bluuebunny/crossref_metadata_2025_split huggingface dataset:
Beneficial land-use change in Europe: deployment scenarios for multifunctional riparian buffers and windbreaks
Authors: Englund Oskar , Börjesson Pål , Mola-Yudego Blas , Berndes Göran , Dimitriou Ioannis , Cederberg Christel , Scarlat Nicolae 
Published: January 2021

Abstract
The land sector needs to increase biomass production to meet multiple demands while reducing negative land use impacts and transitioning from being a source to being a sink of carbon. The new Common Agricultural Policy of the EU (CAP) steers towards a more needs-based, targeted approach to addressing multiple environmental and climatic objectives, in coherence with other EU policies. In relation to this, new schemes are developed to offer farmers direct payments to adapt practices beneficial for climate, water, soil, air and biodiversity. Multifunctional biomass production systems have potential to reduce environmental impacts from agriculture while maintaining or increasing biomass production for the bioeconomy across Europe. Here, we present the first attempt to model the deployment of two such systems, riparian buffers and windbreaks, across >81.000 landscapes in Europe (EU27 + UK), aiming to quantify the resulting ecosystem services and environmental benefits, considering three deployment scenarios with different incentives for implementation. We found that these multifunctional biomass production systems can reduce N emissions to water and soil loss by wind erosion, respectively, down to a “low” impact level all over Europe, while simultaneously providing substantial environmental co-benefits, using less than 1% of the area under annual crops in the EU. The GHG emissions savings of utilizing the biomass produced in these systems for replacing fossil alternatives, combined with the increases in soil organic carbon, correspond to 1-1,4% of total GHG emissions in EU28. The introduction of “eco-schemes” in the new CAP may resolve some of the main barriers to implementation of large-scale multifunctional biomass production systems. Increasing the knowledge of these opportunities among all EU member states, before designing and introducing country-specific Eco-scheme options in the new CAP, is critical.
Fluorescence umpolung enables light-up sensing of N-acetyltransferases and nerve agents
Authors: Yan Chenxu , Guo Zhiqian , Chi Weijie , Fu Wei , Liu Xiaogang , Tian He , Zhu Wei-Hong 
Published: January 2021

Abstract
Intramolecular charge transfer (ICT) is a fundamental mechanism that enables the development of numerous fluorophores and probes for bioimaging and sensing. However, the electron-withdrawing targets (EWTs)-induced fluorescence quenching is a long-standing and unsolved issue in ICT fluorophores, and significantly limits the widespread applicability. Here we report a simple and generalizable structural-modification for completely overturning the intramolecular rotation driving energy, and thus fully reversing the ICT fluorophores’ quenching mode into light-up mode. Specifically, the insertion of an indazole unit into ICT scaffold can fully amplify the intramolecular rotation in donor-indazole-π-acceptor fluorophores (fluorescence OFF), whereas efficiently suppressing the rotation in their EWT-substituted system (fluorescence ON). The novel molecular strategy is generalizable, yielding a palette of chromophores with fluorescence umpolung that spans visible and near-infrared range. This strategy expands the bio-analytical toolboxes and has for the first time allowed exploiting ICT fluorophores for unprecedented light-up sensing of EWTs including N-acetyltransferases and nerve agents.
Synbiotic Combinations of Lactobacillus Gasseri 505 and Cudrania Tricuspidata Leaf Extracts Ameliorate Reproductive Dysfunction in Mice Under Chronic Stress
Authors: Oh Nam Su , Kim Sae Hun , Joung Jae Yeon , Lim Whasun , Ham Jiyeon , Seo Yeon Jeong 
Published: January 2021

Abstract
The objective of this study was to investigate the effects of Lactobacillus gasseri 505 (505) and the synbiotic combination of 505 and Cudrania tricuspidata leaf extracts (CT) on the hypothalamic-pituitary-gonadal axis in mice during chronic stress. In our previous study, a synbiotic combination (Syn) of a fermented CT-supplemented milk with 505 exhibited good anti-inflammatory and hepatoprotective activities in mice. Therefore, we hypothesized that a Syn may exert some preventive effects in the male reproductive system when suffering from unpredictable chronic mild stress (UCMS). UCMS significantly decreased the serum levels of corticosterone, however, treatment with 505 and its Syn suppressed UCMS-induced decreases. Histopathological analysis of the testes showed that these organs experienced some damage during UCMS, but this was repaired following treatment with 505 or Syn. Similarly, the transcription levels of gonadotropin-releasing hormone (GnRH), GnRH receptor, and gonadotropins, moreover, testicular development (i.e., Adam5, Adam29, and Spam1) - and steroidogenesis (i.e., Lhr, Egfr, and StAR) -related genes were significantly downregulated by UCMS. These UCMS-induced changes were inhibited following the administration of 505 or Syn, which was confirmed by the results of in situ hybridization analysis. These results suggest that the administration of a Syn could attenuate the testicular dysfunctions induced by UCMS.
Embedding Supervised Exercise Training for Men on Androgen Deprivation Therapy Into Standard Prostate Cancer Care: A Feasibility and Acceptability Study
Authors: Reale Sophie , Turner Rebecca , Sutton Eileen , Steed Liz , Taylor Stephanie , Morrissey Dylan , Doherty Patrick , Greenfield Diana , Collinson Michelle , Hewison Jenny , Brown Janet , Ibeggazene Said , Mason Malcolm , Rosario Derek , Bourke Liam 
Published: January 2021

Abstract
Lifestyle interventions involving exercise training offset the adverse effects of androgen deprivation therapy in men with prostate cancer (PCa). Yet provision of integrated exercise pathways in cancer care is sparse. This study assessed the feasibility and acceptability of an embedded supervised exercise training intervention into standard PCa care in a single-arm, multicentre prospective cohort study. Feasibility included recruitment, retention, adherence, fidelity and safety. Acceptability of behaviourally informed healthcare and exercise professional training was assessed qualitatively. Despite the imposition of lockdown for the COVID-19 pandemic, referral rates into and adherence to, the intervention was high. Of the 45 men eligible for participation, 79% received the intervention. Patients completed a mean of 27 minutes of aerobic exercise per session (SD=3.48), at 77% heart rate maximum (92% of target dose), and 3 sets of 10 reps of 3 resistance exercises twice weekly for 12 weeks, without serious adverse event. The intervention was delivered by healthcare and exercise professionals with moderate to high fidelity and the intervention was deemed highly acceptable to patients. The impact of societal changes due to the pandemic on the delivery of this face-to-face intervention remain uncertain but positive impacts of embedding exercise provision into PCa care warrant long-term investigation.
Reconstructing Network Structures from Partial Measurements
Authors: Tyloo Melvyn , Delabays Robin , Jacquod Philippe 
Published: January 2021

Abstract
The dynamics of systems of interacting agents is determined by the structure of their coupling
network. The knowledge of the latter is therefore highly desirable, for instance to develop efficient
control schemes, to accurately predict the dynamics or to better understand inter-agent processes.
In many important and interesting situations, the network structure is not known, however, and
previous investigations have shown how it may be inferred from complete measurement time series,
on each and every agent. These methods implicitly presuppose that, even though the network is not
known, all its nodes are. A major shortcoming of theirs is that they cannot provide any reliable
information, not even on partial network structures, as soon as some agents are unobservable.
Here, we construct a novel method that determines network structures even when not all agents
are measurable. We establish analytically and illustrate numerically that velocity signal correlators
encode not only direct couplings, but also geodesic distances in the coupling network, within the
subset of measurable agents. When dynamical data are accessible for all agents, our method is
furthermore algorithmically more efficient than the traditional ones, because it does not rely on
matrix inversion.
Immunological Off-Target Effects of microRNA Control Sequences.
Authors: Al-Modawi Rua , Brinchmann Jan , Karlsen Tommy 
Published: January 2021

Abstract
Immunological off-target effects of RNA and RNAi therapy are a considerable challenge in research and the future of RNA-therapy. Here we investigated some of the hurdles we previously encountered when transfecting mircroRNA (miRNA) control sequences into chondrocytes in an inflammatory model simulating osteoarthritis (OA). We investigated different negative control sequences of different technologies; Pre-miR miRNA Precursor and mirVana from Thermo Fisher Scientific. We used RT-qPCR, western blot analysis and mass spectrometry to asses for the effects of the transfected control sequences.The data did not show a global immunological off-target effect, however a specific off-target effect on IL6 and IL8 was observed. IL6 and IL8 were both upregulated by the negative control from the Pre-miR miRNA Precursor technology (Pre-neg #1), and downregulated by the negative control from the mirVana technology (mirVana-neg). Moreover, the results suggested that the effect on IL6 and IL8 was dependent on both sequence and type of chemical modifications in addition to donor variation. We conclude that negative controls should be selected wisely, and suggest that scientists need to test several controls to ensure correct interpretation of data before drawing any conclusions.
Whole exome sequencing and gene expression analysis of canine osteosarcomas identify mutant TP53 and enriched immune pathways associated with longer survival
Authors: Das Sunetra , Idate Rupa , Regan Daniel , Fowles Jared , Lana Susan , Thamm Douglas , Gustafson Daniel , Duval Dawn 
Published: January 2021

Abstract
Osteosarcoma affects about 2.8% of dogs with cancer, with a one-year survival rate of approximately 45%. The purpose of this study was to characterize the mutation and expression profiles of canine osteosarcoma associated with outcome in samples from dogs treated by amputation and chemotherapy.
The number of somatic variants identified across 26 samples ranged from 145 to 2,697 with top recurrent mutations observed in TP53 (82% of the samples) and SETD2 (22%). Additionally, 47 cancer genes were identified with copy number variations in at least 58% of the samples. We observed transcriptional down-regulation of myogenesis genes and up-regulation of extracellular matrix genes in tumors compared to normal bone. Patients with longer disease-free intervals (DFI) showed increased transcript levels of anti-tumor immune response genes. Wild-type/NULL TP53 mutation status and high pre-treatment blood monocyte counts were associated with a shorter DFI. Immune cell infiltration was quantified via immunohistochemistry and gene expression profiling. CD3+ and MAC387+ myeloid cell quantifications were not significantly associated with outcome. Expression of immune related genes PDL-1, CD160 and ICOS were correlated with T-cell abundance.
Overall, the association of gene expression and mutation profiles to outcome provides insights into pathogenesis and therapeutic interventions in osteosarcoma patients.
Realising and Compressing Quantum Circuits With Quantum Reservoir Computing
Authors: Ghosh Sanjib , Krisnanda Tanjung , Paterek Tomasz , Liew Timothy 
Published: January 2021

Abstract
Quantum computers require precise control over parameters and careful engineering of the underlying physical system. In contrast, neural networks have evolved to tolerate imprecision and inhomogeneity. Here, using a reservoir computing architecture we show how a random network of quantum nodes can be used as a robust hardware for quantum computing. It induces quantum operations by optimising only a single layer of quantum nodes, a key advantage over the traditional neural networks where many layers of neurons have to be optimised. We demonstrate how a single network can induce different quantum gates, including a universal gate set. Moreover, we show that sequences of multiple quantum gates in quantum circuits can be compressed with a single operation, greatly reducing the operation time and complexity. As the key resource is a random network of nodes, with no specific topology or structure, this architecture is a hardware friendly alternative paradigm for quantum computation.
Global Health Effects of Future Atmospheric Mercury Emissions
Authors: Zhang Yanxu , Song Zhengcheng , Huang Shaojian , Zhang Peng , Peng Yiming , Wu Peipei , Gu Jing , Dutkiewicz Stephanie , Zhang Huanxin , Wu Shiliang , Wang Feiyue , Chen Long , Wang Shuxiao , Li Ping 
Published: January 2021

Abstract
Mercury (Hg) is a potent neurotoxin that poses health risks to the global population. Anthropogenic Hg emissions to the atmosphere are projected to decrease in the future due to enhanced policy efforts such as the Minamata Convention, a legally-binding international treaty entered into force in 2017. To project the health benefits of emission reduction requires considering both primary sources and recycling of previously deposited Hg from the land and ocean. Here we report the development of a comprehensive climate-atmosphere-land-ocean-ecosystem and exposure-risk model framework for Hg and its application to project the health effects of future atmospheric emissions. We find the projected Hg health risk changes nonlinearly with emission changes, and the most optimistic scenario (maximum feasible reduction, MFR) leads to Hg levels in the freshwater and marine biota half of the present-day levels. Our results show that the accumulated health effects associated with Hg exposure during 2010–2050 are $19 (range: 10–27) trillion (2020 USD) realized to 2050 (3% discount rate) for the current policy scenario. The MFR scenario is projected to have a health benefit of $2.4 trillion, while a business-as-usual scenario results in an additional $4.9 trillion health loss. Our results suggest a substantial increase in global human health cost if emission reduction actions are delayed. This comprehensive modeling approach provides a much-needed tool to help parties to evaluate the effectiveness of Hg emission controls as required by the Minamata Convention.
Regulation of Abnormal Expression of hsa_circRNA_0127523 on Proliferation, Migration and Invasion and miR-515-5p Expression in Oral Squamous Cell Carcinoma.
Authors: Wei Jianing , Wang Zekun , Gao Jiping , Liang Yuxiang , Xu Guoqiang , Wang Xiaotang , Xiao Lanfei , Yan Xiaoru , Song Guohua 
Published: January 2021

Abstract
Circular RNA (circRNA) play an important role in many biological processes of occurrence and development of cancers. In this research, we established an animal model by DMBA-induced buccal sac tissue and discovered the differential expression of circRNAs by the second-generation sequencing. Models were identified by HE staining and ultrastructural observation. We found total of 3485 circRNAs were differentially expressed which the top 8 different expression circRNAs in sequencing results were confirmed by qRT-PCR. GO and KEGG analyses showed that differently expressed circRNAs function and pathway. Moreover, the axis relationship of circRNA-miRNA was predicted by miRanda. Silencing hsa_circ_0127523 significantly suppressed the proliferation, migration and invasion abilities of oral squamous cell carcinoma (OSCC) cells by RNAi, CCK-8, transwell migration and invasion assays. Furthermore, bioinformatics databases suggested that hsa_circ_0127523 might function by sponging miR-515-5p to regulate the expression of TRIP13. It was subsequently identified that hsa_circ_0127523 may inhibit miR-515-5p expression and increase TRIP13 expression in the OSCC cells. In summary, the results of the present study revealed that OSCC tissues have abundant circRNAs and we firstly explore the role of the hsa_circ_0127523 in the behavior regulation of OSCC cells. Its demonstrating that hsa_circ_0127523 may be a potential biomarker and therapeutic target of OSCC.
SARS-CoV-2 protein encoded by ORF8 contains a histone mimic that disrupts chromatin regulation
Authors: Kee John , Thudium Samuel , Glastad Karl , Palozola Katherine , Zhang Zhen , Li Yize , Cesare Joseph , Truitt Rachel , Cardenas Fabian , Kotton Darrell , Alysandratos Konstantinos-Dionysios , Yang Wenli , Morrisey Edward , Garcia Benjamin , Weiss Susan , Berger Shelley , Korb Erica 
Published: January 2021

Abstract
SARS-CoV-2 emerged in China at the end of 2019 and caused the global pandemic of COVID-19, a disease with high morbidity and mortality. While our understanding of this novel virus is rapidly increasing, gaps remain in our understanding of how SARS-CoV-2 can effectively suppress host cell antiviral responses. Recent work on other viruses has demonstrated a novel mechanism through which viral proteins can mimic critical regions of human histone proteins. Histone proteins are responsible for governing genome accessibility and their precise regulation is critical for a cell’s ability to control transcription and respond to viral threats. Here, we show that the protein encoded by ORF8 (Orf8) in SARS-CoV-2 functions as a histone mimic of two critical histone 3 sites containing an ARKS motif. Orf8 expression in cells disrupts multiple critical histone post-translational modifications (PTMs) while Orf8 lacking this histone mimic motif does not. Orf8 binds to numerous histone-associated proteins and to DNA, and is itself acetylated within the histone mimic site. Importantly, SARS-CoV-2 infection of multiple susceptible cell types causes the same global changes of histone post-translational modifications that are disrupted by Orf8 expression; these include induced pluripotent stem cell-derived alveolar type 2 cells (iAT2) and cardiomyocytes (iCM) and postmortem patient lung tissue. These findings demonstrate a novel function for the poorly understood SARS-CoV-2 ORF8 encoded protein and a mechanism through which SARS-CoV-2 disrupts host cell epigenetic regulation. Notably, this work provides a potential mechanism for emerging findings from human patients indicating that ORF8 deletion results in less severe illness and describes a potentially druggable pathway that may contribute to the virulence of SARS-CoV-2.
Geothermal as resource for megacities
Authors: Vargas Carlos , Caracciolo Luca , Ball Philip 
Published: January 2021

Abstract
33 Megacities are distributed around the world, a number that will increase to 43 by 2030. Megacities are critical for the world’s economy, however, their management is particularly challenging in terms of transportation, water, waste, sanitation, security, electricity, and environmental impact. The increase of energy demand, in parallel to population growth and climate change, requires investment in sustainable energies. Geothermal energy – differently from solar, wind and hydroelectric is independent from weather conditions. A number of megacities around the world are located in areas with anomalous geothermal gradients, proximal to the margins of tectonic plates. This colocation makes geothermal an attractive resilient, baseload, low-carbon, energy source helping Megacities reduce their environmental impact. In this paper, we discuss the advantages of using geothermal energy, leading the study for the city of Bogotá, and applying the same workflow for Los Angeles and Jakarta. We aim to provoke the inclusion of geothermal in energy policies of other megacities around the world.
CRISPRi mediated Down regulation of SFPQ Gene Expression in Human induced Pluripotent Stem Cells Results in Massive Cell Death
Authors: Lam Navya , Yamanaka Shinya , Perli Samuel 
Published: January 2021

Abstract
CRISPR-Cas9 is widely used for targeted genome editing for a wide range of organisms. In this study, we used CRISPR interference (CRISPRi) which employs a catalytically inactive version of Cas9 (known as Dead Cas9 or dCas9) fused to KRAB a chromatin modifier. Similar to Cas9, the dCas9 protein forms a complex along with single guide RNA (sgRNA) and binds desired DNA sequences in the presence of a protospacer adjacent motif (PAM). However, unlike Cas9, dCas9 doesn’t cleave the DNA sequence but can repress gene expression when fused with KRAB. The role of paraspeckles in human cell biology is relatively unknown. In this study, we used CRISPRi to investigate the role of splicing factor proline and glutamine rich (SFPQ), also known as PSF (PTB-associated splicing factor), which is a conserved and core component of paraspeckles. We designed and constructed six different sgRNAs to target different locations of the SFPQ gene in Human induced Pluripotent Stem Cells (HiPSCs). The most effective sgRNA (sgRNA #5) knocked down the expression of SFPQ up to > 99%. We also observed that the knockdown of SFPQ exhibits severe cell-death phenotype in HiPSCs. This finding suggests that CRISPRi based SFPQ repression can modulate stem cell proliferation and maintenance. This study also suggests that SFPQ could play a vital role in proliferating cells such as cancer cells. Most importantly, these results are significant because in mice, knocking out another core component of paraspeckles results in no apparent phenotype despite the complete loss of paraspeckles. Given that traditional drug testing approaches rely on animal models, it is consequential to consider that human cell biology is more distinct than previously imagined. This study provides a new insight for role and function of SFPQ in iPSCs.
Cationic Nanostructures for the Treatment of Inflammatory Bone Loss
Authors: Huang Hanyao , Pan Weiyi , Wang Yi-Fan , Kim Hyesung , Shao Dan , Huang Baoding , Ho Tzu-Chieh , Lao Yeh-Hsing , Quek Chai Hoon , Shi Jiayu , Shi Bing , Zhang Sheng-Min , Zhao Lei , Leong Kam W. 
Published: January 2021

Abstract
Periodontitis is a common type of inflammatory bone loss and is a risk factor for systemic diseases. The pathogenesis of periodontitis relies on inflammatory dysregulation, which represents a target for new therapeutic strategies to treat periodontitis. Here we demonstrate that cell-free DNA (cfDNA) is correlated with periodontitis in patient samples, and that cfDNA/TLR9 interactions participate in the immune response of periodontitis. We then tested the hypothesis that removing cfDNA would benefit periodontitis treatment. To create nucleic acid-binding nanoparticles (NABNs) specific for periodontitis, we coated bone-mimicking selenium-doped hydroxyapatite nanoparticles with cationic polyamidoamine dendrimers (PAMAM-G3), and compared the activities of these NABNs with those of soluble PAMAM-G3 polymers. Both NABNs and PAMAM-G3 inhibited periodontitis-related inflammation in vitro by scavenging cfDNA, and alleviated inflammatory bone loss in a mouse model of ligature-induced periodontitis. Both cfDNA scavengers also regulated the mononuclear phagocyte system in a periodontitis environment, promoting the M1 over the M2 macrophage phenotype. However, NABNs showed greater therapeutic effects than PAMAM-G3 in terms of scavenging and reducing inflammation and bone loss in vivo. Our findings demonstrate the importance of cfDNA in periodontitis and the potential for using cfDNA-scavenging and hydroxyapatite-based NABNs to ameliorate inflammation and bone loss in periodontitis.