Smart Align—a new tool for robust non-rigid registration of scanning microscope data

AbstractMany microscopic investigations of materials may benefit from the recording of multiple successive images. This can include techniques common to several types of microscopy such as frame averaging to improve signal-to-noise ratios (SNR) or time series to study dynamic processes or more specific applications. In the scanning transmission electron microscope, this might include focal series for optical sectioning or aberration measurement, beam damage studies or camera-length series to study the effects of strain; whilst in the scanning tunnelling microscope, this might include bias-voltage series to probe local electronic structure. Whatever the application, such investigations must begin with the careful alignment of these data stacks, an operation that is not always trivial. In addition, the presence of low-frequency scanning distortions can introduce intra-image shifts to the data. Here, we describe an improved automated method of performing non-rigid registration customised for the challenges unique to scanned microscope data specifically addressing the issues of low-SNR data, images containing a large proportion of crystalline material and/or local features of interest such as dislocations or edges. Careful attention has been paid to artefact testing of the non-rigid registration method used, and the importance of this registration for the quantitative interpretation of feature intensities and positions is evaluated.</jats:p

The influence of Arctic Fe and Atlantic fixed N on summertime primary production in Fram Strait, North Greenland Sea

Climate change has led to a ~ 40% reduction in summer Arctic sea-ice cover extent since the 1970s. Resultant increases in light availability may enhance phytoplankton production. Direct evidence for factors currently constraining summertime phytoplankton growth in the Arctic region is however lacking. GEOTRACES cruise GN05 conducted a Fram Strait transect from Svalbard to the NE Greenland Shelf in summer 2016, sampling for bioessential trace metals (Fe, Co, Zn, Mn) and macronutrients (N, Si, P) at ~ 79°N. Five bioassay experiments were conducted to establish phytoplankton responses to additions of Fe, N, Fe + N and volcanic dust. Ambient nutrient concentrations suggested N and Fe were deficient in surface seawater relative to typical phytoplankton requirements. A west-to-east trend in the relative deficiency of N and Fe was apparent, with N becoming more deficient towards Greenland and Fe more deficient towards Svalbard. This aligned with phytoplankton responses in bioassay experiments, which showed greatest chlorophyll-a increases in + N treatment near Greenland and + N + Fe near Svalbard. Collectively these results suggest primary N limitation of phytoplankton growth throughout the study region, with conditions potentially approaching secondary Fe limitation in the eastern Fram Strait. We suggest that the supply of Atlantic-derived N and Arctic-derived Fe exerts a strong control on summertime nutrient stoichiometry and resultant limitation patterns across the Fram Strait region.S.K. was financed by GEOMAR and the German Research Foundation (DFG Award Number AC 217/1-1 to E.P.A). T.J.B. acknowledges funding from a Marie Skłodowska-Curie Postdoctoral European Fellowship (OceanLiNES; Project ID 658035). Open Access funding provided by Projekt DEAL

Social disorganization and history of child sexual abuse against girls in sub-Saharan Africa : a multilevel analysis

Background: Child sexual abuse (CSA) is a considerable public health problem. Less focus has been paid to the role of community level factors associated with CSA. The aim of this study was to examine the association between neighbourhood-level measures of social disorganization and CSA. Methods: We applied multiple multilevel logistic regression analysis on Demographic and Health Survey data for 6,351 adolescents from six countries in sub-Saharan Africa between 2006 and 2008. Results: The percentage of adolescents that had experienced CSA ranged from 1.04% to 5.84%. There was a significant variation in the odds of reporting CSA across the communities, suggesting 18% of the variation in CSA could be attributed to community level factors. Respondents currently employed were more likely to have reported CSA than those who were unemployed (odds ratio [OR] = 2.05, 95% confidence interval [CI] 1.48 to 2.83). Respondents from communities with a high family disruption rate were 57% more likely to have reported CSA (OR=1.57, 95% CI 1.14 to 2.16). Conclusion: We found that exposure to CSA was associated with high community level of family disruption, thus suggesting that neighbourhoods may indeed have significant important effects on exposure to CSA. Further studies are needed to explore pathways that connect the individual and neighbourhood levels, that is, means through which deleterious neighbourhood effects are transmitted to individuals

Strong Dynamo Action in Rapidly Rotating Suns

Stellar dynamos are driven by complex couplings between rotation and turbulent convection, which drive global-scale flows and build and rebuild stellar magnetic fields. When stars like our sun are young, they rotate much more rapidly than the current solar rate. Observations generally indicate that more rapid rotation is correlated with stronger magnetic activity and perhaps more effective dynamo action. Here we examine the effects of more rapid rotation on dynamo action in a star like our sun. We find that vigorous dynamo action is realized, with magnetic field generated throughout the bulk of the convection zone. These simulations do not possess a penetrative tachocline of shear where global-scale fields are thought to be organized in our sun, but despite this we find strikingly ordered fields, much like sea-snakes of toroidal field, which are organized on global scales. We believe this to be a novel finding.Comment: 8 pages, 4 figs. Published in conference proceedings "Unsolved Problems in Stellar Physics", held July 2-6 2007 Cambridge, Englan

Transformation of in-plane ρ(T)\rho (T) in YBa2Cu3O7−δYBa_{2}Cu_{3}O_{7-\delta} at fixed oxygen content

This paper reveals the origin of variation in the magnitude and temperature dependence of the normal state resistivity frequently observed in different YBCO single crystal or thin film samples with the same $T_{c}$. We investigated temperature dependence of resistivity in $YBa_{2}Cu_{3}O_{7-\delta}$ thin films with 7- $\delta = 6.95$ and 6.90, which were subjected to annealing in argon at 400-420 K ($120-140^{o}C$). Before annealing these films exhibited a non-linear $\rho_{ab}(T)$, with a flattening below 230 K, similar to $\rho_{b}(T)$ and $\rho_{ab}(T)$ observed in untwinned and twinned YBCO crystals, respectively. For all films the annealing causes an increase of resistivity and a transformation of $\rho_{ab}(T)$ from a non-linear dependence towards a more linear one (less flattening). In films with 7- $\delta = 6.90$ the increase of resistivity is also associated with an increase in $T_{c}$. We proposed the model that provides an explanation of these phenomena in terms of thermally activated redistribution of residual O(5) oxygens in the chain-layer of YBCO. Good agreement between the experimental data for $\rho_{ab}(t,T)$, where t is the annealing time, and numerical calculations was obtained.Comment: 8 pages, 9 figures, submitted to PR

GCN2-dependent phosphorylation of eukaryotic translation initiation factor-2α in Arabidopsis

The yeast regulatory protein kinase, general control non-derepressible-2 (GCN2) plays a key role in general amino acid control. GCN2 phosphorylates the α subunit of the trimeric eukaryotic translation initiation factor-2 (eIF2), bringing about a decrease in the general rate of protein synthesis but an increase in the synthesis of GCN4, a transcription factor that promotes the expression of genes encoding enzymes for amino acid biosynthesis. The present study concerned the phosphorylation of Arabidopsis eIF2α (AteIF2α) by the Arabidopsis homologue of GCN2, AtGCN2, and the role of AtGCN2 in regulating genes encoding enzymes of amino acid biosynthesis and responding to virus infection. A null mutant for AtGCN2 called GT8359 was obtained and western analysis confirmed that it lacked AtGCN2 protein. GT8359 was more sensitive than wild-type Arabidopsis to herbicides that affect amino acid biosynthesis. Phosphorylation of AteIF2α occurred in response to herbicide treatment but only in wild-type Arabidopsis, not GT8359, showing it to be AtGCN2-dependent. Expression analysis of genes encoding key enzymes for amino acid biosynthesis and nitrate assimilation revealed little effect of loss of AtGCN2 function in GT8359 except that expression of a nitrate reductase gene, NIA1, was decreased. Analysis of wild-type and GT8359 plants infected with Turnip yellow mosaic virus or Turnip crinkle virus showed that AteIF2α was not phosphorylated

Antarctic climate, Southern Ocean circulation patterns, and deep water formation during the Eocene

We assess early-to-middle Eocene seawater neodymium (Nd) isotope records from seven Southern Ocean deep-sea drill sites to evaluate the role of Southern Ocean circulation in long-term Cenozoic climate change. Our study sites are strategically located on either side of the Tasman Gateway and are positioned at a range of shallow (Nd(t) = −9.3 ± 1.5). IODP Site U1356 off the coast of Adélie Land, a locus of modern-day Antarctic Bottom Water production, is identified as a site of persistent deep water formation from the early Eocene to the Oligocene. East of the Tasman Gateway an additional local source of intermediate/deep water formation is inferred at ODP Site 277 in the SW Pacific Ocean (εNd(t) = −8.7 ± 1.5). Antarctic-proximal shelf sites (ODP Site 1171 and Site U1356) reveal a pronounced erosional event between 49 and 48 Ma, manifested by ~2 εNd unit negative excursions in seawater chemistry toward the composition of bulk sediments at these sites. This erosional event coincides with the termination of peak global warmth following the Early Eocene Climatic Optimum and is associated with documented cooling across the study region and increased export of Antarctic deep waters, highlighting the complexity and importance of Southern Ocean circulation in the greenhouse climate of the Eocene