Background: Mobile genetic elements (MGEs), including viruses, plasmids, and transposons, are major drivers of evolution in bacteria and archaea. Host-parasite conflicts drive the emergence of a broad variety of defense and counter-defense systems. Recent advances in metagenomics and functional annotation have shown that many defense systems are located on MGEs. The fact that MGEs are, essentially, genomic parasites raises an intriguing question: why do these parasites carry defense systems at high prevalence, often even higher than the host chromosome? Results: We developed a simple mathematical model to investigate the factors that promote evolution of defense systems in MGEs and the ecological implications of MGE-encoded defense. Our analysis points to the strength of inter-MGE interference as a key determinant of the evolution of defense systems in MGEs. We identify two qualitatively distinct regimes, depending on the basic reproductive number in mixed coinfections. Weakly interfering MGEs tend to carry low-cost defense systems that enhance the survival of their hosts upon exposure to more damaging MGEs. Although these systems can be occasionally transferred to the host, they typically remain in MGEs. In contrast, strongly interfering MGEs, such as plasmids from the same incompatibility group, can carry high-cost defense systems that are detrimental to the host and the population as a whole, but help their carriers spread by actively replacing their competitors. Conclusions: Analysis of our model shows that the key determinant of the evolution and spread of defense systems in MGEs is the strength of cross-MGE interference. Weakly interfering MGEs would serve as "MGE banks", typically carrying low-cost defense systems that can benefit the host by protecting it from more damaging MGEs. In contrast, strongly interfering MGEs would carry costly defense systems that mediate inter-MGE conflicts but are deleterious to the host. These MGEs could serve as proving grounds for emerging defense systems, which might eventually become cost-effective once optimized by selection.
Automating the manipulation of branched deformable linear objects (e.g. wire harnesses) with multiple robots is a complex challenge due to the object's flexibility. In this paper, a coordinated planning and simulation pipeline is presented enabling multiple industrial robot arms to jointly manipulate a deformable object in a manufacturing context. The pipeline is modular, consisting of task definition, physicsbased deformable linear object (DLO) modeling, coordinated multi-robot trajectory planning with deformation constraints, inter-robot collision checking, and simulation-based validation of planned motions. The system is validated primarily in simulation, showing that three robots can successfully route DLOs through complex geometries without entanglement or collisions, and a qualitative real-world demo to illustrate feasibility. The proposed approach is the first to demonstrate a multi-robot planning pipeline for branched DLO manipulation with multiple robots. The results highlight how careful coordination and planning can enable multi-robot deformable object manipulation, offering a foundation for automating wire harness installation in manufacturing.
Electron microscopy has been instrumental in our understanding of complex biological systems. Although electron microscopy reveals cellular morphology with nanoscale resolution, it does not provide information on the location of different types of proteins. An electron-microscopy-based bioimaging technology capable of localizing individual proteins and resolving protein-protein interactions with respect to cellular ultrastructure would provide important insights into the molecular biology of a cell. Here, we synthesize small lanthanide-doped nanoparticles and measure the absolute photon emission rate of individual nanoparticles resulting from a given electron excitation flux (cathodoluminescence). Our results suggest that the optimization of nanoparticle composition, synthesis protocols and electron imaging conditions can lead to sub-20-nm nanolabels that would enable high signal-to-noise localization of individual biomolecules within a cellular context. In ensemble measurements, these labels exhibit narrow spectra of nine distinct colours, so the imaging of biomolecules in a multicolour electron microscopy modality may be possible.
We report the results of P31 NMR measurements on trioctylphosphine oxide (TOPO) passivated InP quantum dots. The spectra show distinct surface-capping sites, implying a manifold of crystal–ligand bonding configurations. Two In 31P surface components are resolved and related to different electronic surroundings. With decreasing particle size the In 31P core resonance reveals an increasing upfield chemical shift related to the overall size dependence of the InP electronic structure.
The covariates included within the multivariable models fitted by each paper. This is a data microarray in which the studies run along the Y-axis and the covariates run along the X-axis. Rows and columns are ordered in descending order, based on the total number each covariate was included in the multivariable models fitted by each study. Where patterns were similar between studies or covariates, those studies or covariates were placed next to each other. (PDF 82 kb)
Read moreThe studies eligible for systematic review. (DOC 444 kb)
Read moreFemtosecond-resolved Faraday rotation is used to probe spin dynamics in chemically synthesized CdSe quantum dots 22--80 \AA{} in diameter from T=6--282 K. The precession of optically injected spins in a transverse magnetic field indicates that the measured relaxation lifetime of the spin polarization is dominated by inhomogeneous dephasing, ranging from \ensuremath{\sim}3 ns at zero field to 100 ps at 4 T. Fourier analysis reveals a multiperiodic Larmor precession, with several distinct g factors ranging from \ensuremath{\sim}1.1 to 1.7.
Read moreColloidal nanocrystal/DNA conjugates hold the promise of becoming powerful probes for biological diagnostics as well as versatile building blocks for nanotechnology. To fully realize this potential, it is important to precisely control the number of oligonucleotides bound to the nanocrystal. Here we demonstrate electrophoretic isolation of 5 and 10 nm gold nanocrystals bearing discrete numbers of single-stranded DNA (1−5). The potential use of these discrete conjugates in the fabrication of novel nanostructures is discussed.
Read moreViruses are obligate symbionts of cellular life forms that can replicate only within host cells and typically form virions (virus particles) to spread among host organisms. Virions numerically dominate the biosphere, exceeding the number of cells several-fold, and also comprise the main reservoir of genetic diversity on earth. Nearly all organisms host multiple, diverse viruses. Unlike cellular organisms, viruses have genomes (genetic information carriers incorporated into virions) that consist of all forms of RNA and DNA, suggesting an evolutionary connection between extant viruses and the primordial replicator pool. Lately, extensive mining of metagenomes and metatranscriptomes has dramatically expanded the world of viruses (virosphere), revealing an unsuspected and unprecedented diversity. Viruses share no universal genes and have multiple origins. However, about 15 viral hallmark genes each bring together multiple, diverse groups of viruses, and many other genes are shared within such groups. Evolution of viruses is inextricably intertwined with the evolution of their hosts. A key aspect of virus-host coevolution is the arms race resulting in accelerated evolution on both sides, especially of host defenses and viral counter-defenses. A complementary, prominent feature of this coevolution is exaptation, whereby viral genes are coopted by the hosts for antiviral defense and other roles, and conversely, viruses capture host genes for diverse functions in virus replication, virion morphogenesis and virus-host interaction. In this review, we attempt a synthesis of the current understanding of the global organization of the virosphere, the major trends and events in the evolution of viruses, and the high-level taxonomy of viruses.
Read moreResearch capabilities in nanoscience, molecular biology and computation have advanced to the point where it is possible to define research activities in which the development of nano-bio systems will support major DOE science goals. Specifically, we identify two major long term research goals which can motivate research at the intersection of nanoscience and biology: 1) Development of biological-systems-control for bioremediation, carbon dioxide sequestration and tailored biomaterials fabrication. 2) Development of artificial nanosystems with biomimetic functionality but without biological fragility. Basic research in support of these goals can be focused by identifying immediate research challenges involving the integration of physical nanostructures and biological nanostructures (i.e. proteins, with a strong emphasis on membrane-bound proteins) in a program of closely correlated theoretical and experimental research.
Read moreAbstract Abstract Pressure-induced structural phase transitions have been studied in CdSe, CdS, InP and Si semiconductor nanocrystals. Nanocrystals transform via single nucleation of the phase transition with a kinetic barrier that increases in increasing cluster size. The structural transition path causes a shape change in the nanocrystals, which dictates the surface energy and thus the kinetic and thermodynamic stability of the transformed nanocrystal. These finite size effects can be used to tune the metastability of the nanocrystals versus pressure. Enhanced metastability allows structural and optical measurements in a regime inaccessible to the bulk solid, as well as possible recovery of the dense high pressure phase to atmospheric pressure. Key Words: MetastabilityNanocrystalPhase transitionHigh pressureKinetics
Read moreCancer has become the second leading cause of death, the global cancer burden is rapidly increasing, and there are marked disparities between and within countries worldwide. Population-based cancer registries systematically collect data on cancer patients in defined populations, which play a crucial role in planning and assessing cancer prevention and control strategies. While the development of cancer registration has been marked by increasing standardization of definitions and methods and the electronic processing of data, the advent of artificial intelligence (AI) offers opportunities to further reduce the labor-intensive nature of registry operations, particularly where registry resources are scarce. These include enabling the processing of large datasets, extracting complex or unstructured data patterns to support cancer registration data abstraction, and facilitating data quality and control. The analysis and dissemination of registry data are also increasingly integrating AI methodologies. This paper provides a comprehensive overview of the application of AI in cancer registration. We investigate the challenges associated with integrating AI into existing cancer registry structures, with a particular emphasis on network and computational constraints, uneven resource allocation, and potential biases and limitations within AI systems. We propose a forward-looking AI-enhanced framework for cancer registration, highlighting AI's potential to optimize efficiency in cancer registration and the use of registry data for cancer control and cancer research.
Read moreThis paper presents a component-resolved decision logic that enables automated disassembly systems to select optimal second-life pathways for control and switchgear cabinets. A two-tier scoring model, calibrated through the weighting of qualitative criteria, is employed to screen component types against reuse and remanufacturing indicators. Where necessary, a recycling assessment is applied to distinguish between recoverable and scrap parts. The framework has been enriched with ECLASS 14.0 classifications in order to generalise results across a range of heterogeneous mechatronic products. However, the results show that coarse taxonomic granularity can mask divergent second-life suitability and thus refinement of the framework is needed. The method has been validated on an industrial cabinet that has been repurchased from service, containing 842 mechanical, mechatronic and electrical components. Direct reuse is a viable option for 229 components (27.2 %), while 460 components (54.8 %) necessitate minor repair work and are thus directed towards the remanufacturing process. A further 144 items (17.1 %) proceed to material recycling, leaving only 0.72 % of components for disposal. In summary, 99.28 % of the cabinet’s components remains available for a second life. These outcomes achieve a balance between environmental and economic imperatives by utilising the residual value of components, whose manufacturing accounts for the majority of costs. The proposed logic therefore offers manufacturers a practical tool for operationalising circular-economy objectives and informs future research on taxonomy refinement and robotic disassembly. This paper addresses therefore two research gaps, the absence of (i) a quantitative framework linking component condition, feasibility, and demand for end-of-life decisions, and (ii) tools aligning ecological gains with economical break-even, validated in an industrial case study.
Read moreAbstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Read moreBACKGROUND: The global rise in cancer incidence and survivorship is contributing to escalating health-care expenditure. Yet comprehensive and internationally comparable data on direct cancer costs worldwide remain scarce, limiting insights into cross-country spending patterns, their relationship to cancer outcomes, and future cost trajectories. METHODS: We assembled data on direct cancer costs up to the year 2022 from academic journals, government statistical reports, and the grey literature. Drawing from 19 sources in 39 countries, we estimated total, per-patient, and per-capita cancer expenditure in US dollars (US$) by cancer type, assessing associations between spending and cancer outcomes, alongside recent trends. RESULTS: Annual cancer costs varied substantially and reflected differences in national income, ranging from US$1989 per diagnosis (Ethiopia) to US$129 494 per diagnosis (United States). Annual costs per capita ranged from US$1.43 (Ethiopia) to US$713 (United States). Annual expenditure was positively correlated with survival for most cancers but showed diminishing returns in high-income countries. Moreover, expenditure had no apparent relation with overall cancer mortality. Where data were available, spending patterns by cancer type reflected country-specific incidence profiles. Across all countries, the 4 costliest cancers accounted for one-third to almost one-half (37%-48%) of direct cancer costs. In countries with reliable time series, costs rose steadily over time, with growth rates ranging from 1.4% (Japan, 2009-2022) to 9.3% (Republic of Korea, 2004-2022). These increases consistently outpaced gross domestic product growth by 1.0%-7.7% over the respective observation periods. CONCLUSION: Greater reforms to cancer control, and health-care more broadly, are required to ensure long-term fiscal sustainability while maximizing population health outcomes.
Read moreThe development, characterization, and exploitation of novel materials based on the assembly of molecular components is an exceptionally active and rapidly expanding field. For this reason, the topic of molecule-based materials (MBMs) was chosen as the subject of a workshop sponsored by the Chemical Sciences Division of the United States Department of Energy. The purpose of the workshop was to review and discuss the diverse research trajectories in the field from a chemical perspective, and to focus on the critical elements that are likely to be essential for rapid progress. The MBMs discussed encompass a diverse set of compositions and structures, including clusters, supramolecular assemblies, and assemblies incorporating biomolecule-based components. A full range of potentially interesting materials properties, including electronic, magnetic, optical, structural, mechanical, and chemical characteristics were considered. Key themes of the workshop included synthesis of novel components, structural control, characterization of structure and properties, and the development of underlying principles and models. MBMs, defined as “useful substances prepared from molecules or molecular ions that maintain aspects of the parent molecular framework” are of special significance because of the capacity for diversity in composition, structure, and properties, both chemical and physical. Key attributes are the ability in MBMs to access the additional dimension of multiple length scales and available structural complexity via organic chemistry synthetic methodologies and the innovative assembly of such diverse components. The interaction among the assembled components can thus lead to unique behavior. A consequence of the complexity is the need for a multiplicity of both existing and new tools for materials synthesis, assembly, characterization, and theoretical analysis. For some technologically useful properties, e.g., ferro- or ferrimagnetism and superconductivity, the property is not a property of a molecule or ion; it is a cooperative solid-state (bulk) property—a property of the entire solid. Hence, the desired properties are a consequence of the interactions between the molecules or ions, and understanding the solid-state structure as well as methods to predict, control, and modulate the structure are essential to understanding and manipulating such behaviors. As challenging as this is, molecules enable a substantially greater ability of control than atoms as building blocks for new materials and thus are well positioned to contribute significantly to new materials. The diversity of components and processes leads to the recognition of the critical role of cross-disciplinary research, including not only that between traditionally different areas within chemistry, but also between chemistry and biochemistry, physics, and a number of engineering disciplines. Enhancing communication and active collaboration between these groups was seen as a critical goal for the research area.
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