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The Sierra Platinum Service for generating peak-calls for replicated ChIP-seq experiments

BMC Research Notes 2018年第1期11卷 1-5页

作者： Wiegreffe, Daniel Müller, Lydia Steuck, Jens Zeckzer, Dirk Stadler, Peter F. Image and Signal Processing Group Department of Computer Science University of Leipzig Augustusplatz 10 Leipzig 04109 Germany Natural Language Processing Department Department of Computer Science University of Leipzig Augustusplatz 10 Leipzig 04109 Germany Bioinformatics Group Department of Computer Science University of Leipzig Härtelstraße 16-18 Leipzig 04107 Germany Interdisciplinary Center for Bioinformatics University of Leipzig Härtelstraße 16-18 Leipzig 04107 Germany Max Planck Institute MIS Inselstraße 22 Leipzig 04103 Germany Fraunhofer Institute for Cell Therapy and Immunology IZI Perlickstraße 1 Leipzig 04103 Germany Institute for Theoretical Chemistry University of Vienna Währinger Straße 17 Vienna 1090 Austria Center for Non-coding RNA in Technology and Health University of Copenhagen Grønnegårdsvej 3 Copenhagen 1870 Denmark Santa Fe Institute 1399 Hyde Park Road Santa Fe 87501 NM United States

Objective: Sierra Platinum is a fast and robust peak-caller for replicated ChIP-seq experiments with visual quality-control and -steering. The required computing resources are optimized but still may exceed the resources available to researchers at biological research institutes. Results: Sierra Platinum Service provides the full functionality of Sierra Platinum: using a web interface, a new instance of the service can be generated. Then experimental data is uploaded and the computation of the peaks is started. Upon completion, the results can be inspected interactively and then downloaded for further analysis, at which point the service terminates. © 2018 The Author(s).

关键词： ChIP-seq Histone modifications Peak-caller Replicate analysis

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Double-network hydrogel enhanced by SS31-loaded mesoporous polydopamine nanoparticles:Symphonic collaboration of near-infrared photothermal antibacterial effect and mitochondrial maintenance for full-thickness wound healing in diabetes mellitus

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Bioactive Materials 2023年第9期27卷 409-428页

作者： Qing-Song Deng Yuan Gao Bi-Yu Rui Xu-Ran Li Po-Lin Liu Zi-Yin Han Zhan-Ying Wei Chang-Ru Zhang Fei Wang Helen Dawes Tong-He Zhu Shi-Cong Tao Shang-Chun Guo Department of Orthopedic Surgery Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine600 Yishan RoadShanghai200233China School of Medicine Shanghai Jiao Tong University227 South Chongqing RoadShanghai200025China Institute of Microsurgery on Extremities Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine600 Yishan RoadShanghai200233China Department of Rheumatology The Affiliated Changzhou No.2 People’s Hospital of Nanjing Medical UniversityNo.29XinglongxiangTianning DistrictChangzhou213000China Shanghai Clinical Research Centre of Bone Diseases Department of Osteoporosis and Bone DiseasesShanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghai200233China Shanghai Key Laboratory of Orthopedic Implants Department of Orthopedic SurgeryShanghai Ninth People’s HospitalShanghai Jiao Tong University School of MedicineNo.639 Zhizaoju RoadShanghai200011China Clinical and Translational Research Center for 3D Printing Technology Medical 3D Printing Innovation Research CenterShanghai Ninth People’s HospitalShanghai Jiao Tong University School of MedicineShanghai200125China Department of Orthopedics Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint DiseasesShanghai Institute of Traumatology and OrthopedicsRuijin HospitalShanghai Jiao Tong University School of Medicine197 Ruijin Second RoadShanghai200025China Faculty of Health and Life Science Oxford Brookes UniversityHeadington RoadOxfordOX30BPUK NIHR Oxford Health Biomedical Research Centre OxfordOX37JXUK College of Medicine and Health St Lukes CampusUniversity of ExeterHeavitree RoadExeterEX12LUUK School of Chemistry and Chemical Engineering Shanghai Engineering Research Center of Pharmaceutical Intelligent EquipmentShanghai Frontiers Science Research Center for Druggability of Cardiovascular Non-Coding RNAInstitute for Frontier Medical TechnologyShanghai University of

Diabetic wound healing has become a serious healthcare *** high-glucose environment leads to persistent bacterial infection and mitochondrial dysfunction,resulting in chronic inflammation,abnormal vascular function,and tissue *** solve these issues,we developed a double-network hydrogel,constructed with pluronic F127 diacrylate(F127DA)and hyaluronic acid methacrylate(HAMA),and enhanced by SS31-loaded mesoporous polydopamine nanoparticles(MPDA NPs).As components,SS31,a mitochondria-targeted peptide,maintains mitochondrial function,reduces mitochondrial reactive oxygen species(ROS)and thus regulates macrophage polarization,as well as promoting cell proliferation and migration,while MPDA NPs not only scavenge ROS and exert an anti-bacterial effect by photothermal treatment under near-infrared light irradiation,but also control release of SS31 in response to *** F127DA/HAMA-MPDA@SS31(FH-M@S)hydrogel has characteristics of adhesion,superior biocompatibility and mechanical properties which can adapt to irregular wounds at different body sites and provide sustained release of MPDA@SS31(M@S)*** addition,in a diabetic rat full thickness skin defect model,the FH-M@S hydrogel promoted macrophage M2 polarization,collagen deposition,neovascularization and wound ***,the FH-M@S hydrogel exhibits promising therapeutic potential for skin regeneration.

关键词： Mesoporous polydopamine nanoparticles(MPDA NPs) SS31 Photothermal antibacterial Mitochondrial function maintenance Diabetic wound healing

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Erratum to: Targeting the PELP1-KDM1 axis as a potential therapeutic strategy for breast cancer

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Breast Cancer Research 2012年第6期14卷 1-2页

作者： Valerie Cortez Monica Mann Seshidhar Tekmal Ratna K Vadlamudi Takayoshi Suzuki Naoki Miyata Cristian Rodriguez-Aguayo Gabriel Lopez-Berestein Anil K Sood Department of Obstetrics and Gynecology University of Texas Health Science Center San Antonio TX 78229 USA Department of Cell and Structural Biology University of Texas Health Science Center San Antonio TX 78229 USA Cancer Therapy and Research Center University of Texas Health Science Center San Antonio TX 78229 USA Graduate School of Medical Science Kyoto Prefectural University of Medicine 13 Taishogun Nishitakatsukasa-Cho Kita-ku Kyoto 403-8334 Japan PRESTO Japan Science and Technology Agency 4-1-8 Honcho Kawaguchi Saitama 332-0012 Japan Graduate School of Pharmaceutical Sciences Nagoya City University 3-1 Tanabe-dori Mizuho-ku Nagoya Aichi 467-8673 Japan Department of Gynecologic Oncology University of Texas MD Anderson Cancer Center Houston TX 78030 USA Center for RNA Interference and Non-coding RNA University of Texas MD Anderson Cancer Center Houston TX 78030 USA Department of Cancer Biology University of Texas MD Anderson Cancer Center Houston TX 78030 USA

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Profiling of Ribose Methylations in rna by High‐Throughput Sequencing†

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Angewandte Chemie 2014年第2期127卷

作者： Ulf Birkedal Mikkel Christensen‐Dalsgaard Nicolai Krogh Radhakrishnan Sabarinathan Jan Gorodkin Henrik Nielsen Department of Cellular and Molecular Medicine University of Copenhagen Blegdamsvej 3B 2200 Copenhagen N (Denmark) Center for Non‐coding RNA in Technology and Health Department of Veterinary Clinical and Animal Science University of Copenhagen Grønnegårdsvej 3 1870 Frederiksberg C (Denmark)

Ribose methylations are the most abundant chemical modifications of ribosomal rna and are critical for ribosome assembly and fidelity of translation. Many aspects of ribose methylations have been difficult to study due to lack of efficient mapping methods. Here, we present a sequencing‐based method (RiboMeth‐seq) and its application to yeast ribosomes, presently the best‐studied eukaryotic model system. We demonstrate detection of the known as well as new modifications, reveal partial modifications and unexpected communication between modification events, and determine the order of modification at several sites during ribosome biogenesis. Surprisingly, the method also provides information on a subset of other modifications. Hence, RiboMeth‐seq enables a detailed evaluation of the importance of rna modifications in the cells most sophisticated molecular machine. RiboMeth‐seq can be adapted to other rna classes, for example, mrna, to reveal new biology involving rna modifications.

关键词： Ribosome Ribozyme rna‐Erkennung rna‐Strukturen Transferasen

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Clinical and genetic delineation of autosomal recessive and dominant ACTL6B-related developmental brain disorders

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Genetics in Medicine 2025年第4期27卷 101251页

作者： Cali, Elisa Quirin, Tania Rocca, Clarissa Efthymiou, Stephanie Riva, Antonella Marafi, Dana Zaki, Maha S. Suri, Mohnish Dominguez, Roberto Elbendary, Hasnaa M. Alavi, Shahryar Abdel-Hamid, Mohamed S. Morsy, Heba Mau-Them, Frederic Tran Nizon, Mathilde Tesner, Pavel Ryba, Lukáš Zafar, Faisal Rana, Nuzhat Saadi, Nebal W. Firoozfar, Zahra Gencpinar, Pinar Unay, Bulent Ustun, Canan Bruel, Ange-Line Coubes, Christine Stefanich, Jennifer Sezer, Ozlem Agolini, Emanuele Novelli, Antonio Vasco, Gessica Lettori, Donatella Milh, Mathieu Villard, Laurent Zeidler, Shimriet Opperman, Henry Strehlow, Vincent Issa, Mahmoud Y. El Khassab, Hebatallah Chand, Prem Ibrahim, Shahnaz Rashidi-Nezhad, Ali Miryounesi, Mohammad Larki, Pegah Morrison, Jennifer Cristian, Ingrid Thiffault, Isabelle Bertsch, Nicole L. Noh, Grace J. Pappas, John Moran, Ellen Marinakis, Nikolaos M. Traeger-Synodinos, Joanne Hosseini, Susan Abbaszadegan, Mohammad Reza Caumes, Roseline Vissers, Lisenka E.L.M. Neshatdoust, Maedeh Montazer Zohour, Mostafa El Fahime, Elmostafa Canavati, Christina Kamal, Lara Kanaan, Moien Askander, Omar Voinova, Victoria Levchenko, Olga Haider, Shahzhad Halbach, Sara S. Elias Maia, Rayana Mansoor, Salehi Jain, Vivek Tawde, Sanjukta Challa, Viveka Santhosh R. Gowda, Vykuntaraju K. Srinivasan, Varunvenkat M. Victor, Lucas Alves Pinero-Banos, Benito Hague, Jennifer ElAwady, Heba Ahmed Maria de Miranda Henriques-Souza, Adelia Cheema, Huma Arshad Anjum, Muhammad Nadeem Idkaidak, Sara Alqarajeh, Firas Atawneh, Osama Mor-Shaked, Hagar Harel, Tamar Zifarelli, Giovanni Bauer, Peter Kok, Fernando Kitajima, Joao Paulo Monteiro, Fabiola Josahkian, Juliana Lesca, Gaetan Chatron, Nicolas Ville, Dorothe Murphy, David Neul, Jeffrey L. Mullegama, Sureni V. Begtrup, Amber Herman, Isabella Mitani, Tadahiro Posey, Jennifer E. Tay, Chee Geap Javed, Iram Carr, Lucinda Kanani, Farah Beecroft, Fiona Hane, Lee Abdelkreem, Elsayed Macek, Milan Bispo, Luciana Elmaksoud, Marwa Abd Hashemi-Gorji, Farzad Pehlivan, Davut Amor, David J. Jamra, Rami Abou Chung, Wend Department of Neuromuscular Diseases University College London Queen Square Institute of Neurology London United Kingdom RNA Molecular Biology Fonds de la Recherche Scientifique (F.R.S./FNRS) Université libre de Bruxelles (ULB) Biopark campus Gosselies Belgium Department of Neurosciences Rehabilitation Ophthalmology Genetics Maternal and Child Health University of Genoa Genoa Italy Department of Molecular and Human Genetics Baylor College of Medicine Houston TX United States Department of Pediatrics Faculty of Medicine Kuwait University Safat Kuwait Clinical Genetics Department Human Genetics and Genome Research Institute National Research Centre Cairo Egypt UK National Paediatric Ataxia Telangiectasia Clinic Nottingham University Hospitals NHS Trust Nottingham United Kingdom Nottingham Clinical Genetics Service Nottingham University Hospitals NHS Trust Nottingham United Kingdom Department of Physiology Perelman School of Medicine University of Pennsylvania Philadelphia PA United States Palindrome Isfahan Iran Medical Molecular Genetics Department Human Genetics and Genome Research Institute National Research Centre Cairo Egypt Human Genetics Department Medical Research Institute Alexandria University Egypt Unité Fonctionnelle 6254 d'Innovation en Diagnostique Génomique des Maladies Rares Pôle de Biologie CHU Dijon Bourgogne Dijon France INSERM UMR1231 GAD Dijon France Service de génétique médicale CHU de Nantes Nantes France Institut du thorax INSERM CNRS UNIV Nantes Nantes France Department of Biology and Medical Genetics 2nd Faculty of Medicine Charles University and Motol University Hospital Prague Czech Republic Department of Paediatric Neurology Children's Hospital and Institute of Child Health Multan Pakistan College of Medicine/University of Baghdad Unit of Pediatric Neurology Children Welfare Teaching Hospital Baghdad Iraq İzmir Katip Çelebi University Tepecik Training and Research Department of Pediatric Neurology Izmir Türkiye U

Purpose: This study aims to comprehensively delineate the phenotypic spectrum of ACTL6B-related disorders, previously associated with both autosomal recessive and autosomal dominant neurodevelopmental disorders. Molecularly, the role of the nucleolar protein ACTL6B in contributing to the disease has remained unclear. Methods: We identified 105 affected individuals, including 39 previously reported cases, and systematically analyzed detailed clinical and genetic data for all individuals. Additionally, we conducted knockdown experiments in neuronal cells to investigate the role of ACTL6B in ribosome biogenesis. Results: Biallelic variants in ACTL6B are associated with severe-to-profound global developmental delay/intellectual disability, infantile intractable seizures, absent speech, autistic features, dystonia, and increased lethality. De novo monoallelic variants result in moderate-to-severe global developmental delay/intellectual disability, absent speech, and autistic features, whereas seizures and dystonia were less frequently observed. Dysmorphic facial features and brain abnormalities, including hypoplastic corpus callosum, and parenchymal volume loss/atrophy, are common findings in both groups. We reveal that in the nucleolus, ACTL6B plays a crucial role in ribosome biogenesis, particularly in pre-rrna processing. Conclusion: This study provides a comprehensive characterization of the clinical spectrum of both autosomal recessive and dominant forms of ACTL6B-associated disorders. It offers a comparative analysis of their respective phenotypes provides a plausible molecular explanation and suggests their inclusion within the expanding category of “ribosomopathies.” © 2024 The Authors

关键词： ACTL6B Autism BAFopathies Epileptic-dyskinetic encephalopathy Ribosomopathies

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DNA origami technology for biomedical applications: Challenges and opportunities

MedComm - Biomaterials and Applications

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MedComm - Biomaterials and Applications 2023年第2期2卷

作者： Li, Ling Nie, Shihong Du, Ting Zhao, Jiaxuan Chen, Xiaoyuan West China School of Public Health West China Fourth Hospital and State Key Laboratory of Biotherapy Sichuan University Chengdu China Department of Radiation Oncology Cancer Center West China Hospital Sichuan University Chengdu China Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province Chengdu Medical College Chengdu China Departments of Diagnostic Radiology Surgery Chemical and Biomolecular Engineering and Biomedical Engineering Yong Loo Lin School of Medicine and Faculty of Engineering National University of Singapore Singapore Singapore Clinical Imaging Research Centre Centre for Translational Medicine Yong Loo Lin School of Medicine National University of Singapore Singapore Singapore Nanomedicine Translational Research Program NUS Center for Nanomedicine Yong Loo Lin School of Medicine National University of Singapore Singapore Singapore Institute of Molecular and Cell Biology Agency for Science Technology and Research (A*STAR) Singapore Singapore

DNA origami, a promising branch of structural DNA technology, refers to the technique of folding a single-stranded DNA scaffold into well-defined nanostructures. In recent years, DNA origami nanostructures have shown considerable promise in a variety of biomedical applications, owing to their biodegradability, unique programmability, and addressability. Despite their popularity, the biomedical application of DNA origami techniques, which exploits their unique programmability and addressability, is rare in previous studies. Most recently, mounting evidence has demonstrated the robustness of DNA origami nanostructures in the spatial organization of functional components at the nanoscale in the biomedical field. These examples provide typical paradigms to fully realize the potential of DNA origami techniques by taking advantage of their unique programmability and addressability. This minireview summarizes the recent advancements of DNA origami techniques in biosensing, biocatalysis, and drug delivery, and the representative examples using DNA origami nanostructures for the spatial organization of functional molecules with nanometric precision are highlighted. We further discuss the possible limitations and challenges for in vivo applications, including stability issues and potential immunogenicity, and finally, propose some strategies to overcome these obstacles to fully realize the potential of DNA origami techniques in biomedical applications. © 2023 The Authors. MedComm – Biomaterials and Applications published by John Wiley & Sons Australia, Ltd on behalf of Sichuan International Medical Exchange & Promotion Association (SCIMEA).

关键词： biocatalysis biosensing DNA nanotechnology DNA origami

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The Theory of Gene Family Histories

arXiv

引用

arXiv 2023年

作者： Hellmuth, Marc Stadler, Peter F. Department of Mathematics Faculty of Science Stockholm University StockholmSE - 106 91 Sweden Bioinformatics Group Department of Computer Science Interdisciplinary Center for Bioinformatics University of Leipzig Härtelstraße 16-18 LeipzigD-04107 Germany Max Planck Institute for Mathematics in the Sciences Inselstraße 22 LeipzigD-04103 Germany Fraunhofer Institute for Cell Therapy and Immunology Perlickstraße 1 LeipzigD-04103 Germany Institute for Theoretical Chemistry University of Vienna Währingerstraße 17 WienA-1090 Austria Center for Non-coding RNA in Technology and Health University of Copenhagen Grønnegårdsvej 3 Frederiksberg CDK-1870 Denmark Santa Fe Institute 1399 Hyde Park Rd Santa FeNM87501 United States

Most genes are part of larger families of evolutionary related genes. The history of gene families typically involves duplications and losses of genes as well as horizontal transfers into other organisms. The reconstruction of detailed gene family histories, i.e., the precise dating of evolutionary events relative to phylogenetic tree of the underlying species has remained a challenging topic despite their importance as a basis for detailed investigations into adaptation and functional evolution of individual members of the gene family. The identification of orthologs, moreover, is a particularly important subproblem of the more general setting considered here. In the last few years, an extensive body of mathematical results has appeared that tightly links orthology, a formal notion of best matches among genes, and horizontal gene transfer. The purpose of this chapter is the broadly outline some of the key mathematical insights and to discuss their implication for practical applications. In particular, we focus on tree-free methods, i.e., methods to infer orthology or horizontal gene transfer as well as gene trees, species trees and reconciliations between them without using a priori knowledge of the underlying trees or statistical models for the inference of phylogenetic trees. Instead, the initial step aims to extract binary relations among genes. Copyright © 2023, The Authors. All rights reserved.

关键词： Genes

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Global, regional, and national burden of diabetes from 1990 to 2021, with projections of prevalence to 2050: a systematic analysis for the Global Burden of Disease Study 2021

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The Lancet 2023年第10397期402卷 203-234页

作者： Ong, Kanyin Liane Stafford, Lauryn K. McLaughlin, Susan A. Boyko, Edward J. Vollset, Stein Emil Smith, Amanda E. Dalton, Bronte E. Duprey, Joe Cruz, Jessica A. Hagins, Hailey Lindstedt, Paulina A. Aali, Amirali Abate, Yohannes Habtegiorgis Abate, Melsew Dagne Abbasian, Mohammadreza Abbasi-Kangevari, Zeinab Abbasi-Kangevari, Mohsen ElHafeez, Samar Abd Abd-Rabu, Rami Abdulah, Deldar Morad Abdullah, Abu Yousuf Md Abedi, Vida Abidi, Hassan Aboagye, Richard Gyan Abolhassani, Hassan Abu-Gharbieh, Eman Abu-Zaid, Ahmed Adane, Tigist Demssew Adane, Denberu Eshetie Addo, Isaac Yeboah Adegboye, Oyelola A. Adekanmbi, Victor Adepoju, Abiola Victor Adnani, Qorinah Estiningtyas Sakilah Afolabi, Rotimi Felix Agarwal, Gina Aghdam, Zahra Babaei Agudelo-Botero, Marcela Arriagada, Constanza Elizabeth Aguilera Agyemang-Duah, Williams Ahinkorah, Bright Opoku Ahmad, Danish Ahmad, Rizwan Ahmad, Sajjad Ahmad, Aqeel Ahmadi, Ali Ahmadi, Keivan Ahmed, Ali Ahmed, Luai A. Ahmed, Syed Anees Ajami, Marjan Akinyemi, Rufus Olusola Al Hamad, Hanadi Al Hasan, Syed Mahfuz AL-Ahdal, Tareq Mohammed Ali Alalwan, Tariq A. Al-Aly, Ziyad AlBataineh, Mohammad T. Alcalde-Rabanal, Jacqueline Elizabeth Alemi, Sharifullah Ali, Hassam Alinia, Tahereh Aljunid, Syed Mohamed Almustanyir, Sami Al-Raddadi, Rajaa M. Alvis-Guzman, Nelson Amare, Firehiwot Ameyaw, Edward Kwabena Amiri, Sohrab Amusa, Ganiyu Adeniyi Andrei, Catalina Liliana Anjana, Ranjit Mohan Ansar, Adnan Ansari, Golnoosh Ansari-Moghaddam, Alireza Anyasodor, Anayochukwu Edward Arabloo, Jalal Aravkin, Aleksandr Y. Areda, Demelash Arifin, Hidayat Arkew, Mesay Armocida, Benedetta Arnlov, Johan Artamonov, Anton A. Arulappan, Judie Aruleba, Raphael Taiwo Arumugam, Ashokan Aryan, Zahra Asemu, Mulu Tiruneh Asghari-Jafarabadi, Mohammad Askari, Elaheh Asmelash, Daniel Astell-Burt, Thomas Athar, Mohammad Athari, Seyyed Shamsadin Atout, Maha Moh'd Wahbi Avila-Burgos, Leticia Awaisu, Ahmed Azadnajafabad, Sina Darshan, B.B. Babamohamadi, Hassan Badar, Muhammad Badawi, Alaa Badiye, Ashish D. Baghcheghi, Nayereh Baghe Institute for Health Metrics and Evaluation School of Medicine General Medicine Service Department of Veterans Affairs Seattle WA United States Department of Health Metrics Sciences School of Medicine Faculty of Medicine France Department of Clinical Governance and Quality Improvement Aleta Wondo Hospital Aleta Wondo Ethiopia Department of Nursing Woldia University Woldia Ethiopia Department of Nursing Department of Orthopedic Surgery Orthopaedic Surgery Social Determinants of Health Research Center Non-communicable Diseases Research Center Epidemiology Department Evidence-Based Practice Center Community and Maternity Nursing Unit University of Duhok Duhok Iraq School of Planning Faculty of Environment Department of Public Health Sciences Penn State College of Medicine Pennsylvania State University Hershey PA United States Biocomplexity Institute Virginia Tech Blacksburg VA United States College of Medicine Department of Public Health Laboratory Technology Sciences Department Department of Family and Community Health University of Health and Allied Sciences Ho Ghana Research Center for Immunodeficiencies Department of Biosciences and Nutrition Karolinska University Hospital Huddinge Sweden Clinical Sciences Department Department of Surgery Department of Surgery Department of Obstetrics & Gynecology College of Graduate Health Sciences University of Tennessee Memphis TN United States Department of Obstetrics & Gynecology Department of Clinical and Psychosocial Epidemiology Department of Anesthesia and Critical Care Centre for Social Research in Health Quality and Systems Performance Unit Cancer Institute NSW Sydney NSW Australia Department of Public Health and Tropical Medicine HIV and Infectious Diseases Department Jhpiego Abuja Nigeria Adolescent Research and Care Department Adolescent Friendly Research Initiative and Care Ado Ekiti Nigeria Department of Epidemiology Department of Epidemiology and Medical Statistics Department of Family Medicine McMaster University

Background: Diabetes is one of the leading causes of death and disability worldwide, and affects people regardless of country, age group, or sex. Using the most recent evidentiary and analytical framework from the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD), we produced location-specific, age-specific, and sex-specific estimates of diabetes prevalence and burden from 1990 to 2021, the proportion of type 1 and type 2 diabetes in 2021, the proportion of the type 2 diabetes burden attributable to selected risk factors, and projections of diabetes prevalence through 2050. Methods: Estimates of diabetes prevalence and burden were computed in 204 countries and territories, across 25 age groups, for males and females separately and combined;these estimates comprised lost years of healthy life, measured in disability-adjusted life-years (DALYs;defined as the sum of years of life lost [YLLs] and years lived with disability [YLDs]). We used the Cause of Death Ensemble model (CODEm) approach to estimate deaths due to diabetes, incorporating 25 666 location-years of data from vital registration and verbal autopsy reports in separate total (including both type 1 and type 2 diabetes) and type-specific models. Other forms of diabetes, including gestational and monogenic diabetes, were not explicitly modelled. Total and type 1 diabetes prevalence was estimated by use of a Bayesian meta-regression modelling tool, DisMod-MR 2.1, to analyse 1527 location-years of data from the scientific literature, survey microdata, and insurance claims;type 2 diabetes estimates were computed by subtracting type 1 diabetes from total estimates. Mortality and prevalence estimates, along with standard life expectancy and disability weights, were used to calculate YLLs, YLDs, and DALYs. When appropriate, we extrapolated estimates to a hypothetical population with a standardised age structure to allow comparison in populations with different age structures. We used the comparative r

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Chemical transformation motifs - Modelling pathways as integer hyperflows

arXiv

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arXiv 2017年

作者： Andersen, Jakob L. Flamm, Christoph Merkle, Daniel Stadler, Peter F. Earth-Life Science Institute Tokyo Institute of Technology Tokyo 152-8550 Japan Department of Mathematics and Computer Science University of Southern Denmark Odense M DK-5230 Denmark Research group Bioinformatics and Computational Biology Faculty of Computer Science University of Vienna Vienna 1090 Austria Institute for Theoretical Chemistry University of Vienna Wien 1090 Austria Halle-Jena-Leipzig and Competence Center for Scalable Data Services Solutions Dresden-Leipzig Leipzig Research Center for Civilization Diseases University of Leipzig Leipzig D-04107 Germany Max Planck Institute for Mathematics in the Sciences Leipzig D-04103 Germany Fraunhofer Institute for Cell Therapy and Immunology Leipzig D-04103 Germany Center for non-coding RNA in Technology and Health University of Copenhagen Frederiksberg C DK-1870 Denmark Santa Fe Institute 1399 Hyde Park Rd Santa Fe NM 87501 United States Research Network Chemistry Meets Microbiology University of Vienna Wien A-1090 Austria

We present an elaborate framework for formally modelling pathways in chemical reaction networks on a mechanistic level. Networks are modelled mathematically as directed multi-hypergraphs, with vertices corresponding to molecules and hyperedges to reactions. Pathways are modelled as integer hyperflows and we expand the network model by detailed routing constraints. In contrast to the more traditional approaches like Flux Balance Analysis or Elementary Mode analysis we insist on integer-valued flows. While this choice makes it necessary to solve possibly hard integer linear programs, it has the advantage that more detailed mechanistic questions can be formulated. It is thus possible to query networks for general transformation motifs, and to automatically enumerate optimal and near-optimal pathways. Similarities and differences between our work and traditional approaches in metabolic network analysis are discussed in detail. To demonstrate the applicability of the mathematical framework to real-life problems we first explore the design space of possible non-oxidative glycolysis pathways and show that recent manually designed pathways can be further optimised. We then use a model of sugar chemistry to investigate pathways in the autocatalytic formose process. A graph transformation-based approach is used to automatically generate the reaction networks of interest. Copyright © 2017, The Authors. All rights reserved.

关键词： Integer programming

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Mapping geographical inequalities in childhood diarrhoeal morbidity and mortality in low-income and middle-income countries, 2000-17: analysis for the Global Burden of Disease Study 2017 (vol 395, pg 1779, 2020)

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LANCET 2020年第10239期395卷 1762-1762页

作者： Reiner, R. C., Jr. Hay, S., I Institute for Health Metrics and Evaluation University of Washington Seattle WA United States Department of Global Health School of Medicine University of Washington Seattle WA United States Department of Health Metrics Sciences School of Medicine University of Washington Seattle WA United States College of Health and Medical Sciences Haramaya University Harar Ethiopia Department of Epidemiology and Biostatistics Haramaya University Harar Ethiopia Department of Medical Laboratory Sciences Haramaya University Harar Ethiopia School of Nursing and Midwifery Haramaya University Harar Ethiopia School of Pharmacy Haramaya University Harar Ethiopia School of Public Health Haramaya University Harar Ethiopia Haramaya University Harar Ethiopia Advanced Diagnostic and Interventional Radiology Research Center Tehran University of Medical Sciences Tehran Iran Cancer Biology Research Center Tehran University of Medical Sciences Tehran Iran Cancer Research Institute Tehran University of Medical Sciences Tehran Iran Department of Economics and Management Sciences for Health Tehran University of Medical Sciences Tehran Iran Department of Environmental Health Engineering Tehran University of Medical Sciences Tehran Iran Department of Epidemiology and Biostatistics Tehran University of Medical Sciences Tehran Iran Department of Health Management and Economics Tehran University of Medical Sciences Tehran Iran Department of Microbiology Tehran University of Medical Sciences Tehran Iran Department of Pharmacology Tehran University of Medical Sciences Tehran Iran Digestive Diseases Research Institute Tehran University of Medical Sciences Tehran Iran Endocrinology and Metabolism Research Center Tehran University of Medical Sciences Tehran Iran Hematology-Oncology and Stem Cell Transplantation Research Center Tehran University of Medical Sciences Tehran Iran Iran National Institute of Health Research Tehran University of Medical Sciences Tehran Iran Metabolomics and

Summary Background Across low-income and middle-income countries (LMICs), one in ten deaths in children younger than 5 years is attributable to diarrhoea. The substantial between-country variation in both diarrhoea incidence and mortality is attributable to interventions that protect children, prevent infection, and treat disease. Identifying subnational regions with the highest burden and mapping associated risk factors can aid in reducing preventable childhood *** We used Bayesian model-based geostatistics and a geolocated dataset comprising 15 072 746 children younger than 5 years from 466 surveys in 94 LMICs, in combination with findings of the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2017, to estimate posterior distributions of diarrhoea prevalence, incidence, and mortality from 2000 to 2017. From these data, we estimated the burden of diarrhoea at varying subnational levels (termed units) by spatially aggregating draws, and we investigated the drivers of subnational patterns by creating aggregated risk factor *** The greatest declines in diarrhoeal mortality were seen in south and southeast Asia and South America, where 54·0% (95% uncertainty interval [UI] 38·1-65·8), 17·4% (7·7-28·4), and 59·5% (34·2-86·9) of units, respectively, recorded decreases in deaths from diarrhoea greater than 10%. Although children in much of Africa remain at high risk of death due to diarrhoea, regions with the most deaths were outside Africa, with the highest mortality units located in Pakistan. Indonesia showed the greatest within-country geographical inequality; some regions had mortality rates nearly four times the average country rate. Reductions in mortality were correlated to improvements in water, sanitation, and hygiene (WASH) or reductions in child growth failure (CGF). Similarly, most high-risk areas had poor WASH, high CGF, or low oral rehydration therapy *** By co-analysing geospatial trends in d

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