Science Collected Works - Research Publications
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ItemYCu(TeO3)2(NO3)(H2O)3: a novel layered tellurite.(International Union of Crystallography (IUCr), 2016-08-01)A new hydrated yttrium copper tellurite nitrate, yttrium(III) copper(II) bis-[trioxidotellurate(IV)] nitrate trihydrate, has been synthesized hydro-thermally in a Teflon-lined autoclave and structurally determined using synchrotron radiation. The new phase is the first example containing yttrium, copper and tellurium in one structure. Its crystal structure is unique, with relatively strongly bound layers extending parallel to (020), defined by YO8, CuO4 and TeO3 polyhedra, while the NO3 (-) anions and one third of the water mol-ecules lie between those layers. The structural unit consists of [Cu2(TeO3)4](4-) loop-branched chains of {Cu⋯Te⋯Cu⋯Te} squares running parallel to [001], which are linked further into layers only through Y(O,H2O)8 polyhedra. Weak 'secondary' Te bonds and O-H⋯O hydrogen-bonding inter-actions, involving water mol-ecules and layer O atoms, link the layers and inter-layer species. IR spectroscopic data are also presented.
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ItemNo Preview AvailableEffect of Cissus quadrangularis on Fracture Healing in Laboratory Animal(Instituto para o Desenvolvimento da Educacao, 2022-02-16)
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ItemSperm Syringe: 3D Sorting Platform for Assisted Reproduction(WILEY, 2022-03-04)
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ItemActivation of the viral sensor oligoadenylate synthetase 2 (Oas2) prevents pregnancy-driven mammary cancer metastases(BMC, 2022-05-03)BACKGROUND: The interferon response can influence the primary and metastatic activity of breast cancers and can interact with checkpoint immunotherapy to modulate its effects. Using N-ethyl-N-nitrosourea mutagenesis, we found a mouse with an activating mutation in oligoadenylate synthetase 2 (Oas2), a sensor of viral double stranded RNA, that resulted in an interferon response and prevented lactation in otherwise healthy mice. METHODS: To determine if sole activation of Oas2 could alter the course of mammary cancer, we combined the Oas2 mutation with the MMTV-PyMT oncogene model of breast cancer and examined disease progression and the effects of checkpoint immunotherapy using Kaplan-Meier survival analysis with immunohistochemistry and flow cytometry. RESULTS: Oas2 mutation prevented pregnancy from increasing metastases to lung. Checkpoint immunotherapy with antibodies against programmed death-ligand 1 was more effective when the Oas2 mutation was present. CONCLUSIONS: These data establish OAS2 as a therapeutic target for agents designed to reduce metastases and increase the effectiveness of checkpoint immunotherapy.
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ItemInsights into the Vertical Stratification of Microbial Ecological Roles across the Deepest Seawater Column on Earth.(MDPI AG, 2020-08-27)The Earth's oceans are a huge body of water with physicochemical properties and microbial community profiles that change with depth, which in turn influences their biogeochemical cycling potential. The differences between microbial communities and their functional potential in surface to hadopelagic water samples are only beginning to be explored. Here, we used metagenomics to investigate the microbial communities and their potential to drive biogeochemical cycling in seven different water layers down the vertical profile of the Challenger Deep (0-10,500 m) in the Mariana Trench, the deepest natural point in the Earth's oceans. We recovered 726 metagenome-assembled genomes (MAGs) affiliated to 27 phyla. Overall, biodiversity increased in line with increased depth. In addition, the genome size of MAGs at ≥4000 m layers was slightly larger compared to those at 0-2000 m. As expected, surface waters were the main source of primary production, predominantly from Cyanobacteria. Intriguingly, microbes conducting an unusual form of nitrogen metabolism were identified in the deepest waters (>10,000 m), as demonstrated by an enrichment of genes encoding proteins involved in dissimilatory nitrate to ammonia conversion (DNRA), nitrogen fixation and urea transport. These likely facilitate the survival of ammonia-oxidizing archaea α lineage, which are typically present in environments with a high ammonia concentration. In addition, the microbial potential for oxidative phosphorylation and the glyoxylate shunt was enhanced in >10,000 m waters. This study provides novel insights into how microbial communities and their genetic potential for biogeochemical cycling differs through the Challenger deep water column, and into the unique adaptive lifestyle of microbes in the Earth's deepest seawater.
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ItemHigh-Frequency Ultrasound Boosts Bull and Human Sperm Motility.(Wiley, 2022-04)Sperm motility is a significant predictor of male fertility potential and is directly linked to fertilization success in both natural and some forms of assisted reproduction. Sperm motility can be impaired by both genetic and environmental factors, with asthenozoospermia being a common clinical presentation. Moreover, in the setting of assisted reproductive technology clinics, there is a distinct absence of effective and noninvasive technology to increase sperm motility without detriment to the sperm cells. Here, a new method is presented to boost sperm motility by increasing the intracellular rate of metabolic activity using high frequency ultrasound. An increase of 34% in curvilinear velocity (VCL), 10% in linearity, and 32% in the number of motile sperm cells is shown by rendering immotile sperm motile, after just 20 s exposure. A similar effect with an increase of 15% in VCL treating human sperm with the same setting is also identified. This cell level mechanotherapy approach causes no significant change in cell viability or DNA fragmentation index, and, as such, has the potential to be applied to encourage natural fertilization or less invasive treatment choices such as in vitro fertilization rather than intracytoplasmic injection.
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ItemDiTing: A Pipeline to Infer and Compare Biogeochemical Pathways From Metagenomic and Metatranscriptomic Data(FRONTIERS MEDIA SA, 2021-08-02)Metagenomics and metatranscriptomics are powerful methods to uncover key micro-organisms and processes driving biogeochemical cycling in natural ecosystems. Databases dedicated to depicting biogeochemical pathways (for example, metabolism of dimethylsulfoniopropionate (DMSP), which is an abundant organosulfur compound) from metagenomic/metatranscriptomic data are rarely seen. Additionally, a recognized normalization model to estimate the relative abundance and environmental importance of pathways from metagenomic and metatranscriptomic data has not been organized to date. These limitations impact the ability to accurately relate key microbial-driven biogeochemical processes to differences in environmental conditions. Thus, an easy-to-use, specialized tool that infers and visually compares the potential for biogeochemical processes, including DMSP cycling, is urgently required. To solve these issues, we developed DiTing, a tool wrapper to infer and compare biogeochemical pathways among a set of given metagenomic or metatranscriptomic reads in one step, based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) and a manually created DMSP cycling gene database. Accurate and specific formulae for over 100 pathways were developed to calculate their relative abundance. Output reports detail the relative abundance of biogeochemical pathways in both text and graphical format. DiTing was applied to simulated metagenomic data and resulted in consistent genetic features of simulated benchmark genomic data. Subsequently, when applied to natural metagenomic and metatranscriptomic data from hydrothermal vents and the Tara Ocean project, the functional profiles predicted by DiTing were correlated with environmental condition changes. DiTing can now be confidently applied to wider metagenomic and metatranscriptomic datasets, and it is available at https://github.com/xuechunxu/DiTing.
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ItemBiogeography of functional trait diversity in the Taiwanese reef fish fauna(WILEY, 2019-01-01)The richness of Taiwanese reef fish species is inversely correlated to latitude as a direct consequence of the abiotic environment and its effects on benthic habitats. However, to date, no studies have investigated the variations in the diversity of traits (FD) linked with the role of these fishes in the ecosystem. FD is usually considered more sensitive than species richness in detecting early changes in response to disturbances, and therefore could serve as an indicator of ecological resilience to environmental changes. Here, we aim to characterize FD in the Taiwanese reef fish fauna and to document its regional variations. Six traits were used to categorize the 1,484 reef fish species occurring in four environmentally contrasted regions around Taiwan. The number of unique trait combinations (FEs), their richness (FRic), their redundancy (FR), their over-redundancy (FOR), and their vulnerability (FV) were compared among these regions. Overall, 416 FEs were identified. Their number decreased from south to north in step with regional species richness but FRic remained similar among regions. FR and FOR were higher to the south. At the local scale, variations in FEs and FRic are in concordance with the worldwide pattern of FD. High-latitude, impoverished fish assemblages, offer a range of trait combinations similar to diversified tropical assemblages. Increasing diversity in the latter mainly contributes to raising FR and supports already over-redundant entities. High vulnerability makes many combinations highly sensitive to species loss, and was higher at intermediate latitudes when using a fine resolution in trait categories. It suggests that the loss of FEs may first be characterized by an increase in their vulnerability, a pattern that could have been overlooked in previous global scale analyses. Overall, this study provides new insights into reef fish trait biogeography with potential ramifications for ecosystem functioning.
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ItemRethinking the distribution of urban green spaces in Mexico City: Lessons from the COVID-19 outbreak(ELSEVIER GMBH, 2022-04-01)The COVID-19 pandemic has exposed inequalities that are expected to widen if no action is taken to support the most marginalized populations. One such inequality is the distribution of urban green spaces (UGS), which are essential to pandemic recovery. Cities that aim to be inclusive and resilient should assess whether access to their UGS is equitably distributed among the population and identify the areas where these spaces are most needed. This study therefore examines the equity of access to UGS in Mexico City at the neighborhood level using network analysis. First, access to UGS was identified at a threshold of 300 m, regardless of UGS size. Second, access was differentiated by the functional level of the UGS, which primarily depends on their size, with larger UGS having more extensive catchment areas. The results of this study suggest a deficit of access to small green spaces in most of the neighborhoods of Mexico City, with the neighborhoods with higher rates of poverty showing an even lower average of UGS access. The results further highlight which neighborhoods in Mexico City should receive priority attention and funding for UGS to mitigate the disproportionate effects of public health crises. This is critical for future city planning and may be used as a roadmap for identifying priority neighborhoods in other cities with similar segregation patterns.
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ItemHolocene sea-level change and estuary infill in North West Nelson, central New Zealand(SAGE PUBLICATIONS LTD, 2021-11-21)The sedimentary sequences found within estuaries in the north west Nelson region of central New Zealand are investigated in order to quantify the timing of the end of the Post Glacial Marine Transgression. This region has been identified as being relatively stable in terms of vertical tectonic movement during the Holocene, but is yet to yield any reconstructions of eustatic sea level. In this study, we investigate the Holocene infill of a barrier estuary (Parapara Inlet) through sedimentological analysis and radiocarbon dating of 18 vibracores up to 4.2 m in length. It is found that the estuary infilled through a combination of lateral flood tide and fluvial delta progradation as well as vertical central basin infill. The central basin infilled at a consistent rate of 0.4 mm/year in both the mid (7.0–6.0 ka) and late-Holocene (2.5–1.5 ka). By the time of early human (Maori) settlement (c. 1 ka), the estuary surface was at low intertidal elevations with sediment being transported from the fluvial to tidal delta. A discernible change in sedimentation rates could not be associated with Maori settlement; however, infill rates increased to at least 12.5 mm/year in the past 150 years due hydraulic sluicing associated with mining. The sedimentary history of Parapara Inlet is compared to nearby Whanganui Inlet, d’Urville Island and Nelson to establish the character of regional Holocene sea level movement. It is found that relative sea level reached modern elevations between 8 and 7 ka in the region. The similarity between sea level curves for the end of the post glacial marine transgression (PMT) to other tectonically stable sites in northern New Zealand suggests that this curve can now be considered a true eustatic signal for the New Zealand archipelago.