Characterization of clastic sedimentary enviroments by clustering algorithm and several statistical approaches — case study, Sava Depression in Northern Croatia

Abstract This study demonstrates a method to identify and characterize some facies of turbiditic depositional environments. The study area is a hydrocarbon field in the Sava Depression (Northern Croatia). Its Upper Miocene reservoirs have been proved to represent a lacustrine turbidite system. In the workflow, first an unsupervised neural network was applied as clustering method for two sandstone reservoirs. The elements of the input vectors were the basic petrophysical parameters. In the second step autocorrelation surfaces were used to reveal the hidden anisotropy of the grid. This anisotropy is supposed to identify the main continuity directions in the geometrical analyses of sandstone bodies. Finally, in the description of clusters several parametric and nonparametric statistics were used to characterize the identified facies. Obtained results correspond to the previously published interpretation of those reservoir facies

Tectono-stratigraphic response of the Sandino Forearc Basin (N-Costa Rica and W-Nicaragua) to episodes of rough crust and oblique subduction

The southern Central American active margin is a world-class site where past and present subduction processes have been extensively studied. Tectonic erosion/accretion and oblique/orthogonal subduction are thought to alternate in space and time along the Middle American Trench. These processes may cause various responses in the upper plate, such as uplift/subsidence, deformation, and volcanic arc migration/ shut-off. We present an updated stratigraphic framework of the Late Cretaceous– Cenozoic Sandino Forearc Basin (SFB) which provides evidence of sedimentary response to tectonic events. Since its inception, the basin was predominantly filled with deep-water volcaniclastic deposits. In contrast, shallow-water deposits appeared episodically in the basin record and are considered as tectonic event markers. The SFB stretches for about 300 km and varies in thickness from 5 km (southern part) to about 16 km (northern part). The drastic, along-basin, thickness variation appears to be the result of (1) differential tectonic evolutions and (2) differential rates of sediment supply. (1) The northern SFB did not experience major tectonic events. In contrast, the reduced thickness of the southern SFB (5 km) is the result of at least four uplift phases related to the collision/accretion of bathymetric reliefs on the incoming plate: (i) the accretion of a buoyant oceanic plateau (Nicoya Complex) during the middle Campanian; (ii) the collision of an oceanic plateau (?) during the late Danian–Selandian; (iii) the collision/accretion of seamounts during the late Eocene–early Oligocene; (iv) the collision of seamounts and ridges during the Pliocene–Holocene. (2) The northwestward thickening of the SFB may have been enhanced by high sediment supply in the Fonseca Gulf area which reflects sourcing from wide, high relief drainage basins. In contrast, sedimentary input has possibly been lower along the southern SFB, due to the proximity of the narrow, lowland isthmus of southern Central America. Moreover, two phases of strongly oblique subduction affected the margin, producing strike-slip faulting in the forearc basin: (1) prior to the Farallon Plate breakup, an Oligocene transpressional phase caused deformation and uplift of the basin depocenter, triggering shallowing-upward of the Nicaraguan Isthmus in the central and northern SFB; (2) a Pleistocene–Holocene transtensional phase drives the NW-directed motion of a forearc sliver and reactivation of the graben-bounding faults of the late Neogene Nicaraguan Depression. We discuss arguments in favour of a Pliocene development of the Nicaraguan Depression and propose that the Nicaraguan Isthmus, which is the apparent rift shoulder of the depression, represents a structure inherited from the Oligocene transpressional phase

s-Process Nucleosynthesis in AGB Stars: A Test for Stellar Evolution

[abridged] We study the s-process in AGB stars using three different stellar evolutionary models computed for a 3Msun and solar metallicity star. First we investigate the formation and the efficiency of the main neutron source. We parametrically vary the number of protons mixed from the envelope into the C12 rich core. For p/C12 > 0.3, mainly N14 is produced, which represent a major neutron poison. The amount of C12 in the He intershell and the maximum value of the time-integrated neutron flux are proportional. Then we generate detailed s-process calculations on the basis of stellar evolutionary models constructed with three different codes. One code considers convective hydrodynamic overshoot that depends on a free parameter f, and results in partial mixing beyond convective boundaries, the most efficient third dredge up and the formation of the C13 pocket. For the other two codes an identical C13 pocket is introduced in the post-processing nucleosynthesis calculations. The models generally reproduce the spectroscopically observed s-process enhancements. The results of the cases without overshoot are remarkably similar. The code including hydrodynamic overshoot produces a He intershell composition near to that observed in H-deficient central stars of planetary nebulae. As a result of this intershell dredge up the neutron fluxes have a higher efficiency, both during the interpulse periods and within thermal pulses. The s-element distribution is pushed toward the heavier s-process elements and large abundances of neutron-rich isotopes fed by branching points in the s-process path are produced. Several observational constraints are better matched by the models without overshoot. Our study need to be extended to different masses and metallicities and in the space of the free overshoot parameter f.Comment: 44 pages, incl 10 figures, accepted for publication in Ap

Six Year Refractive Change among White Children and Young Adults: Evidence for Significant Increase in Myopia among White UK Children

OBJECTIVE:To determine six-year spherical refractive error change among white children and young adults in the UK and evaluate differences in refractive profiles between contemporary Australian children and historical UK data. DESIGN:Population-based prospective study. PARTICIPANTS:The Northern Ireland Childhood Errors of Refraction (NICER) study Phase 1 examined 1068 children in two cohorts aged 6-7 years and 12-13 years. Prospective data for six-year follow-up (Phase 3) are available for 212 12-13 year olds and 226 18-20 year olds in each cohort respectively. METHODS:Cycloplegic refractive error was determined using binocular open-field autorefraction (Shin-Nippon NVision-K 5001, cyclopentolate 1%). Participants were defined by spherical equivalent refraction (SER) as myopic SER ≤-0.50D, emmetropic -0.50D<SER<+2.00 or hyperopic SER≥+2.00D. MAIN OUTCOME MEASURES:Proportion and incidence of myopia. RESULTS:The proportion of myopes significantly increased between 6-7 years (1.9%) and 12-13 years (14.6%) (p<0.001) but not between 12-13 and 18-20 years (16.4% to 18.6%, p = 0.51). The estimated annual incidence of myopia was 2.2% and 0.7% for the younger and older cohorts respectively. There were significantly more myopic children in the UK at age 12-13 years in the NICER study (16.4%) than reported in Australia (4.4%) (p<0.001). However by 17 years the proportion of myopia neared equivalence in the two populations (NICER 18.6%, Australia 17.7%, p = 0.75). The proportion of myopic children aged 12-13 years in the present study (2006-2008) was 16.4%, significantly greater than that reported for children aged 10-16 years in the 1960's (7.2%, p = 0.01). The proportion of hyperopes in the younger NICER cohort decreased significantly over the six year period (from 21.7% to 14.2%, p = 0.04). Hyperopes with SER ≥+3.50D in both NICER age cohorts demonstrated persistent hyperopia. CONCLUSIONS:The incidence and proportion of myopia are relatively low in this contemporary white UK population in comparison to other worldwide studies. The proportion of myopes in the UK has more than doubled over the last 50 years in children aged between 10-16 years and children are becoming myopic at a younger age. Differences between the proportion of myopes in the UK and in Australia apparent at 12-13 years were eliminated by 17 years of age

Second-Generation Sequencing Supply an Effective Way to Screen RNAi Targets in Large Scale for Potential Application in Pest Insect Control

The key of RNAi approach success for potential insect pest control is mainly dependent on careful target selection and a convenient delivery system. We adopted second-generation sequencing technology to screen RNAi targets. Illumina's RNA-seq and digital gene expression tag profile (DGE-tag) technologies were used to screen optimal RNAi targets from Ostrinia furnalalis. Total 14690 stage specific genes were obtained which can be considered as potential targets, and 47 were confirmed by qRT-PCR. Ten larval stage specific expression genes were selected for RNAi test. When 50 ng/µl dsRNAs of the genes DS10 and DS28 were directly sprayed on the newly hatched larvae which placed on the filter paper, the larval mortalities were around 40∼50%, while the dsRNAs of ten genes were sprayed on the larvae along with artificial diet, the mortalities reached 73% to 100% at 5 d after treatment. The qRT-PCR analysis verified the correlation between larval mortality and the down-regulation of the target gene expression. Topically applied fluorescent dsRNA confirmed that dsRNA did penetrate the body wall and circulate in the body cavity. It seems likely that the combination of DGE-tag with RNA-seq is a rapid, high-throughput, cost less and an easy way to select the candidate target genes for RNAi. More importantly, it demonstrated that dsRNAs are able to penetrate the integument and cause larval developmental stunt and/or death in a lepidopteron insect. This finding largely broadens the target selection for RNAi from just gut-specific genes to the targets in whole insects and may lead to new strategies for designing RNAi-based technology against insect damage

In vitro and in vivo characterization of highly purified Human Mesothelioma derived cells

<p>Abstract</p> <p>Background</p> <p>Malignant pleural mesothelioma is a rare disease known to be resistant to conventional therapies. A better understanding of mesothelioma biology may provide the rationale for new therapeutic strategies. In this regard, tumor cell lines development has been an important tool to study the biological properties of many tumors. However all the cell lines established so far were grown in medium containing at least 10% serum, and it has been shown that primary cell lines cultured under these conditions lose their ability to differentiate, acquire gene expression profiles that differ from that of tissue specific stem cells or the primary tumor they derive from, and in some cases are neither clonogenic nor tumorigenic. Our work was aimed to establish from fresh human pleural mesothelioma samples cell cultures maintaining tumorigenic properties.</p> <p>Methods</p> <p>The primary cell cultures, obtained from four human pleural mesotheliomas, were expanded in vitro in a low serum proliferation-permissive medium and the expression of different markers as well as the tumorigenicity in immunodeficient mice was evaluated.</p> <p>Results</p> <p>The established mesothelioma cell cultures are able to engraft, after pseudo orthotopic intraperitoneal transplantation, in immunodeficient mouse and maintain this ability to after serial transplantation. Our cell cultures were strongly positive for CD46, CD47, CD56 and CD63 and were also strongly positive for some markers never described before in mesothelioma cell lines, including CD55, CD90 and CD99. By real time PCR we found that our cell lines expressed high mRNA levels of typical mesothelioma markers as mesothelin (MSLN) and calretinin (CALB2), and of BMI-1, a stemness marker, and DKK1, a potent Wingless [WNT] inhibitor.</p> <p>Conclusions</p> <p>These cell cultures may provide a valuable in vitro and in vivo model to investigate mesothelioma biology. The identification of new mesothelioma markers may be useful for diagnosis and/or prognosis of this neoplasia as well as for isolation of mesothelioma tumor initiating cells.</p

p53 modeling as a route to mesothelioma patients stratification and novel therapeutic identification

Background Malignant pleural mesothelioma (MPM) is an orphan disease that is difficult to treat using traditional chemotherapy, an approach which has been effective in other types of cancer. Most chemotherapeutics cause DNA damage leading to cell death. Recent discoveries have highlighted a potential role for the p53 tumor suppressor in this disease. Given the pivotal role of p53 in the DNA damage response, here we investigated the predictive power of the p53 interactome model for MPM patients’ stratification. Methods We used bioinformatics approaches including omics type analysis of data from MPM cells and from MPM patients in order to predict which pathways are crucial for patients’ survival. Analysis of the PKT206 model of the p53 network was validated by microarrays from the Mero-14 MPM cell line and RNA-seq data from 71 MPM patients, whilst statistical analysis was used to identify the deregulated pathways and predict therapeutic schemes by linking the affected pathway with the patients’ clinical state. Results In silico simulations demonstrated successful predictions ranging from 52 to 85% depending on the drug, algorithm or sample used for validation. Clinical outcomes of individual patients stratified in three groups and simulation comparisons identified 30 genes that correlated with survival. In patients carrying wild-type p53 either treated or not treated with chemotherapy, FEN1 and MMP2 exhibited the highest inverse correlation, whereas in untreated patients bearing mutated p53, SIAH1 negatively correlated with survival. Numerous repositioned and experimental drugs targeting FEN1 and MMP2 were identified and selected drugs tested. Epinephrine and myricetin, which target FEN1, have shown cytotoxic effect on Mero-14 cells whereas marimastat and batimastat, which target MMP2 demonstrated a modest but significant inhibitory effect on MPM cell migration. Finally, 8 genes displayed correlation with disease stage, which may have diagnostic implications. Conclusions Clinical decisions related to MPM personalized therapy based on individual patients’ genetic profile and previous chemotherapeutic treatment could be reached using computational tools and the predictions reported in this study upon further testing in animal models

The (n, gamma) campaigns at EXILL

At the PF1B cold neutron beam line at the Institut Laue Langevin, the EXILL array consisting of EXOGAM, GASP and ILL-Clover detectors was used to perform (n, gamma) measurements at very high coincidence rates. About ten different reactions were measured in autumn 2012 using a highly collimated cold neutron beam. In spring 2013, the EXOGAM array was combined with 16 LaBr3(Ce) scintillators in the EXILL&FATIMA campaign for the measurement of lifetimes using the generalised centroid difference method. We report on the properties of the set-ups and present first results from both campaigns