Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Facile Sulfurization under Ambient Condition with Na2S to Fabricate Nanostructured Copper Sulfide

The sulfurization reaction was investigated as a promising fabrication method for preparing metal sulfide nanomaterials. Traditional sulfurization processes generally require high vacuum systems, high reaction temperatures, and toxic chemicals, utilizing complicated procedures with poor composition and morphology controllability. Herein, a facile method is reported for synthesizing nanostructured copper sulfide using a sulfurization reaction with Na2S at room temperature under non-vacuum conditions. Moreover, we demonstrate that the morphology, composition, and optical properties of nanostructured copper sulfides could be controlled by the Na2S solution concentration and the reaction time. Nanostructured copper sulfides were synthesized in nanospheres, nanoplates, and nanoplate-based complex morphologies with various oxidation states. Furthermore, by comparing the optical properties of nanostructured copper sulfides with different oxidation states, we determined that reflectivity in the near infrared (NIR) region decreases with increasing oxidation states. These results reveal that the Na2S solution concentration and reaction time are key factors for designing nanostructured copper sulfides, providing new insights for synthesis methods of metal sulfide nanomaterials

Electrophoretic Deposition of Aged and Charge Controlled Colloidal Copper Sulfide Nanoparticles

Colloidal nanoparticles (NPs) have been recently spotlighted as building blocks for various nanostructured devices. Their collective properties have been exhibited by arranging them on a substrate to form assembled NPs. In particular, electrophoretic deposition (EPD) is an emerging fabrication method for such nanostructured films. To maximize the benefits of this method, further studies are required to fully elucidate the key parameters that influence the NP deposition. Herein, two key parameters are examined, namely: (i) the aging of colloidal NPs and (ii) the charge formation by surface ligands. The aging of Cu2-xS NPs changes the charge states, thus leading to different NP deposition behaviors. The SEM images of NP films, dynamic light scattering, and zeta potential results demonstrated that the charge control and restoration of interparticle interactions for aged NPs were achieved via simple ligand engineering. The charge control of colloidal NPs was found to be more dominant than the influence of aging, which can alter the surface charges of the NPs. The present results thus reveal that the charge formation on the colloidal NPs, which depends on the surface ligands, is an important controllable parameter in EPD

Selective Etching of Copper Sulfide Nanoparticles and Heterostructures through Sulfur Abstraction: Phase Transformations and Optical Properties

Integrating top-down methods, such as chemical etching, for the precise removal of excess material in nanostructures with the bottom-up size and shape control of colloidal nanoparticle synthesis could greatly expand the range of accessible nanoparticle morphologies. We present mechanistic insights into an unusual reaction in which trialkylphosphines (“phosphines”), which are commonly used to protect nanoparticle surfaces as a surfactant ligand, chemically etch copper sulfide, Cu_2–<i>x</i>S, nanostructures in the presence of oxygen. Furthermore, Cu_2–<i>x</i>S is removed highly selectively from zinc sulfideCu_2–<i>x</i>S heterostructures. Structural and optical characterizations show that the addition of phosphine destabilizes the highly Cu-deficient roxbyite phase and injects Cu into the interiors of the nanoparticles, even at room temperature. Analysis of the etching products confirms that chalcogens are removed in the form of phosphine chalcogenides and shows that the removed copper is solubilized as Cu²⁺. The morphology of etched Cu_2–<i>x</i>S particles changes dramatically as the concentration of phosphine is reduced, producing anisotropically etched particles indicative of facet-selective surface chemical reactions. Additionally, ceric ammonium nitrate, another oxidizing agent, can be used to control the etching reaction; the use of this redox agent affords strictly isotropically etched particles. These results demonstrate the highly pliable structural and chemical properties of nanocrystalline Cu_2–<i>x</i>S and raise the possibility of using surface-active ligands formerly thought to be passivating to dramatically reshape as-synthesized colloidal nanostructures into more functional forms

Binder-Free and Carbon-Free Nanoparticle Batteries: A Method for Nanoparticle Electrodes without Polymeric Binders or Carbon Black

In this work, we have developed a new fabrication method for nanoparticle (NP) assemblies for Li-ion battery electrodes that require no additional support or conductive materials such as polymeric binders or carbon black. By eliminating these additives, we are able to improve the battery capacity/weight ratio. The NP film is formed by using electrophoretic deposition (EPD) of colloidally synthesized, monodisperse cobalt NPs that are transformed through the nanoscale Kirkendall effect into hollow Co₃O₄. EPD forms a network of NPs that are mechanically very robust and electrically connected, enabling them to act as the Li-ion battery anode. The morphology change through cycles indicates stable 5–10 nm NPs form after the first lithiation remained throughout the cycling process. This NP-film battery made without binders and conductive additives shows high gravimetric (>830 mAh/g) and volumetric capacities (>2100 mAh/cm³) even after 50 cycles. Because similar films made from drop-casting do not perform well under equal conditions, EPD is seen as the critical step to create good contacts between the particles and electrodes resulting in this significant improvement in battery electrode assembly. This is a promising system for colloidal nanoparticles and a template for investigating the mechanism of lithiation and delithiation of NPs

Tuning of aluminum concentration distribution in high nickel cathode particles for lithium ion batteries

© 2019 This study focuses on a novel approach for the structural design of LiNi0.86Co0.12Al0.02O2 cathodes by tailoring the distribution of Al elements using milled-Al(OH)3. The distribution of Al in the cathode material is investigated using an electron probe micro analyzer. By controlling milled-Al(OH)3 addition time at 3 and 6 h, thickness of Al-rich layer is varied during co-precipitation process and following calcination with LiOH produces cathode materials with the variant Al distribution. Initial discharge capacities of the cathodes with the Al addition at 3 and 6 h are 202 and 195 mA h g−1 and the IE (initial efficiency) is 92.5 and 86.6%, respectively. The capacity retentions from the cycling test of the individual cathodes are as high as 96.7 and 92.6% at 50 cycles under 1 C rate, respectively. This advanced electrochemical performance is attributed to gradual increase of Al element from inner to outer in active material11sciescopu

Synthesis and Properties of Electrically Conductive, Ductile, Extremely Long (∼50 μm) Nanosheets of K_<i>x</i>CoO₂·<i>y</i>H₂O

Extremely long, electrically conductive, ductile, free-standing nanosheets of water-stabilized K_<i>x</i>CoO₂·<i>y</i>H₂O are synthesized using the sol–gel and electric-field induced kinetic-demixing (SGKD) process. Room temperature in-plane resistivity of the K_<i>x</i>CoO₂·<i>y</i>H₂O nanosheets is less than ∼4.7 mΩ·cm, which corresponds to one of the lowest resistivity values reported for metal oxide nanosheets. The synthesis produces tens of thousands of very high aspect ratio (50,000:50,000:1 = length/width/thickness), millimeter length nanosheets stacked into a macro-scale pellet. Free-standing nanosheets up to ∼50 μm long are readily delaminated from the stacked nanosheets. High-resolution transmission electron microscopy (HR-TEM) studies of the free-standing nanosheets indicate that the delaminated pieces consist of individual nanosheet crystals that are turbostratically stacked. X-ray diffraction (XRD) studies confirm that the nanosheets are stacked in perfect registry along their <i>c</i>-axis. Scanning electron microscopy (SEM) based statistical analysis show that the average thickness of the nanosheets is ∼13 nm. The nanosheets show ductility with a bending radius as small as ∼5 nm

Activity and stability of cobalt phosphides for hydrogen evolution upon water splitting

Late transition metal phosphides have been reported to have high activity for catalyzing hydrogen evolution reaction (HER), yet their active site and stability are not well-understood. Here we report systematic activity and stability study of CoP for HER by combining electrochemical measurements for CoP nanoparticles (NPs) with ex situ and in situ synchrotron X-ray absorption (XAS) spectroscopy at phosphorus and cobalt K edges, as well as density functional theory (DFT) calculations. Colloidally synthesized CoP NPs showed high HER activity in both acid and base electrolytes, comparable to previous work, where no significant pH dependence was observed. Transmission electron microscopy-energy dispersive spectroscopy study of CoP NPs before and after exposure to potentials in the range from 0 to 1.4 V vs. the reversible hydrogen electrode (RHE) revealed that the P/Co ratio reduced with increasing potential in the potentiostatic measurements prior to HER measurements. The reduced P/Co ratio was accompanied with the emergence of (oxy)phosphate(s) as revealed by XAS, and reduced specific HER activity, suggesting the important role of P in catalyzing HER. This hypothesis was further supported by DFT calculations of HER on the most stable (011) surface of CoP and voltage dependent intensities of both phosphide and phosphate components from P-K edge X-ray spectroscopy. This work highlights the need of stabilizing metal phosphides and optimizing their surface P sites in order to realize the practical use of metal phosphides to catalyze HER in electrochemical and photoelectrochemical devices. Keywords: Metal phosphide; Hydrogen evolution reaction; HER; Catalysis; Water splitting; Electrocatalysi