Direction dependent Point spread function reconstruction for Multi-Conjugate Adaptive Optics on Giant Segmented Mirror Telescopes

Modern Giant Segmented Mirror Telescopes (GSMT) like the Extremely Large Telescope (ELT), currently under construction depend heavily on Adaptive Optics (AO) systems to correct for atmospheric turbulence. To be able to correct wider fields of view (FoV), Multi-Conjugate Adaptive Optics (MCAO) systems were introduced, which use multiple guide stars to obtain an almost uniform correction over the FoV. However, a residual blur remains in the astronmical images due to the time delay stemming from the wavefront sensor (WFS) integration time and temporal response of the deformable mirror(s) (DM). This results in a blur which can be mathematically described by a convolution of the true image with the point spread function (PSF). Due to the nature of the atmosphere and its correction, the PSF is spatially varying. In this paper, we present an algorithm for MCAO PSF reconstruction adapted to the needs of GSMTs in a storage efficient way. In particular, the PSF reconstruction algorithm for Single Conjugate Adaptive Optics (SCAO) from [40] is combined with an algorithm for atmospheric tomography from [33] to obtain a direction dependent reconstruction of the post-AO PSF. Results obtained in an end-to-end simulation tool show qualitatively good reconstruction of the PSF compared to the PSF calculated directly from the simulated incoming wavefront. Furthermore, the used algorithm has a reasonable runtime and memory consumption.Comment: submitted for publicatio

Against all odds? Forming the planet of the HD196885 binary

HD196885Ab is the most "extreme" planet-in-a-binary discovered to date, whose orbit places it at the limit for orbital stability. The presence of a planet in such a highly perturbed region poses a clear challenge to planet-formation scenarios. We investigate this issue by focusing on the planet-formation stage that is arguably the most sensitive to binary perturbations: the mutual accretion of kilometre-sized planetesimals. To this effect we numerically estimate the impact velocities $dv$ amongst a population of circumprimary planetesimals. We find that most of the circumprimary disc is strongly hostile to planetesimal accretion, especially the region around 2.6AU (the planet's location) where binary perturbations induce planetesimal-shattering $dv$ of more than 1km/s. Possible solutions to the paradox of having a planet in such accretion-hostile regions are 1) that initial planetesimals were very big, at least 250km, 2) that the binary had an initial orbit at least twice the present one, and was later compacted due to early stellar encounters, 3) that planetesimals did not grow by mutual impacts but by sweeping of dust (the "snowball" growth mode identified by Xie et al., 2010b), or 4) that HD196885Ab was formed not by core-accretion but by the concurent disc instability mechanism. All of these 4 scenarios remain however highly conjectural.Comment: accepted for publication by Celestial Mechanics and Dynamical Astronomy (Special issue on EXOPLANETS

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Deficient histone H3 propionylation by BRPF1-KAT6 complexes in neurodevelopmental disorders and cancer

Lysine acetyltransferase 6A (KAT6A) and its paralog KAT6B form stoichiometric complexes with bromodomain- and PHD finger-containing protein 1 (BRPF1) for acetylation of histone H3 at lysine 23 (H3K23). We report that these complexes also catalyze H3K23 propionylati

The Origin, Early Evolution and Predictability of Solar Eruptions

Coronal mass ejections (CMEs) were discovered in the early 1970s when space-borne coronagraphs revealed that eruptions of plasma are ejected from the Sun. Today, it is known that the Sun produces eruptive flares, filament eruptions, coronal mass ejections and failed eruptions; all thought to be due to a release of energy stored in the coronal magnetic field during its drastic reconfiguration. This review discusses the observations and physical mechanisms behind this eruptive activity, with a view to making an assessment of the current capability of forecasting these events for space weather risk and impact mitigation. Whilst a wealth of observations exist, and detailed models have been developed, there still exists a need to draw these approaches together. In particular more realistic models are encouraged in order to asses the full range of complexity of the solar atmosphere and the criteria for which an eruption is formed. From the observational side, a more detailed understanding of the role of photospheric flows and reconnection is needed in order to identify the evolutionary path that ultimately means a magnetic structure will erupt

Driver Fusions and Their Implications in the Development and Treatment of Human Cancers.

Gene fusions represent an important class of somatic alterations in cancer. We systematically investigated fusions in 9,624 tumors across 33 cancer types using multiple fusion calling tools. We identified a total of 25,664 fusions, with a 63% validation rate. Integration of gene expression, copy number, and fusion annotation data revealed that fusions involving oncogenes tend to exhibit increased expression, whereas fusions involving tumor suppressors have the opposite effect. For fusions involving kinases, we found 1,275 with an intact kinase domain, the proportion of which varied significantly across cancer types. Our study suggests that fusions drive the development of 16.5% of cancer cases and function as the sole driver in more than 1% of them. Finally, we identified druggable fusions involving genes such as TMPRSS2, RET, FGFR3, ALK, and ESR1 in 6.0% of cases, and we predicted immunogenic peptides, suggesting that fusions may provide leads for targeted drug and immune therapy

Ação do cepa e do ácido giberélico na frutificação da videira 'niagara rosada'

Studies were carried out to establish the effects of exogenous growth regulators on Vitis (labrusca x vinifera) 'Niagara Rosada' fruiting. The investigations were done in the Jundiaí Research Station, Agronomic Institute State of São Paulo, always using disease-free vineyards of good productivity. The morphological transformations of clusters were carried out under the following aspects: weight, length and width of cluster; number of berries; weight, length average and width average of berries; length average/width average ratio of berries; number of seeds; length and diameter of secondary rachis. That characteristics were determined at the time of maturity plus the total sugars, total acid, Maturity Index and reducing sugars in samples of all treatments. The experiment were conduced in order to determine the doses that resulted in the most beneficial effects, always using applications by immersion of the inflorescence. The experiment consisted of appplications of (2-chloroethyl) phosphonic acid (CEPA) at concentrations of 50, 100, 250, 500, 1,000 and 2,000 ppm, 14 days before flowering; treatments with gibberellic acid at concentrations of 100 and 200 ppm before full bloom, 10 days after full bloom, and both before plus after full bloom. Treatment with CEPA 100 ppm plus gibberellic acid 100 ppm before full bloom and check treatment were also used. The use of CEPA before flowering at the concentrations used, did not result in good results in 'Niagara Rosada' clusters; applications of gibberellic acid did not differ significantly from the nontreated vines under the conditions studied.Estudou-se o efeito da aplicação, por imersão, do CEPA (ácido 2-cloroetil fosfônico) e do ácido giberélico, 14 dias antes do florescimento, nas características morfológicas da panícula da videira Vitis (labrus-ca x vinifera) "Niagara Rosada". Alguns tratamentos com ácido giberélico foram concluídos com nova aplicação 10 dias após o florescimento. Neste experimento verificou-se que, aplicação do CEPA na concentração de 250 ppm resultou na formação de panículas com a maioria de características indesejáveis. o tratamento misto CEPA 100 ppm + ácido giberélico 100 ppm também promoveu o aparecimento de panículas subdesenvolvidas. Aplicação de ácido giberélico na concentração de 100 ppm em pré e pós-ílorescimento, resultou médias mais elevadas, com relação ao peso da panícula, comprimento da panícula, peso das bagas e comprimento da ráquis. Ácido giberélico na concentração de 100 ppm aplicado em pós-ílorescimento, promoveu uma tendência de aumento nas médias do tratamento quanto ao comprimento médio das bagas, largura média das bagas, largura do engaço e comprimento da ráquila. Devemos considerar porém, que os resultados obtidos não apresentaram diferenças significativas com relação ao controle, quanto às características das frutificações, nas condições de estudo

Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas

DNA damage repair (DDR) pathways modulate cancer risk, progression, and therapeutic response. We systematically analyzed somatic alterations to provide a comprehensive view of DDR deficiency across 33 cancer types. Mutations with accompanying loss of heterozygosity were observed in over 1/3 of DDR genes, including TP53 and BRCA1/2. Other prevalent alterations included epigenetic silencing of the direct repair genes EXO5, MGMT, and ALKBH3 in 3c20% of samples. Homologous recombination deficiency (HRD) was present at varying frequency in many cancer types, most notably ovarian cancer. However, in contrast to ovarian cancer, HRD was associated with worse outcomes in several other cancers. Protein structure-based analyses allowed us to predict functional consequences of rare, recurrent DDR mutations. A new machine-learning-based classifier developed from gene expression data allowed us to identify alterations that phenocopy deleterious TP53 mutations. These frequent DDR gene alterations in many human cancers have functional consequences that may determine cancer progression and guide therapy. Knijnenburg et al. present The Cancer Genome Atlas (TCGA) Pan-Cancer analysis of DNA damage repair (DDR) deficiency in cancer. They use integrative genomic and molecular analyses to identify frequent DDR alterations across 33 cancer types, correlate gene- and pathway-level alterations with genome-wide measures of genome instability and impaired function, and demonstrate the prognostic utility of DDR deficiency scores

The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma

Renal cell carcinoma(RCC) is not a single disease, but several histologically defined cancers with different genetic drivers, clinical courses, and therapeutic responses. The current study evaluated 843 RCC from the three major histologic subtypes, including 488 clear cell RCC, 274 papillary RCC, and 81 chromophobe RCC. Comprehensive genomic and phenotypic analysis of the RCC subtypes reveals distinctive features of each subtype that provide the foundation for the development of subtype-specific therapeutic and management strategies for patients affected with these cancers. Somatic alteration of BAP1, PBRM1, and PTEN and altered metabolic pathways correlated with subtype-specific decreased survival, while CDKN2A alteration, increased DNA hypermethylation, and increases in the immune-related Th2 gene expression signature correlated with decreased survival within all major histologic subtypes. CIMP-RCC demonstrated an increased immune signature, and a uniform and distinct metabolic expression pattern identified a subset of metabolically divergent (MD) ChRCC that associated with extremely poor survival