bluuebunny/crossref_metadata_2025 huggingface dataset:
Influence of visual cues on host‐searching and learning behaviour of the egg parasitoids Telenomus podisi and Trissolcus basalis
Authors: Ferreira Santos de Aquino Michely , Dias Aline Moreira , Borges Miguel , Moraes Maria Carolina Blassioli , Laumann Raul Alberto
Published: September 2012

Insect parasitoids use a variety of chemical and physical cues when foraging for hosts and food. Parasitoids can learn cues that lead them to the hosts, thus contributing to better foraging. One of the cues that influence host‐searching behaviour could be colour. In this study, we investigated the ability of females of the parasitoid wasps Telenomus podisi Ashmead and Trissolcus basalis Wollaston (both Hymenoptera: Scelionidae) to respond to colours and to associate the presence of hosts – eggs of Euschistus heros (Fabricius) (Hemiptera: Pentatomidae) – with coloured substrates after training (associative learning). Two sets of experiments were conducted: in one the innate preference for substrate colours was examined, in the other associative learning of substrate colour and host presence was tested in multiple‐choice and dual‐choice experiments. In the associative learning experiments, Te. podisi and Tr. basalis were trained to respond to differently coloured substrates containing hosts in two sessions of 2 h each, with 1‐h intervals. In multiple‐choice experiments, the wasps displayed innate preference for yellow substrates over green, brown, black, or white ones. Even after being trained on substrates of different colours, both parasitoids continued to show preference for yellow substrates. The response to the colours of substrates of both parasitoids was related with the orientation to the plant foliage during the search for hosts.
Color Effects of Gingiva on Cervical Regions of All‐Ceramic Crowns
Authors: Wang Jian , Lin Jin , Seliger Alison , Gil Mindy , da Silva John D. , Ishhikawa‐Nagai Shigemi
Published: September 2012

Statement of Problem:  The final color of all‐ceramic crowns is influenced by the color of both the remaining tooth structure and the surrounding gingival tissue. The optical effects of gingival tissue on an all‐ceramic crown have never been fully studied.

Purpose:  The purpose of this study is to investigate the effects of gingival color on ceramic crowns in the cervical region.

Materials and Methods:  Thirty‐one all‐ceramic crowns of differing shades were included in this study. Using a spectrophotometer, the color values of each crown were measured on a typodont in the absence of an artificial gingiva (control group) and in the presence of an artificial gingiva (test group). CIELAB color coordinates (L*, a*, b*) were collected from three regions of the cervical area in descending order from the gingival margin (upper region, middle region, and lower region). Color difference values (ΔE*) were calculated for each cervical region between the test and control groups. ΔE* between the test and control groups from the upper to lower cervical regions was also compared with each other. The statistical analysis was performed using the student t‐test and one‐way analysis of variance (ANOVA) test.

Results:  The mean ΔE* values between the test group and control group at the upper, middle, and lower cervical regions were 5.8, 2.8, and 1.8, respectively. Significant color differences between the test and control group were detected in all three incremental regions (p < 0.001 at ΔE* = 1.6 threshold), with all color coordinates (L*, a*, and b*) contributing significantly to the color differences in these regions (p < 0.001). The color variations in the cervical area also varied significantly from the upper region to the lower region, with L* and a* contributing most to the differences.

Conclusions:  The presence of artificial gingiva is a critical factor in precise color matching and color reproduction for all‐ceramic crowns.

CLINICAL SIGNIFICANCE

Gingival tissue has significant optical effects on the color of all‐ceramic crowns at the cervical areas; therefore, it is suggested that artificial gingiva be used by both dentists and ceramists while matching and replicating tooth color with ceramic restorations.

(J Esthet Restor Dent ••:••–••, 2012)
Spontaneous clostridial myonecrosis after pregnancy – emergency treatment to the limb salvage and functional recovery: a case report
Authors: De Angelis Barbara , Cerulli Paolo , Lucilla Lucarini , Fusco Augusto , Di Pasquali Camilla , Bocchini Ilaria , Orlandi Fabrizio , Agovino Annarita , Cervelli Valerio
Published: September 2012

Clostridial myonecrosis (CM) is a rare, life threatening necrotizing infection of a skeletal muscle caused by Clostridium perfringens in the majority of cases. The diagnosis may be difficult because of few diagnostic and cutaneous signs early in its course. Standard therapy involves surgical debridements of a devitalized tissue and high‐dose organism‐specific antibiotic therapy. The hyperbaric oxygen has also showed its usefulness in the treatment of these infections. Autograft systems as tissue replacement, based on bioengineered materials, have been demonstrated to be safe and effective treatments for chronic wounds and a suitable physiotherapy is recommended for the recovery of functional impairments of upper extremities. We present a rare case of CM of right upper limb treated with a combination of standard treatments and new techniques.
Vulnerology: a new term to describe the discipline of wound care
Authors: Costagliola Michel , Atiyeh Bishara
Published: September 2012

Although wound healing is probably the most critical aspect of essential medical and surgical care, it has been neglected for a long time. With the tremendous surge over the last two decades in basic research, wound healing is emerging as a well‐defined medical entity transcending existing specialties and subdivisions. In view of the multitude of health professionals interested in the field of wounds and wound healing, it seems reasonably warranted to group them under one and single appellation. We suggest ‘vulnerology’ as a new term to describe the discipline of wound care.
A Critical Review of Some Qualitative Research Methods Used to Explore Rater Cognition
Authors: Suto Irenka
Published: September 2012

Internationally, many assessment systems rely predominantly on human raters to score examinations. Arguably, this facilitates the assessment of multiple sophisticated educational constructs, strengthening assessment validity. It can introduce subjectivity into the scoring process, however, engendering threats to accuracy. The present objectives are to examine some key qualitative data collection methods used internationally to research this potential trade‐off, and to consider some theoretical contexts within which the methods are usable. Self‐report methods such as Kelly's Repertory Grid, think aloud, stimulated recall, and the NASA task load index have yielded important insights into the competencies needed for scoring expertise, as well as the sequences of mental activity that scoring typically involves. Examples of new data and of recent studies are used to illustrate these methods’ strengths and weaknesses. This investigation has significance for assessment designers, developers and administrators. It may inform decisions on the methods’ applicability in American and other rater cognition research contexts.
Reciting the Qur’ān and Reading the Torah: Muslim and Jewish Attitudes and Practices in a Comparative Historical Perspective
Authors: Talmon‐Heller Daniella
Published: September 2012

Verses of Torah and Qur’ān are incorporated into statutory and supererogatory prayers, communal services, talismanic practices, rites of passage and social gatherings of Jews and Muslims. In both traditions correct pronunciation is held to preserve the authentic voice of the revelation and to incur powerful benevolent effects. In Islam, the recital of the memorized text, or parts of it, is the privileged practice; in Judaism – public reading of weekly consecutive portions is ceremoniously performed from special Torah scrolls. While the Qur’ān is absolutely dominant in Muslim liturgy and piety, texts other than the Torah constitute the lion’s share of daily liturgical reading and expressions of piety of Jews.
Comparative Journalism Research – An Overview
Authors: Örnebring Henrik
Published: September 2012

This overview focuses on the most common type of comparative journalism research, which is cross‐national comparative research. The overview presents a typology for different types of comparative journalism research, based on whether the research interest is in journalism as an activity or as a product; and, in the case of journalism as an activity, whether the interest is in the system level, the organizational level, or the individual level of journalism. The overview finds that the analysis of journalism on the individual level and of journalism as a product are the most common types of comparative research, whereas comparative analysis of journalism on the organizational level is much under‐studied.
Appearance‐based interventions to reduce ultraviolet exposure and/or increase sun protection intentions and behaviours: A systematic review and meta‐analyses
Authors: Williams Alison L. , Grogan Sarah , Clark‐Carter David , Buckley Emily
Published: September 2012

Objectives

A systematic review and meta‐analyses were conducted to identify and review research examining the impact of appearance‐based interventions on sun protection intentions and/or ultraviolet (UV) exposure behaviour.

Methods

A search of 16 databases including PsycARTICLES, Cochrane Library and Web of Knowledge was conducted to identify studies examining the impact of appearance‐based interventions on reducing UV exposure and/or increasing sun protection intentions and behaviours. A total of 21 articles met the inclusion criteria, and these studies were subjected to a systematic review and meta‐analyses to determine the effectiveness of the interventions.

Results

Interventions used a variety of techniques including UV technology and photoaging information. Study design and outcome measures varied. The research indicated that appearance‐based interventions have a positive effect on UV exposure and sun protection intentions and behaviour.

Conclusions

Findings suggest that interventions based on the appearance‐damaging effects of UV exposure, and the positive effects of sun protection, may have a role in health promotion. It is concluded that there is a need for further research incorporating a wider range of participants, and using qualitative and mixed methods designs.

Statement of contribution

What is already known on the subject? Recreational exposure to ultraviolet (UV) radiation, are the primary causes of all melanomas, leading to skin cancer. A previous systematic review (Dodd & Forshaw, ) looking at the efficacy of appearance‐focussed interventions in skin cancer prevention, suggested that there were significant effects for UV protection behaviour after such interventions.

What does this study add? An up‐to‐date systematic review of studies that has carried out appearance‐based interventions to reduce UV exposure and/or increase sun protection intentions and behaviours. A meta‐analysis of data providing statistical evidence indicating that appearance‐based interventions have a positive effect on UV exposure and sun protection intentions and behaviour.
First Record of Didymella anemones sp. nov. Teleomorph of Ascochyta anemones, the Causal Agent of Leaf Spots on Pulsatilla korreana in China
Authors: Su Dan , Fu Junfan , Irfan Muhammad
Published: September 2012

The teleomorph of Ascochyta anemones has been recorded for the first time on overwintering windflower stalk in Liaoning, China. The features of this new species were described, and it was distinguished from other species to which it is similar. The morphological characteristics of this species, such as asci and ascospores, phylogenetic analysis based on internal transcribed spacer sequences, comparison with similar fungi so far described from Ranunculaceae indicated that the teleomorph is an undescribed species of Didymella.
Variability of the Ramularia collo‐cygni Population in Central Europe
Authors: Leisova‐Svobodova Leona , Matusinsky Pavel , Kucera Ladislav
Published: September 2012

The genetic structure of the fungal barley pathogen Ramularia collo‐cygni (Rcc) population in Central Europe involving the isolates from the Czech Republic, the Slovak Republic, Germany and Swiss was determined using amplified fragment length polymorphism (AFLP) analysis. One hundred and eighty‐four markers were chosen to determine genetic and genotypic diversity and to test the hypothesis of random mating and population differentiation of Rcc isolates. Among the 337 isolates collected, the overall gene diversity was moderate ( = 0.216). The level of multilocus genotypic diversity was higher within populations than among them. All individuals had unique multilocus genotypes. Genetic differentiation was significant among populations in localities, but at a moderate level (θ = 0.12; P < 0.001), suggesting that gene flow is occurring among populations. The isolates from all twelve clusters produced by Structure were found in all local populations, although at different frequencies. Therefore, the inferred clusters did not represent geographical populations. Although the null hypothesis of random mating in Rcc populations was rejected, the high level of genotypic diversity suggests that the Rcc population structure appears to be generated by a mixed reproductive system including both asexual and sexual reproduction, along with a rather high migration rate.
Comparison of filtering methods for extracellular gastric slow wave recordings
Authors: Paskaranandavadivel N. , O’Grady G. , Du P. , K Cheng L.
Published: September 2012

Background  Extracellular recordings are used to define gastric slow wave propagation. Signal filtering is a key step in the analysis and interpretation of extracellular slow wave data; however, there is controversy and uncertainty regarding the appropriate filtering settings. This study investigated the effect of various standard filters on the morphology and measurement of extracellular gastric slow waves.

Methods  Experimental extracellular gastric slow waves were recorded from the serosal surface of the stomach from pigs and humans. Four digital filters: finite impulse response filter (0.05–1 Hz); Savitzky‐Golay filter (0–1.98 Hz); Bessel filter (2–100 Hz); and Butterworth filter (5–100 Hz); were applied on extracellular gastric slow wave signals to compare the changes temporally (morphology of the signal) and spectrally (signals in the frequency domain).

Key Results  The extracellular slow wave activity is represented in the frequency domain by a dominant frequency and its associated harmonics in diminishing power. Optimal filters apply cutoff frequencies consistent with the dominant slow wave frequency (3–5 cpm) and main harmonics (up to ∼2 Hz). Applying filters with cutoff frequencies above or below the dominant and harmonic frequencies was found to distort or eliminate slow wave signal content.

Conclusions & Inferences  Investigators must be cognizant of these optimal filtering practices when detecting, analyzing, and interpreting extracellular slow wave recordings. The use of frequency domain analysis is important for identifying the dominant and harmonics of the signal of interest. Capturing the dominant frequency and major harmonics of slow wave is crucial for accurate representation of slow wave activity in the time domain. Standardized filter settings should be determined.
The pharmacokinetics of methadone in adolescents undergoing posterior spinal fusion
Authors: Stemland Christopher J. , Witte Jurgen , Colquhoun Douglas A. , Durieux Marcel E. , Langman Loralie J. , Balireddy Ravi , Thammishetti Swapna , Abel Mark F. , Anderson Brian J.
Published: September 2012

Background

The optimal methadone dosing regimen for children undergoing spinal surgery is uncertain because of sparse pediatric pharmacokinetic data and a paucity of analgesic effect data. The minimum effective analgesic concentration of methadone in opioid naïve adults is 58 mcg·L−1.

Methods

Adolescents aged 12–19 years undergoing idiopathic scoliosis correction were administered 0.25 mg·kg−1 racemic methadone IV prior to surgical incision. Arterial blood samples for methadone assay were obtained at 0 min, 5 min, 10 min, 15 min, 20 min, 40 min, 1 h, 2 h, 4 h, 5 h, 6 h, 8 h, 10 h, 12 h, 24 h, and 48 h. Compartment analysis was undertaken using nonlinear mixed effects models. Parameter estimates were standardized to a 70‐kg person using allometric models.

Results

A three‐compartment linear disposition model best described observed time–concentration profiles. Population parameter estimates (between‐subjects variability) were central volume (V1) 19.1 (126%) L 70 kg−1, peripheral volumes of distribution V2 65.5 (60%) L 70 kg−1, V3 485 (23%) L 70 kg−1, clearance (CL) 9.3 (11%) L·h−1·70 kg−1, and inter‐compartment clearances Q2 282 (95%) L·h−1 70 kg−1, Q3 139 (42%) L·h−1 70 kg−1. The terminal elimination half‐life was 44.4 h. The mean observed methadone concentration was <58 mcg·L−1 by the first hour after administration.

Conclusions

Current pharmacokinetic parameter estimates in adolescents are similar to those reported in adults. Methadone undergoes rapid redistribution after bolus administration. This may result in plasma concentrations that provide inadequate analgesia postoperatively. We would suggest following the bolus (0.25 mg.kg‐1) with an infusion (0.1–0.15 mg·kg−1·h−1 for 4 h) during spinal surgery to ensure adequate plasma concentrations for 24 h.
The evolution of submarine channels under the influence of Coriolis forces: experimental observations of flow structures
Authors: Cossu Remo , Wells Mathew G.
Published: September 2012

Terra Nova, 25, 65–71, 2013

We present results from experimental gravity and turbidity currents to show that at high latitudes, the Coriolis effect strongly influences the internal flow structure in submarine channel systems. At high latitudes, Coriolis forces deflect the downstream velocity core, and consequently areas of deposition and erosion, to one side of the channel system. Over time, this supports the evolution of low‐sinuosity submarine channels. These findings help explain the recently found relation that channels at low latitudes often show strongly sinuous planform geometries, whereas channels at high latitudes tend to be much less sinuous. On the basis of our observations and an existing conceptual model for channel evolution, we propose a process model for sedimentation regimes in turbidity currents, which is applicable to all latitudinal settings.
Role of galactolipid biosynthesis in coordinated development of photosynthetic complexes and thylakoid membranes during chloroplast biogenesis in Arabidopsis
Authors: Kobayashi Koichi , Narise Takafumi , Sonoike Kintake , Hashimoto Haruki , Sato Naoki , Kondo Maki , Nishimura Mikio , Sato Mayuko , Toyooka Kiminori , Sugimoto Keiko , Wada Hajime , Masuda Tatsuru , Ohta Hiroyuki
Published: September 2012

The galactolipids monogalactosyldiacylglycerol (MGDG) and digalactosyldiacylglycerol (DGDG) are the predominant lipids in thylakoid membranes and indispensable for photosynthesis. Among the three isoforms that catalyze MGDG synthesis in Arabidopsis thaliana, MGD1 is responsible for most galactolipid synthesis in chloroplasts, whereas MGD2 and MGD3 are required for DGDG accumulation during phosphate (Pi) starvation. A null mutant of Arabidopsis MGD1 (mgd1‐2), which lacks both galactolipids and shows a severe defect in chloroplast biogenesis under nutrient‐sufficient conditions, accumulated large amounts of DGDG, with a strong induction of MGD2/3 expression, during Pi starvation. In plastids of Pi‐starved mgd1‐2 leaves, biogenesis of thylakoid‐like internal membranes, occasionally associated with invagination of the inner envelope, was observed, together with chlorophyll accumulation. Moreover, the mutant accumulated photosynthetic membrane proteins upon Pi starvation, indicating a compensation for MGD1 deficiency by Pi stress‐induced galactolipid biosynthesis. However, photosynthetic activity in the mutant was still abolished, and light‐harvesting/photosystem core complexes were improperly formed, suggesting a requirement for MGDG for proper assembly of these complexes. During Pi starvation, distribution of plastid nucleoids changed concomitantly with internal membrane biogenesis in the mgd1‐2 mutant. Moreover, the reduced expression of nuclear‐ and plastid‐encoded photosynthetic genes observed in the mgd1‐2 mutant under Pi‐sufficient conditions was restored after Pi starvation. In contrast, Pi starvation had no such positive effects in mutants lacking chlorophyll biosynthesis. These observations demonstrate that galactolipid biosynthesis and subsequent membrane biogenesis inside the plastid strongly influence nucleoid distribution and the expression of both plastid‐ and nuclear‐encoded photosynthetic genes, independently of photosynthesis.
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.
Atomically precise surface engineering of silicon CCDs for enhanced UV quantum efficiency
Authors: Greer Frank , Hamden Erika , Jacquot Blake C. , Hoenk Michael E. , Jones Todd J. , Dickie Matthew R. , Monacos Steve P. , Nikzad Shouleh
Published: September 2012

The authors report here on a new technique, combining the atomic precision of molecular beam epitaxy and atomic layer deposition, to fabricate back illuminated silicon CCD detectors that demonstrate world record detector quantum efficiency (>50%) in the near and far ultraviolet (155–300 nm). This report describes in detail the unique surface engineering approaches used and demonstrates the robustness of detector performance that is obtained by achieving atomic level precision at key steps in the fabrication process. The characterization, materials, and devices produced in this effort will be presented along with comparison to other approaches.
Gas chopping etching process for InP based nanostructures with high aspect ratios
Authors: Afzal Sohaib , Peter Reithmaier Johann
Published: September 2012

The authors report a novel etching process for the fabrication of nanostructured III-V semiconductors with ultra-high aspect ratios. For the very first time, a time multiplexed etching process (gas chopping process) for an InP based material system has been successfully developed and demonstrated. The repetition of a Cl2/H2/Ar based etching step together with passivation and removal steps ensures very deep etching with straight walls without general restrictions by the etch depth. The newly developed process is very promising for the fabrication of deeply etched feedback gratings for lasers or nanophotonic devices requesting high aspect ratios, like lasers with surface defined distributed Bragg reflector/distributed feedback gratings or deeply etched photonic crystals. This new process allows the formation of vertical profiles with smooth surfaces and reduced footing effect. Using this gas chopping process for InP, a high mask selectivity of 15, good etching rate of 95 nm/min, and record values of the aspect ratio up to 41 could be demonstrated.
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.
Low-cost diffuse optical tomography for the classroom
Authors: Minagawa Taisuke , Zirak Peyman , Weigel Udo M. , Kristoffersen Anna K. , Mateos Nicolas , Valencia Alejandra , Durduran Turgut
Published: September 2012

Diffuse optical tomography (DOT) is an emerging imaging modality with potential applications in oncology, neurology, and other clinical areas. It allows the non-invasive probing of the tissue function using relatively inexpensive and safe instrumentation. An educational laboratory setup of a DOT system could be used to demonstrate how photons propagate through tissues, basics of medical tomography, and the concepts of multiple scattering and absorption. Here, we report a DOT setup that could be introduced to the advanced undergraduate or early graduate curriculum using inexpensive and readily available tools. The basis of the system is the LEGO Mindstorms NXT platform which controls the light sources, the detectors (photo-diodes), a mechanical 2D scanning platform, and the data acquisition. A basic tomographic reconstruction is implemented in standard numerical software, and 3D images are reconstructed. The concept was tested and developed in an educational environment that involved a high-school student and a group of post-doctoral fellows.
A semiclassical optics derivation of Einstein’s rate equations
Authors: Höppner Robert , Roldán Eugenio , de Valcárcel Germán J.
Published: September 2012

We provide a semiclassical optics derivation of Einstein’s rate equations (ERE) for a two-level system illuminated by a broadband light field, setting a limit on their validity that depends on the spectral properties of the light field. Starting from the optical Bloch equations for individual atoms, the ensemble averaged atomic inversion is shown to follow ERE under two concurrent hypotheses: (i) the decorrelation of the inversion at a given time from the field at later times and (ii) a Markov approximation owing to the short correlation time of the light field. When the latter hypothesis is relaxed, we find effective Bloch equations for the ensemble average in which the atomic polarization decay rate is increased by an amount equal to the width of the light spectrum, which allows its adiabatic elimination for a large enough spectral width. The use of a phase-diffusion model of light allows us to check our results and hypotheses using numerical simulations of the corresponding stochastic differential equations. We take into account both light bandwidth and atomic linewidth, which allows us to discuss the differences existing between rate equations in the limits of large light bandwidth or large atomic linewidth. Only in the former case does one obtain ERE with the correct expression for Einstein’s B coefficient.
Video-based spatial portraits of a nonlinear vibrating string
Authors: Hassan Umer , Usman Zubair , Sabieh Anwar Muhammad
Published: September 2012

The article describes a systematic experimental study of a string vibrating nonlinearly. The string is tracked in real time using strategically located cameras; the video tracking enables a remote observation of the oscillator without perturbing its inherent nonlinearities. We show that our technique can help probe the parametrically excited oscillations and study phenomena such as elliptical and circular trajectories near resonance, resonance fold-over, jump, hysteresis, and subharmonic resonance. The experiment has been successfully employed in the advanced physics laboratory.
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

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

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

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

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

Urinary 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

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.