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- ItemComparing a global high-resolution downscaled fossil fuel CO2 emission dataset to local inventory-based estimates over 14 global cities(London : Biomed Central, 2020) Chen, Jingwen; Zhao, Fang; Zeng, Ning; Oda, TomohiroBackground: Compilation of emission inventories (EIs) for cities is a whole new challenge to assess the subnational climate mitigation effort under the Paris Climate Agreement. Some cities have started compiling EIs, often following a global community protocol. However, EIs are often difficult to systematically examine because of the ways they were compiled (data collection and emission calculation) and reported (sector definition and direct vs consumption). In addition, such EI estimates are not readily applicable to objective evaluation using modeling and observations due to the lack of spatial emission extents. City emission estimates used in the science community are often based on downscaled gridded EIs, while the accuracy of the downscaled emissions at city level is not fully assessed. Results: This study attempts to assess the utility of the downscaled emissions at city level. We collected EIs from 14 major global cities and compare them to the estimates from a global high-resolution fossil fuel CO2 emission data product (ODIAC) commonly used in the science research community. We made necessary adjustments to the estimates to make our comparison as reasonable as possible. We found that the two methods produce very close area-wide emission estimates for Shanghai and Delhi (< 10% difference), and reach good consistency in half of the cities examined (< 30% difference). The ODIAC dataset exhibits a much higher emission compared to inventory estimates in Cape Town (+ 148%), Sao Paulo (+ 43%) and Beijing (+ 40%), possibly related to poor correlation between nightlight intensity with human activity, such as the high-emission and low-lighting industrial parks in developing countries. On the other hand, ODIAC shows lower estimates in Manhattan (-62%), New York City (-45%), Washington D.C. (-42%) and Toronto (-33%), all located in North America, which may be attributable to an underestimation of residential emissions from heating in ODIAC's nightlight-based approach, and an overestimation of emission from ground transportation in registered vehicles statistics of inventory estimates. Conclusions: The relatively good agreement suggests that the ODIAC data product could potentially be used as a first source for prior estimate of city-level CO2 emission, which is valuable for atmosphere CO2 inversion modeling and comparing with satellite CO2 observations. Our compilation of in-boundary emission estimates for 14 cities contributes towards establishing an accurate inventory in-boundary global city carbon emission dataset, necessary for accountable local climate mitigation policies in the future. © 2020 The Author(s).
- ItemImprovement of the optical properties after surface error correction of aluminium mirror surfaces(London : Biomed Central, 2021) Ulitschka, M.; Bauer, J.; Frost, F.; Arnold, T.Ion beam finishing techniques of aluminium mirrors have a high potential to meet the increasing demands on applications of high-performance mirror devices for visible and ultraviolet spectral range. Reactively driven ion beam machining using oxygen and nitrogen gases enables the direct figure error correction up to 1 μm machining depth while preserving the initial roughness. However, the periodic turning mark structures, which result from preliminary device shaping by single-point diamond turning, often limit the applicability of mirror surfaces in the short-periodic spectral range. Ion beam planarization with the aid of a sacrificial layer is a promising process route for surface smoothing, resulting in successfully reduction of the turning mark structures. A combination with direct surface smoothing to perform a subsequent improvement of the microroughness is presented with a special focus on roughness evolution, chemical composition, and optical surface properties. As a result, an ion beam based process route is suggested, which allows almost to recover the reflective properties and an increased long-term stability of smoothed aluminium surfaces.
- ItemDesign and performance analysis of integrated focusing grating couplers for the transverse-magnetic TM00 mode in a photonic BiCMOS technology(London : Biomed Central, 2020) Georgieva, Galina; Voigt, Karsten; Peczek, Anna; Mai, Christian; Zimmermann, LarsFocusing grating couplers for the excitation of the fundamental transverse-magnetic (TM) mode in integrated silicon photonic waveguides are designed and characterized under the boundary conditions of a photonic BiCMOS foundry. Two types of waveguide geometries are considered – a nanowire and a rib waveguide. Wafer-scale experimental results for nanowire TM grating couplers are in excellent agreement with numerical investigations and demonstrate a robust behavior on the wafer. The mean coupling loss and the 3s interval are -3.9 ± 0.3 dB. The on wafer variation is three times lower than for the fundamental transverse-electric (TE) polarization. Similarly, the coupling in rib waveguides is examined as well. The results indicate that the rib waveguides require a modified geometry when designed for TM. In general, the nanowire waveguide type is more suitable for TM coupling, showing a stable and repeatable performance. © 2020, The Author(s).
- ItemElectroactive nanoinjection platform for intracellular delivery and gene silencing(London : Biomed Central, 2023) Shokouhi, Ali-Reza; Chen, Yaping; Yoh, Hao Zhe; Murayama, Takahide; Suu, Koukou; Morikawa, Yasuhiro; Brenker, Jason; Alan, Tuncay; Voelcker, Nicolas H.; Elnathan, RoeyBackground: Nanoinjection—the process of intracellular delivery using vertically configured nanostructures—is a physical route that efficiently negotiates the plasma membrane, with minimal perturbation and toxicity to the cells. Nanoinjection, as a physical membrane-disruption-mediated approach, overcomes challenges associated with conventional carrier-mediated approaches such as safety issues (with viral carriers), genotoxicity, limited packaging capacity, low levels of endosomal escape, and poor versatility for cell and cargo types. Yet, despite the implementation of nanoinjection tools and their assisted analogues in diverse cellular manipulations, there are still substantial challenges in harnessing these platforms to gain access into cell interiors with much greater precision without damaging the cell’s intricate structure. Here, we propose a non-viral, low-voltage, and reusable electroactive nanoinjection (ENI) platform based on vertically configured conductive nanotubes (NTs) that allows for rapid influx of targeted biomolecular cargos into the intracellular environment, and for successful gene silencing. The localization of electric fields at the tight interface between conductive NTs and the cell membrane drastically lowers the voltage required for cargo delivery into the cells, from kilovolts (for bulk electroporation) to only ≤ 10 V; this enhances the fine control over membrane disruption and mitigates the problem of high cell mortality experienced by conventional electroporation. Results: Through both theoretical simulations and experiments, we demonstrate the capability of the ENI platform to locally perforate GPE-86 mouse fibroblast cells and efficiently inject a diverse range of membrane-impermeable biomolecules with efficacy of 62.5% (antibody), 55.5% (mRNA), and 51.8% (plasmid DNA), with minimal impact on cells’ viability post nanoscale-EP (> 90%). We also show gene silencing through the delivery of siRNA that targets TRIOBP, yielding gene knockdown efficiency of 41.3%. Conclusions: We anticipate that our non-viral and low-voltage ENI platform is set to offer a new safe path to intracellular delivery with broader selection of cargo and cell types, and will open opportunities for advanced ex vivo cell engineering and gene silencing. Graphical abstract: [Figure not available: see fulltext.]
- ItemOptically transparent vertical silicon nanowire arrays for live-cell imaging(London : Biomed Central, 2021) Elnathan, Roey; Holle, Andrew W.; Young, Jennifer; George, Marina; Heifler, Omri; Goychuk, Andriy; Frey, Erwin; Kemkemer, Ralf; Spatz, Joachim P.; Kosloff, Alon; Patolsky, Fernando; Voelcker, Nicolas H.Programmable nano-bio interfaces driven by tuneable vertically configured nanostructures have recently emerged as a powerful tool for cellular manipulations and interrogations. Such interfaces have strong potential for ground-break-ing advances, particularly in cellular nanobiotechnology and mechanobiology. However, the opaque nature of many nanostructured surfaces makes non-destructive, live-cell characterization of cellular behavior on vertically aligned nanostructures challenging to observe. Here, a new nanofabrication route is proposed that enables harvesting of vertically aligned silicon (Si) nanowires and their subsequent transfer onto an optically transparent substrate, with high efficiency and without artefacts. We demonstrate the potential of this route for efficient live-cell phase contrast imaging and subsequent characterization of cells growing on vertically aligned Si nanowires. This approach provides the first opportunity to understand dynamic cellular responses to a cell-nanowire interface, and thus has the potential to inform the design of future nanoscale cellular manipulation technologies.
- ItemEffectiveness of porous silicon nanoparticle treatment at inhibiting the migration of a heterogeneous glioma cell population(London : Biomed Central, 2021) Abdalla, Youssef; Luo, Meihua; Mäkilä, Ermei; Day, Bryan W.; Voelcker, Nicolas H.; Tong, YinBACKGROUND: Approximately 80% of brain tumours are gliomas. Despite treatment, patient mortality remains high due to local metastasis and relapse. It has been shown that transferrin-functionalised porous silicon nanoparticles (Tf@pSiNPs) can inhibit the migration of U87 glioma cells. However, the underlying mechanisms and the effect of glioma cell heterogeneity, which is a hallmark of the disease, on the efficacy of Tf@pSiNPs remains to be addressed. RESULTS: Here, we observed that Tf@pSiNPs inhibited heterogeneous patient-derived glioma cells’ (WK1) migration across small perforations (3 μm) by approximately 30%. A phenotypical characterisation of the migrated subpopulations revealed that the majority of them were nestin and fibroblast growth factor receptor 1 positive, an indication of their cancer stem cell origin. The treatment did not inhibit cell migration across large perforations (8 μm), nor cytoskeleton formation. This is in agreement with our previous observations that cellular-volume regulation is a mediator of Tf@pSiNPs’ cell migration inhibition. Since aquaporin 9 (AQP9) is closely linked to cellular-volume regulation, and is highly expressed in glioma, the effect of AQP9 expression on WK1 migration was investigated. We showed that WK1 migration is correlated to the differential expression patterns of AQP9. However, AQP9-silencing did not affect WK1 cell migration across perforations, nor the efficacy of cell migration inhibition mediated by Tf@pSiNPs, suggesting that AQP9 is not a mediator of the inhibition. CONCLUSION: This in vitro investigation highlights the unique therapeutic potentials of Tf@pSiNPs against glioma cell migration and indicates further optimisations that are required to maximise its therapeutic efficacies.
- ItemRole of actin cytoskeleton in cargo delivery mediated by vertically aligned silicon nanotubes(London : Biomed Central, 2022) Chen, Yaping; Yoh, Hao Zhe; Shokouhi, Ali-Reza; Murayama, Takahide; Suu, Koukou; Morikawa, Yasuhiro; Voelcker, Nicolas H.; Elnathan, RoeyNanofabrication technologies have been recently applied to the development of engineered nano–bio interfaces for manipulating complex cellular processes. In particular, vertically configurated nanostructures such as nanoneedles (NNs) have been adopted for a variety of biological applications such as mechanotransduction, biosensing, and intracellular delivery. Despite their success in delivering a diverse range of biomolecules into cells, the mechanisms for NN-mediated cargo transport remain to be elucidated. Recent studies have suggested that cytoskeletal elements are involved in generating a tight and functional cell–NN interface that can influence cargo delivery. In this study, by inhibiting actin dynamics using two drugs—cytochalasin D (Cyto D) and jasplakinolide (Jas), we demonstrate that the actin cytoskeleton plays an important role in mRNA delivery mediated by silicon nanotubes (SiNTs). Specifically, actin inhibition 12 h before SiNT-cellular interfacing (pre-interface treatment) significantly dampens mRNA delivery (with efficiencies dropping to 17.2% for Cyto D and 33.1% for Jas) into mouse fibroblast GPE86 cells, compared to that of untreated controls (86.9%). However, actin inhibition initiated 2 h after the establishment of GPE86 cell–SiNT interface (post-interface treatment), has negligible impact on mRNA transfection, maintaining > 80% efficiency for both Cyto D and Jas treatment groups. The results contribute to understanding potential mechanisms involved in NN-mediated intracellular delivery, providing insights into strategic design of cell–nano interfacing under temporal control for improved effectiveness.
- ItemBog ecosystems as a playground for plant-microbe coevolution: bryophytes and vascular plants harbour functionally adapted bacteria(London : Biomed Central, 2021) Wicaksono, Wisnu Adi; Cernava, Tomislav; Berg, Christian; Berg, GabrieleBackground: Bogs are unique ecosystems inhabited by distinctive, coevolved assemblages of organisms, which play a global role for carbon storage, climate stability, water quality and biodiversity. To understand ecology and plant–microbe co-occurrence in bogs, we selected 12 representative species of bryophytes and vascular plants and subjected them to a shotgun metagenomic sequencing approach. We explored specific plant–microbe associations as well as functional implications of the respective communities on their host plants and the bog ecosystem. Results: Microbial communities were shown to be functionally adapted to their plant hosts; a higher colonization specificity was found for vascular plants. Bryophytes that commonly constitute the predominant Sphagnum layer in bogs were characterized by a higher bacterial richness and diversity. Each plant group showed an enrichment of distinct phylogenetic and functional bacterial lineages. Detailed analyses of the metabolic potential of 28 metagenome-assembled genomes (MAGs) supported the observed functional specification of prevalent bacteria. We found that novel lineages of Betaproteobacteria and Actinobacteria in the bog environment harboured genes required for carbon fixation via RuBisCo. Interestingly, several of the highly abundant bacteria in both plant types harboured pathogenicity potential and carried similar virulence factors as found with corresponding human pathogens. Conclusions: The unexpectedly high specificity of the plant microbiota reflects intimate plant–microbe interactions and coevolution in bog environments. We assume that the detected pathogenicity factors might be involved in coevolution processes, but the finding also reinforces the role of the natural plant microbiota as a potential reservoir for human pathogens. Overall, the study demonstrates how plant–microbe assemblages can ensure stability, functioning and ecosystem health in bogs. It also highlights the role of bog ecosystems as a playground for plant–microbe coevolution. [MediaObject not available: see fulltext.] © 2021, The Author(s).
- ItemStatistical stopping criteria for automated screening in systematic reviews(London : Biomed Central, 2020) Callaghan, Max W.; Müller-Hansen, FinnActive learning for systematic review screening promises to reduce the human effort required to identify relevant documents for a systematic review. Machines and humans work together, with humans providing training data, and the machine optimising the documents that the humans screen. This enables the identification of all relevant documents after viewing only a fraction of the total documents. However, current approaches lack robust stopping criteria, so that reviewers do not know when they have seen all or a certain proportion of relevant documents. This means that such systems are hard to implement in live reviews. This paper introduces a workflow with flexible statistical stopping criteria, which offer real work reductions on the basis of rejecting a hypothesis of having missed a given recall target with a given level of confidence. The stopping criteria are shown on test datasets to achieve a reliable level of recall, while still providing work reductions of on average 17%. Other methods proposed previously are shown to provide inconsistent recall and work reductions across datasets.