bluuebunny/crossref_metadata_2025_split huggingface dataset:
SIRT2 promotes the viability, invasion and metastasis of osteosarcoma cells by inhibiting the degradation of Snail
Authors: Tian Yonghao , Liu Ruijuan , Hou Xiaoyan , Gao Zhixiao , Liu Xinyu , Zhang Weifang 
Published: November 2022

AbstractOsteosarcomas (OS) are highly metastatic and usually lead to poor outcomes. Epithelial-mesenchymal transition (EMT) is reported to be a critical event in metastasis. SIRT2 exerts dual functions in many different tumors. However, the underlying molecular mechanisms of SIRT2 in osteosarcoma cell metastasis and the question of whether SIRT2 regulates EMT have not been fully explored. In this study, we confirmed that SIRT2 was highly-expressed in human osteosarcoma MG63 and Saos-2 cell lines. The viability, migration and invasion of osteosarcoma cells were inhibited by knockdown of SIRT2 and were enhanced by overexpression of SIRT2. Moreover, SIRT2 positively regulated EMT and upregulated the protein levels of the mesenchymal markers N-cadherin and Vimentin and the levels of MMP2 and MMP9. A xenograft mouse model showed that SIRT2 knockdown in osteosarcoma cells led to reduced tumor growth, decreased expression of mesenchymal markers and impaired lung and liver metastasis in vivo. Furthermore, we showed that SIRT2 interacted with and upregulated the protein level of the EMT-associated transcription factor Snail. SIRT2 inhibited Snail degradation via its deacetylase activity. Knockdown of Snail abrogated the promoting effects of SIRT2 on migration and invasion of osteosarcoma cells. In conclusion, SIRT2 plays a crucial role in osteosarcoma metastasis by inhibiting Snail degradation and may serve as a novel therapeutic target to manage osteosarcoma.
Specialist multidisciplinary input maximises rare disease diagnoses from whole genome sequencing
Authors: Macken William L. , Falabella Micol , McKittrick Caroline , Pizzamiglio Chiara , Ellmers Rebecca , Eggleton Kelly , Woodward Cathy E. , Patel Yogen , Labrum Robyn ,   Genomics England Research Consortium, Ambrose J. C. , Arumugam P. , Bevers R. , Bleda M. , Boardman-Pretty F. , Boustred C. R. , Brittain H. , Brown M. A. , Caulfield M. J. , Chan G. C. , Giess A. , Griffin J. N. , Hamblin A. , Henderson S. , Hubbard T. J. P. , Jackson R. , Jones L. J. , Kasperaviciute D. , Kayikci M. , Kousathanas A. , Lahnstein L. , Lakey A. , Leigh S. E. A. , Leong I. U. S. , Lopez F. J. , Maleady-Crowe F. , McEntagart M. , Minneci F. , Mitchell J. , Moutsianas L. , Mueller M. , Murugaesu N. , Need A. C. , O’Donovan P. , Odhams C. A. , Patch C. , Perez-Gil D. , Pereira M. B. , Pullinger J. , Rahim T. , Rendon A. , Rogers T. , Savage K. , Sawant K. , Scott R. H. , Siddiq A. , Sieghart A. , Smith S. C. , Sosinsky A. , Stuckey A. , Tanguy M. , Taylor Tavares A. L. , Thomas E. R. A. , Thompson S. R. , Tucci A. , Welland M. J. , Williams E. , Witkowska K. , Wood S. M. , Zarowiecki M. , Phadke Rahul , Reilly Mary M. , DeVile Catherine , Sarkozy Anna , Footitt Emma , Davison James , Rahman Shamima , Houlden Henry , Bugiardini Enrico , Quinlivan Rosaline , Hanna Michael G. , Vandrovcova Jana , Pitceathly Robert D. S. 
Published: November 2022

AbstractDiagnostic whole genome sequencing (WGS) is increasingly used in rare diseases. However, standard, semi-automated WGS analysis may overlook diagnoses in complex disorders. Here, we show that specialist multidisciplinary analysis of WGS, following an initial ‘no primary findings’ (NPF) report, improves diagnostic rates and alters management. We undertook WGS in 102 adults with diagnostically challenging primary mitochondrial disease phenotypes. NPF cases were reviewed by a genomic medicine team, thus enabling bespoke informatic approaches, co-ordinated phenotypic validation, and functional work. We enhanced the diagnostic rate from 16.7% to 31.4%, with management implications for all new diagnoses, and detected strong candidate disease-causing variants in a further 3.9% of patients. This approach presents a standardised model of care that supports mainstream clinicians and enhances diagnostic equity for complex disorders, thereby facilitating access to the potential benefits of genomic healthcare. This research was made possible through access to the data and findings generated by the 100,000 Genomes Project: http://www.genomicsengland.co.uk.
DNA barcoding reveals ongoing immunoediting of clonal cancer populations during metastatic progression and immunotherapy response
Authors: Baldwin Louise A. , Bartonicek Nenad , Yang Jessica , Wu Sunny Z. , Deng Niantao , Roden Daniel L. , Chan Chia-Ling , Al-Eryani Ghamdan , Zanker Damien J. , Parker Belinda S. , Swarbrick Alexander , Junankar Simon 
Published: November 2022

AbstractCancers evade the immune system through the process of cancer immunoediting. While immune checkpoint inhibitors are effective for reactivating tumour immunity in some cancer types, many other solid cancers, including breast cancer, remain largely non-responsive. Understanding how non-responsive cancers evade immunity and whether this occurs at the clonal level will improve immunotherapeutic design. Here we use DNA barcoding to track murine mammary cancer cell clones during immunoediting and determine clonal transcriptional profiles that allow immune evasion following anti-PD1 plus anti-CTLA4 immunotherapy. Clonal diversity is significantly restricted by immunotherapy treatment in both primary tumours and metastases, demonstrating selection for pre-existing breast cancer cell populations and ongoing immunoediting during metastasis and treatment. Immunotherapy resistant clones express a common gene signature associated with poor survival of basal-like breast cancer patient cohorts. At least one of these genes has an existing small molecule that can potentially be used to improve immunotherapy response.
Differences in water and vapor transport through angstrom-scale pores in atomically thin membranes
Authors: Cheng Peifu , Fornasiero Francesco , Jue Melinda L. , Ko Wonhee , Li An-Ping , Idrobo Juan Carlos , Boutilier Michael S. H. , Kidambi Piran R. 
Published: November 2022

AbstractThe transport of water through nanoscale capillaries/pores plays a prominent role in biology, ionic/molecular separations, water treatment and protective applications. However, the mechanisms of water and vapor transport through nanoscale confinements remain to be fully understood. Angstrom-scale pores (~2.8–6.6 Å) introduced into the atomically thin graphene lattice represent ideal model systems to probe water transport at the molecular-length scale with short pores (aspect ratio ~1–1.9) i.e., pore diameters approach the pore length (~3.4 Å) at the theoretical limit of material thickness. Here, we report on orders of magnitude differences (~80×) between transport of water vapor (~44.2–52.4 g m−2 day−1 Pa−1) and liquid water (0.6–2 g m−2 day−1 Pa−1) through nanopores (~2.8–6.6 Å in diameter) in monolayer graphene and rationalize this difference via a flow resistance model in which liquid water permeation occurs near the continuum regime whereas water vapor transport occurs in the free molecular flow regime. We demonstrate centimeter-scale atomically thin graphene membranes with up to an order of magnitude higher water vapor transport rate (~5.4–6.1 × 104 g m−2 day−1) than most commercially available ultra-breathable protective materials while effectively blocking even sub-nanometer (>0.66 nm) model ions/molecules.
Circuit-guided population acclimation of a synthetic microbial consortium for improved biochemical production
Authors: Kang Chae Won , Lim Hyun Gyu , Won Jaehyuk , Cha Sanghak , Shin Giyoung , Yang Jae-Seong , Sung Jaeyoung , Jung Gyoo Yeol 
Published: November 2022

AbstractMicrobial consortia have been considered potential platforms for bioprocessing applications. However, the complexity in process control owing to the use of multiple strains necessitates the use of an efficient population control strategy. Herein, we report circuit-guided synthetic acclimation as a strategy to improve biochemical production by a microbial consortium. We designed a consortium comprising alginate-utilizing Vibrio sp. dhg and 3-hydroxypropionic acid (3-HP)-producing Escherichia coli strains for the direct conversion of alginate to 3-HP. We introduced a genetic circuit, named “Population guider”, in the E. coli strain, which degrades ampicillin only when 3-HP is produced. In the presence of ampicillin as a selection pressure, the consortium was successfully acclimated for increased 3-HP production by 4.3-fold compared to that by a simple co-culturing consortium during a 48-h fermentation. We believe this concept is a useful strategy for the development of robust consortium-based bioprocesses.
Hippocampal astrocytes modulate anxiety-like behavior
Authors: Cho Woo-Hyun , Noh Kyungchul , Lee Byung Hun , Barcelon Ellane , Jun Sang Beom , Park Hye Yoon , Lee Sung Joong 
Published: November 2022

AbstractAstrocytes can affect animal behavior by regulating tripartite synaptic transmission, yet their influence on affective behavior remains largely unclear. Here we showed that hippocampal astrocyte calcium activity reflects mouse affective state during virtual elevated plus maze test using two-photon calcium imaging in vivo. Furthermore, optogenetic hippocampal astrocyte activation elevating intracellular calcium induced anxiolytic behaviors in astrocyte-specific channelrhodopsin 2 (ChR2) transgenic mice (hGFAP-ChR2 mice). As underlying mechanisms, we found ATP released from the activated hippocampal astrocytes increased excitatory synaptic transmission in dentate gyrus (DG) granule cells, which exerted anxiolytic effects. Our data uncover a role of hippocampal astrocytes in modulating mice anxiety-like behaviors by regulating ATP-mediated synaptic homeostasis in hippocampal DG granule cells. Thus, manipulating hippocampal astrocytes activity can be a therapeutic strategy to treat anxiety.
Structural basis of organic cation transporter-3 inhibition
Authors: Khanppnavar Basavraj , Maier Julian , Herborg Freja , Gradisch Ralph , Lazzarin Erika , Luethi Dino , Yang Jae-Won , Qi Chao , Holy Marion , Jäntsch Kathrin , Kudlacek Oliver , Schicker Klaus , Werge Thomas , Gether Ulrik , Stockner Thomas , Korkhov Volodymyr M. , Sitte Harald H. 
Published: November 2022

AbstractOrganic cation transporters (OCTs) facilitate the translocation of catecholamines, drugs and xenobiotics across the plasma membrane in various tissues throughout the human body. OCT3 plays a key role in low-affinity, high-capacity uptake of monoamines in most tissues including heart, brain and liver. Its deregulation plays a role in diseases. Despite its importance, the structural basis of OCT3 function and its inhibition has remained enigmatic. Here we describe the cryo-EM structure of human OCT3 at 3.2 Å resolution. Structures of OCT3 bound to two inhibitors, corticosterone and decynium-22, define the ligand binding pocket and reveal common features of major facilitator transporter inhibitors. In addition, we relate the functional characteristics of an extensive collection of previously uncharacterized human genetic variants to structural features, thereby providing a basis for understanding the impact of OCT3 polymorphisms.
Bayesian deep learning for error estimation in the analysis of anomalous diffusion
Authors: Seckler Henrik , Metzler Ralf 
Published: November 2022

AbstractModern single-particle-tracking techniques produce extensive time-series of diffusive motion in a wide variety of systems, from single-molecule motion in living-cells to movement ecology. The quest is to decipher the physical mechanisms encoded in the data and thus to better understand the probed systems. We here augment recently proposed machine-learning techniques for decoding anomalous-diffusion data to include an uncertainty estimate in addition to the predicted output. To avoid the Black-Box-Problem a Bayesian-Deep-Learning technique named Stochastic-Weight-Averaging-Gaussian is used to train models for both the classification of the diffusion model and the regression of the anomalous diffusion exponent of single-particle-trajectories. Evaluating their performance, we find that these models can achieve a well-calibrated error estimate while maintaining high prediction accuracies. In the analysis of the output uncertainty predictions we relate these to properties of the underlying diffusion models, thus providing insights into the learning process of the machine and the relevance of the output.
Gate-tunable Veselago interference in a bipolar graphene microcavity
Authors: Zhang Xi , Ren Wei , Bell Elliot , Zhu Ziyan , Tsai Kan-Ting , Luo Yujie , Watanabe Kenji , Taniguchi Takashi , Kaxiras Efthimios , Luskin Mitchell , Wang Ke 
Published: November 2022

AbstractThe relativistic charge carriers in monolayer graphene can be manipulated in manners akin to conventional optics. Klein tunneling and Veselago lensing have been previously demonstrated in ballistic graphene pn-junction devices, but collimation and focusing efficiency remains relatively low, preventing realization of advanced quantum devices and controlled quantum interference. Here, we present a graphene microcavity defined by carefully-engineered local strain and electrostatic fields. Electrons are manipulated to form an interference path inside the cavity at zero magnetic field via consecutive Veselago refractions. The observation of unique Veselago interference peaks via transport measurement and their magnetic field dependence agrees with the theoretical expectation. We further utilize Veselago interference to demonstrate localization of uncollimated electrons and thus improvement in collimation efficiency. Our work sheds new light on relativistic single-particle physics and provide a new device concept toward next-generation quantum devices based on manipulation of ballistic electron trajectory.
Structure of the IscB–ωRNA ribonucleoprotein complex, the likely ancestor of CRISPR-Cas9
Authors: Kato Kazuki , Okazaki Sae , Kannan Soumya , Altae-Tran Han , Esra Demircioglu F. , Isayama Yukari , Ishikawa Junichiro , Fukuda Masahiro , Macrae Rhiannon K. , Nishizawa Tomohiro , Makarova Kira S. , Koonin Eugene V. , Zhang Feng , Nishimasu Hiroshi 
Published: November 2022

AbstractTransposon-encoded IscB family proteins are RNA-guided nucleases in the OMEGA (obligate mobile element-guided activity) system, and likely ancestors of the RNA-guided nuclease Cas9 in the type II CRISPR-Cas adaptive immune system. IscB associates with its cognate ωRNA to form a ribonucleoprotein complex that cleaves double-stranded DNA targets complementary to an ωRNA guide segment. Although IscB shares the RuvC and HNH endonuclease domains with Cas9, it is much smaller than Cas9, mainly due to the lack of the α-helical nucleic-acid recognition lobe. Here, we report the cryo-electron microscopy structure of an IscB protein from the human gut metagenome (OgeuIscB) in complex with its cognate ωRNA and a target DNA, at 2.6-Å resolution. This high-resolution structure reveals the detailed architecture of the IscB–ωRNA ribonucleoprotein complex, and shows how the small IscB protein assembles with the ωRNA and mediates RNA-guided DNA cleavage. The large ωRNA scaffold structurally and functionally compensates for the recognition lobe of Cas9, and participates in the recognition of the guide RNA–target DNA heteroduplex. These findings provide insights into the mechanism of the programmable DNA cleavage by the IscB–ωRNA complex and the evolution of the type II CRISPR-Cas9 effector complexes.
Regulome-based characterization of drug activity across the human diseasome
Authors: Iwata Michio , Kosai Keisuke , Ono Yuya , Oki Shinya , Mimori Koshi , Yamanishi Yoshihiro 
Published: November 2022

AbstractDrugs are expected to recover the cell system away from the impaired state to normalcy through disease treatment. However, the understanding of gene regulatory machinery underlying drug activity or disease pathogenesis is far from complete. Here, we perform large-scale regulome analysis for various diseases in terms of gene regulatory machinery. Transcriptome signatures were converted into regulome signatures of transcription factors by integrating publicly available ChIP-seq data. Regulome-based correlations between diseases and their approved drugs were much clearer than the transcriptome-based correlations. For example, an inverse correlation was observed for cancers, whereas a positive correlation was observed for immune system diseases. After demonstrating the usefulness of the regulome-based drug discovery method in terms of accuracy and applicability, we predicted new drugs for nonsmall cell lung cancer and validated the anticancer activity in vitro. The proposed method is useful for understanding disease–disease relationships and drug discovery.
Predicting vaccine effectiveness against invasive pneumococcal disease in children using immunogenicity data
Authors: Ryman Josiah , Weaver Jessica , Hu Tianyan , Weinberger Daniel M. , Yee Ka Lai , Sachs Jeffrey R. 
Published: November 2022

AbstractThe strength of the immune response, as measured by antibody concentrations, varies between pneumococcal conjugate vaccines (PCVs). Linking immunogenicity and effectiveness is necessary to assess whether changes in immune response from currently recommended PCVs to next-generation vaccines could impact effectiveness. Simulated reverse cumulative distribution curves were generated using published serotype-specific IgG concentrations with placebo or PCV7. This was combined with the published estimates of serotype-specific vaccine effectiveness of PCV7 against invasive pneumococcal disease to estimate the protective antibody concentration for each serotype in PCV7. Then, based on the published serotype-specific IgG concentrations in PCV13 recipients, reverse cumulative distribution curves were generated for the serotypes shared between PCV13 and PCV7. These estimated protective antibody concentration values were then used to predict the vaccine effectiveness of PCV13. The results were compared to published aggregate values for vaccine effectiveness. The aggregate median predicted vaccine effectiveness values were similar to previously reported observed values for the United Kingdom (93% versus 90%), Australia (71% versus 70%), and Germany (91% versus 90%). These results demonstrate that IgG concentrations of next-generation PCVs can be used to generate reliable estimates of vaccine effectiveness for serotypes shared with established PCVs.
Photoswitchable gating of non-equilibrium enzymatic feedback in chemically communicating polymersome nanoreactors
Authors: Rifaie-Graham Omar , Yeow Jonathan , Najer Adrian , Wang Richard , Sun Rujie , Zhou Kun , Dell Tristan N. , Adrianus Christopher , Thanapongpibul Chalaisorn , Chami Mohamed , Mann Stephen , de Alaniz Javier Read , Stevens Molly M. 
Published: November 2022

AbstractThe circadian rhythm generates out-of-equilibrium metabolite oscillations that are controlled by feedback loops under light/dark cycles. Here we describe a non-equilibrium nanosystem comprising a binary population of enzyme-containing polymersomes capable of light-gated chemical communication, controllable feedback and coupling to macroscopic oscillations. The populations consist of esterase-containing polymersomes functionalized with photo-responsive donor–acceptor Stenhouse adducts (DASA) and light-insensitive semipermeable urease-loaded polymersomes. The DASA–polymersome membrane becomes permeable under green light, switching on esterase activity and decreasing the pH, which in turn initiates the production of alkali in the urease-containing population. A pH-sensitive pigment that absorbs green light when protonated provides a negative feedback loop for deactivating the DASA–polymersomes. Simultaneously, increased alkali production deprotonates the pigment, reactivating esterase activity by opening the membrane gate. We utilize light-mediated fluctuations of pH to perform non-equilibrium communication between the nanoreactors and use the feedback loops to induce work as chemomechanical swelling/deswelling oscillations in a crosslinked hydrogel. We envision possible applications in artificial organelles, protocells and soft robotics.
On-surface synthesis of disilabenzene-bridged covalent organic frameworks
Authors: Sun Kewei , Silveira Orlando J. , Ma Yujing , Hasegawa Yuri , Matsumoto Michio , Kera Satoshi , Krejčí Ondřej , Foster Adam S. , Kawai Shigeki 
Published: November 2022

AbstractSubstituting carbon with silicon in organic molecules and materials has long been an attractive way to modify their electronic structure and properties. Silicon-doped graphene-based materials are known to exhibit exotic properties, yet conjugated organic materials with atomically precise Si substitution have remained difficult to prepare. Here we present the on-surface synthesis of one- and two-dimensional covalent organic frameworks whose backbones contain 1,4-disilabenzene (C4Si2) linkers. Silicon atoms were first deposited on a Au(111) surface, forming a AuSix film on annealing. The subsequent deposition and annealing of a bromo-substituted polyaromatic hydrocarbon precursor (triphenylene or pyrene) on this surface led to the formation of the C4Si2-bridged networks, which were characterized by a combination of high-resolution scanning tunnelling microscopy and photoelectron spectroscopy supported by density functional theory calculations. Each Si in a hexagonal C4Si2 ring was found to be covalently linked to one terminal Br atom. For the linear structure obtained with the pyrene-based precursor, the C4Si2 rings were converted into C4Si pentagonal siloles by further annealing.
Cellpose 2.0: how to train your own model
Authors: Pachitariu Marius , Stringer Carsen 
Published: November 2022

AbstractPretrained neural network models for biological segmentation can provide good out-of-the-box results for many image types. However, such models do not allow users to adapt the segmentation style to their specific needs and can perform suboptimally for test images that are very different from the training images. Here we introduce Cellpose 2.0, a new package that includes an ensemble of diverse pretrained models as well as a human-in-the-loop pipeline for rapid prototyping of new custom models. We show that models pretrained on the Cellpose dataset can be fine-tuned with only 500–1,000 user-annotated regions of interest (ROI) to perform nearly as well as models trained on entire datasets with up to 200,000 ROI. A human-in-the-loop approach further reduced the required user annotation to 100–200 ROI, while maintaining high-quality segmentations. We provide software tools such as an annotation graphical user interface, a model zoo and a human-in-the-loop pipeline to facilitate the adoption of Cellpose 2.0.