Samarabandu Amila , Holdsworth David W. , Fenster Aaron , Lacefield James C. 
Published: September 2012

Purpose:Volumetric x‐ray microcomputed tomography (CT) can be employed in a variety of quantitative research applications such as image‐guided interventions or characterization of medical devices. To ensure the highest geometric fidelity of images for these applications, a phantom and image processing algorithm have been developed to calibrate the scaling accuracy of micro‐CT scanners to a traceable standard and provide corrections to image voxel sizing.Methods:The calibration phantom contains six borosilicate beads whose separations have been measured to a traceable standard. An image processing algorithm compares the known separations of the beads to their separations in micro‐CT images. A least‐squares solution is used to determine linear scaling correction factors along each of the three scanner axes to minimize errors in the bead separations within the images by correcting the image voxel size. The correction factors were applied to images of a similar phantom with beads at different positions to evaluate the ability of the correction factors to reduce errors at points independent of the fiducial locations in the calibration phantom. The calibration phantom was used to evaluate the scaling accuracy of five different micro‐CT scanners representing four different scanner models.Results:In two of the five scanners evaluated, the correction factors significantly reduced the mean error in bead separations in the images from 0.17% to 0.05% and from 0.37% to 0.07% of the actual bead separations, respectively. Scanners yielding similar voxel sizes possessed comparable geometric errors after correction using the phantom.Conclusions:Although the magnitude of the corrections is small, such corrections can be important for demanding micro‐CT applications. Even if no voxel size correction is required, the phantom provides an easily implemented method to verify the geometric fidelity of micro‐CT scanners to a traceable standard of measurement.
Quantitative comparison of noise texture across CT scanners from different manufacturers
Authors: Solomon Justin B. , Christianson Olav , Samei Ehsan 
Published: September 2012

Purpose:To quantitatively compare noise texture across computed tomography (CT) scanners from different manufacturers using the noise power spectrum (NPS).Methods:The American College of Radiology CT accreditation phantom (Gammex 464, Gammex, Inc., Middleton, WI) was imaged on two scanners: Discovery CT 750HD (GE Healthcare, Waukesha, WI), and SOMATOM Definition Flash (Siemens Healthcare, Germany), using a consistent acquisition protocol (120 kVp, 0.625/0.6 mm slice thickness, 250 mAs, and 22 cm field of view). Images were reconstructed using filtered backprojection and a wide selection of reconstruction kernels. For each image set, the 2D NPS were estimated from the uniform section of the phantom. The 2D spectra were normalized by their integral value, radially averaged, and filtered by the human visual response function. A systematic kernel‐by‐kernel comparison across manufacturers was performed by computing the root mean square difference (RMSD) and the peak frequency difference (PFD) between the NPS from different kernels. GE and Siemens kernels were compared and kernel pairs that minimized the RMSD and |PFD| were identified.Results:The RMSD (|PFD|) values between the NPS of GE and Siemens kernels varied from 0.01 mm2 (0.002 mm−1) to 0.29 mm2 (0.74 mm−1). The GE kernels “Soft,” “Standard,” “Chest,” and “Lung” closely matched the Siemens kernels “B35f,” “B43f,” “B41f,” and “B80f” (RMSD < 0.05 mm2, |PFD| < 0.02 mm−1, respectively). The GE “Bone,” “Bone+,” and “Edge” kernels all matched most closely with Siemens “B75f” kernel but with sizeable RMSD and |PFD| values up to 0.18 mm2 and 0.41 mm−1, respectively. These sizeable RMSD and |PFD| values corresponded to visually perceivable differences in the noise texture of the images.Conclusions:It is possible to use the NPS to quantitatively compare noise texture across CT systems. The degree to which similar texture across scanners could be achieved varies and is limited by the kernels available on each scanner.
Bacterial Resistance to Antisense Peptide Phosphorodiamidate Morpholino Oligomers
Authors: Puckett Susan E. , Reese Kaleb A. , Mitev Georgi M. , Mullen Valerie , Johnson Rudd C. , Pomraning Kyle R. , Mellbye Brett L. , Tilley Lucas D. , Iversen Patrick L. , Freitag Michael , Geller Bruce L. 
Published: September 2012

ABSTRACT

Peptide phosphorodiamidate morpholino oligomers (PPMOs) are synthetic DNA mimics that bind cRNA and inhibit bacterial gene expression. The PPMO (RFF)
3
RXB-AcpP (where R is arginine, F, phenylalanine, X is 6-aminohexanoic acid, B is β-alanine, and AcpP is acyl carrier protein) is complementary to 11 bases of the essential gene
acpP
(which encodes acyl carrier protein). The MIC of (RFF)
3
RXB-AcpP was 2.5 μM (14 μg/ml) in
Escherichia coli
W3110. The rate of spontaneous resistance of
E. coli
to (RFF)
3
RXB-AcpP was 4 × 10
−7
mutations/cell division. A spontaneous (RFF)
3
RXB-AcpP-resistant mutant (PR200.1) was isolated. The MIC of (RFF)
3
RXB-AcpP was 40 μM (224 μg/ml) for PR200.1. The MICs of standard antibiotics for PR200.1 and W3110 were identical. The sequence of
acpP
was identical in PR200.1 and W3110. PR200.1 was also resistant to other PPMOs conjugated to (RFF)
3
RXB or peptides with a similar composition or pattern of cationic and nonpolar residues. Genomic sequencing of PR200.1 identified a mutation in
sbmA
, which encodes an active transport protein. In separate experiments, a (RFF)
3
RXB-AcpP-resistant isolate (RR3) was selected from a transposome library, and the insertion was mapped to
sbmA
. Genetic complementation of PR200.1 or RR3 with
sbmA
restored susceptibility to (RFF)
3
RXB-AcpP. Deletion of
sbmA
caused resistance to (RFF)
3
RXB-AcpP. We conclude that resistance to (RFF)
3
RXB-AcpP was linked to the peptide and not the phosphorodiamidate morpholino oligomer, dependent on the composition or repeating pattern of amino acids, and caused by mutations in
sbmA
. The data further suggest that (RFF)
3
R-XB PPMOs may be transported across the plasma membrane by SbmA.
Comparative
In Vitro
and
In Vivo
Efficacies of Human Simulated Doses of Ceftazidime and Ceftazidime-Avibactam against Pseudomonas aeruginosa
Authors: Crandon Jared L. , Schuck Virna J. , Banevicius Mary Anne , Beaudoin Marie-Eve , Nichols Wright W. , Tanudra M. Angela , Nicolau David P. 
Published: September 2012

ABSTRACT

The combination of ceftazidime and avibactam possesses potent activity against resistant Gram-negative pathogens, including
Pseudomonas aeruginosa
. We compared the efficacies of human simulated doses of ceftazidime and ceftazidime-avibactam using a hollow-fiber system and neutropenic and immunocompetent murine thigh infection models. Twenty-seven clinical
P. aeruginosa
isolates with ceftazidime MICs of 8 to 128 mg/liter and ceftazidime-avibactam MICs of 4 to 32 mg/liter were utilized in neutropenic mouse studies; 15 of the isolates were also evaluated in immunocompetent mice. Six isolates were studied in both the hollow-fiber system and the neutropenic mouse. In both systems, the free drug concentration-time profile seen in humans given 2 g of ceftazidime every 8 h (2-h infusion), with or without avibactam at 500 mg every 8 h (2-h infusion), was evaluated.
In vivo
activity was pharmacodynamically predictable based on the MIC. Ceftazidime decreased bacterial densities by ≥0.5 log unit for 10/27 isolates, while ceftazidime-avibactam did so for 22/27 isolates. In immunocompetent animals, enhancements in activity were seen for both drugs, with ceftazidime achieving reductions of ≥0.3 log unit for 10/15 isolates, whereas ceftazidime-avibactam did so against all 15 isolates.
In vitro
, ceftazidime resulted in regrowth by 24 h against all isolates, while ceftazidime-avibactam achieved stasis or better against 4/7 isolates. Mutants with elevated ceftazidime-avibactam MICs appeared after 24 h from 3/7 isolates studied
in vitro
; however, no resistant mutants were detected
in vivo
. Against this highly ceftazidime-nonsusceptible population of
P. aeruginosa
, treatment with human simulated doses of ceftazidime-avibactam resulted in pharmacodynamically predictable activity, particularly
in vivo
, against isolates with MICs of ≤16 mg/liter, and this represents a potential new option to combat these difficult-to-treat pathogens.
Phylogenetically Novel LuxI/LuxR-Type Quorum Sensing Systems Isolated Using a Metagenomic Approach
Authors: Nasuno Eri , Kimura Nobutada , Fujita Masaki J. , Nakatsu Cindy H. , Kamagata Yoichi , Hanada Satoshi 
Published: September 2012

ABSTRACT

A great deal of research has been done to understand bacterial cell-to-cell signaling systems, but there is still a large gap in our current knowledge because the majority of microorganisms in natural environments do not have cultivated representatives. Metagenomics is one approach to identify novel quorum sensing (QS) systems from uncultured bacteria in environmental samples. In this study, fosmid metagenomic libraries were constructed from a forest soil and an activated sludge from a coke plant, and the target genes were detected using a green fluorescent protein (GFP)-based
Escherichia coli
biosensor strain whose fluorescence was screened by spectrophotometry. DNA sequence analysis revealed two pairs of new LuxI family
N
-acyl-
l
-homoserine lactone (AHL) synthases and LuxR family transcriptional regulators (clones N16 and N52, designated AubI/AubR and AusI/AusR, respectively). AubI and AusI each produced an identical AHL,
N
-dodecanoyl-
l
-homoserine lactone (C
12
-HSL), as determined by nuclear magnetic resonance (NMR) and mass spectrometry. Phylogenetic analysis based on amino acid sequences suggested that AusI/AusR was from an uncultured member of the
Betaproteobacteria
and AubI/AubR was very deeply branched from previously described LuxI/LuxR homologues in isolates of the
Proteobacteria
. The phylogenetic position of AubI/AubR indicates that they represent a QS system not acquired recently from the
Proteobacteria
by horizontal gene transfer but share a more ancient ancestry. We demonstrated that metagenomic screening is useful to provide further insight into the phylogenetic diversity of bacterial QS systems by describing two new LuxI/LuxR-type QS systems from uncultured bacteria.
Novel Method for Enumeration of Viable Lactobacillus plantarum WCFS1 Cells after Single-Droplet Drying
Authors: Perdana Jimmy , Bereschenko Ludmila , Roghair Mark , Fox Martijn B. , Boom Remko M. , Kleerebezem Michiel , Schutyser Maarten A. I. 
Published: September 2012

ABSTRACT

Survival of probiotic bacteria during drying is not trivial. Survival percentages are very specific for each probiotic strain and can be improved by careful selection of drying conditions and proper drying carrier formulation. An experimental approach is presented, comprising a single-droplet drying method and a subsequent novel screening methodology, to assess the microbial viability within single particles. The drying method involves the drying of a single droplet deposited on a flat, hydrophobic surface under well-defined drying conditions and carrier formulations. Semidried or dried particles were subjected to rehydration, fluorescence staining, and live/dead enumeration using fluorescence microscopy. The novel screening methodology provided accurate survival percentages in line with conventional plating enumeration and was evaluated in single-droplet drying experiments with
Lactobacillus plantarum
WCFS1 as a model probiotic strain. Parameters such as bulk air temperatures and the carrier matrices (glucose, trehalose, and maltodextrin DE 6) were varied. Following the experimental approach, the influence on the viability as a function of the drying history could be monitored. Finally, the applicability of the novel viability assessment was demonstrated for samples obtained from drying experiments at a larger scale.
Immune Modulation by Group B Streptococcus Influences Host Susceptibility to Urinary Tract Infection by Uropathogenic Escherichia coli
Authors: Kline Kimberly A. , Schwartz Drew J. , Gilbert Nicole M. , Hultgren Scott J. , Lewis Amanda L. 
Published: September 2012

ABSTRACTUrinary tract infection (UTI) is most often caused by uropathogenicEscherichia coli(UPEC). UPEC inoculation into the female urinary tract (UT) can occur through physical activities that expose the UT to an inherently polymicrobial periurethral, vaginal, or gastrointestinal flora. We report that a common urogenital inhabitant and opportunistic pathogen, group BStreptococcus(GBS), when present at the time of UPEC exposure, undergoes rapid UPEC-dependent exclusion from the murine urinary tract, yet it influences acute UPEC-host interactions and alters host susceptibility to persistent outcomes of bladder and kidney infection. GBS presence results in increased UPEC titers in the bladder lumen during acute infection and reduced inflammatory responses of murine macrophages to live UPEC or purified lipopolysaccharide (LPS), phenotypes that require GBS mimicry of host sialic acid residues. Taken together, these studies suggest that despite low titers, the presence of GBS at the time of polymicrobial UT exposure may be an overlooked risk factor for chronic pyelonephritis and recurrent UTI in susceptible groups, even if it is outcompeted and thus absent by the time of diagnosis.
Coupling of σ
G
Activation to Completion of Engulfment during Sporulation of Bacillus subtilis Survives Large Perturbations to DNA Translocation and Replication
Authors: Regan Genevieve , Itaya Mitsuhiro , Piggot Patrick J. 
Published: September 2012

ABSTRACT

Spore formation in
Bacillus subtilis
is characterized by activation of RNA polymerase sigma factors, including the late-expressed σ
G
. During spore formation an asymmetric division occurs, yielding the smaller prespore and the larger mother cell. At division, only 30% of the chromosome is in the prespore, and the rest is then translocated into the prespore. Following completion of engulfment of the prespore by the mother cell, σ
G
is activated in the prespore. Here we tested the link between engulfment and σ
G
activation by perturbing DNA translocation and replication, which are completed before engulfment. One approach was to have large DNA insertions in the chromosome; the second was to have an impaired DNA translocase; the third was to use a strain in which the site of termination of chromosome replication was relocated. Insertion of 2.3 Mb of
Synechocystis
DNA into the
B. subtilis
genome had the largest effect, delaying engulfment by at least 90 min. Chromosome translocation was also delayed and was completed shortly before the completion of engulfment. Despite the delay, σ
G
became active only after the completion of engulfment. All results are consistent with a strong link between completion of engulfment and σ
G
activation. They support a link between completion of chromosome translocation and completion of engulfment.
Sequence-Verified Two-Allele Transposon Mutant Library for Pseudomonas aeruginosa PAO1
Authors: Held Kiara , Ramage Elizabeth , Jacobs Michael , Gallagher Larry , Manoil Colin 
Published: September 2012

ABSTRACT

Mutant hunts using comprehensive sequence-defined libraries make it possible to identify virtually all of the nonessential functions required for different bacterial processes. However, the success of such screening depends on the accuracy of mutant identification in the mutant library used. To provide a high-quality library for
Pseudomonas aeruginosa
PAO1, we created a sequence-verified collection of 9,437 transposon mutants that provides genome coverage and includes two mutants for most genes. Mutants were cherry-picked from a larger library, colony-purified, and resequenced both individually using Sanger sequencing and in a pool using Tn-seq. About 8% of the insertion assignments were corrected, and in the final library nearly 93% of the transposon locations were confirmed by at least one of the resequencing procedures. The extensive sequence verification and inclusion of more than one mutant for most genes should help minimize missed or erroneous genotype-phenotype assignments in studies using the new library.