Importance of charge capture in interphase regions during readout of charge-coupled devices

The current understanding of charge transfer dynamics in charge-coupled devices (CCDs) is that charge is moved so quickly from one phase to the next in a clocking sequence and with a density so low that trapping of charge in the interphase regions is negligible. However, simulation capabilities developed at the Centre for Electronic Imaging, which includes direct input of electron density simulations, have made it possible to investigate this assumption further. As part of the radiation testing campaign of the Euclid CCD273 devices, data have been obtained using the trap pumping method, a method that can be used to identify and characterize single defects within CCDs. Combining these data with simulations, we find that trapping during the transfer of charge among phases is indeed necessary to explain the results of the data analysis. This result could influence not only trap pumping theory and how trap pumping should be performed but also how a radiation-damaged CCD is readout in the most optimal way

Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae

We investigated the dynamics of a gene regulatory network controlling the cold shock response in budding yeast, Saccharomyces cerevisiae. The medium-scale network, derived from published genome-wide location data, consists of 21 transcription factors that regulate one another through 31 directed edges. The expression levels of the individual transcription factors were modeled using mass balance ordinary differential equations with a sigmoidal production function. Each equation includes a production rate, a degradation rate, weights that denote the magnitude and type of influence of the connected transcription factors (activation or repression), and a threshold of expression. The inverse problem of determining model parameters from observed data is our primary interest. We fit the differential equation model to published microarray data using a penalized nonlinear least squares approach. Model predictions fit the experimental data well, within the 95 % confidence interval. Tests of the model using randomized initial guesses and model-generated data also lend confidence to the fit. The results have revealed activation and repression relationships between the transcription factors. Sensitivity analysis indicates that the model is most sensitive to changes in the production rate parameters, weights, and thresholds of Yap1, Rox1, and Yap6, which form a densely connected core in the network. The modeling results newly suggest that Rap1, Fhl1, Msn4, Rph1, and Hsf1 play an important role in regulating the early response to cold shock in yeast. Our results demonstrate that estimation for a large number of parameters can be successfully performed for nonlinear dynamic gene regulatory networks using sparse, noisy microarray data

Exposure of individual harbour seals (Phoca vitulina) and waters surrounding protected habitats to acoustic deterrent noise from aquaculture

This work was funded by the European Social Fund and Scottish Funding Council as part of Developing Scotland's Workforce in the Scotland 2014–2020 European Structural and Investment Fund Programme. NDM and AF were funded by the Centre for Environment, Fisheries and Aquaculture Science (Cefas). Funding for the seal tagging was provided by the Scottish Government to the Sea Mammal Research Unit (SMRU) as part of the Marine Mammal Scientific Support Program MMSS/002/15, with additional resources from the Natural Environment Research Council (grant numbers NE/J004251/1 and SMRU1001).1. Pinniped depredation at aquaculture sites is a globally recognized problem. To mitigate depredation, the aquaculture sector uses acoustic deterrent devices (ADDs) as a non-lethal alternative to shooting pinnipeds interacting with caged finfish. However, it is unclear whether sound emissions from ADDs have the potential to also impact non-target pinnipeds at spatial scales relevant to populations. 2. Global Positioning System (GPS) tracking data from seven harbour seals tagged in a non-aquaculture context, on the west coast of Scotland, in 2017 were combined with modelled maps of ADD noise to quantify sound exposure and estimate the potential for auditory impairment. The acoustic model applied an energy flux approach across the main frequency range of ADDs (2–40 kHz). Predictions of temporary and permanent auditory threshold shifts were made using seal location data and published noise exposure criteria. The acoustic exposure of waters (10-km buffers) surrounding protected habitats (i.e. designated haul outs and Special Areas of Conservation (SACs)) on the west coast of Scotland was also assessed. 3. All tagged seals and waters surrounding 51 of 56 protected sites were predicted to be exposed to ADD noise exceeding median ambient sound levels. Temporary auditory impairment was predicted to occur in one of the seven tagged harbour seals and across 1.7% of waters surrounding protected habitats over a 24-hour period, when assuming a 100% ADD duty cycle. 4. Although the predicted risk of auditory impairment appears to be relatively low, these findings suggest that harbour seals inhabiting inshore waters off western Scotland are routinely exposed to ADD noise that exceeds median ambient sound levels. This chronic exposure risks negative consequences for individual harbour seals among the wider population in this region. The use of ADDs to mitigate pinniped depredation should be carefully considered to reduce unintended habitat-wide impacts on non-target species, including pinnipeds that are not specifically interacting with aquaculture.Publisher PDFPeer reviewe

No effect of New Zealand blackcurrant extract on recovery of muscle damage following running a half-marathon

New Zealand blackcurrant (NZBC) contains anthocyanins, known to moderate blood flow and display anti-inflammatory properties that may improve recovery from exercise-induced muscle damage. The authors examined whether NZBC extract supplementation enhances recovery from exercise-induced muscle damage after a half-marathon race. Following a randomized, double-blind, independent groups design, 20 (eight women) recreational runners (age 30 ± 6 years, height 1.73 ± 0.74 m, body mass 68.5 ± 7.8 kg, half-marathon finishing time 1:56:33 ± 0:18:08 hr:min:s) ingested either two 300-mg/day capsules of NZBC extract (CurraNZ™) or a visually matched placebo, for 7 days prior to and 2 days following a half-marathon. Countermovement jump performance variables, urine interleukin-6, and perceived muscle soreness and fatigue were measured pre, post, and at 24 and 48 hr after the half-marathon and analyzed using a mixed linear model with statistical significance set a priori at p  .05). Urine interleukin-6 increased 48-hr post-half-marathon in the NZBC group only (p  .05). Perceived muscle soreness and fatigue increased immediately post-half-marathon (p  .05). Supplementation with NZBC extract had no effect on the recovery of countermovement jump variables and perceptions of muscle soreness or fatigue following a half-marathon in recreational runners

Is tagging with visual implant elastomer a reliable technique for marking earthworms?

Visual implant elastomer (VIE) has recently been employed to investigate different aspects of earthworm ecology. However, a number of fundamental questions relating to the detection and positioning of the tag, its persistence and potential effects on earthworms remain unknown. Seven earthworm species belonging to three ecological groupings, with different pigmentation and burrowing behaviour, were tagged using different coloured VIE. External inspection after two days, one week and 1, 10 and 27 months were followed by preservation, dissection and internal inspection. Tags could be seen in living specimens to 27 months, and dissection revealed that in most cases they were lodged in the coelomic cavity, held in place by septa. However, over longer time periods (more than two years), the chlorogogenous tissue tended to bind to the tags and made external observation increasingly difficult. Migration of the VIE material towards the posterior of the earthworm and potential loss of the tag were only observed on rare occasions, and a recovery rate in excess of 98% was recorded. By introducing a reasonable amount of VIE into segments, just after the clitellum, this technique can become a valuable tool in earthworm ecology and life history studies, particularly in short-medium term laboratory and field experiments

A model for sequential evolution of ligands by exponential enrichment (SELEX) data

A Systematic Evolution of Ligands by EXponential enrichment (SELEX) experiment begins in round one with a random pool of oligonucleotides in equilibrium solution with a target. Over a few rounds, oligonucleotides having a high affinity for the target are selected. Data from a high throughput SELEX experiment consists of lists of thousands of oligonucleotides sampled after each round. Thus far, SELEX experiments have been very good at suggesting the highest affinity oligonucleotide, but modeling lower affinity recognition site variants has been difficult. Furthermore, an alignment step has always been used prior to analyzing SELEX data. We present a novel model, based on a biochemical parametrization of SELEX, which allows us to use data from all rounds to estimate the affinities of the oligonucleotides. Most notably, our model also aligns the oligonucleotides. We use our model to analyze a SELEX experiment containing double stranded DNA oligonucleotides and the transcription factor Bicoid as the target. Our SELEX model outperformed other published methods for predicting putative binding sites for Bicoid as indicated by the results of an in-vivo ChIP-chip experiment.Comment: Published in at http://dx.doi.org/10.1214/12-AOAS537 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Drug-Resistant Tuberculosis--Current Dilemmas, Unanswered Questions, Challenges and Priority Needs

Tuberculosis was declared a global emergency by the World Health Organization (WHO) in 1993. Following the declaration and the promotion in 1995 of directly observed treatment short course (DOTS), a cost-effective strategy to contain the tuberculosis epidemic, nearly 7 million lives have been saved compared with the pre-DOTS era, high cure rates have been achieved in most countries worldwide, and the global incidence of tuberculosis has been in a slow decline since the early 2000s. However, the emergence and spread of multidrug-resistant (MDR) tuberculosis, extensively drug-resistant (XDR) tuberculosis, and more recently, totally drug-resistant tuberculosis pose a threat to global tuberculosis control. Multidrug-resistant tuberculosis is a man-made problem. Laboratory facilities for drug susceptibility testing are inadequate in most tuberculosis-endemic countries, especially in Africa; thus diagnosis is missed, routine surveillance is not implemented, and the actual numbers of global drug-resistant tuberculosis cases have yet to be estimated. This exposes an ominous situation and reveals an urgent need for commitment by national programs to health system improvement because the response to MDR tuberculosis requires strong health services in general. Multidrug-resistant tuberculosis and XDR tuberculosis greatly complicate patient management within resource-poor national tuberculosis programs, reducing treatment efficacy and increasing the cost of treatment to the extent that it could bankrupt healthcare financing in tuberculosis-endemic areas. Why, despite nearly 20 years of WHO-promoted activity and >12 years of MDR tuberculosis–specific activity, has the country response to the drug-resistant tuberculosis epidemic been so ineffectual? The current dilemmas, unanswered questions, operational issues, challenges, and priority needs for global drug resistance screening and surveillance, improved treatment regimens, and management of outcomes and prevention of DR tuberculosis are discussed

Auditory impairment from acoustic seal deterrents predicted for harbour porpoises in a marine protected area

Management interventions to reduce human–wildlife conflict can have unintended consequences for non-target species. Acoustic deterrent devices (ADDs) are used globally by the aquaculture sector. However, the potential for these sound emissions to impact non-target species, such as cetaceans, has not yet been quantified at population relevant spatial scales. To better understand the extent of potential impacts on cetaceans, such as harbour porpoises, we used acoustic modelling to investigate levels of ADD noise throughout the west coast of Scotland and across a Special Area of Conservation (SAC) for this species. Using an energy-flux acoustic propagation model and data on aquaculture sites known to be using ADDs, we predicted the spatial extent of ADD noise on the Scottish west coast from 1 February 2017 to 31 January 2018. Noise maps were produced to determine the risk of auditory impairment for harbour porpoises under a range of scenarios which assumed single or multiple ADDs and simultaneous use across all sites. The acoustic propagation model performed well when tested against field measurements up to 5 km, with 98% of sound exposure level (SEL) predictions within ±10% of the measurements. Predictions of SELs over a 24-hr period suggested extensive temporary hearing loss zones (median radius: ~28 km) for harbour porpoises around aquaculture sites. Assuming a single device at each site, 23% of the harbour porpoise SAC was predicted to be exposed to ADD noise sufficient to induce a temporary threshold shift, and under the worst-case scenario (multiple, continuously running devices per site with an aggregate duty cycle of 100%), levels exceeding permanent threshold shift could reach 0.9% of the SAC. Policy implications. This study highlights the potential for ‘collateral damage’ from interventions such as acoustic deterrent devices (ADDs) which are intended to reduce human–wildlife conflicts with pinnipeds but may affect the long-term health and habitat use of non-target species. This is especially true for harbour porpoises which are protected under the EU and UK Habitats Regulations. The aquaculture industry, policymakers and regulators in countries where ADDs are used should consider these findings when attempting to mitigate pinniped depredation