Mining the British Isles oak tree-ring data set. Part A: Rationale, data, software, and proof of concept

From stuttering early beginnings, archaeological oak dendrochronology in the British Isles developed rapidly in the latter decades of the 20th century, to the present situation where dozens of new crossdated site chronologies are produced each year. Although unevenly spread in both space and time, the available data set is now so large (several thousand sites) that it has the potential to be mined for applications that were not envisaged when the data were originally collected. Here we compile available data into an oak database of archaeological and modern (living) sites, develop a software tool to visualise spatial patterns and correlations, and explore six potential data-mining applications (crossdating methodology, crossdating error detection, regional chronologies, pointer years, provenancing, past climate reconstruction). Results indicate variable data-mining potential, but with viable prospects in each case

Patterns and drivers of movement for a coastal benthopelagic fish, Pseudocaranx georgianus, on Australia's southeast coast.

Knowledge of connectivity and population structure is integral to the sustainable management of fished populations, yet such information is unavailable for many species over scales relevant to their exploitation. We examined broad-scale patterns and drivers of adult movement for a putatively mobile carangid (Pseudocaranx georgianus) on Australia's southeast coast using an angler tag-recapture dataset. More than 6300 individuals were tagged and released across 1007 km of coastline, with anglers recapturing 157 (2.48%) individuals during a 14-year period. Median distance moved was 5 km and a substantial proportion of individuals (19%) were recaptured at their release location. Recapture latitude was also strongly predicted by release latitude (r2 = 0.87). However, a broad range of movements were observed (0-508 km), with 6% of individuals moving further than 100 km. Most individuals recaptured in areas now designated as Marine Protected Areas (MPAs) were originally released in the same area (79.2%). Larger body size, longer periods at liberty, and releases during Spring all positively influenced distance moved. Results support restricted movement over an intermediate scale, punctuated by occasional large movements. Our findings suggest adult movement of P. georgianus in southeastern Australia primarily occurs over smaller distances than the current spatial scale of management

Supernatants derived from chemotherapy-treated cancer cell lines can modify angiogenesis

BACKGROUND: There is evidence that tumours produce substances such as cytokines and microvesicular bodies bearing bioactive molecules, which support the carcinogenic process. Furthermore, chemotherapy has also been shown to modify these exudates and in doing so, neutralise their tumourigenic influence. METHODS: In the current study, we have investigated the effect of chemotherapy agents on modifying the cytokine profile and microvesicular cargo of supernatants derived from cancer cell lines. In addition, we have explored the effect of these tumour-derived supernatants on angiogenesis, and how chemotherapy can alter the supernatants rendering them less pro-angiogenic. RESULTS: Herein, we show that supernatants contain a rich cocktail of cytokines, a number of which are potent modulators of angiogenesis. They also contain microvesicular bodies containing RNA transcripts that code for proteins involved in transcription, immune modulation and angiogenesis. These supernatants altered intracellular signalling molecules in endothelial cells and significantly enhanced their tubulogenic character; however, this was severely compromised when supernatants from tumours treated with chemotherapy was used instead. CONCLUSION: This study suggests tumour exudates and bioactive material from tumours can influence cellular functions, and that treatment with some chemotherapy can serve to negate these pro-tumourigenic processes

Empirically-determined statistical significance of the Baillie and Pilcher (1973) t statistic for British Isles oak

The “Belfast method” of statistical crossdating has been widely used in the British Isles since public domain software was released by Baillie and Pilcher (1973). Although the conceptual merits of the approach are accepted, the details of the methodology have been severely criticised, including the fact that serially correlated tree-ring time series violate a fundamental requirement for the use of Students t statistic as a measure of statistical significance. An unfortunate consequence of this has been that t values are often published without reference to the associated probability of the specific value being obtained by chance. Here we present an empirical method for determining statistical significance from analysis of many misaligned inter-site correlations amongst over 2000 dated British Isles oak chronologies. Results indicate that a t value of 3.5 has a probability of about one in 600 for series lengths of 100+ years, but this declines (becomes less rare) as series length decreases

Validating and improving the uncertainty assumptions for the assimilation of ocean‐colour‐derived chlorophyll aa a into a marine biogeochemistry model of the Northwest European Shelf Seas

The correct specification of all sources of uncertainty is critical to the success of data assimilation (DA) in improving the realism and accuracy of forecasts and reanalyses. This work focuses on improving the uncertainty assumptions made during the assimilation of ocean-colour-derived chlorophyll a$$a$$ into an operational marine coupled physical–biogeochemical DA system, which produces daily biogeochemistry forecasts on the Northwest European Shelf Seas. Analysis of the observation–model misfits shows significant biases in chlorophyll a$$a$$, which vary strongly with season. The behaviour of these misfits agrees well with previous studies and can be attributed to systematic errors within the coupled model. Diagnostic metrics, used frequently within numerical weather prediction, are applied to separate out the random component of the observation and model errors, allowing for the derivation of new error covariance matrices. These new error covariance matrices are then modified to account for the biases in the model that cannot be treated explicitly within the operational DA system. This has the effect of inflating both the error variances and the correlation length-scales. Experiments show that the new error covariances can result in significant improvements in the accuracy of the analysis and forecast. In particular, the new error covariance matrices reduce the bias in the spring phytoplankton bloom present when using the previous error covariances. Validation against independent glider observations in the North Sea also shows reductions in bias in chlorophyll a$$a$$ and oxygen that extend below the surface to the depth of the mixed layer. Accounting for the biases in the model in the error correlations can lead to much larger improvements than not accounting for them; however, there are also regions where large degradations are seen that may indicate model instabilities. This may be improved by estimating the bias separately for the different regions on the shelf

An empirical resampling method for determining optimal high-pass filters used in correlation-based tree-ring crossdating

Visual crossdating of tree-ring series focusses on high-frequency variations. Automated correlation-based crossdating tools mimic this by transforming raw ring widths into indices that emphasise the high frequency signal, prior to calculating the goodness-of-fit between series. Here we present a resampling methodology to determine the relative merits of alternative simple high-pass filters and demonstrate it using two tree-ring data sets (British Isles oak, New Zealand kauri). Results indicate that: (a) high-pass filtering is a critical step; (b) the efficacy of alternative filters is variable, and; (c) efficacy appears to be species specific. These results have implications for crossdating in the two contexts investigated, and also for future software developments, especially the desirability of flexible implementations of high-pass filtering

Prostate Cancer and Race

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/72215/1/j.1525-1497.2003.30801.x.pd

From quantum fusiliers to high-performance networks

Our objective was to design a quantum repeater capable of achieving one million entangled pairs per second over a distance of 1000km. We failed, but not by much. In this letter we will describe the series of developments that permitted us to approach our goal. We will describe a mechanism that permits the creation of entanglement between two qubits, connected by fibre, with probability arbitrarily close to one and in constant time. This mechanism may be extended to ensure that the entanglement has high fidelity without compromising these properties. Finally, we describe how this may be used to construct a quantum repeater that is capable of creating a linear quantum network connecting two distant qubits with high fidelity. The creation rate is shown to be a function of the maximum distance between two adjacent quantum repeaters.Comment: 2 figures, Comments welcom

PAC1 receptor-mediated clearance of tau in postsynaptic compartments attenuates tau pathology in mouse brain

Accumulation of pathological tau in synapses has been identified as an early event in Alzheimer's disease (AD) and correlates with cognitive decline in patients with AD. Tau is a cytosolic axonal protein, but under disease conditions, tau accumulates in postsynaptic compartments and presynaptic terminals, due to missorting within neurons, transsynaptic transfer between neurons, or a failure of clearance pathways. Using subcellular fractionation of brain tissue from rTg4510 tau transgenic mice with tauopathy and human postmortem brain tissue from patients with AD, we found accumulation of seed-competent tau predominantly in postsynaptic compartments. Tau-mediated toxicity in postsynaptic compartments was exacerbated by impaired proteasome activity detected by measuring lysine-48 polyubiquitination of proteins targeted for proteasomal degradation. To combat the accumulation of tau and proteasome impairment in the postsynaptic compartments of rTg4510 mouse brain, we stimulated the pituitary adenylate cyclase-activating polypeptide (PACAP) type 1 receptor (PAC1R) with its ligand PACAP administered intracerebroventricularly to rTg4510 mice. We observed enhanced synaptic proteasome activity and reduced total tau in postsynaptic compartments in mouse brain after PACAP treatment. The clearance of tau from postsynaptic compartments correlated with attenuated tauopathy and improved cognitive performance of rTg4510 transgenic mice on two behavioral tests. These results suggest that activating PAC1R could prevent accumulation of aggregate-prone tau and indicate a potential therapeutic approach for AD and other tauopathies