IF 64.8 1区综合性期刊

Nature Pub Date : 2024-11-20 DOI: 10.1038/s41586-024-08208-z

Marc Robin, Elodie Mouloungui, Gabriel Castillo Dali, Yan Wang, Jean-Louis Saffar, Graciela Pavon-Djavid, Thibaut Divoux, Sébastien Manneville, Luc Behr, Delphine Cardi, Laurence Choudat, Marie-Madeleine Giraud-Guille, Anne Meddahi-Pellé, Fannie Baudimont, Marie-Laure Colombier, Nadine Nassif

{"title":"Mineralized collagen plywood contributes to bone autograft performance","authors":"Marc Robin, Elodie Mouloungui, Gabriel Castillo Dali, Yan Wang, Jean-Louis Saffar, Graciela Pavon-Djavid, Thibaut Divoux, Sébastien Manneville, Luc Behr, Delphine Cardi, Laurence Choudat, Marie-Madeleine Giraud-Guille, Anne Meddahi-Pellé, Fannie Baudimont, Marie-Laure Colombier, Nadine Nassif","doi":"10.1038/s41586-024-08208-z","DOIUrl":"https://doi.org/10.1038/s41586-024-08208-z","url":null,"abstract":"Autologous bone (AB) is the gold standard for bone-replacement surgeries1, despite its limited availability and the need for an extra surgical site. Traditionally, competitive biomaterials for bone repair have focused on mimicking the mineral aspect of bone, as evidenced by the widespread clinical use of bioactive ceramics2. However, AB also exhibits hierarchical organic structures that might substantially affect bone regeneration. Here, using a range of cell-free biomimetic-collagen-based materials in murine and ovine bone-defect models, we demonstrate that a hierarchical hybrid microstructure—specifically, the twisted plywood pattern of collagen and its association with poorly crystallized bioapatite—favourably influences bone regeneration. Our study shows that the most structurally biomimetic material has the potential to stimulate bone growth, highlighting the pivotal role of physicochemical properties in supporting bone formation and offering promising prospects as a competitive bone-graft material.","PeriodicalId":18787,"journal":{"name":"Nature","volume":"14 1","pages":""},"PeriodicalIF":64.8,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142673857","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Combining quantum processors with real-time classical communication 量子处理器与实时经典通信的结合

IF 64.8 1区综合性期刊

Nature Pub Date : 2024-11-20 DOI: 10.1038/s41586-024-08178-2

Almudena Carrera Vazquez, Caroline Tornow, Diego Ristè, Stefan Woerner, Maika Takita, Daniel J. Egger

{"title":"Combining quantum processors with real-time classical communication","authors":"Almudena Carrera Vazquez, Caroline Tornow, Diego Ristè, Stefan Woerner, Maika Takita, Daniel J. Egger","doi":"10.1038/s41586-024-08178-2","DOIUrl":"https://doi.org/10.1038/s41586-024-08178-2","url":null,"abstract":"Quantum computers process information with the laws of quantum mechanics. Current quantum hardware is noisy, can only store information for a short time and is limited to a few quantum bits, that is, qubits, typically arranged in a planar connectivity1. However, many applications of quantum computing require more connectivity than the planar lattice offered by the hardware on more qubits than is available on a single quantum processing unit (QPU). The community hopes to tackle these limitations by connecting QPUs using classical communication, which has not yet been proven experimentally. Here we experimentally realize error-mitigated dynamic circuits and circuit cutting to create quantum states requiring periodic connectivity using up to 142 qubits spanning two QPUs with 127 qubits each connected in real time with a classical link. In a dynamic circuit, quantum gates can be classically controlled by the outcomes of mid-circuit measurements within run-time, that is, within a fraction of the coherence time of the qubits. Our real-time classical link enables us to apply a quantum gate on one QPU conditioned on the outcome of a measurement on another QPU. Furthermore, the error-mitigated control flow enhances qubit connectivity and the instruction set of the hardware thus increasing the versatility of our quantum computers. Our work demonstrates that we can use several quantum processors as one with error-mitigated dynamic circuits enabled by a real-time classical link.","PeriodicalId":18787,"journal":{"name":"Nature","volume":"99 1","pages":""},"PeriodicalIF":64.8,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142673858","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Half of the top 20 science cities are now in China — and regional city growth is the key 排名前 20 位的科学城有一半在中国--区域城市的发展是关键所在

IF 64.8 1区综合性期刊

Nature Pub Date : 2024-11-20 DOI: 10.1038/d41586-024-03521-z

引用次数: 0

Ferocity of Atlantic hurricanes surges as the ocean warms 随着海洋变暖，大西洋飓风的威力不断增强

IF 64.8 1区综合性期刊

Nature Pub Date : 2024-11-20 DOI: 10.1038/d41586-024-03783-7

引用次数: 0

Human HDAC6 senses valine abundancy to regulate DNA damage 人类 HDAC6 感知缬氨酸丰度以调控 DNA 损伤

IF 64.8 1区综合性期刊

Nature Pub Date : 2024-11-20 DOI: 10.1038/s41586-024-08248-5

Jiali Jin, Tong Meng, Yuanyuan Yu, Shuheng Wu, Chen-Chen Jiao, Sihui Song, Ya-Xu Li, Yu Zhang, Yuan-Yuan Zhao, Xinran Li, Zixin Wang, Yu-Fan Liu, Runzhi Huang, Jieling Qin, Yihua Chen, Hao Cao, Xiao Tan, Xin Ge, Cong Jiang, Jianhuang Xue, Jian Yuan, Dianqing Wu, Wei Wu, Ci-Zhong Jiang, Ping Wang

{"title":"Human HDAC6 senses valine abundancy to regulate DNA damage","authors":"Jiali Jin, Tong Meng, Yuanyuan Yu, Shuheng Wu, Chen-Chen Jiao, Sihui Song, Ya-Xu Li, Yu Zhang, Yuan-Yuan Zhao, Xinran Li, Zixin Wang, Yu-Fan Liu, Runzhi Huang, Jieling Qin, Yihua Chen, Hao Cao, Xiao Tan, Xin Ge, Cong Jiang, Jianhuang Xue, Jian Yuan, Dianqing Wu, Wei Wu, Ci-Zhong Jiang, Ping Wang","doi":"10.1038/s41586-024-08248-5","DOIUrl":"https://doi.org/10.1038/s41586-024-08248-5","url":null,"abstract":"As an essential branched amino acid, valine is pivotal for protein synthesis, neurological behaviour, haematopoiesis and leukaemia progression1,2,3. However, the mechanism by which cellular valine abundancy is sensed for subsequent cellular functions remains undefined. Here we identify that human histone deacetylase 6 (HDAC6) serves as a valine sensor by directly binding valine through a primate-specific SE14 repeat domain. The nucleus and cytoplasm shuttling of human, but not mouse, HDAC6 is tightly controlled by the intracellular levels of valine. Valine deprivation leads to HDAC6 retention in the nucleus and induces DNA damage. Mechanistically, nuclear-localized HDAC6 binds and deacetylates ten-eleven translocation 2 (TET2) to initiate active DNA demethylation, which promotes DNA damage through thymine DNA glycosylase-driven excision. Dietary valine restriction inhibits tumour growth in xenograft and patient-derived xenograft models, and enhances the therapeutic efficacy of PARP inhibitors. Collectively, our study identifies human HDAC6 as a valine sensor that mediates active DNA demethylation and DNA damage in response to valine deprivation, and highlights the potential of dietary valine restriction for cancer treatment.","PeriodicalId":18787,"journal":{"name":"Nature","volume":"73 1","pages":""},"PeriodicalIF":64.8,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142673850","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A cell atlas foundation model for scalable search of similar human cells 可扩展搜索相似人类细胞的细胞图谱基础模型

IF 64.8 1区综合性期刊

Nature Pub Date : 2024-11-20 DOI: 10.1038/s41586-024-08411-y

Graham Heimberg, Tony Kuo, Daryle J. DePianto, Omar Salem, Tobias Heigl, Nathaniel Diamant, Gabriele Scalia, Tommaso Biancalani, Shannon J. Turley, Jason R. Rock, Héctor Corrada Bravo, Josh Kaminker, Jason A. Vander Heiden, Aviv Regev

{"title":"A cell atlas foundation model for scalable search of similar human cells","authors":"Graham Heimberg, Tony Kuo, Daryle J. DePianto, Omar Salem, Tobias Heigl, Nathaniel Diamant, Gabriele Scalia, Tommaso Biancalani, Shannon J. Turley, Jason R. Rock, Héctor Corrada Bravo, Josh Kaminker, Jason A. Vander Heiden, Aviv Regev","doi":"10.1038/s41586-024-08411-y","DOIUrl":"https://doi.org/10.1038/s41586-024-08411-y","url":null,"abstract":"Single-cell RNA-seq (scRNA-seq) has profiled hundreds of millions of human cells across organs, diseases, development, and perturbations to date. Mining these growing atlases could reveal cell-disease associations, discover cell states in unexpected tissue contexts, and relate in vivo biology to in vitro models. These require a common measure of cell similarity across the body and an efficient way to search. Here, we develop SCimilarity, a metric learning framework to learn a unified and interpretable representation that enables rapid queries of tens of millions of cell profiles from diverse studies for cells that are transcriptionally similar to an input cell profile or state. We use SCimilarity to query a 23.4 million cell atlas of 412 scRNA-seq studies for macrophage and fibroblast profiles from interstitial lung disease1 and reveal similar cell profiles across other fibrotic diseases and tissues. The top scoring in vitro hit for the macrophage query was a 3D hydrogel system2, which we experimentally demonstrated reproduces this cell state. SCimilarity serves as a foundation model for single-cell profiles that enables researchers to query for similar cellular states across the human body, providing a powerful tool for generating biological insights from the Human Cell Atlas.","PeriodicalId":18787,"journal":{"name":"Nature","volume":"19 1","pages":""},"PeriodicalIF":64.8,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142678295","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Liver X receptor unlinks intestinal regeneration and tumorigenesis 肝 X 受体将肠道再生与肿瘤发生联系在一起

IF 64.8 1区综合性期刊

Nature Pub Date : 2024-11-20 DOI: 10.1038/s41586-024-08247-6

Srustidhar Das, S. Martina Parigi, Xinxin Luo, Jennifer Fransson, Bianca C. Kern, Ali Okhovat, Oscar E. Diaz, Chiara Sorini, Paulo Czarnewski, Anna T. Webb, Rodrigo A. Morales, Sacha Lebon, Gustavo Monasterio, Francisca Castillo, Kumar P. Tripathi, Ning He, Penelope Pelczar, Nicola Schaltenberg, Marjorie De la Fuente, Francisco López-Köstner, Susanne Nylén, Hjalte List Larsen, Raoul Kuiper, Per Antonson, Marcela A. Hermoso, Samuel Huber, Moshe Biton, Sandra Scharaw, Jan-Åke Gustafsson, Pekka Katajisto, Eduardo J. Villablanca

{"title":"Liver X receptor unlinks intestinal regeneration and tumorigenesis","authors":"Srustidhar Das, S. Martina Parigi, Xinxin Luo, Jennifer Fransson, Bianca C. Kern, Ali Okhovat, Oscar E. Diaz, Chiara Sorini, Paulo Czarnewski, Anna T. Webb, Rodrigo A. Morales, Sacha Lebon, Gustavo Monasterio, Francisca Castillo, Kumar P. Tripathi, Ning He, Penelope Pelczar, Nicola Schaltenberg, Marjorie De la Fuente, Francisco López-Köstner, Susanne Nylén, Hjalte List Larsen, Raoul Kuiper, Per Antonson, Marcela A. Hermoso, Samuel Huber, Moshe Biton, Sandra Scharaw, Jan-Åke Gustafsson, Pekka Katajisto, Eduardo J. Villablanca","doi":"10.1038/s41586-024-08247-6","DOIUrl":"https://doi.org/10.1038/s41586-024-08247-6","url":null,"abstract":"Uncontrolled regeneration leads to neoplastic transformation1,2,3. The intestinal epithelium requires precise regulation during continuous homeostatic and damage-induced tissue renewal to prevent neoplastic transformation, suggesting that pathways unlinking tumour growth from regenerative processes must exist. Here, by mining RNA-sequencing datasets from two intestinal damage models4,5 and using pharmacological, transcriptomics and genetic tools, we identified liver X receptor (LXR) pathway activation as a tissue adaptation to damage that reciprocally regulates intestinal regeneration and tumorigenesis. Using single-cell RNA sequencing, intestinal organoids, and gain- and loss-of-function experiments, we demonstrate that LXR activation in intestinal epithelial cells induces amphiregulin (Areg), enhancing regenerative responses. This response is coordinated by the LXR-ligand-producing enzyme CYP27A1, which was upregulated in damaged intestinal crypt niches. Deletion of Cyp27a1 impaired intestinal regeneration, which was rescued by exogenous LXR agonists. Notably, in tumour models, Cyp27a1 deficiency led to increased tumour growth, whereas LXR activation elicited anti-tumour responses dependent on adaptive immunity. Consistently, human colorectal cancer specimens exhibited reduced levels of CYP27A1, LXR target genes, and B and CD8 T cell gene signatures. We therefore identify an epithelial adaptation mechanism to damage, whereby LXR functions as a rheostat, promoting tissue repair while limiting tumorigenesis.","PeriodicalId":18787,"journal":{"name":"Nature","volume":"38 1","pages":""},"PeriodicalIF":64.8,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142678357","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Learning high-accuracy error decoding for quantum processors 为量子处理器学习高精度错误解码

IF 64.8 1区综合性期刊

Nature Pub Date : 2024-11-20 DOI: 10.1038/s41586-024-08148-8

Johannes Bausch, Andrew W. Senior, Francisco J. H. Heras, Thomas Edlich, Alex Davies, Michael Newman, Cody Jones, Kevin Satzinger, Murphy Yuezhen Niu, Sam Blackwell, George Holland, Dvir Kafri, Juan Atalaya, Craig Gidney, Demis Hassabis, Sergio Boixo, Hartmut Neven, Pushmeet Kohli

{"title":"Learning high-accuracy error decoding for quantum processors","authors":"Johannes Bausch, Andrew W. Senior, Francisco J. H. Heras, Thomas Edlich, Alex Davies, Michael Newman, Cody Jones, Kevin Satzinger, Murphy Yuezhen Niu, Sam Blackwell, George Holland, Dvir Kafri, Juan Atalaya, Craig Gidney, Demis Hassabis, Sergio Boixo, Hartmut Neven, Pushmeet Kohli","doi":"10.1038/s41586-024-08148-8","DOIUrl":"https://doi.org/10.1038/s41586-024-08148-8","url":null,"abstract":"Building a large-scale quantum computer requires effective strategies to correct errors that inevitably arise in physical quantum systems1. Quantum error-correction codes2 present a way to reach this goal by encoding logical information redundantly into many physical qubits. A key challenge in implementing such codes is accurately decoding noisy syndrome information extracted from redundancy checks to obtain the correct encoded logical information. Here we develop a recurrent, transformer-based neural network that learns to decode the surface code, the leading quantum error-correction code3. Our decoder outperforms other state-of-the-art decoders on real-world data from Google’s Sycamore quantum processor for distance-3 and distance-5 surface codes4. On distances up to 11, the decoder maintains its advantage on simulated data with realistic noise including cross-talk and leakage, utilizing soft readouts and leakage information. After training on approximate synthetic data, the decoder adapts to the more complex, but unknown, underlying error distribution by training on a limited budget of experimental samples. Our work illustrates the ability of machine learning to go beyond human-designed algorithms by learning from data directly, highlighting machine learning as a strong contender for decoding in quantum computers.","PeriodicalId":18787,"journal":{"name":"Nature","volume":"193 1","pages":""},"PeriodicalIF":64.8,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142678360","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Photocatalytic low-temperature defluorination of PFASs 光催化低温脱氟处理全氟辛烷磺酸

IF 50.5 1区综合性期刊

Nature Pub Date : 2024-11-20 DOI: 10.1038/s41586-024-08179-1

Hao Zhang, Jin-Xiang Chen, Jian-Ping Qu, Yan-Biao Kang

{"title":"Photocatalytic low-temperature defluorination of PFASs","authors":"Hao Zhang, Jin-Xiang Chen, Jian-Ping Qu, Yan-Biao Kang","doi":"10.1038/s41586-024-08179-1","DOIUrl":"10.1038/s41586-024-08179-1","url":null,"abstract":"Polyfluoroalkyl and perfluoroalkyl substances (PFASs) are found in many everyday consumer products, often because of their high thermal and chemical stabilities, as well as their hydrophobic and oleophobic properties1. However, the inert carbon–fluorine (C–F) bonds that give PFASs their properties also provide resistance to decomposition through defluorination, leading to long-term persistence in the environment, as well as in the human body, raising substantial safety and health concerns1–5. Despite recent advances in non-incineration approaches for the destruction of functionalized PFASs, processes for the recycling of perfluorocarbons (PFCs) as well as polymeric PFASs such as polytetrafluoroethylene (PTFE) are limited to methods that use either elevated temperatures or strong reducing reagents. Here we report the defluorination of PFASs with a highly twisted carbazole-cored super-photoreductant KQGZ. A series of PFASs could be defluorinated photocatalytically at 40–60 °C. PTFE gave amorphous carbon and fluoride salts as the major products. Oligomeric PFASs such as PFCs, perfluorooctane sulfonic acid (PFOS), polyfluorooctanoic acid (PFOA) and derivatives give carbonate, formate, oxalate and trifluoroacetate as the defluorinated products. This allows for the recycling of fluorine in PFASs as inorganic fluoride salt. The mechanistic investigation reveals the difference in reaction behaviour and product components for PTFE and oligomeric PFASs. This work opens a window for the low-temperature photoreductive defluorination of the ‘forever chemicals’ PFASs, especially for PTFE, as well as the discovery of new super-photoreductants. Photocatalysis at 40–60 °C is shown to be able to defluorinate perfluoroalkyl substances, known as ‘forever chemicals’, allowing the recycling of fluorine in polyfluoroalkyl and perfluoroalkyl substances as inorganic fluoride salt.","PeriodicalId":18787,"journal":{"name":"Nature","volume":"635 8039","pages":"610-617"},"PeriodicalIF":50.5,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142678304","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

How students and grandparents could solve the global mental-health crisis 学生和祖父母如何解决全球心理健康危机

IF 50.5 1区综合性期刊

Nature Pub Date : 2024-11-20 DOI: 10.1038/d41586-024-03757-9

Simar Bajaj

引用次数: 0

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