Progress dissecting the oral microbiome in caries and health

Recent rapid advances in "-omics" technologies have yielded new insights into the interaction of the oral microbiome with its host. Associations of species that are usually considered to be acid-tolerant with caries have been confirmed, while some recognized as health-associated are often present in greater proportions in the absence of caries. In addition, some newly identified bacteria have been suggested as potential contributors to the caries process. In spite of this progress, two major challenges remain. The first is that there is a great deal of heterogeneity in the phenotypic capabilities of individual species of oral bacteria. The second is that the most abundant taxa in oral biofilms display remarkable phenotypic plasticity, i.e., the bacteria associated most strongly with health or with caries can morph rapidly in response to alterations in environmental pH, carbohydrate availability and source, and oxygen tension and redox environment. However, new technologic advances coupled with "old-fashioned microbiology" are starting to erode the barriers to a more complete understanding of oral biofilm physiology and ecology, and in doing so are beginning to provide insights for the creation of novel cost-effective caries control therapies.

A galactose-specific sugar: phosphotransferase permease is prevalent in the non-core genome of Streptococcus mutans

Three genes predicted to encode the A, B and C domains of a sugar : phosphotransferase system (PTS) permease specific for galactose\(EII(Gal) ) were identified in the genomes of 35 of 57 recently sequenced isolates of Streptococcus mutans, the primary etiological agent of human dental caries. Mutants defective in the EII(Gal) complex were constructed in six of the isolates and showed markedly reduced growth rates on galactose-based medium relative to the parental strains. An EII(Gal) -deficient strain constructed using the invasive serotype f strain OMZ175 (OMZ/IIGal) expressed significantly lower PTS activity when galactose was present as the substrate. Galactose was shown to be an effective inducer of catabolite repression in OMZ175, but not in the EII(Gal) -deficient strain. In a mixed-species competition assay with galactose as the sole carbohydrate source, OMZ/IIGal was less effective than the parental strain at competing with the oral commensal bacterium Streptococcus gordonii, which has a high-affinity galactose transporter. Hence, a significant proportion of S. mutans strains encode a galactose PTS permease that could enhance the ability of these isolates to compete more effectively with commensal streptococci for galactose in salivary constituents and the diet.

Observation of a critical gradient threshold for electron temperature fluctuations in the DIII-D Tokamak

A critical gradient threshold has been observed for the first time in a systematic, controlled experiment for a locally measured turbulent quantity in the core of a confined high-temperature plasma. In an experiment in the DIII-D tokamak where L(T(e))(-1) = |∇T(e)|/T(e) and toroidal rotation were varied, long wavelength (k(θ)ρ(s) ≲ 0.4) electron temperature fluctuations exhibit a threshold in L(T(e))(-1): below, they change little; above, they steadily increase. The increase in δT(e)/T(e) is concurrent with increased electron heat flux and transport stiffness. Observations were insensitive to rotation. Accumulated evidence strongly enforces the identification of the experimentally observed threshold with ∇T(e)-driven trapped electron mode turbulence.

The added challenges of bone metastases treatment in elderly patients

Most cancers occur in those older than the age of 65 years. As the population of the world ages and life expectancies continue to increase, it is important to address treatment challenges for elderly patients. This narrative review details the challenges of palliative radiotherapy treatment for elderly patients with bone metastases. We begin with the definition of elderly and its appropriateness, outlining recent demographic data of patients with cancer. The current status of elderly participation in clinical trials is discussed by reviewing the recent literature and clinical trial data. Factors affecting enrolment of the elderly are assessed, with a focus on palliative radiotherapy trials, and what we can do to improve accrual in this data-driven setting. At present, there is a lack of level 1 evidence that evaluates the optimal treatment for elderly patients with bone metastases. Therefore, a review of safety and efficacy is given based on previously published reports. Palliative radiotherapy for elderly patients is a worthwhile treatment and should be recommended regardless of age, as supported by available evidence. Patient, family and physician concerns about physical burden may be reduced as single treatments (that often can be done in a single visit) are as beneficial as multiple treatments for painful bone metastases. In elderly patients, radiotherapy may even be the best treatment for these cases as opioid-related adverse events are amplified in this group and often dosages are more difficult to titrate. Clinicians should continue to encourage the enrolment of elderly patients on to clinical trials as these data form the basis of optimal treatment guidelines. Radiation oncologists are encouraged to reduce the physical burden for elderly patients by offering single treatments where appropriate and completing consultation, treatment simulation and treatment in a single clinical visit.

Design of a millimeter-wave polarimeter for NSTX-Upgrade and initial test on DIII-D

Polarimetry is a powerful diagnostic technique to probe plasma equilibria and magnetic fluctuations in fusion plasmas. In a high beta plasma such as the National Spherical Torus eXperiment (NSTX), these measurements are important to understand plasma stability and anomalous transport. A 288 GHz polarimeter operating along a major radial chord in retroreflection geometry has been developed and is being tested on the DIII-D tokamak to prepare for future implementation on NSTX-Upgrade. The system launches a rotating linearly polarized beam and detects the phase shift directly related to the polarization change caused by the plasma. To accomplish this, a pair of orthogonal linearly polarized beams with a stable difference frequency is generated using a single sideband modulation technique, then combined and transformed to be counter-rotating circularly polarized. To improve phase resolution, quasi-optical isolation, using Faraday rotators and polarizers, is utilized to eliminate a multi-path feedback effect, which is found to be the primary source of phase error. The bench tests in the laboratory and DIII-D power supply test discharges indicate ≤1° phase resolution.

Inter-rater reliability between musculoskeletal radiologists and orthopedic surgeons on computed tomography imaging features of spinal metastases

INTRODUCTION

The primary objective of this pilot study was to examine the inter-rater reliability in scoring the computed tomography (ct) imaging features of spinal metastases in patients referred for radiotherapy (rt) for bone pain.

METHODS

In a retrospective review, 3 musculoskeletal radiologists and 2 orthopedic spinal surgeons independently evaluated ct imaging features for 41 patients with spinal metastases treated with rt in an outpatient radiation clinic from January 2007 to October 2008. The evaluation used spinal assessment criteria that had been developed in-house, with reference to osseous and soft tissue tumour extent,presence of a pathologic fracture,severity of vertebral height loss, andpresence of kyphosis.The Cohen kappa coefficient between the two specialties was calculated.

RESULTS

Mean patient age was 69.2 years (30 men, 11 women). The mean total daily oral morphine equivalent was 73.4 mg. Treatment dose-fractionation schedules included 8 Gy/1 (n = 28), 20 Gy/5 (n = 12), and 20 Gy/8 (n = 1). Areas of moderate agreement in identifying the ct imaging appearance of spinal metastasis included extent of vertebral body involvement (κ = 0.48) and soft-tissue component (κ = 0.59). Areas of fair agreement included extent of pedicle involvement (κ = 0.28), extent of lamina involvement (κ = 0.35), and presence of pathologic fracture (κ = 0.20). Areas of poor agreement included nerve-root compression (κ = 0.14) and vertebral body height loss (κ = 0.19).

CONCLUSIONS

The range of agreement between musculoskeletal radiologists and orthopedic surgeons for most spinal assessment criteria is moderate to poor. A consensus for managing challenging vertebral injuries secondary to spinal metastases needs to be established so as to best triage patients to the most appropriate therapeutic modality.

Involvement of decreased hypoxia-inducible factor 1 activity and resultant G1-S cell cycle transition in radioresistance of perinecrotic tumor cells

Cancer patients often suffer from local tumor recurrence after radiation therapy. Some intracellular and extracellular factors, such as activity of hypoxia-inducible factor 1 (HIF-1), cell cycle status and oxygen availability, have been suggested to affect DNA damage responses and eventual radioresistant characteristics of cancer cells. But when, where, and how these factors affect one another and induce cellular radioresistance is largely unknown. Here, we analyzed mechanistic and spatio-temporal relationships among them in highly heterogeneous tumor microenvironments. Experiments in vitro demonstrated that a decrease in the glucose concentration reduced the transcriptional activity of HIF-1 and expression of a downstream gene for the cell cycle regulator p27^Kip1 even under hypoxic conditions. Then, the proportion of cells in the radioresistant S phase increased, whereas that in the radiosensitive G₁ phase decreased, significantly. Immunohistochemical analyses showed that cancer cells in perinecrotic hypoxic regions, which should be under low-glucose conditions, expressed little HIF-1α, and therefore, were mainly in S phase and less damaged by radiation treatment. Continuous administration of glucagon, which increases the blood glucose concentration and so improves glucose availability in perinecrotic hypoxic regions, induced HIF-1α expression and increased radiation-induced DNA damage. Taken all together, these results indicate that cancer cells in perinecrotic regions, which would be under low-glucose and hypoxic conditions, obtain radioresistance by decreasing the level of both HIF-1 activity and p27^Kip1 expression, and adjusting their cell cycle to the radioresistant S phase.

Role of zonal flow predator-prey oscillations in triggering the transition to H-mode confinement

Direct evidence of zonal flow (ZF) predator-prey oscillations and the synergistic roles of ZF- and equilibrium E×B flow shear in triggering the low- to high-confinement (L- to H-mode) transition in the DIII-D tokamak is presented. Periodic turbulence suppression is first observed in a narrow layer at and just inside the separatrix when the shearing rate transiently exceeds the turbulence decorrelation rate. The final transition to H mode with sustained turbulence and transport reduction is controlled by equilibrium E×B shear due to the increasing ion pressure gradient.

Association of β-cell function and insulin sensitivity with fasting and 2-h plasma glucose in a large Chinese population

AIM

Our aim was to provide a quantitative analysis of the changes in the principal determinants of insulin sensitivity and secretion in relation to fasting plasma glucose (FPG) or 2-h plasma glucose (2h PG) in a Chinese population with a wide range of glucose tolerance.

METHODS

A total of 5728 adults spanning the entire range of glucose tolerance were included. Insulin sensitivity was measured by Matsuda insulin sensitivity index (ISI(M)) and homeostasis model assessment of 1/homeostasis model assessment of insulin resistance (HOMA-IR). β-Cell function adjusted by insulin sensitivity was assessed from disposition index (DI) at early-phase DI(30) and total DI(120). The exponential curve was established as the best fit for the relationship between insulin sensitivity or β-cell function and FPG or 2h PG.

RESULTS

Relative to the trend classified as increasing 2h PG, hepatic insulin sensitivity and insulin secretion showed a decreasing trend to a substantial degree as FPG increased. A 1 mmol/l increase in FPG and 2h PG concentration was associated with a -22 and -21% decline in ISI(M), -16 and -4% in 1/HOMA-IR, -38 and -35% in DI(30) and -36 and -26% in DI(120). The decay constant of ISI(M) and DI(30) in IFG or ISI(M), 1/HOMA-IR, DI(30) and DI(120) in IGT was lower than that in normal glucose tolerance. Significant interactions between sex and glucose levels determining DI were found.

CONCLUSIONS

We conclude that impairment of insulin sensitivity and insulin secretion contributes to both FPG or 2h PG hyperglycaemia in a Chinese population, but that the decline in insulin secretion is more pronounced with increasing fasting than 2h PG.

A Bayesian approach to risk-adjusted outcome monitoring in healthcare

Clinical outcomes are commonly monitored in healthcare practices to detect changes in care providers' performance. One key challenge in outcome monitoring is the need of adjustment for patient base-line risks. Various control charting methods have been developed to conduct risk-adjusted outcome monitoring, but they all rely on the availability of a large number of historical data. We propose a Bayesian approach to this type of monitoring for cases where historical data are not available. In our approach, detection of change is formulated as a model-selection problem and solved using a popular Bayesian tool for variable selection, the Bayes factor. Issues in decision-making about whether there is a change point in the observed patient outcomes are addressed, including specification of priors and computation of Bayes factors. This approach is applied to a real data set on cardiac surgeries, and its performance under different parameter scenarios is studied through simulations.

Single-virus tracking reveals a spatial receptor-dependent search mechanism

Viral infection begins with the binding of a virus to a specific target on the surface of the host cell, followed by viral genome delivery into the host and a continuation of the infection process. Before binding occurs, the virus must first find its receptor by a process whose details are largely unknown. We applied high-resolution fluorescence microscopy and single-particle tracking to elucidate the target-finding process in bacteriophage λ as it infects an Escherichia coli cell. By monitoring the motion of individual viruses through the early stages of infection, we identified a unique spatial focusing process that allows a virus to arrive from its initial random landing site to its destination at the cell pole. The search process is governed by the interaction between the virus and the LamB receptors, and by the spatial organization of the receptor network on the cell surface. Our findings allowed us to develop a theoretical model for the target-finding process that reproduces the key features observed in experiment. We discuss the possible implications of our findings for the process of viral receptor-finding in higher systems.

Update on the systematic review of palliative radiotherapy trials for bone metastases

AIMS

To update previous meta-analyses of randomised palliative radiotherapy trials comparing single fractions versus multiple fractions.

MATERIALS AND METHODS

All published randomised controlled trials comparing single fraction versus multiple fraction schedules for the palliation of uncomplicated bone metastases were included in this analysis. Odds ratios and 95% confidence intervals were calculated for each trial. Forest plots were created using a random effects model and the Mantel-Haenszel statistic.

RESULTS

In total, 25 randomised controlled trials were identified. For intention-to-treat patients, the overall response rate was similar in patients receiving single fractions (1696 of 2818; 60%) and multiple fractions (1711 of 2799; 61%). Complete response rates were 620 of 2641 (23%) in the single fraction arm and 634 of 2622 (24%) in the multiple fraction arm. No significant difference was seen in overall or complete response rates. Pathological fracture did not favour either arm, but spinal cord compression trended towards favouring multiple fractions; however, neither was statistically significant (P = 0.72 and P = 0.13, respectively). Retreatment rates favoured patients in the multiple fraction arm, where the likelihood of requiring re-irradiation was 2.6-fold greater in the single fraction arm (95% confidence interval: 1.92-3.47; P < 0.00001). Repeated analyses excluding drop-out patients did not alter these findings. In general, no significant differences in acute toxicities were seen.

CONCLUSION

Overall and complete response rates were similar in both intention-to-treat and assessable patients. Single and multiple fraction regimens provided equal pain relief; however, significantly higher retreatment rates occurred in those receiving single fractions.

Following cell-fate in E. coli after infection by phage lambda

The system comprising bacteriophage (phage) lambda and the bacterium E. coli has long served as a paradigm for cell-fate determination^1,2. Following the simultaneous infection of the cell by a number of phages, one of two pathways is chosen: lytic (virulent) or lysogenic (dormant)^3,4. We recently developed a method for fluorescently labeling individual phages, and were able to examine the post-infection decision in real-time under the microscope, at the level of individual phages and cells⁵. Here, we describe the full procedure for performing the infection experiments described in our earlier work⁵. This includes the creation of fluorescent phages, infection of the cells, imaging under the microscope and data analysis. The fluorescent phage is a "hybrid", co-expressing wild- type and YFP-fusion versions of the capsid gpD protein. A crude phage lysate is first obtained by inducing a lysogen of the gpD-EYFP (Enhanced Yellow Fluorescent Protein) phage, harboring a plasmid expressing wild type gpD. A series of purification steps are then performed, followed by DAPI-labeling and imaging under the microscope. This is done in order to verify the uniformity, DNA packaging efficiency, fluorescence signal and structural stability of the phage stock. The initial adsorption of phages to bacteria is performed on ice, then followed by a short incubation at 35°C to trigger viral DNA injection⁶. The phage/bacteria mixture is then moved to the surface of a thin nutrient agar slab, covered with a coverslip and imaged under an epifluorescence microscope. The post-infection process is followed for 4 hr, at 10 min interval. Multiple stage positions are tracked such that ~100 cell infections can be traced in a single experiment. At each position and time point, images are acquired in the phase-contrast and red and green fluorescent channels. The phase-contrast image is used later for automated cell recognition while the fluorescent channels are used to characterize the infection outcome: production of new fluorescent phages (green) followed by cell lysis, or expression of lysogeny factors (red) followed by resumed cell growth and division. The acquired time-lapse movies are processed using a combination of manual and automated methods. Data analysis results in the identification of infection parameters for each infection event (e.g. number and positions of infecting phages) as well as infection outcome (lysis/lysogeny). Additional parameters can be extracted if desired.