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At least 703 records · Page 39

Proteogenomic characterization of difficult-to-treat breast cancer with tumor cells enriched through laser microdissection

Abstract Background Breast cancer (BC) is the most commonly diagnosed cancer and the leading cause of cancer death among women globally. Despite advances, there is considerable variation in clinical outcomes for patients with non-luminal A tumors, classified as difficult-to-treat breast cancers (DTBC). This study aims to delineate the proteogenomic landscape of DTBC tumors compared to luminal A (LumA) tumors. Methods We retrospectively collected a total of 117 untreated primary breast tumor specimens, focusing on DTBC subtypes. Breast tumors were processed by laser microdissection (LMD) to enrich tumor cells. DNA, RNA, and protein were simultaneously extracted from each tumor preparation, followed by whole genome sequencing, paired-end RNA sequencing, global proteomics and phosphoproteomics. Differential feature analysis, pathway analysis and survival analysis were performed to better understand DTBC and investigate biomarkers. Results We observed distinct variations in gene mutations, structural variations, and chromosomal alterations between DTBC and LumA breast tumors. DTBC tumors predominantly had more mutations inTP53,PLXNB3, Zinc finger genes, and fewer mutations inSDC2,CDH1,PIK3CA,SVIL, andPTEN. Notably, Cytoband 1q21, which contains numerous cell proliferation-related genes, was significantly amplified in the DTBC tumors. LMD successfully minimized stromal components and increased RNA–protein concordance, as evidenced by stromal score comparisons and proteomic analysis. Distinct DTBC and LumA-enriched clusters were observed by proteomic and phosphoproteomic clustering analysis, some with survival differences. Phosphoproteomics identified two distinct phosphoproteomic profiles for high relapse-risk and low relapse-risk basal-like tumors, involving several genes known to be associated with breast cancer oncogenesis and progression, includingKIAA1522,DCK,FOXO3,MYO9B,ARID1A,EPRS,ZC3HAV1, andRBM14. Lastly, an integrated pathway analysis of multi-omics data highlighted a robust enrichment of proliferation pathways in DTBC tumors. Conclusions This study provides an integrated proteogenomic characterization of DTBC vs LumA with tumor cells enriched through laser microdissection. We identified many common features of DTBC tumors and the phosphopeptides that could serve as potential biomarkers for high/low relapse-risk basal-like BC and possibly guide treatment selections.

Oncology↗

Hybrid quantum nanophotonic devices with color centers in nanodiamonds [Invited]

Optically active color centers in nanodiamonds offer unique opportunities for generating and manipulating quantum states of light. These mechanically, chemically, and optically robust emitters can be produced in mass quantities, deterministically manipulated, and integrated with a variety of quantum device geometries and photonic material platforms. Nanodiamonds with deeply sub-wavelength sizes coupled to nanophotonic structures feature a giant enhancement of light-matter interaction, promising high bitrates in quantum photonic systems. We review the recent advances in controlled techniques for synthesizing, selecting, and manipulating nanodiamond-based color centers for their integration with quantum nanophotonic devices.

Sahoo, Swetapadma (ORCID:0000000179281391)↗

Metal-containing photopolymer resins generated by reduction of dissolved metal salts

According to one embodiment, a three-dimensional structure includes: at least one photopolymer having at least one metal dispersed throughout at least portions of a bulk of the structure. The structure is characterized by features having a horizontal and/or vertical feature resolution in a range from several hundred nanometers to several hundred microns. The portions of the bulk throughout which metal is dispersed may optionally be selectively determined. In more embodiments, the structure may have electroless plated metal formed on surfaces thereof, alternatively or in addition to the metal dispersed throughout the bulk of the structure. The electroless plating may be achieved without the use of a surface activation bath. Corresponding methods for forming various embodiments of such three dimensional structures are also disclosed.

36 MATERIALS SCIENCE↗

Tunable assembly of hybrid colloids induced by regioselective depletion

Assembling colloidal particles using site-selective directional interactions into predetermined colloidal superlattices with desired properties is broadly sought-after, but challenging to achieve. Here in this paper, we exploit regioselective depletion interactions to engineer the directional bonding and assembly of non-spherical colloidal hybrid microparticles. We report that the crystallization of a binary colloidal mixture can be regulated by tuning the depletion conditions. Subsequently, we fabricate triblock biphasic colloids with controlled aspect ratios to achieve regioselective bonding. Without any surface treatment, these biphasic colloids assemble into various colloidal superstructures and superlattices featuring optimized pole-to-pole or center-to-center interactions. Additionally, we observe polymorphic crystallization, quantify the abundancy of each form using algorithms we developed, and investigate the crystallization process in real time. We demonstrate selective control of attractive interactions between specific regions on an anisotropic colloid with no need of site-specific surface functionalization, leading to a general method for achieving colloidal structures with yet unforeseen arrangements and properties.

36 MATERIALS SCIENCE↗

Distributive Nd-to-Yb Energy Transfer within Pure [YbNdYb] Heterometallic Molecules

Facile access to site-selective hetero-lanthanide molecules will open new avenues in the search of novel photophysical phenomena based on Ln-to-Ln' energy transfer (ET). This challenge demands strategies to segregate efficiently different Ln metal ions among different positions in a molecule. We report here the one-step synthesis and structure of a pure [YbNdYb] (1) coordination complex featuring short Yb···Nd distances, ideal to investigate a potential distributive (i.e., from one donor to two acceptors) intramolecular ET from one Nd 3+ ion to two Yb 3+ centers within a well-characterized molecule. The difference in ionic radius is the mechanism allowing to allocate selectively both types of metal ion within the molecular structure, exploited with the simultaneous use of two β-diketone-type ligands. To assist the photophysical investigation of this heterometallic species, the analogues [YbLaYb] (2) and [LuNdLu] (3) have also been prepared. Sensitization of Yb 3+ and Nd 3+ in the last two complexes, respectively, was observed, with remarkably long decay times, facilitating the determination of the Nd-to-Yb ET within the [YbNdYb] composite. This ET was demonstrated by comparing the emission of iso-absorbant solutions of 1, 2, and 3 and through lifetime determinations in solution and solid state. The comparatively high efficiency of this process corroborates the facilitating effect of having two acceptors for the nonradiative decay of Nd 3+ created within the [YbNdYb] molecule.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Designing molecular qubits: computational insights into first-row and group 6 transition metal complexes

In the realm of optically addressable qubits, a previously synthesized and characterized Cr( IV ) pseudo-tetrahedral complex, featuring four strongly donating ligands surrounding the chromium center, has demonstrated potential as a qubit candidate. This study proposes analogs of this complex through a metal substitution strategy, extending the investigation to different complexes based on metal centers selected from first-row and Group 6 transition metals. Computational modeling based on multiconfigurational methods CASPT2 and MC-PDFT was utilized to calculate energy gaps between ground and excited electronic spin states, and zero-field splitting parameters. Simulations were applied to each equilibrium geometry and related deformations based on vibrational modes. All results align with previous experimental findings, but also show that qubits based on V and Ti centers could be more electronically stable than the Cr one, suggesting a lower electronic features dependency from their related geometry. In some cases geometrical deformations provide changes in relative energy gaps between triplet and singlet excited state, that could potentially swap, offering a different initialization process, and some inspiration for ligand design based on such deformations. Additionally, this study identifies an unsynthesized Ti( II ) compound as a promising candidate for molecular qubits. This finding highlights the role of computational multireference methods in the rational design of qubit systems.

Sauza-de la Vega, Arturo [Univ. of Chicago, IL (Un↗

Computational discovery of a tetragonal MBene phase: diamond-shaped boron lattices, viable MAB precursors, and selective CO 2 reduction

MBenes are a class of two-dimensional transition-metal borides derived from layered MAB phases. Here, we use first-principles calculations to predict a new tetragonal MB (1 : 1) MBene phase featuring a diamond-shaped B–B lattice and systematically assess its phase stability, synthetic accessibility, and catalytic performance towards the CO 2 reduction reaction (CO 2 RR). Four tetragonal configurations are benchmarked against known hexagonal and orthorhombic phases, and a multi-tier screening identifies six robust members (CrB, FeB, MoB, WB, IrB, and PtB). Exploration of the I4/mmm MAB space reveals 11 viable precursors, including the experimentally synthesized Ir 2 ZnB 2 , which validates our screening approach. CO 2 RR free-energy diagrams show that CrB favors CH 3 OH while FeB, MoB, WB, IrB, and PtB preferentially yield HCOOH. The corresponding limiting potentials are competitive with, and in some cases superior to, those reported for state-of-the-art orthorhombic and hexagonal MBenes. These findings expand the MBene landscape by establishing a tetragonal phase with structural, synthetic, and catalytic promise.

Lu, Linguo [University of Puerto Rico, San Juan, P↗

Design complexity and performance analysis in additively manufactured heat exchangers

The main objective of this research is to investigate the tradeoffs between design complexity and thermal performance in additively manufactured metallic heat exchangers. Such heat exchangers have become a favorite topic for investigation in various fields ranging from air conditioning to aircraft gas turbine engines. In particular, high manufacturing cost has emerged as the major drawback in broad applications of manifold-microchannel heat exchanger (MMHXs). The possibility of cost-effective manufacturing has generated wide interest in applying additive manufacturing (AM) for fabricating MMHXs. Furthermore, AM technologies will provide an opportunity for enhanced design and superior heat transfer performance. In this study, innovative MMHXs are designed and fabricated through selective laser melting. An experimental setup was designed to measure pressure drop and heat transfer for the developed MMHXs with a wide range of Reynolds numbers. Furthermore, the coefficient of performance was calculated based on the heat flow rate, air pressure drop, and air flow rate. Measurement results demonstrated that in some scenarios adding more internal features, i.e., increasing design complexity, does not necessarily improve the MMHX performance.

10 SYNTHETIC FUELS↗

Differences in substrate use linked to divergent carbon flow during litter decomposition

ABSTRACT Discovering widespread microbial processes that create variation in soil carbon (C) cycling within ecosystems may improve soil C modeling. Toward this end, we screened 206 soil communities decomposing plant litter in a common garden microcosm environment and examined features linked to divergent patterns of C flow. C flow was measured as carbon dioxide (CO2) and dissolved organic carbon (DOC) from 44-days of litter decomposition. Two large groups of microbial communities representing ‘high’ and ‘low’ DOC phenotypes from original soil and 44-day microcosm samples were down-selected for fungal and bacterial profiling. Metatranscriptomes were also sequenced from a smaller subset of communities in each group. The two groups exhibited differences in average rate of CO2 production, demonstrating that the divergent patterns of C flow arose from innate functional constraints on C metabolism, not a time-dependent artefact. To infer functional constraints, we identified features – traits at the organism, pathway or gene level – linked to the high and low DOC phenotypes using RNA-Seq approaches and machine learning approaches. Substrate use differed across the high and low DOC phenotypes. Additional features suggested that divergent patterns of C flow may be driven in part by differences in organism interactions that affect DOC abundance directly or indirectly by controlling community structure.

59 BASIC BIOLOGICAL SCIENCES↗

E ‐selective Semi‐hydrogenation of Alkynes under Mild Conditions by a Diruthenium Hydride Complex

Abstract The synthesis, characterization and catalytic activity of a new class of diruthenium hydrido carbonyl complexes bound to the t Bu PNNP expanded pincer ligand is described. Reacting t Bu PNNP with two equiv of RuHCl(PPh 3 ) 3 (CO) at 140 °C produces an insoluble air‐stable complex, which was structurally characterized as [Ru 2 ( t Bu PNNP)H(μ‐H)Cl(μ‐Cl)(CO) 2 ] ( 1 ) using solid‐state NMR, IR and X‐ray absorption spectroscopies and follow‐up reactivity. A reaction with KO t Bu results in deprotonation of a methylene linker to produce [Ru 2 ( t Bu PNNP * )H(μ‐H)(μ‐O t Bu)(CO) 2 ] ( 3 ) featuring a partially dearomatized naphthyridine core. This enables metal‐ligand cooperative activation of H 2 analogous to the mononuclear analogue, [Ru( t Bu PNP*)H(CO)]. In contrast to the mononuclear system, the bimetallic analogue 3 catalyzes the E ‐selective semi‐hydrogenation of alkynes at ambient temperature and atmospheric H 2 pressure with good functional group tolerance. Monitoring the semi‐hydrogenation of diphenylacetylene by 1 H NMR spectroscopy shows the intermediacy of Z ‐stilbene, which is subsequently isomerized to the E ‐isomer. Initial findings into the mode of action of this system are provided, including the spectroscopic characterization of a polyhydride intermediate and the isolation of a deactivated species with a partially hydrogenated naphthyridine backbone.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Two Mesoporous Domains Are Better Than One for Catalytic Deconstruction of Polyolefins

Catalytic hydrogenolysis of polyolefins into valuable liquid, oil, or wax-like hydrocarbon chains for second-life applications is typically accompanied by the hydrogen-wasting co-formation of low value volatiles, notably methane, that increase greenhouse gas emissions. Catalytic sites confined at the bottom of mesoporous wells, under conditions in which the pore exerts the greatest influence over the mechanism, are capable of producing less gases than unconfined sites. A new architecture was designed to emphasize this pore effect, with the active platinum nanoparticles embedded between linear, hexagonal mesoporous silica and gyroidal cubic MCM-48 silica (mSiO 2 /Pt/MCM-48). This catalyst deconstructs polyolefins selectively into ~C 20 –C 40 paraffins and cleaves C–C bonds at a rate (TOF = 4.2 ± 0.3 s –1 ) exceeding that of materials lacking these combined features while generating negligible volatile side products including methane. The time-independent product distribution is consistent with a processive mechanism for polymer deconstruction. In contrast to time- and polymer length-dependent products obtained from non-porous catalysts, mSiO 2 /Pt/MCM-48 yields a C 28 -centered Gaussian distribution of waxy hydrocarbons from polyolefins of varying molecular weight, composition, and physical properties, including low-density polyethylene, isotactic polypropylene, ultrahigh-molecular-weight polyethylene, and mixtures of multiple, post-industrial polyolefins. Here, coarse-grained simulation reveals that the porous-core architecture enables the paraffins to diffuse away from the active platinum site, preventing secondary reactions that produce gases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Efficient separation of xylene isomers by using a robust calcium-based metal–organic framework through a synergetic thermodynamically and kinetically controlled mechanism

Adsorptive separation of physically and chemically similar molecules and understanding the underlying host–guest interactions at the molecular level are of significant scientific and practical importance. Here we report the development of a novel calcium-based metal–organic framework, formulated as Ca 3 (Htcpp) 2 (H 4 tcpp = 2,3,5,6-tetrakis(4-carboxyphenyl)-pyrazine) featuring microporosity and high stability. This compound shows distinct adsorption behavior toward xylene isomers and is capable of separating them efficiently at an industrially relevant temperature. The selective adsorption is attributed to a synergetic thermodynamic and kinetic effect. Here, the host–guest interactions were probed directly by single-crystal X-ray diffraction analysis and the adsorption affinity was evaluated through computational molecular simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The Completed SDSS-IV extended Baryon Oscillation Spectroscopic Survey: measurement of the BAO and growth rate of structure of the emission line galaxy sample from the anisotropic power spectrum between redshift 0.6 and 1.1

We analyse the large-scale clustering in Fourier space of emission line galaxies (ELG) from the Data Release 16 of the Sloan Digital Sky Survey IV extended Baryon Oscillation Spectroscopic Survey. The ELG sample contains 173,736 galaxies covering 1,170 square degrees in the redshift range 0.6 < z < 1.1. We perform a BAO measurement from the post-reconstruction power spectrum monopole, and study redshift space distortions (RSD) in the first three even multipoles. Furthermore, photometric variations yield fluctuations of both the angular and radial survey selection functions. Those are directly inferred from data, imposing integral constraints which we model consistently. The full data set has only a weak preference for a BAO feature (1.4σ). At the effective redshift zeff = 0.845 we measure $D_{\rm V}(z_{\rm eff})/r_{\rm drag} = 18.33_{-0.62}^{+0.57}$, with DV the volume-averaged distance and rdrag the comoving sound horizon at the drag epoch. In combination with the RSD measurement, at zeff = 0.85 we find $f\sigma _8(z_{\rm eff}) = 0.289_{-0.096}^{+0.085}$, with f the growth rate of structure and σ8 the normalisation of the linear power spectrum, $D_{\rm H}(z_{\rm eff})/r_{\rm drag} = 20.0_{-2.2}^{+2.4}$ and DM(zeff)/rdrag = 19.17 ± 0.99 with DH and DM the Hubble and comoving angular distances, respectively. These results are in agreement with those obtained in configuration space, thus allowing a consensus measurement of fσ8(zeff) = 0.315 ± 0.095, $D_{\rm H}(z_{\rm eff})/r_{\rm drag} = 19.6_{-2.1}^{+2.2}$ and DM(zeff)/rdrag = 19.5 ± 1.0. This measurement is consistent with a flat ΛCDM model with Planck parameters.

79 ASTRONOMY AND ASTROPHYSICS↗

DECADE+ DES Y3 Weak Lensing Mass Map: A 13,000 deg $\^{} 2$ View of Cosmic Structure from 270 Million Galaxies

We present the largest galaxy weak lensing mass map of the late-time Universe, reconstructed from 270 million galaxies in the DECADE and DES Year 3 datasets, covering 13,000 square degrees. We validate the map through systematic tests against observational conditions (depth, seeing, etc.), finding the map is statistically consistent with no contamination. The large area covered by the mass map makes it a well-suited tool for cosmological analyses, cross-correlation studies and the identification of large-scale structure features. We demonstrate its potential by detecting cosmic filaments directly from the mass map for the first time and validating them through their association with galaxy clusters selected using the Sunyaev-Zeldovich effect from Planck and ACT DR6.

Gatti, M.↗

Tier 2 Safety Basis Document: Weapons and Complex Integration - Building 225

This Safety Basis Document (SBD) covers operations in the Weapons and Complex Integration (WCI) Building 225 (B225) facility. B225 is located in the southwestern quadrant of Lawrence Livermore National Laboratory (LLNL) and is operated and owned by WCI. This SBD satisfies the requirements of LLNL ES&H Manual Document 3.1, Nonnuclear Safety Basis Program (Ref. 2). B225 is classified as a Low Hazard Facility based on the inventory of radiological materials. Other hazards in B225: chemicals, radiation generating devices, and industrial hazards are managed at the Light Science and Industry (LSI) level. Biological and explosive hazards are not authorized in B225. There are four general Administrative Controls (ACs) identified as the B225 Operational Safety Requirements (OSRs). These administrative controls are deemed sufficient to ensure safe operations with respect to co-located workers and the public. Other safety features and administrative requirements are required by the LLNL ES&H Manual, including those to protect the facility workers and the environment, but these have not been selected as credited controls to protect the co-located workers or the public, which are the target populations of concern for the SBD.

61 RADIATION PROTECTION AND DOSIMETRY↗

Computed Tomography Scanning and Geophysical Measurements of UW Enterprises LP 1-250512-129 Well in Southwestern Indiana

The computed tomography (CT) facilities and the Multi-Sensor Core Logger (MSCL) at the National Energy Technology Laboratory (NETL) in Morgantown, West Virginia, were used to characterize Illinois Basin core of the Upper Devonian-Early Mississippian New Albany Shale Formation from Posey County, Indiana. The primary impetus of this work is a collaboration between Indiana Geological and Water Survey at Indiana University Bloomington, NETL, and Woolsey Operating Company LLC to characterize and make publicly available core information from the New Albany Shale of the Illinois Basin. Core characterization of this unconventional oil/gas well will aid in understanding the lithology changes and the fracture complexity of the New Albany Shale. There is a potential for this formation to be developed in the future for critical mineral and rare earth element (CM/REE) extraction. The resultant datasets are presented in this report and can be accessed from NETL's Energy Data eXchange (EDX) online system using the following link: https://edx.netl.doe.gov/dataset/uw-enterprises. All equipment and techniques used were non-destructive, enabling future examinations and analyses to be performed on this core. None of the equipment used was suitable for direct visualization of the pore space in the fine-grained structures studied; however, fractures, discontinuities, and millimeter-scale features were readily detectable with the methods tested. Imaging with the NETL medical CT scanner was performed on the entire core. Targeted higher resolution CT scanning of select sections was performed with NETL’s industrial and micro-CT scanner. Qualitative analysis of the medical CT images, coupled with X-ray fluorescence (XRF), P-wave, and magnetic susceptibility measurements from the MSCL were useful in identifying zones of interest for more detailed analysis. The ability to quickly identify key areas for more detailed study with higher resolution will save time and resources in future studies. The combination of methods used provides a multi-scale analysis of the core; the resulting macro and micro descriptions are relevant to many subsurface energy related examinations traditionally performed at NETL.

58 GEOSCIENCES↗

A Combined Water and CO 2 Direct Air Capture System (Final Technical Report)

The primary objective of the project was to demonstrate the technical and economic performance of a technology that simultaneously captures CO 2 and water from the air – a Hybrid Direct Air Capture system (HDAC). In HDAC, air is passed over water capture section as well as a CO 2 selective sorbent to remove CO 2 from the air stream. Combining potable water generation and CO 2 capture in a single device with the unique energy conserving features of the proposed design enables long-term projected CAPEX under $\$$750/t-CO 2 and levelized cost of capture (LCOC) of $\$$140/t-CO 2 . Project DE-FE-0031970 "A Combined Water and CO 2 Direct Air Capture System" ran for four years and three months from 10/01/2020 to 12/31/2024 for three budget periods and an extension period. The total project budget at completion was $\$$3,534,408 consisting of a $\$$2,680,064 federal share and $\$$854,344 cost share. The pilot plant was successfully designed, engineered, built and commissioned during the initial three budget periods. The plant demonstrated successful water capture during this period, whereas initial CO 2 capture was well below target values. The project team requested an extension period during which alternate materials and beds were evaluated. By the end of the project, both moisture swing adsorption of CO 2 and water capture had successfully been demonstrated at target capture rates making further scale-up of the technology viable.

42 ENGINEERING↗