The human face is a valuable biomarker of aging,but the collection and use of its image raise significant privacy concerns.Here we present an approach for facial data masking that preserves age-related features using ...The human face is a valuable biomarker of aging,but the collection and use of its image raise significant privacy concerns.Here we present an approach for facial data masking that preserves age-related features using coordinate-wise monotonic transformations.We first develop a deep learning model that estimates age directly from non-registered face point clouds with high accuracy and generalizability.We show that the model learns a highly indistinguishable mapping using faces treated with coordinate-wise monotonic transformations,indicating that the relative positioning of facial information is a low-level biomarker of facial aging.Through visual perception tests and computational3D face verification experiments,we demonstrate that transformed faces are significantly more difficult to perceive for human but not for machines,except when only the face shape information is accessible.Our study leads to a facial data protection guideline that has the potential to broaden public access to face datasets with minimized privacy risks.展开更多
Super-enhancers are defined as cluster of enhancers with dense TF binding, which can activate proximal cell-identity gene expression. Here we review the identification, func- tional significance of super-enhancers, an...Super-enhancers are defined as cluster of enhancers with dense TF binding, which can activate proximal cell-identity gene expression. Here we review the identification, func- tional significance of super-enhancers, and their relation- ships with cancer. With the current intense interests in su- per-enhancers, more super-enhancers will be defined and studied in different cell types and tissues and in different developmental and biological contexts to reveal molecular mechanisms of their functions.展开更多
Aging is characterized by a progressive deterioration of physiological integrity,leading to impaired functional ability and ultimately increased susceptibility to death.It is a major risk factor for chronic human dise...Aging is characterized by a progressive deterioration of physiological integrity,leading to impaired functional ability and ultimately increased susceptibility to death.It is a major risk factor for chronic human diseases,including cardiovascular disease,diabetes,neurological degeneration,and cancer.Therefore,the growing emphasis on “healthy aging” raises a series of important questions in life and social sciences.In recent years,there has been unprecedented progress in aging research,particularly the discovery that the rate of aging is at least partly controlled by evolutionarily conserved genetic pathways and biological processes.In an attempt to bring full-fledged understanding to both the aging process and age-associated diseases,we review the descriptive,conceptual,and interventive aspects of the landscape of aging composed of a number of layers at the cellular,tissue,organ,organ system,and organismal levels.展开更多
Age-associated changes in immune cells have been linked to an increased risk for infection.However,a global and detailed characterization of the changes that human circulating immune cells undergo with age is lacking....Age-associated changes in immune cells have been linked to an increased risk for infection.However,a global and detailed characterization of the changes that human circulating immune cells undergo with age is lacking.Here,we combined scRNA-seq,mass cytometry and sCATAC-seq to compare immune cell types in peripheral blood collected from young and old subjects and patients with COVID-19.We found that the immune cell landscape was reprogrammed with age and was characterized by T cell polarization from naive and memory cells to effector,cytotoxic,exhausted and reg-ulatory cells,along with increased late natural killer cells,age-associated B cells,inflammatory monocytes and age-associated dendritic cells.In addition,the expression of genes,which were implicated in coron-avirus susceptibility,was upregulated in a cell subtype-specific manner with age.Notably,COVID-19 promoted age-induced immune cell polarization and gene expression related to inflammation and cellular senes-cence.Therefore,these findings suggest that a dysreg-ulated immune system and increased gene expression associated with SARS-CoV-2 susceptibility may at least partially account for COVID-19 vulnerability in the elderly.展开更多
COVID-19 is now rapidly spreading worldwide.While the majority of COVID-19 patients show only mild or moderate symptoms,some could deteriorate quickly and may succumb to a sudden death.It is therefore important to ide...COVID-19 is now rapidly spreading worldwide.While the majority of COVID-19 patients show only mild or moderate symptoms,some could deteriorate quickly and may succumb to a sudden death.It is therefore important to identify who will be more likely to develop severe outcomes and be treated with particular or preventive care.Here in this literature survey,we collected epidemiologic and clinical data from 36 articles on 51,270 patients with different severity of COVID-19,aiming to characterize the population that are prone to severe condition and bad outcomes.These data reveal that old males and those with high BMI or underlying diseases,especially cardiovascular disease,hypertension and diabetes,are overrepresented among severe cases.High leukocyte and lymphopenia are common features in severe and critical patients.Upon deterioration of the disease,both CD4^(+) and CD8^(+)T cells are decreased,while almost all serum cytokines,especially pro-inflammatory cytokines,increased.展开更多
With the rapid development of biotechnology,data-driven bioinformatics research is increasingly dependent on data generation from biological wet-labs.At the same time,to gain in-depth knowledge of various biological s...With the rapid development of biotechnology,data-driven bioinformatics research is increasingly dependent on data generation from biological wet-labs.At the same time,to gain in-depth knowledge of various biological systems,conventional biology laboratories have become more reliant on the establishment and optimization of advanced bioinformatics methods.Many bioinformatics labs are debating whether to build their own wet-bench or to seek collaborations,while many wet-bench labs are also confused over whether they should build their own dry-labs or likewise seek collaborations.展开更多
HDAC6 is involved in several biological processes related to aging-associated diseases.However,it was unknown whether HDAC6 could directly regulate lifespan and healthspan.We found that HDAC6 knockdown induced transcr...HDAC6 is involved in several biological processes related to aging-associated diseases.However,it was unknown whether HDAC6 could directly regulate lifespan and healthspan.We found that HDAC6 knockdown induced transcriptome changes to attenuate the aging changes in the Drosophila head,particularly on the inflammation and innate immunity-related genes.Whole-body knockdown of HDAC6 extended lifespan in the fly,furthermore brain-specific knockdown of HDAC6 extended both lifespan and healthspan in the fly.Our results established HDAC6 as a lifespan regulator and provided a potential anti-aging target.展开更多
The investigation of the interplay between genes,proteins,metabolites and diseases plays a central role in molecular and cellular biology.Whole genome sequencing has made it possible to examine the behavior of all the...The investigation of the interplay between genes,proteins,metabolites and diseases plays a central role in molecular and cellular biology.Whole genome sequencing has made it possible to examine the behavior of all the genes in a genome by high-throughput experimental techniques and to pinpoint molecular interactions on a genome-wide scale,which form the backbone of systems biology.In particular,Bayesian network(BN)is a powerful tool for the ab-initial identification of causal and non-causal relationships between biological factors directly from experimental data.However,scalability is a crucial issue when we try to apply BNs to infer such interactions.In this paper,we not only introduce the Bayesian network formalism and its applications in systems biology,but also review recent technical developments for scaling up or speeding up the structural learning of BNs,which is important for the discovery of causal knowledge from large-scale biological datasets.Specifically,we highlight the basic idea,relative pros and cons of each technique and discuss possible ways to combine different algorithms towards making BN learning more accurate and much faster.展开更多
During the last two centuries, there have been many spectacular advances in medical science, the main consequence of which has been the dramatically reduced burden of infectious diseases. While in the 1800s many peopl...During the last two centuries, there have been many spectacular advances in medical science, the main consequence of which has been the dramatically reduced burden of infectious diseases. While in the 1800s many people died before reaching adult- hood, nowadays most people survive. Hence average life ex- pectancy in 1800s was around 30-40, which was barely higher than it had been in Greek and Roman times (Finch, 2010), but nowadays life expectancy in most modernised economies is around 75 - 80. This demographic shift, which has happened in only 200 years, has created a dramatic change in the causes of mortality. The major killers in the modern world are non- communicable diseases (NCDs): principally cardiovascular disease, cancer and neurodegenerative disorders such as Alz- heimer's disease. A major factor that influences susceptibility to all these diseases is age. As we get older, our risk of developing these NCDs increases enormously. For example, the rate of breast cancer in females at age 15-19 is less than 10 per 100,000 population, but this increases to 100 at age 40-44, 275 at age 55--59 and 450 at age 85 + (http://www.cancerresearchuk.org/ cancer-info/cancerstats/types/breast/incidence/#age). Ageing has consequently become a major medical, social and economic burden to many countries.展开更多
基金supported by the National Natural Science Foundation of China(92049302,92374207,32088101,32330017)the National Key Research and Development Program of China(2020YFA0804000)。
文摘The human face is a valuable biomarker of aging,but the collection and use of its image raise significant privacy concerns.Here we present an approach for facial data masking that preserves age-related features using coordinate-wise monotonic transformations.We first develop a deep learning model that estimates age directly from non-registered face point clouds with high accuracy and generalizability.We show that the model learns a highly indistinguishable mapping using faces treated with coordinate-wise monotonic transformations,indicating that the relative positioning of facial information is a low-level biomarker of facial aging.Through visual perception tests and computational3D face verification experiments,we demonstrate that transformed faces are significantly more difficult to perceive for human but not for machines,except when only the face shape information is accessible.Our study leads to a facial data protection guideline that has the potential to broaden public access to face datasets with minimized privacy risks.
基金supported by the National Natural Science Foundation of China(3121010391691329302 and 91519330)+2 种基金the Progress on CAS Strategic Priority Research Program(XDA01010303)the Instrument Developing Project of the Chinese Academy of Sciences(YZ201243)the National Basic Research Program of China(2015CB964803 and 2011CB504206)to Jing-Dong J.Han
文摘Super-enhancers are defined as cluster of enhancers with dense TF binding, which can activate proximal cell-identity gene expression. Here we review the identification, func- tional significance of super-enhancers, and their relation- ships with cancer. With the current intense interests in su- per-enhancers, more super-enhancers will be defined and studied in different cell types and tissues and in different developmental and biological contexts to reveal molecular mechanisms of their functions.
基金supported by the National Natural Science Foundation of China(31871380,32000500,32070730,32170756,32170804,81330008,81671377,81725010,81725010,81872874,81921006,81922027,81971312,81991512,82030041,82103167,82122024,82125009,82125011,82130044,91749126,91949101,91949207,92049302)the National Key Research and Development Program of China(2017YFA0506400,2018YFA0800200,2018YFA0800700,2018YFA0900200,2018YFC2000100,2018YFC2000400,2018YFE-0203700,20192ACB70002,2019YFA0802202,2020YFA0113400,2020YFA0803401,2020YFA0804000,2020YFC2002800,2020YFC-2002900,2021ZD0202401)+11 种基金the Strategic Priority Research Program of the Chinese Academy of Sciences(XDA16010100,XDA16010603,XDA16020400,XDB29020000,XDB39000000,XDB39000000,XDB39030300)the China Association for Science and Technology(2021QNRC001)the Beijing Municipal Science and Technology Commission(Z200022)the Natural Science Foundation of Shanghai(21JC1406400)the Key Programs of the Jiangxi ProvinceChina(20192ACB70002)the“Shu Guang”Project supported by the Shanghai Municipal Education Commission and Shanghai Education Development Foundation(19SG18)the Shanghai Sailing Program(22YF1434300)the Research Project of Joint Laboratory of University of Science and Technology of China and Anhui Mental Health Center(2019LH03)the Fundamental Research Funds for the Central Universities(WK2070210004)the Young Elite Scientists Sponsorship Program by China Association for Science and Technology(YESS20210002)the Youth Innovation Promotion Association of Chinese Academy of Sciences(2022083)。
文摘Aging is characterized by a progressive deterioration of physiological integrity,leading to impaired functional ability and ultimately increased susceptibility to death.It is a major risk factor for chronic human diseases,including cardiovascular disease,diabetes,neurological degeneration,and cancer.Therefore,the growing emphasis on “healthy aging” raises a series of important questions in life and social sciences.In recent years,there has been unprecedented progress in aging research,particularly the discovery that the rate of aging is at least partly controlled by evolutionarily conserved genetic pathways and biological processes.In an attempt to bring full-fledged understanding to both the aging process and age-associated diseases,we review the descriptive,conceptual,and interventive aspects of the landscape of aging composed of a number of layers at the cellular,tissue,organ,organ system,and organismal levels.
基金This work was supported by the National Key Research and Development Program of China(2017YFA0105804)the Strategic Priority Research Program of the Chinese Academy of Sciences(XDA16010000)+8 种基金the National Key Research and Development Program of China(2018YFC2000100,2017YFA0103304,2017YFA0102802,2018YFA0107203)the National Natural Science Foundation of China(81670897,81625009,91749202.81861168034,81921006,31671429,91949209,91749123,81671377,81822018,81870228,81922027,81701388,81601233)the Program of the Beijing Municipal Science and Technology Commission(Z191100001519005)Bejing Natural Science Foun-dation(Z190019)Bejing Municipal Commission of Health and Family Planning(PXM2018026283_000002)Advanced Innovation Center for Human Brain Protection(3500-1192012)the Key Research Program of the Chinese Academy of Sciences(KFZD-SW-221)K.C.Wong Education Foundation(GJTD-2019-06,GJTD-2019-08),Youth Innovation Promotion Association of CAS(2016093)the State Key Laboratory of Membrane Biology and the State Key Laboratory of Stem Cell and Reproductive Biology.
文摘Age-associated changes in immune cells have been linked to an increased risk for infection.However,a global and detailed characterization of the changes that human circulating immune cells undergo with age is lacking.Here,we combined scRNA-seq,mass cytometry and sCATAC-seq to compare immune cell types in peripheral blood collected from young and old subjects and patients with COVID-19.We found that the immune cell landscape was reprogrammed with age and was characterized by T cell polarization from naive and memory cells to effector,cytotoxic,exhausted and reg-ulatory cells,along with increased late natural killer cells,age-associated B cells,inflammatory monocytes and age-associated dendritic cells.In addition,the expression of genes,which were implicated in coron-avirus susceptibility,was upregulated in a cell subtype-specific manner with age.Notably,COVID-19 promoted age-induced immune cell polarization and gene expression related to inflammation and cellular senes-cence.Therefore,these findings suggest that a dysreg-ulated immune system and increased gene expression associated with SARS-CoV-2 susceptibility may at least partially account for COVID-19 vulnerability in the elderly.
基金This work was supported by grants from the National Natural Science Foundation of China(No.91749205)China Ministry of Science and Technology(No.2016YFE0108700)to J.D.J.H.
文摘COVID-19 is now rapidly spreading worldwide.While the majority of COVID-19 patients show only mild or moderate symptoms,some could deteriorate quickly and may succumb to a sudden death.It is therefore important to identify who will be more likely to develop severe outcomes and be treated with particular or preventive care.Here in this literature survey,we collected epidemiologic and clinical data from 36 articles on 51,270 patients with different severity of COVID-19,aiming to characterize the population that are prone to severe condition and bad outcomes.These data reveal that old males and those with high BMI or underlying diseases,especially cardiovascular disease,hypertension and diabetes,are overrepresented among severe cases.High leukocyte and lymphopenia are common features in severe and critical patients.Upon deterioration of the disease,both CD4^(+) and CD8^(+)T cells are decreased,while almost all serum cytokines,especially pro-inflammatory cytokines,increased.
文摘With the rapid development of biotechnology,data-driven bioinformatics research is increasingly dependent on data generation from biological wet-labs.At the same time,to gain in-depth knowledge of various biological systems,conventional biology laboratories have become more reliant on the establishment and optimization of advanced bioinformatics methods.Many bioinformatics labs are debating whether to build their own wet-bench or to seek collaborations,while many wet-bench labs are also confused over whether they should build their own dry-labs or likewise seek collaborations.
基金This work was supported by grants from the National Natural Science Foundation of China(31771545,92049301,31821002,91329302,and 31210103916)China Ministry of Science and Technology(2015CB964803,2016YFE0108700,and 2016YFA0500600),and Max Planck fellowship to J.D.J.H.
文摘HDAC6 is involved in several biological processes related to aging-associated diseases.However,it was unknown whether HDAC6 could directly regulate lifespan and healthspan.We found that HDAC6 knockdown induced transcriptome changes to attenuate the aging changes in the Drosophila head,particularly on the inflammation and innate immunity-related genes.Whole-body knockdown of HDAC6 extended lifespan in the fly,furthermore brain-specific knockdown of HDAC6 extended both lifespan and healthspan in the fly.Our results established HDAC6 as a lifespan regulator and provided a potential anti-aging target.
基金We thank the support from the China National Science Foundation(Grant No.30890033,30588001 and 30620120433)Chinese Ministry of Science and Technology(No.2006CB910700)to J.D.J.H.
文摘The investigation of the interplay between genes,proteins,metabolites and diseases plays a central role in molecular and cellular biology.Whole genome sequencing has made it possible to examine the behavior of all the genes in a genome by high-throughput experimental techniques and to pinpoint molecular interactions on a genome-wide scale,which form the backbone of systems biology.In particular,Bayesian network(BN)is a powerful tool for the ab-initial identification of causal and non-causal relationships between biological factors directly from experimental data.However,scalability is a crucial issue when we try to apply BNs to infer such interactions.In this paper,we not only introduce the Bayesian network formalism and its applications in systems biology,but also review recent technical developments for scaling up or speeding up the structural learning of BNs,which is important for the discovery of causal knowledge from large-scale biological datasets.Specifically,we highlight the basic idea,relative pros and cons of each technique and discuss possible ways to combine different algorithms towards making BN learning more accurate and much faster.
文摘During the last two centuries, there have been many spectacular advances in medical science, the main consequence of which has been the dramatically reduced burden of infectious diseases. While in the 1800s many people died before reaching adult- hood, nowadays most people survive. Hence average life ex- pectancy in 1800s was around 30-40, which was barely higher than it had been in Greek and Roman times (Finch, 2010), but nowadays life expectancy in most modernised economies is around 75 - 80. This demographic shift, which has happened in only 200 years, has created a dramatic change in the causes of mortality. The major killers in the modern world are non- communicable diseases (NCDs): principally cardiovascular disease, cancer and neurodegenerative disorders such as Alz- heimer's disease. A major factor that influences susceptibility to all these diseases is age. As we get older, our risk of developing these NCDs increases enormously. For example, the rate of breast cancer in females at age 15-19 is less than 10 per 100,000 population, but this increases to 100 at age 40-44, 275 at age 55--59 and 450 at age 85 + (http://www.cancerresearchuk.org/ cancer-info/cancerstats/types/breast/incidence/#age). Ageing has consequently become a major medical, social and economic burden to many countries.