Natural age dispersion arising from the analysis of broken crystals, part I. Theoretical basis and implications for the apatite (U-Th)/He thermochronometer

Over the last decade major progress has been made in developing both the theoretical and practical aspects of apatite (U-Th)/He thermochronometry and it is now standard practice, and generally seen as best practice, to analyse single grain aliquots. These individual prismatic crystals are often broken and are fragments of larger crystals that have broken during mineral separation along the weak basal cleavage in apatite. This is clearly indicated by the common occurrence of only 1 or no clear crystal terminations present on separated apatite grains, and evidence of freshly broken ends when grains are viewed using a scanning electron microscope. This matters because if the 4He distribution within the whole grain is not homogeneous, because of partial loss due to thermal diffusion for example, then the fragments will all yield ages different from each other and from the whole grain age. Here we use a numerical model with a finite cylinder geometry to approximate 4He ingrowth and thermal diffusion within hexagonal prismatic apatite crystals. This is used to quantify the amount and patterns of inherent, natural age dispersion that arises from analysing broken crystals. A series of systematic numerical experiments were conducted to explore and quantify the pattern and behaviour of this source of dispersion using a set of 5 simple thermal histories that represent a range of plausible geological scenarios. In addition some more complex numerical experiments were run to investigate the pattern and behaviour of grain dispersion seen in several real data sets. The results indicate that natural dispersion of a set of single fragment ages (defined as the range divided by the mean) arising from fragmentation alone varies from c. 7% even for rapid (c. 10 ∘C/Ma), monotonic cooling to over 50% for protracted, complex histories that cause significant diffusional loss of 4He. The magnitude of dispersion arising from fragmentation scales with the grain cylindrical radius, and is of a similar magnitude to dispersion expected from differences in absolute grain size alone (spherical equivalent radii of 40 to 150 μm). This source of dispersion is significant compared with typical analytical uncertainties on individual grain analyses (c. 6%) and standard deviations on multiple grain analyses from a single sample (c. 10-20%). Where there is a significant difference in the U and Th concentration of individual grains (eU), the effect of radiation damage accumulation on 4He diffusivity (assessed using the RDAAM model of Flowers et al. (2009)) is the primary cause of dispersion for samples that have experienced a protracted thermal history, and can cause dispersion in excess of 100% for realistic ranges of eU conentration (i.e. 5-100 ppm). Expected natural dispersion arising from the combined effects of reasonable variations in grain size (radii 40-125 μm), eU concentration (5-150 ppm) and fragmentation would typically exceed 100% for complex thermal histories. In addition to adding a significant component of natural dispersion to analyses, the effect of fragmentation also acts to decouple and corrupt expected correlations between grain ages and absolute grain size and to a lesser extent between grain age and effective uranium concentration (eU). Considering fragmentation explicitly as a source of dispersion and analysing how the different sources of natural dispersion all interact with each other provides a quantitative framework for understanding patterns of dispersion that otherwise appear chaotic. An important outcome of these numerical experiments is that they demonstrate that the pattern of age dispersion arising from fragmentation mimics the pattern of 4He distribution within the whole grains, thus providing an important source of information about the thermal history of the sample. We suggest that if the primary focus of a study is to extract the thermal history information from (U-Th)/He analyses then sampling and analytical strategies should aim to maximise the natural dispersion of grain ages, not minimise it, and should aim to analyse circa 20-30 grains from each sample. The key observations and conclusions drawn here are directly applicable to other thermochronometers, such as the apatite, rutile and titanite U-Pb systems, where the diffusion domain is approximated by the physical grain size

ATM and Artemis promote homologous recombination of radiation-induced DNA double-strand breaks in G2

Homologous recombination (HR) and non‐homologous end joining (NHEJ) represent distinct pathways for repairing DNA double‐strand breaks (DSBs). Previous work implicated Artemis and ATM in an NHEJ‐dependent process, which repairs a defined subset of radiation‐induced DSBs in G1‐phase. Here, we show that in G2, as in G1, NHEJ represents the major DSB‐repair pathway whereas HR is only essential for repair of ∼15% of X‐ or γ‐ray‐induced DSBs. In addition to requiring the known HR proteins, Brca2, Rad51 and Rad54, repair of radiation‐induced DSBs by HR in G2 also involves Artemis and ATM suggesting that they promote NHEJ during G1 but HR during G2. The dependency for ATM for repair is relieved by depleting KAP‐1, providing evidence that HR in G2 repairs heterochromatin‐associated DSBs. Although not core HR proteins, ATM and Artemis are required for efficient formation of single‐stranded DNA and Rad51 foci at radiation‐induced DSBs in G2 with Artemis function requiring its endonuclease activity. We suggest that Artemis endonuclease removes lesions or secondary structures, which inhibit end resection and preclude the completion of HR or NHEJ

The chronology and tectonic style of landscape evolution along the elevated Atlantic continental margin of South Africa resolved by joint apatite fission track and (U-Th-Sm)/He thermochronology

Atlantic-type continental margins have long been considered “passive” tectonic settings throughout the entire postrift phase. Recent studies question the long-term stability of these margins and have shown that postrift uplift and reactivation of preexisting structures may be a common feature of a continental margin’s evolution. The Namaqualand sector of the western continental margin of South Africa is characterized by a ubiquitously faulted basement but lacks preservation of younger geological strata to constrain postrift tectonic fault activity. Here we present the first systematic study using joint apatite fission track and apatite (U-Th-Sm)/He thermochronology to achieve a better understanding on the chronology and tectonic style of landscape evolution across this region. Apatite fission track ages range from 58.3 ± 2.6 to 132.2 ± 3.6Ma, with mean track lengths between 10.9 ± 0.19 and 14.35 ± 0.22 μm, and mean (U-Th-Sm)/He sample ages range from 55.8 ± 31.3 to 120.6 ± 31.4Ma. Joint inverse modeling of these data reveals two distinct episodes of cooling at approximately 150–130Ma and 110–90Ma with limited cooling during the Cenozoic. Estimates of denudation based on these thermal histories predict approximately 1–3 km of denudation coinciding with two major tectonic events. The first event, during the Early Cretaceous, was driven by continental rifting and the development and removal of synrift topography. The second event, during the Late Cretaceous, includes localized reactivation of basement structures as well as regional mantle-driven uplift. Relative tectonic stability prevailed during the Cenozoic, and regional denudation over this time is constrained to be less than 1 km

Deciphering the nitrate signaling pathway leading to a reduction of primary root growth in Medicago truncatula

In the model legume Medicago truncatula, nitrate has been shown to inhibit primary root growth through the reduction of root cell elongation. Nitrate, as an essential nutrient, also acts as a signal molecule that is sensed and transduced through a nitrate transporter MtNPF6.8, with RNAi mutants deficient in MtNPF6.8 being insensitive to nitrate [1, 2]. We tested here whether reactive oxygen species (ROS) could be downstream mediators of the nitrate signal since ROS are able to transduce ABA signal in other contexts and also govern the primary root growth. Thus, we analyzed the distribution of ROS (H2O2, O2•−, •OH) and peroxidase activity all along the primary root of seedlings sensitive or insensitive to nitrate using different genotypes of M. truncatula, three wild types and a npf6.8RNAi mutant grown with or without nitrate, to determine whether nitrate modifies ROS and peroxidase patterns. We found that nitrate modified the morphology of the root tip, induced an increase in H2O2, and a decrease in O2•− and •OH in seedlings sensitive to nitrate (R108, A17, and DZA315-16), but not in seedlings insensitive to nitrate (npf6.8RNAi mutant). These results suggest that ROS and peroxidases are downstream mediators in the nitrate signaling pathway. The origin of the change in ROS accumulation in response to nitrate was further investigated following the activity of major enzymes (peroxidase, SOD, Nox) able to interfere with ROS accumulation

Statistical Gaussian Model of Image Regions in Stochastic Watershed Segmentation

International audienceStochastic watershed is an image segmentation technique based on mathematical morphology which produces a probability density function of image contours. Estimated probabilities depend mainly on local distances between pixels. This paper introduces a variant of stochastic watershed where the probabilities of contours are computed from a Gaussian model of image regions. In this framework, the basic ingredient is the distance between pairs of regions, hence a distance between normal distributions. Hence several alternatives of statistical distances for normal distributions are compared, namely Bhattacharyya distance, Hellinger metric distance and Wasserstein metric distance

AFTER, the front end ASIC of the T2K Time Projection Chambers

The T2K (Tokai-to-Kamioka) experiment is a long baseline neutrino oscillation experiment in Japan. A near detector, located at 280m of the production target, is used to characterize the beam. One of its key elements is a tracker, made of three Time Projection Chambers (TPC) read by Micromegas endplates. A new readout system has been developed to collect, amplify, condition and acquire the data produced by the 124,000 detector channels of these detectors. The front-end element of this system is a a new 72-channel application specific integrated circuit. Each channel includes a low noise charge preamplifier, a pole zero compensation stage, a second order Sallen-Key low pass filter and a 511-cell Switched Capacitor Array. This electronics offers a large flexibility in sampling frequency, shaping time, gain, while taking advantage of the low physics events rate of 0.3 Hz. We detail the design and the performance of this ASIC and report on the deployment of the frond-end electronics on-site

Liver segmentation in MRI: a fully automatic method based on stochastic partitions

There are few fully automated methods for liver segmentation in magnetic resonance images (MRI) despite the benefits of this type of acquisition in comparison to other radiology techniques such as computed tomography (CT). Motivated by medical requirements, liver segmentation in MRI has been carried out. For this purpose, we present a new method for liver segmentation based on the watershed transform and stochastic partitions. The classical watershed over-segmentation is reduced using a marker-controlled algorithm. To improve accuracy of selected contours, the gradient of the original image is successfully enhanced by applying a new variant of stochastic watershed. Moreover, a final classifier is performed in order to obtain the final liver mask. Optimal parameters of the method are tuned using a training dataset and then they are applied to the rest of studies (17 datasets). The obtained results (a Jaccard coefficient of 0.91 +/- 0.02) in comparison to other methods demonstrate that the new variant of stochastic watershed is a robust tool for automatic segmentation of the liver in MRI. (C) 2014 Elsevier Ireland Ltd. All rights reserved.This work has been supported by the MITYC under the project NaRALap (ref. TSI-020100-2009-189), partially by the CDTI under the project ONCOTIC (IDI-20101153), by Ministerio de Educacion y Ciencia Spain, Project Game Teen (TIN2010-20187) projects Consolider-C (SEJ2006-14301/PSIC), "CIBER of Physiopathology of Obesity and Nutrition, an initiative of ISCIII" and Excellence Research Program PROMETEO (Generalitat Valenciana. Conselleria de Educacion, 2008-157). We would like to express our gratitude to the Hospital Clinica Benidorm, for providing the MR datasets and to the radiologist team of Inscanner for the manual segmentation of the MR images.López-Mir, F.; Naranjo Ornedo, V.; Angulo, J.; Alcañiz Raya, ML.; Luna, L. (2014). Liver segmentation in MRI: a fully automatic method based on stochastic partitions. Computer Methods and Programs in Biomedicine. 114(1):11-28. https://doi.org/10.1016/j.cmpb.2013.12.022S1128114