Simple adaptive momentum: new algorithm for training multilayer perceptrons

The speed of convergence while training is an important consideration in the use of neural nets. The authors outline a new training algorithm which reduces both the number of iterations and training time required for convergence of multilayer perceptrons, compared to standard back-propagation and conjugate gradient descent algorithms.

Fluorescence lifetime imaging microscopy (FLIM) to demonstrate the nuclear binding of flavanols and (--epigallocatechin gallate

The use of light microscopy and DMACA staining strongly suggested that plant and animal cell nuclei act as sinks for flavanols [1, 2]. Detailed uv-vis spectroscopic titration experiments indicated that histone proteins are the likely binding sites in the nucleus [2]. Here we report the development of a multi-photon excitation microscopy technique combined with fluorescent lifetime measurements of flavanols. Using this technique, (+) catechin, (-) epicatechin and (-) epigallocatechin gallate (EGCG) showed strikingly different excited state lifetimes in solution. Interaction of histone proteins with flavanols was indicated by the appearance of a significant τ2-component of 1.7 to 4.0ns. Tryptophan interference could be circumvented in the in vivo fluorescence lifetime imaging microscopy (FLIM) experiments with 2-photon excitation at 630nm. This enabled visualisation and semi-quantitative measurements that demonstrated unequivocally the absorption of (+)catechin, (-)epicatechin and EGCG by nuclei of onion cells. 3D FLIM revealed for the first time that externally added EGCG penetrated the whole nucleus in onion cells. The relative proportions of EGCG in cytoplasm: nucleus: nucleoli were ca. 1:10:100. FLIM experiments may therefore facilitate probing the health effects of EGCG, which is the major constituent of green tea.

Two-photon excitation with pico-second fluorescence lifetime imaging to detect nuclear association of flavanols

Two-photon excitation enabled for the first time the observation and measurement of excited state fluorescence lifetimes from three flavanols in solution, which were ∼1.0 ns for catechin and epicatechin, but <45 ps for epigallocatechin gallate (EGCG). The shorter lifetime for EGCG is in line with a lower fluorescence quantum yield of 0.003 compared to catechin (0.015) and epicatechin (0.018). In vivo experiments with onion cells demonstrated that tryptophan and quercetin, which tend to be major contributors of background fluorescence in plant cells, have sufficiently low cross sections for two-photon excitation at 630 nm and therefore do not interfere with detection of externally added or endogenous flavanols in Allium cepa or Taxus baccata cells. Applying two-photon excitation to flavanols enabled 3-D fluorescence lifetime imaging microscopy and showed that added EGCG penetrated the whole nucleus of onion cells. Interestingly, EGCG and catechin showed different lifetime behaviour when bound to the nucleus: EGCG lifetime increased from <45 to 200 ps, whilst catechin lifetime decreased from 1.0 ns to 500 ps. Semi-quantitative measurements revealed that the relative ratios of EGCG concentrations in nucleoli associated vesicles: nucleus: cytoplasm were ca. 100:10:1. Solution experiments with catechin, epicatechin and histone proteins provided preliminary evidence, via the appearance of a second lifetime (τ2 = 1.9–3.1 ns), that both flavanols may be interacting with histone proteins. We conclude that there is significant nuclear absorption of flavanols. This advanced imaging using two-photon excitation and biophysical techniques described here will prove valuable for probing the intracellular trafficking and functions of flavanols, such as EGCG, which is the major flavanol of green tea.

Impact of a drier Early-Mid-Holocene climate upon Amazonian forests

This paper uses a palaeoecological approach to examine the impact of drier climatic conditions of the Early-Mid-Holocene (ca 8000-4000 years ago) upon Amazonia's forests and their fire regimes. Palaeovegetation (pollen data) and palaeofire (charcoal) records are synthesized from 20 sites within the present tropical forest biome, and the underlying causes of any emergent patterns or changes are explored by reference to independent palaeoclimate data and present-day patterns of precipitation, forest cover and fire activity across Amazonia. During the Early-Mid-Holocene, Andean cloud forest taxa were replaced by lowland tree taxa as the cloud base rose while lowland ecotonal areas, which are presently covered by evergreen rainforest, were instead dominated by savannahs and/or semi-deciduous dry forests. Elsewhere in the Amazon Basin there is considerable spatial and temporal variation in patterns of vegetation disturbance and fire, which probably reflects the complex heterogeneous patterns in precipitation and seasonality across the basin, and the interactions between climate change, drought- and fire susceptibility of the forests, and Palaeo-Indian land use. Our analysis shows that the forest biome in most parts of Amazonia appears to have been remarkably resilient to climatic conditions significantly drier than those of today, despite widespread evidence of forest burning. Only in ecotonal areas is there evidence of biome replacement in the Holocene. From this palaeoecological perspective, we argue against the Amazon forest 'dieback' scenario simulated for the future.

High-resolution provenance of desert dust deposited on Mt. Elbrus, Caucasus in 2009–2012 using snow pit and firn core records

The first record of dust deposition events on Mt. Elbrus, Caucasus Mountains derived from a snow pit and a shallow firn core is presented for the 2009–2012 period. A combination of isotopic analysis, SEVIRI red-greenblue composite imagery, MODIS atmospheric optical depth fields derived using the Deep Blue algorithm, air mass trajectories derived using the HYSPLIT model and analyses of meteorological data enabled identification of dust source regions with high temporal (hours) and spatial (ca. 20–100 km) resolution. Seventeen dust deposition events were detected; fourteen occurred in March–June, one in February and two in October. Four events originated in the Sahara, predominantly in northeastern Libya and eastern Algeria. Thirteen events originated in the Middle East, in the Syrian Desert and northern Mesopotamia, from a mixture of natural and anthropogenic sources. Dust transportation from Sahara was associated with vigorous Saharan depressions, strong surface winds in the source region and mid-tropospheric southwesterly flow with daily winds speeds of 20–30 m s−1 at 700 hPa level. Although these events were less frequent than those originating in the Middle East, they resulted in higher dust concentrations in snow. Dust transportation from the Middle East was associated with weaker depressions forming over the source region, high pressure centred over or extending towards the Caspian Sea and a weaker southerly or southeasterly flow towards the Caucasus Mountains with daily wind speeds of 12–18 m s−1 at 700 hPa level. Higher concentrations of nitrates and ammonium characterised dust from the Middle East deposited on Mt. Elbrus in 2009 indicating contribution of anthropogenic sources. The modal values of particle size distributions ranged between 1.98 µm and 4.16 µm. Most samples were characterised by modal values of 2.0– 2.8 µm with an average of 2.6 µm and there was no signifi- cant difference between dust from the Sahara and the Middle East.

Implementing systematic review techniques in chemical risk assessment: challenges, opportunities and recommendations

Systematic review (SR) is a rigorous, protocol-driven approach designed to minimise error and bias when summarising the body of research evidence relevant to a specific scientific question. Taking as a comparator the use of SR in synthesising research in healthcare, we argue that SR methods could also pave the way for a “step change” in the transparency, objectivity and communication of chemical risk assessments (CRA) in Europe and elsewhere. We suggest that current controversies around the safety of certain chemicals are partly due to limitations in current CRA procedures which have contributed to ambiguity about the health risks posed by these substances. We present an overview of how SR methods can be applied to the assessment of risks from chemicals, and indicate how challenges in adapting SR methods from healthcare research to the CRA context might be overcome. Regarding the latter, we report the outcomes from a workshop exploring how to increase uptake of SR methods, attended by experts representing a wide range of fields related to chemical toxicology, risk analysis and SR. Priorities which were identified include: the conduct of CRA-focused prototype SRs; the development of a recognised standard of reporting and conduct for SRs in toxicology and CRA; and establishing a network to facilitate research, communication and training in SR methods. We see this paper as a milestone in the creation of a research climate that fosters communication between experts in CRA and SR and facilitates wider uptake of SR methods into CRA.