Restoring native plants following invasive Malephora Crocea (coppery iceplant, Aizoaceae) eradication on Anacapa Island

To avoid unintended complications of invasive species eradication, it is important to understand the potential implications of the techniques used in species eradication efforts. This study aimed to compare how different methods of removing Malephora crocea affect the survivorship of planted seedlings of native perennial plants on Anacapa Island. Employing a randomized complete block design in an M. crocea stand, three removal treatments were tested: 1) hand-pull; 2) spray with herbicide and leave skeletons; and 3) spray and then remove skeletons after 2.5 months. In each treatment, seedlings of three species (Leptosyne gigantea, Frankenia salina, and Grindelia stricta) and seeds of two species (L. gigantea and G. stricta) were planted. Survivorship and seed establishment were monitored quarterly between March 2010 and January 2011. For transplanted seedlings, the spray-and-leave treatment resulted in higher survivorship, while no difference was observed between the pull-treatments. Seed establishment was very low overall, but results of seeding of G. stricta showed that the spray-and-pull treatment provided for higher establishment than other treatments. L. gigantea seed establishment was inconclusive. The spray-and-leave treatment also provided the highest relative soil moisture. My results suggest that the spray-and-leave treatment provided the most suitable conditions for survival of transplanted native perennial vegetation

Stable solar-driven oxidation of water by semiconducting photoanodes protected by transparent catalytic nickel oxide films

Reactively sputtered nickel oxide (NiO_x) films provide transparent, antireflective, electrically conductive, chemically stable coatings that also are highly active electrocatalysts for the oxidation of water to O_2(g). These NiO_x coatings provide protective layers on a variety of technologically important semiconducting photoanodes, including textured crystalline Si passivated by amorphous silicon, crystalline n-type cadmium telluride, and hydrogenated amorphous silicon. Under anodic operation in 1.0 M aqueous potassium hydroxide (pH 14) in the presence of simulated sunlight, the NiO_x films stabilized all of these self-passivating, high-efficiency semiconducting photoelectrodes for >100 h of sustained, quantitative solar-driven oxidation of water to O_2(g)

Performance and failure modes of Si anodes patterned with thin-film Ni catalyst islands for water oxidation

Silicon photoanodes patterned with thin-film Ni catalyst islands exhibited stable oxygen evolution for over 240 h of continuous operation in 1.0 mol L^(−1) KOH under simulated sunlight conditions. Buried-junction np^+-Si(111) photoanodes with an 18.0% filling fraction of a square array of Ni microelectrodes, np^+-Si(111)|NiμE_(18.0%), demonstrated performance equivalent to a Ni anode in series with a photovoltaic device having an open-circuit voltage of 538 ± 20 mV, a short-circuit current density of 20.4 ± 1.3 mA cm^(−2), and a photovoltaic efficiency of 6.7 ± 0.9%. For the np^+-Si(111)|NiμE_(18.0%) samples, the photocurrent density at the equilibrium potential for oxygen evolution was 12.7 ± 0.9 mA cm^(−2), yielding an ideal regenerative cell solar-to-oxygen conversion efficiency of 0.47 ± 0.07%. The photocurrent passed exclusively through the Ni catalyst islands to evolve O_2 with nearly 100% faradaic efficiency, while a passivating, insulating surface layer of SiO_x formed in situ on areas of the Si in direct contact with the electrolyte. The (photo)electrochemical behavior of Si electrodes patterned with varying areal filling fractions of Ni catalyst islands was also investigated. The stability and efficiency of the patterned-catalyst Si electrodes were affected by the filling fraction of the Ni catalyst, the orientation and dopant type of the substrates, and the measurement conditions. The electrochemical behavior at different stages of operation, including Ni catalyst activation, Si passivation, stable operation, and device failure, was affected by the dynamic processes of anodic formation and isotropic dissolution of SiO_x on the exposed Si. Ex situ and operando microscopic and spectroscopic studies revealed that these processes were three-dimensional and spatially non-uniform across the surface of the substrate, and occurred near the active catalyst islands. The patterned catalyst/substrate electrodes serve as a model system for accelerated studies of failure mechanisms in photoanodes protected by multifunctional catalytic coatings or other hole-conductive thin-film coatings that contain defects

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

Blue Hill Ship Building

https://digitalmaine.com/blue_hill_documents/1180/thumbnail.jp

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity.

Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant