Isolating intrinsic noise sources in a stochastic genetic switch

The stochastic mutual repressor model is analysed using perturbation methods. This simple model of a gene circuit consists of two genes and three promotor states. Either of the two protein products can dimerize, forming a repressor molecule that binds to the promotor of the other gene. When the repressor is bound to a promotor, the corresponding gene is not transcribed and no protein is produced. Either one of the promotors can be repressed at any given time or both can be unrepressed, leaving three possible promotor states. This model is analysed in its bistable regime in which the deterministic limit exhibits two stable fixed points and an unstable saddle, and the case of small noise is considered. On small time scales, the stochastic process fluctuates near one of the stable fixed points, and on large time scales, a metastable transition can occur, where fluctuations drive the system past the unstable saddle to the other stable fixed point. To explore how different intrinsic noise sources affect these transitions, fluctuations in protein production and degradation are eliminated, leaving fluctuations in the promotor state as the only source of noise in the system. Perturbation methods are then used to compute the stability landscape and the distribution of transition times, or first exit time density. To understand how protein noise affects the system, small magnitude fluctuations are added back into the process, and the stability landscape is compared to that of the process without protein noise. It is found that significant differences in the random process emerge in the presence of protein noise

Estimating urban flood risk - uncertainty in design criteria

The design of urban stormwater infrastructure is generally performed assuming that climate is static. For engineering practitioners, stormwater infrastructure is designed using a peak flow method, such as the Rational Method as outlined in the Australian Rainfall and Runoff (AR&R) guidelines and estimates of design rainfall intensities. Changes to Australian rainfall intensity design criteria have been made through updated releases of the AR&R77, AR&R87 and the recent 2013 AR&R Intensity Frequency Distributions (IFDs). The primary focus of this study is to compare the three IFD sets from 51 locations Australia wide. Since the release of the AR&R77 IFDs, the duration and number of locations for rainfall data has increased and techniques for data analysis have changed. Updated terminology coinciding with the 2013 IFD release has also resulted in a practical change to the design rainfall. For example, infrastructure that is designed for a 1: 5 year ARI correlates with an 18.13 % AEP, however for practical purposes, hydraulic guidelines have been updated with the more intuitive 20 % AEP. The evaluation of design rainfall variation across Australia has indicated that the changes are dependent upon location, recurrence interval and rainfall duration. The changes to design rainfall IFDs are due to the application of differing data analysis techniques, the length and number of data sets and the change in terminology from ARI to AEP. Such changes mean that developed infrastructure has been designed to a range of different design criteria indicating the likely inadequacy of earlier developments to the current estimates of flood risk. In many cases, the under-design of infrastructure is greater than the expected impact of increased rainfall intensity under climate change scenarios

Vivid Motor Imagery as an Adaptation Method for Head Turns on a Short-Arm Centrifuge

Artificial gravity (AG) has been proposed as a potential countermeasure to the debilitating physiological effects of long duration space flight. The most economical means of implementing AG may be through the use of a short-radius (2m or less) centrifuge. For such a device to produce gravitational forces comparable to those on earth requires rotation rates in excess of 20 revolutions per minute (rpm). Head turns made out of the plane of rotation at these rates, as may be necessary if exercise is combined with AG, result in cross-coupled stimuli (CCS) that cause adverse side effects including motion sickness, illusory sensations of motion, and inappropriate eye movements. Recent studies indicate that people can adapt to CCS and reduce these side effects by making multiple head turns during centrifuge sessions conducted over consecutive days. However, about 25% of the volunteers for these studies have difficulty tolerating the CCS adaptation paradigm and often drop out due to motion sickness symptoms. The goal of this investigation was to determine whether vivid motor imagery could be used as a pseudostimulus for adapting subjects to this unique environment. Twenty four healthy human subjects (14 males, 10 females), ranging in age from 21 to 48 years (mean 33, sd 7 years) took part in this study. The experimental stimuli were produced using the NASA JSC short-arm centrifuge (SAC). Subjects were oriented supinely on this device with the nose pointed toward the ceiling and head centered on the axis of rotation. Thus, centrifuge rotation was in the body roll plane. After ramp-up the SAC rotated clockwise at a constant rate of 23 rpm, producing a centrifugal force of approximately 1 g at the feet. Semicircular canal CCS were produced by having subjects make yaw head turns from the nose up (NU) position to the right ear down (RED) position and from RED to NU. Each head turn was completed in about one second, and a 30 second recovery period separated consecutive head movements. Participants were randomly assigned to one of three groups (n=8 per group): physical adapters (PA), mental adapters (MA), or a control group (CG). Each subject participated in a one hour test session on each of three consecutive days. Each test session consisted of an initial (preadaptation) period during which the subject performed six CCS maneuvers in the dark, followed by an adaptation period with internal lighting on the centrifuge, and a final (postadaptation) period during which six more CCS maneuvers were performed in the dark. For the PA group, the adaptation period consisted of performing 30 additional CCS maneuvers in the light. For the MA and CG group the centrifuge was ramped down to 0 rpm after the pre-adaptation period and ramped back up to 23 rpm before the post-adaptation period. For the both of these groups, the adaptation period consisted of making 30 CCS maneuvers in the light with the centrifuge stationary (so no cross-coupling occurred). MA group subjects were instructed to vividly imagine the provocative sensations produced by the preadaptation CCS maneuvers in terms of magnitude, duration, and direction of illusory body tilt, as well as any accompanying levels of motion sickness. CG group subjects were asked to answer low imagery content questions (trivial pursuit) during each adaptation period head turn. During the 30 second recovery following each head turn, psychophysical data were collected including self reports of motion sickness, magnitude and direction estimates of illusory body tilt, and the overall duration of these sensations. A multilevel mixed effects linear regression analysis performed on all response variables indicated that all three groups experienced some psychophysical adaptation across the three test sessions. For illusory tilt magnitude, the PA group exhibited the most overall adaptation, followed by the MA group, and the CG group. The slopes of these adaptation trajectories by group over day were significantly diffent from one another. For the perceived duration of sensations, the CG group again exhibited the least amount of adaptation. However, the rates of adaptation of the PA and the MA groups were indistinguishable, suggesting that the imagined pseudostimulus appeared to be just as effective a means of adaptation as the actual stimulus. The MA group's rate of adaptation to motion sickness symptoms was also comparable to the PA group. The use of vivid motor imagery may be an effective method for adapting to the illusory sensations and motion sickness symptoms produced by cross-coupled stimuli. For space-based AG applications, this technique may prove quite useful in retaining astronauts considered highly susceptible to motion sickness as it reduces the number of actual CCS required to attain adaptation

Elucidating the Antagonistic Relationship Between Bone Morphogenetic Protein and Activin Signaling Pathways in Osteoprogenitor Cells

Osteoporosis is a disease characterized by low bone mineral density due to the rate of bone resorption exceeding that of bone formation. Substantial evidence indicates the Bone Morphogenetic Protein (BMP) pathway promotes bone formation through action of the effectors SMAD1/5/8 while the Activin pathway negatively influences bone mass through action of the effectors SMAD2/3. Recent studies from our lab suggest that BMP and Activin ligands regulate bone mass in a see-saw-like mechanism via competition for a shared pool of receptors, i.e. receptor-level competition. In the present study we seek to test this hypothesis in vitro via signaling responsiveness assays using pathway-specific western blot analyses in the osteogenic cell line W-20-17. We first confirmed that W-20-17 cells respond to exogenous stimulation by BMP2 and Activin-A. Then, we administered recombinant versions of naturally-occurring extracellular ligand traps for BMP2 or Activin ligands (Noggin and Follistatin, respectively) to examine basal antagonism between these pathways. This revealed that, under basal conditions, SMAD1/5/8 activation is repressed by Activin signaling; interestingly, the converse relationship was not observed. To determine the molecular mechanism allowing for this relationship, we treated W-20-17 cells with SB431542, which is an intracellular inhibitor of Activin signaling that functions downstream of receptor engagement, and found no effect on SMAD1/5/8 activation. Collectively, our results suggest Activin-mediated repression of BMP signaling is ligand-dependent but occurs upstream of SMAD2/3 activation. Current studies seek to identify the specific Activin ligand(s) responsible for this effect; gene expression analyses indicates that W-20-17 cells express multiple Activin subunits including Inhβa and Inhβb. Additionally, overpression studies are ongoing to determine if receptor-level competition is involved in mediating these effects. Collectively, our study seeks to elucidate the mechanism(s) that regulate antagonism BMP and Activin signaling pathways to identify novel opportunities for safer and more effective therapies for low bone mass in humans

Infant feeding knowledge, attitudes,and beliefs predict antenatal intention among first-time mothers in Queensland

Aim: This study assessed infant feeding knowledge, attitudes, and beliefs among women from Queensland, Australia, in their first pregnancy. Antenatal feeding intention in this group was described, and the hypothesis was tested that antenatal knowledge, attitudes, and beliefs about infant feeding are associated with antenatal intention for the duration and exclusivity of breastfeeding for the infant’s first year. Subjects and Methods: The Feeding Queensland Babies Study is a prospective survey of infant feeding attitudes and behaviors among first-time mothers in Queensland, Australia. Data on infant feeding knowledge, attitudes, beliefs, and intention were collected antenatally, and an Infant Feeding Attitudes Score was calculated. Results: Although 85% of respondents endorsed breastfeeding as most appropriate for infants, 11% valued formula feeding equally. Intention to give any breastmilk during the first weeks was 98%, but it fell to 18% during the second year. More than one-quarter of women reported intention to introduce foods other than breastmilk before 5 months of infant age. The infant feeding attitudes and beliefs score correlated positively with feeding intention for breastfeeding and the introduction of complementary solids. Conclusions: Enhancing women’s knowledge of recommendations and their understanding of breastfeeding’s specific benefits and the reasons for recommended scheduling of feeding transitions may positively impact breastfeeding exclusivity and duration and the age-appropriate introduction of complementary solids. Communication of detailed feeding recommendations for the infant’s first year and specific information about the health benefits of breastfeeding should be a goal of healthcare providers working with pregnant women

Phase separated structures in tethered dPS–PMMA copolymer films revealed using X-ray scattering with a novel contrast enhancement agent

Tethered deuterated polystyrene-block-polymethyl methacrylate films have been examined by X-ray scattering both in their native state and following treatment with ruthenium tetroxide. The use of the stain, while increasing the thickness of the films, does not significantly alter the lateral structure or periodicity of the films and provides contrast between the two blocks. Both the periodicity of the films and the structure normal to the surface have been identified following staining. Experiments were also performed on films treated by a solvent exchange process, and the effects of staining on these films are discussed

Photoemission evidence for crossover from Peierls-like to Mott-like transition in highly strained VO2_2

We present a spectroscopic study that reveals that the metal-insulator transition of strained VO$_2$ thin films may be driven towards a purely electronic transition, which does not rely on the Peierls dimerization, by the application of mechanical strain. Comparison with a moderately strained system, which does involve the lattice, demonstrates the crossover from Peierls- to Mott-like transitions

Methodology of a reevaluation of cardiovascular outcomes in the RECORD trial: study design and conduct

Background In 2010, after regulatory review of rosiglitazone licensing, the US Food and Drug Administration (FDA) requested a reevaluation of cardiovascular end points in the RECORD trial.<p></p> Methods Automated screening of the original clinical trial database and manual case report form review were performed to identify all potential cardiovascular and noncardiovascular deaths, and nonfatal myocardial infarction (MI) and stroke events. Search techniques were used to find participants lost to follow-up, and sites were queried for additional source documents. Suspected events underwent blinded adjudication using both original RECORD end point definitions and new FDA end point definitions, before analysis by the Duke Clinical Research Institute.<p></p> Results The reevaluation effort included an additional 328 person-years of follow-up. Automated screening identified 396 suspected deaths, 2,052 suspected MIs, and 468 suspected strokes. Manual review of documents by Duke Clinical Research Institute clinical events classification (CEC) coordinators identified an additional 31 suspected deaths, 49 suspected MIs, and 28 suspected strokes. There were 127 CEC queries issued requesting additional information on suspected deaths; 43 were closed with no site response, 61 were closed with a response that no additional data were available, and additional data were received for 23. Seventy CEC queries were issued requesting additional information for suspected MI and stroke events; 31 were closed with no site response, 20 were closed with a response that no additional data were available, and 19 resulted in additional data.<p></p> Conclusions Comprehensive procedures were used for rigorous event reascertainment and readjudication in a previously completed open-label, global clinical trial. These procedures used in this unique situation were consistent with other common approaches in the field, were enhanced to address the FDA concerns about the original RECORD trial results, and could be considered by clinical trialists designing event readjudication protocols for drug development programs that have been completed.<p></p&gt

Results of a reevaluation of cardiovascular outcomes in the RECORD trial

Background The US Food and Drug Administration (FDA) required a reevaluation of cardiovascular (CV) outcomes in the RECORD trial. This provided an opportunity to assess the implications of event adjudication by 2 groups and quantify the differences as well as to use new FDA end point definitions in development.<p></p> Methods Original data were used to systematically identify all potential deaths, myocardial infarctions (MIs), and strokes. Site investigators were approached for additional source documents and information about participants lost to follow-up. Suspected events were adjudicated using standard procedures, and the results were compared with the original trial outcomes.<p></p> Results Follow-up for mortality was 25,833 person-years, including an additional 328 person-years identified during the reevaluation effort. A total of 184 CV or unknown-cause deaths (88 rosiglitazone, 96 metformin/sulfonylurea), 128 participants with an MI (68 rosiglitazone, 60 metformin/sulfonylurea), and 113 participants with a stroke (50 rosiglitazone, 63 metformin/sulfonylurea) were included. The hazard ratio (HR) for rosiglitazone versus metformin/sulfonylurea for the end point of CV (or unknown cause) death, MI, or stroke was 0.95 (95% CI 0.78-1.17) compared with 0.93 (95% CI 0.74-1.15) for the original RECORD results. Treatment comparisons for MI (HR 1.13, 95% CI 0.80-1.59) and mortality (HR 0.86, 95% CI 0.68-1.08) were also the same compared with the original RECORD results. Sensitivity analyses were also consistent with the original RECORD results. Analyses using the FDA definitions showed similar results.<p></p> Conclusions Only a modest number of additional person-years of follow-up were ascertained from this reevaluation of CV end points in RECORD. Observed HRs and CIs from these analyses using the original RECORD or new FDA end point definitions showed similar treatment effects of rosiglitazone compared with the original RECORD results.<p></p&gt