Dynamics of ERK regulation in the processive limit

We consider a model of extracellular signal-regulated kinase regulation by dual-site phosphorylation and dephosphorylation, which exhibits bistability and oscillations, but loses these properties in the limit in which the mechanisms underlying phosphorylation and dephosphorylation become processive. Our results suggest that anywhere along the way to becoming processive, the model remains bistable and oscillatory. More precisely, in simplified versions of the model, precursors to bistability and oscillations (specifically, multistationarity and Hopf bifurcations, respectively) exist at all "processivity levels". Finally, we investigate whether bistability and oscillations can exist together.

Joining and decomposing reaction networks

In systems and synthetic biology, much research has focused on the behavior and design of single pathways, while, more recently, experimental efforts have focused on how cross-talk (coupling two or more pathways) or inhibiting molecular function (isolating one part of the pathway) affects systems-level behavior. However, the theory for tackling these larger systems in general has lagged behind. Here, we analyze how joining networks (e.g., cross-talk) or decomposing networks (e.g., inhibition or knock-outs) affects three properties that reaction networks may possess-identifiability (recoverability of parameter values from data), steady-state invariants (relationships among species concentrations at steady state, used in model selection), and multistationarity (capacity for multiple steady states, which correspond to multiple cell decisions). Specifically, we prove results that clarify, for a network obtained by joining two smaller networks, how properties of the smaller networks can be inferred from or can imply similar properties of the original network. Our proofs use techniques from computational algebraic geometry, including elimination theory and differential algebra.

Algebraic signatures of convex and non-convex codes

A convex code is a binary code generated by the pattern of intersections of a collection of open convex sets in some Euclidean space. Convex codes are relevant to neuroscience as they arise from the activity of neurons that have convex receptive fields. In this paper, we use algebraic methods to determine if a code is convex. Specifically, we use the neural ideal of a code, which is a generalization of the Stanley-Reisner ideal. Using the neural ideal together with its standard generating set, the canonical form, we provide algebraic signatures of certain families of codes that are non-convex. We connect these signatures to the precise conditions on the arrangement of sets that prevent the codes from being convex. Finally, we also provide algebraic signatures for some families of codes that are convex, including the class of intersection-complete codes. These results allow us to detect convexity and non-convexity in a variety of situations, and point to some interesting open questions.

SU-E-T-188: Evaluation of a 3D Patient Relevant Dose QA Tool: Multiple Institutional Studies

PURPOSE

To evaluate 3DVHTM as a patient dose-verification and analysis tool through multiple institutional studies. Virtual patient doses were measured and compared among different vendors' treatment planning systems (TPS) and delivered by different vendors' LINACS so that we better understand the uncertainty of entire process within a patient undergone radiotherapy.

METHODS

One head-and-neck (H&N) and one lung patient were selected in this study. The DICOM images/RT structures along with clinical protocols including prescription doses (59.4Gy for H&N and 70.2Gy for lung) and normal‐tissues tolerances were distributed to six institutions. Based on the same criteria, each institution generated their IMRT plans for the patients. Four different TPS and six different LINACS were used. The conventional per‐beam IMRT QA using MapCHECK was performed by all participants. All the measured and calculated data were sent back to one institution for 3DVH analysis. Through the use of planned-dose-perturbation (PDP)TM algorithm (Sun Nuclear Corp.), the 'actual-DVHs' were generated and then compared to the 'reference-DVHs' from plans. Their differences represented errors induced from the combination of TPS dose-calculation algorithm and beam-delivery systems.

RESULTS

All plans in the study have met the clinical criteria. The 3D matching rates for 3%global/3mm (DD/DTA) ranged from 95.8-99.9% for H&N and 93.5-100% for lung. The dose-difference-histogram for PTV had a mean of 0.67% [0-2%] for H&N cases and 1% [0.6-2.8%] for lung cases. The QA tool was able to spot the doses outside 3%/3mm criteria for critical structures much easier than conventional planar QA methods. In addition, the hot/cold spots at the boundaries of collimators are attributed to the uncertainty of collimator-positioning greater than 1-mm.

CONCLUSIONS

The analysis of IMRT plans in this study has shown that 3DVH is a vital QA tool for assessing clinically relevant doses as well as diagnosing potential systematic errors from both TPS and delivery systems.

Comparison of pattern detection methods in microarray time series of the segmentation clock

While genome-wide gene expression data are generated at an increasing rate, the repertoire of approaches for pattern discovery in these data is still limited. Identifying subtle patterns of interest in large amounts of data (tens of thousands of profiles) associated with a certain level of noise remains a challenge. A microarray time series was recently generated to study the transcriptional program of the mouse segmentation clock, a biological oscillator associated with the periodic formation of the segments of the body axis. A method related to Fourier analysis, the Lomb-Scargle periodogram, was used to detect periodic profiles in the dataset, leading to the identification of a novel set of cyclic genes associated with the segmentation clock. Here, we applied to the same microarray time series dataset four distinct mathematical methods to identify significant patterns in gene expression profiles. These methods are called: Phase consistency, Address reduction, Cyclohedron test and Stable persistence, and are based on different conceptual frameworks that are either hypothesis- or data-driven. Some of the methods, unlike Fourier transforms, are not dependent on the assumption of periodicity of the pattern of interest. Remarkably, these methods identified blindly the expression profiles of known cyclic genes as the most significant patterns in the dataset. Many candidate genes predicted by more than one approach appeared to be true positive cyclic genes and will be of particular interest for future research. In addition, these methods predicted novel candidate cyclic genes that were consistent with previous biological knowledge and experimental validation in mouse embryos. Our results demonstrate the utility of these novel pattern detection strategies, notably for detection of periodic profiles, and suggest that combining several distinct mathematical approaches to analyze microarray datasets is a valuable strategy for identifying genes that exhibit novel, interesting transcriptional patterns.

The cyclohedron test for finding periodic genes in time course expression studies

The problem of finding periodically expressed genes from time course microarray experiments is at the center of numerous efforts to identify the molecular components of biological clocks. We present a new approach to this problem based on the cyclohedron test, which is a rank test inspired by recent advances in algebraic combinatorics. The test has the advantage of being robust to measurement errors, and can be used to ascertain the significance of top-ranked genes. We apply the test to recently published measurements of gene expression during mouse somitogenesis and find 32 genes that collectively are significant. Among these are previously identified periodic genes involved in the Notch/FGF and Wnt signaling pathways, as well as novel candidate genes that may play a role in regulating the segmentation clock. These results confirm that there are an abundance of exceptionally periodic genes expressed during somitogenesis. The emphasis of this paper is on the statistics and combinatorics that underlie the cyclohedron test and its implementation within a multiple testing framework.

An integrated treatment delivery system for CSRS and CSRT and clinical applications

An integrated treatment delivery system for conformal stereotactic radiosurgery (CSRS) and radiotherapy (CSRT) has been developed through a collaboration involving Siemens Medical Systems, Inc., Tyco/Radionics, Inc., and The University of Texas M. D. Anderson Cancer Center. The system consists of a 6-MV linear accelerator (LINAC) equipped with a Tyco/Radionics miniature multileaf collimator (mMLC). For the conventional SRS treatment, the circular collimator housing can be attached to the opening window of the mMLC. The treatment delivery system is integrated with a radiotherapy treatment planning system and a record-and-verify system. The purpose of this study is to report the characteristics, performance, benefits, and the clinical applications of this delivery system. The technical specifications of the LINAC and mMLC were tested, and all the specifications were met. The 80% to 20% penumbral width for each mMLC leaf is approximately 3 mm and is nearly independent of the off-axis positions of a leaf. The maximum interleaf leakage is 1.4% (1.1% on average) and the maximum intra-leaf leakage is 1.0% (0.9% on average). The leaf position precision is better than 0.5 mm for all the leaves. The integration of the SRS/SRT treatment planning system, mMLC, and LINAC has been evaluated successfully for transferring the patient treatment data file through radiotherapy treatment planning system to the patient information and treatment record-and-verify server and the mMLC controller. Subsequently, the auto-sequential treatment delivery for SRS, CSRS/CSRT, and the step-and-shoot intensity-modulated radiotherapy has also been tested successfully. The accuracy of dose delivery was evaluated for a 2-cm spherical target in a Radiological Physics Center SRS head phantom with GAFChromic films and TLD. Five non-coplanar arcs, using a 2-cm diameter circular collimator, were used for this simulation treatment. The accuracy to aim the center of the spherical target was within 0.5 mm and the deviation of dose delivery to the isocenter of the target was within 2% of the calculated dose. For the irregularly shaped tumor, a tissue-equivalent head phantom was used to evaluate the accuracy of dose delivery for using either geometric conformal treatment or IMRT. The accuracy of dose delivery to the isocenter was within 2% and 3% of the calculated dose, respectively. From October 26, 1999 to September 30, 2002, we treated over 400 SRS patients and 70 SRT patients. Four representative cases are presented to illustrate the capabilities of this dedicated unit in performing conventional SRS, CSRS, and CSRT. For all the cases, the geometric conformal-plan dose distributions showed a high degree of conformity to the target shape. The degree of conformity can be evaluated using the target-volume-ratio (TVR). Our preferred TVR values for highly conformed dose distributions range from 1.6 to 2.0. The patient setup reproducibility for the Gill-Thomas-Cosman (GTC) noninvasive head frame ranges from 0.5 to 1 mm, and the head and neck noninvasive frame is within 2 mm. The integrated treatment delivery system offers excellent conformation for complicated planning target volumes with the stereotactic setup approach, ensuring that dose delivery can be achieved within the specified accuracy. In addition, the treatment time is comparable with that of single isocenter multiple-arc treatments.

Evaluating psychosocial nursing interventions for cardiac clients and their caregivers: a case study of the community rehabilitation network in Hong Kong

AIM OF THE STUDY

The purpose of this exploratory study was to describe the type and nature of psychosocial nursing interventions provided for cardiac clients in Hong Kong's Community Rehabilitation Centres (CRNs).

DESIGN/METHODS

Using a two-phase case study design data were collected from nurses, cardiac clients and their caregivers. The initial phase focused on identifying the types of psychosocial interventions provided. These data were obtained by observing nursing activities and the keeping of daily journals by the nurses. The second phase acquired data from structured telephone interviews, that reviewed clients' perceptions of the psychosocial interventions provided by the nurses and face-to-face interviews with clients and their caregivers.

FINDINGS

These findings revealed that the nurses' interpersonal skills of information giving, social support and counselling were highly valued by cardiac clients and their caregivers. Both clients and caregivers outlined a concern about the lack of individual care and this was reflected in the focus of the CRN on group processes.

CONCLUSION

Recommendations for psychosocial cardiac care are made for public health nurses and nurses working in community settings.

A pencil-beam photon dose algorithm for stereotactic radiosurgery using a miniature multileaf collimator

A computer-controlled miniature multileaf collimator (MMLC) with 4 mm leaf width and a maximum field size of 6 cm X 6 cm has been designed as a tertiary beam-shaping device for linac-based stereotactic radiosurgery. The purpose of this study is to develop an accurate and efficient dose calculation model for use with the MMLC. A pencil-beam based algorithm using a sum of three Gaussian kernels was developed to model the off-axis ratio of MMLC fields. Because the kernel integration over a rectangular field can be solved in closed form, dose to any point from an arbitrary MMLC field can be calculated efficiently by summing dose contribution from a set of rectangular apertures and transmission blocks that model individual leaf openings or leaf transmissions. The model uses an effective rectangular field and equivalent square method for determination of depth dose and dose output. Results showed that the calculated percentage depth dose was within 1% and output factor was within 1.5% of measured data. The parameters of the pencil beam kernels were extracted by fitting measured off-axis profiles for a few field sizes at a few depths. The accuracy of the calculated off-axis ratio was tested by comparison with measured data for a number of MMLC fields. The algorithm was shown to be accurate to within 1.5% or 1 mm for off-axis ratios. The algorithm computes at a speed of 34,600 data points per second on a DEC Alpha server model 2000/433 (Digital Equipment Corp., Maynard, MA), which is about 15 times faster than a Clarkson-type summation method.

Verification of radiosurgery target point alignment with an electronic portal imaging device (EPID)

A procedure has been developed using an electronic portal imaging device (EPID) to verify that the center of a patient's lesion is aligned with the center of a treatment cone prior to treatment in a linac-based stereotactic radiosurgery procedure. The coordinates of the lesion center are set on the Brown-Roberts-Wells phantom base using a target simulator. A 3 mm tungsten ball, mounted on the target simulator, is used as the reference point for the planned isocenter. The target simulator is then attached to an adapter mounted on the linac couch, and an EPID image of the simulated target is acquired. The center of the circular-shaped radiation field is calculated from the centroid of the segmented EPID image, and the center of the tungsten ball is identified by an automated computer search algorithm. A summation filter is used to find the position of the lowest radiation intensity coincident with the center of the ball. The alignment error is defined as the difference between the center of the radiation field and the center of the ball. The accuracy of this method was tested and found to be within 0.2 mm. The advantage of the EPID-based procedure is that it can give quantitative offset values quickly for immediate readjustment. We have found that the method is also a convenient tool for testing room laser alignment and the accuracy of the treatment cones.

An evaluation of the effectiveness of public health nursing: a case study of the maternal and child health centres in Hong Kong

The aim of this study was to evaluate the effectiveness of public health nursing in Hong Kong using the maternal and child health centres as a case study. The case study design, employing both qualitative and quantitative methods of data collection, focused on clients' and nurses' perceptions of the effectiveness of care. The data analysis identified three important factors influencing the effectiveness of care: the need for a health needs data base, the organisation of care and service provision. From these findings the authors suggest that a health needs data base plays an essential role in measuring the effectiveness of care in public health nursing.

Surgery versus radiosurgery in the treatment of brain metastasis

Surgery and radiosurgery are effective treatment modalities for brain metastasis. To compare the results of these treatment modalities, the authors followed 13 patients treated by radiosurgery and 62 patients treated by surgery who were retrospectively matched. Patients were matched according to the following criteria: histological characteristics of the primary tumor, extent of systemic disease, preoperative Karnofsky Performance Scale score, time to brain metastasis, number of brain metastases, and patient age and sex. For patients treated by radiosurgery, the median size of the treated lesion was 1.96 cm3 (range 0.41-8.25 cm3) and the median dose was 20 Gy (range 12-22 Gy). The median survival was 7.5 months for patients treated by radiosurgery and 16.4 months for those treated by surgery; this difference was found to be statistically significant using both univariate (p = 0.0018) and multivariate (p = 0.0009) analyses. The difference in survival was due to a higher rate of mortality from brain metastasis in the radiosurgery group than in the surgery group (p < 0.0001) and not due to a difference in the rate of death from systemic disease (p = 0.28). Log-rank analysis showed that the higher mortality rate found in the radiosurgery group was due to a greater progression rate of the radiosurgically treated lesions (p = 0.0001) and not due to the development of new brain metastasis (p = 0.75). On the basis of their data, the authors conclude that surgery is superior to radiosurgery in the treatment of brain metastasis. Patients who undergo surgical treatment survive longer and have a better local control. The data lead the authors to suggest that the indications for radiosurgery should be limited to surgically inaccessible metastatic tumors or patients in poor medical condition. Surgery should remain the treatment of choice whenever possible.