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Data analysis guidelines for single‑cell RNA‑seq in biomedical studies and clinical applications

Military Medical Research 2023年第4期10卷 529-553页

作者： Min Su Tao Pan Qiu‑Zhen Chen Wei‑Wei Zhou Yi Gong Gang Xu Huan‑Yu Yan Si Li Qiao‑Zhen Shi Ya Zhang Xiao He Chun‑Jie Jiang Shi‑Cai Fan Xia Li Murray J.Cairns Xi Wang Yong‑Sheng Li State Key Laboratory of Reproductive Medicine Nanjing Medical UniversityNanjing 211166China College of Biomedical Information and Engineering the First Affiliated Hospital of Hainan Medical UniversityHainan Medical UniversityHaikou 571199HainanChina College of Bioinformatics Science and Technology Harbin Medical UniversityHarbin 150081HeilongjiangChina Department of Immunology Nanjing Medical UniversityNanjing 211166China Department of Laboratory Medicine Women and Children’s Hospital of Chongqing Medical UniversityChongqing 401174China Baylor College of Medicine HoustonTX 77030USA Shenzhen Institute for Advanced Study University of Electronic Science and Technology of ChinaShenzhen 518110GuangdongChina School of Biomedical Sciences and Pharmacy Faculty of Health and Medicinethe University of NewcastleUniversity DriveCallaghanNSW 2308Australia Precision Medicine Research Program Hunter Medical Research InstituteNew Lambton HeightsNSW 2305Australia

The application of single-cell RNA sequencing(scRNA-seq)in biomedical research has advanced our understanding of the pathogenesis of disease and provided valuable insights into new diagnostic and therapeutic *** the expansion of capacity for high-throughput scRNA-seq,including clinical samples,the analysis of these huge volumes of data has become a daunting prospect for researchers entering this ***,we review the workflow for typical scRNA-seq data analysis,covering raw data processing and quality control,basic data analysis applicable for almost all scRNA-seq data sets,and advanced data analysis that should be tailored to specific scientific *** summarizing the current methods for each analysis step,we also provide an online repository of software and wrapped-up scripts to support the *** and caveats are pointed out for some specific analysis tasks and *** hope this resource will be helpful to researchers engaging with scRNA-seq,in particular for emerging clinical applications.

关键词： Single-cell RNA-sequencing(scRNA-seq) Data analysis Biomedical research Clinical applications

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A Bayesian framework for incorporating exposure uncertainty into health analyses with application to air pollution and stillbirth

arXiv

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arXiv 2022年

作者： Comess, Saskia Chang, Howard H. Warren, Joshua L. Emmett Interdisciplinary Program in Environment and Resources Stanford University StanfordCA94305 United States Department of Biostatistics and Bioinformatics Emory University AtlantaGA30329 United States Department of Biostatistics Yale University New HavenCT06510 United States

Studies of the relationships between environmental exposures and adverse health outcomes often rely on a two-stage statistical modeling approach, where exposure is modeled/predicted in the first stage and used as input to a separately fit health outcome analysis in the second stage. Uncertainty in these predictions is frequently ignored, or accounted for in an overly simplistic manner, when estimating the associations of interest. Working in the Bayesian setting, we propose a flexible kernel density estimation (KDE) approach for fully utilizing posterior output from the first stage modeling/prediction to make accurate inference on the association between exposure and health in the second stage, derive the full conditional distributions needed for efficient model fitting, detail its connections with existing approaches, and compare its performance through simulation. Our KDE approach is shown to generally have improved performance across several settings and model comparison metrics. Using competing approaches, we investigate the association between lagged daily ambient fine particulate matter levels and stillbirth counts in New Jersey (2011-2015), observing an increase in risk with elevated exposure three days prior to delivery. The newly developed methods are available in the R package KDExp. © 2022, CC BY.

关键词： Uncertainty analysis

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Mobile Application Implementation as Agriculture 4.0 Strategy for Sugarcane Yield Prediction

Mobile Application Implementation as Agriculture 4.0 Strateg...

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HCI and UX Conference in Indonesia (CHIuXiD), International

作者： Hangger Gahara Mawandha Reza Rahutomo Teddy Suparyanto Bens Pardamean Faculty of Agricultural Technology Institut Pertanian Stiper Yogyakarta Indonesia Information Systems Department School of Information Systems Bina Nusantara University Jakarta Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta Indonesia

ISBN: (数字)9798350304084

ISBN: (纸本)9798350304091

Information engineering strategies play a significant and transformative role in shaping the landscape of digital agriculture. It drives innovation and efficiency in modern farming practices, with a specific focus on enhancing the value of agricultural commodities, such as sugarcane. The application of mobile technology plays a crucial part in achieving increased sugarcane productivity. Mobile applications, equipped with advanced developer features, offer rapid and user-friendly access to vital information. Traditional methods of estimating sugarcane production relied on manual data recording on paper, followed by data transfer to computer systems, typically managed by sugar factory junior plant officers. This conventional approach presents several inherent weaknesses, including time and effort intensiveness during data recording and entry. Additionally, the potential for errors in calculation and data input is a concern. The storage capacity for paper-based documents is finite, and farmers are often unable to autonomously assess their production potential. The objective of this research is to confront these obstacles by creating a sugarcane production application for Android. This application functions as an information engineering approach focused on forecasting sugarcane yields for plantation owners and their assistants. The development procedure adhered to the systematic waterfall method, following the principles of the Software Development Life Cycle (SDLC) model. Data collection was carried out through observations, while interviews with junior plant officers provided valuable insights into sugarcane estimation techniques. Analysis involved the synthesis of observational and interview data to inform the design of the application’s interface and algorithmic system. The resulting application significantly simplifies the process of estimating production potential for farmers, enabling them to access sugarcane productivity data during harvest. Consequently, sugar

关键词： Productivity Operating systems Estimation Production facilities Raw materials Mobile applications Recording

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The bourque distances for mutation trees of cancers 20

The bourque distances for mutation trees of cancers

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20th International Workshop on Algorithms in bioinformatics, WABI 2020

作者： Jahn, Katharina Beerenwinkel, Niko Zhang, Louxin Department of Biosystems Science and Engineering ETH Zurich Basel Switzerland SIB Swiss Institute of Bioinformatics Basel Switzerland Department of Mathematics and Computational Biology Program National University of Singapore Singapore

ISBN: (纸本)9783959771610

Mutation trees are rooted trees of arbitrary node degree in which each node is labeled with a mutation set. These trees, also referred to as clonal trees, are used in computational oncology to represent the mutational history of tumours. Classical tree metrics such as the popular RobinsonFoulds distance are of limited use for the comparison of mutation trees. One reason is that mutation trees inferred with different methods or for different patients often contain different sets of mutation labels. Here, we generalize the RobinsonFoulds distance into a set of distance metrics called Bourque distances for comparing mutation trees. A connection between the RobinsonFoulds distance and the nearest neighbor interchange distance is also presented. © Katharina Jahn, Niko Beerenwinkel, and Louxin Zhang;licensed under Creative Commons License CC-BY

关键词： Bourque distance Clonal trees Mutation trees Phylogenetic trees Robinson–Foulds distance Tree distance Tree metric

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Construction and Characterization of a Novel Recombinant Attenuated and Replication-Deficient Candidate Human Adenovirus Type 3 Vaccine:"Adenovirus Vaccine Within an Adenovirus Vector"

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Virologica Sinica 2021年第3期36卷 354-364页

作者： Yuqian Yan Shuping Jing Liqiang Feng Jing Zhang Zhiwei Zeng Min Li Shan Zhao Junxian Ou Wendong Lan Wenyi Guan Xiaowei Wu Jianguo Wu Donald Seto Qiwei Zhang Guangdong Provincial Key Laboratory of Tropical Disease Research School of Public HealthSouthern Medical UniversityGuangzhou 510515China Microbiological Laboratory Zhuhai Center for Disease Control and PreventionZhuhai 519000China Guangzhou Institutes of Biomedicine and Health Chinese Academy of SciencesGuangzhou 510530China Guangdong Provincial Key Laboratory of Virology Institute of Medical MicrobiologyJinan UniversityGuangzhou 510632China Bioinformatics and Computational Biology Program School of Systems BiologyGeorge Mason UniversityManassasVA 20110USA

Human adenoviruses(HAd Vs)are highly contagious and result in large number of acute respiratory disease(ARD)cases with severe morbidity and *** adenovirus type 3(HAd V-3)is the most common type that causes ARD outbreaks in Asia,Europe,and the ***,there is currently no vaccine approved for its general *** hexon protein contains the main neutralizing epitopes,provoking strong and lasting *** this study,a novel recombinant and attenuated adenovirus vaccine candidate against HAd V-3 was constructed based on a commercially-available replication-defective HAd V-5 gene therapy and vaccine *** entire HAd V-3 hexon gene was integrated into the E1 region of the vector by homologous recombination using a bacterial *** resultant recombinants expressing the HAd V-3 hexon protein were rescued in AD293 cells,identified and characterized by RT-PCR,Western blots,indirect immunofluorescence,and electron *** potential vaccine candidate had a similar replicative efficacy as the wild-type HAd V-3 ***,and importantly,the vaccine strain had been rendered replication-defective and was incapable of replication in A549 cells after more than twentygeneration passages in AD293 *** represents a significant safety *** mice immunized both intranasally and intramuscularly by this vaccine candidate raised significant neutralizing antibodies against HAd ***,this recombinant,attenuated,and safe adenovirus vaccine is a promising HAd V-3 vaccine *** strategy of using a clinically approved and replication-defective HAd V-5 vector provides a novel approach to develop universal adenovirus vaccine candidates against all the other types of adenoviruses causing ARDs and perhaps other adenovirus-associated diseases.

关键词： Adenovirus vaccine Human adenovirus type 3(HAdV-3) Replication-deficient adenovirus vector Immunity in BALB/c mice Recombination

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Effects of Eimeria tenella on Cecal Luminal and Mucosal Microbiota in Broiler Chickens

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Avian diseases 2022年第1期66卷 39-52页

作者： Campos, Philip M. Miska, Katarzyna B. Kahl, Stanislaw Jenkins, Mark C. Shao, Jonathan Proszkowiec-Weglarz, Monika Oak Ridge Institute for Science and Education (ORISE) USDA-ARS Research Participation Program Oak Ridge TN 37830 NEA Bioinformatics USDA-ARS Beltsville United States NEA Beltsville Agriculture Research Center Animal Biosciences and Biotechnology Laboratory USDA-ARS Beltsville United States NEA Beltsville Agriculture Research Center Animal Parasitic Diseases Laboratory USDA-ARS Beltsville United States NEA Beltsville Agriculture Research Center Animal Biosciences and Biotechnology Laboratory USDA-ARS Beltsville United States

The intestinal disease coccidiosis, caused by parasitic Eimeria species, severely impacts poultry production, leading to an estimated $14 billion in annual losses worldwide. As the poultry industry moves away from antibiotics as a treatment for diseases, a better understanding of the microbiota is required to develop other solutions such as probiotics, prebiotics, and nutritional supplements. This study aimed to investigate the effects of Eimeria tenella infection on luminal (cecal contents [CeC]) and mucosal (cecal epithelial scrapings [CeS]) microbial populations in 288 Ross 708 broiler chickens at multiple time points postinfection (PI). By use of 16S rRNA amplicon sequencing, it was revealed that microbial diversity differed in infected (IF) chickens in comparison to the control (C) in both CeC and CeS microbiota at the peak of infection (7 days PI), when simultaneously IF birds saw reduced body weight gain and a higher feed conversion ratio. Infection resulted in a significant differential abundance of some bacterial taxa, including increases in potential secondary pathogens Escherichia coli, Enterococcus, Clostridium, and Proteus and a decrease in the short chain fatty acid-producing family Lachnospiraceae. Predicted metagenomic pathways associated with E. coli, such as those responsible for amino acid biosynthesis, were differentially expressed in IF birds. In conclusion, our results show that E. tenella infection disturbs luminal and mucosal microbiota balance in chickens. Moreover, the luminal microbiota seems to be more susceptible to prolonged imbalance due to IF, whereas the mucosal microbiota appeared to be affected only in the short term, demonstrating the importance of researching both the luminal and mucosal microbiota of the cecum.;Efectos de Eimeria tenella sobre la microbiota luminal y de la mucosa de los ciegos en pollos de engorde. La coccidiosis, una enfermedad intestinal causada por especies parasitarias de Eimeria, afecta gravemente la produc

关键词： 16S broiler chickens cecum coccidia microbiota

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Correction: Effects of polygenic risk score and sodium and potassium intake on hypertension in Asians: A nationwide prospective cohort study (July,10.1038/s41440-024-01784-7,2024)

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HYPERTENSION RESEARCH 2024年第11期47卷 3286-3286页

作者： Bae, Eunjin Ji, Yunmi Jo, Jinyeon Kim, Yaerim Lee, Jung Pyo Won, Sungho Lee, Jeonghwan Department of Internal Medicine Gyeongsang National University Changwon Hospital Changwon Republic of Korea Department of Internal Medicine College of Medicine Gyeongsang National University Jinju Republic of Korea Institute of Medical Science College of Medicine Gyeongsang National University Jinju Republic of Korea College of Natural Sciences Interdisciplinary Program in Bioinformatics Seoul National University Seoul Republic of Korea Department of Public Health Sciences Institute of Health & Environment Seoul National University Seoul Republic of Korea Interdisciplinary Program for Bioinformatics College of Natural Science Seoul National University Seoul Republic of Korea RexSoft Corps Seoul Republic of Korea Department of Internal Medicine College of Medicine Keimyung University School of Medicine Daegu Republic of Korea Department of Internal Medicine Seoul National University Boramae Medical Center Seoul Republic of Korea Department of Internal Medicine Seoul National University College of Medicine Seoul Republic of Korea

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Biocontrol potential of Vibrio maritimus chitinase: Heterologous expression and insecticidal activity against Acanthoscelides obtectus

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International Journal of Biological Macromolecules 2025年 313卷 144285页

作者： Dikbaş, Neslihan Tülek, Ahmet Uçar, Sevda Alım, Şeyma Servili, Burak Paçal, Nurettin Tozlu, Göksel Ercisli, Sezai Ataturk University Agricultural Faculty Department of Agricultural Biotechnology Erzurum Turkey Iğdır University Department of Bioengineeringand Sciences Iğdır Turkey Sivas Science and Technology University Faculty of Agricultural Sciences and Technology Department of Field Crops Sivas Turkey Kadir Has University of Science and Engineering Bioinformatics and Genetics Program Istanbul Turkey Ataturk University Agricultural Faculty Department of Plant Protection Erzurum Turkey Ataturk University Agricultural Faculty Department of Horticulture Erzurum Turkey

In this study, the chitinase gene from the marine bacterium Vibrio maritimus was heterologously expressed in Escherichia coli, purified via affinity chromatography and tested for its insecticidal activity against the storage pest Acanthoscelides obtectus. The recombinant VmChiA protein exhibited a molecular mass of ∼60 kDa, with optimum activity observed at pH 6.0 and 40 °C. Enzyme kinetic analysis revealed a Km value of 0.042 mM, Vmax of 17.48 μmol min−1, kcat of 1.75 min−1 and catalytic efficiency of 41.61 mM−1 min−1, respectively. Furthermore, a dose of 40 U mL−1 of recombinant VmChiA showed similar efficacy to malathion insecticide against A. obtectus, with 100 % mortality in both treatments. LC50 and LC90 values of VmChiA were 13.95 U mL−1 and 27.66 U mL−1, respectively. Furthermore, the three-dimensional structure of the catalytic site of VmChiA was modeled. Molecular dynamics simulation technique was used to explore and analyze the dynamics and interactions. A salt bridge (GLU274-ARG296) in the α + β domain was observed as a critical feature facilitating substrate (GlcNAc)2 binding and enzymatic activity. These findings demonstrate that recombinant VmChiA possesses potent insecticidal properties, highlighting its potential as a bio-based, eco-friendly alternative for managing significant agricultural pests. © 2025 Elsevier B.V.

关键词： Affinity chromatography

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Graph Fourier MMD for Signals on Graphs

Graph Fourier MMD for Signals on Graphs

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International Conference on Sampling Theory and Applications (SampTA)

作者： Samuel Leone Aarthi Venkat Guillaume Huguet Alexander Tong Guy Wolf Smita Krishnaswamy Applied Math Program New Haven Connecticut Computational Biology & Bioinformatics Program Yale University New Haven Connecticut Dept. of Math. & Stat Mila - Quebec AI Institute Université de Montréal Montreal Canada Dept. of Comp. Sci. & Oper. Res. Mila-Quebec AI Institute Université de Montréal Montreal Canada Department of Computer Science Department of Genetics Yale University New Haven Connecticut

While numerous methods have been proposed for computing distances between probability distributions in Euclidean space, relatively little attention has been given to computing such distances for distributions on graphs. However, there has been a marked increase in data that either lies on graph (such as protein interaction networks) or can be modeled as a graph (single cell data), particularly in the biomedical sciences. Thus, it becomes important to find ways to compare signals defined on such graphs. Here, we propose Graph Fourier MMD (GFMMD), a novel distance between distributions and signals on graphs. GFMMD is defined via an optimal witness function that is both smooth on the graph and maximizes the difference in expectation between the pair of distributions on the graph. We find an analytical solution to this optimization problem as well as an embedding of distributions that results from this method. We also prove several properties of this method including scale invariance and applicability to disconnected graphs. We showcase it on graph benchmark datasets as well on single cell RNA-sequencing data analysis. In the latter, we use the GFMMD-based gene embeddings to find meaningful gene clusters. We also propose a novel type of score for gene selection called gene localization score which helps select genes for cellular state space characterization.

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A Chromosome-Level Genome Assembly and Annotation for the Clouded Apollo Butterfly (Parnassius mnemosyne): A Species of Global Conservation Concern (vol 16, evae031, 2024)

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GENOME BIOLOGY AND EVOLUTION 2024年第5期16卷 evae031页

作者： Hoglund, Jacob Dias, Guilherme Olsen, Remi-Andre Soares, Andre Bunikis, Ignas Talla, Venkat Backstrom, Niclas Animal Ecology Program Department of Ecology and Genetics (IEG) Uppsala University Uppsala SE-752 36 Sweden. National Bioinformatics Infrastructure Sweden (NBIS) Science for Life Laboratory Uppsala 752 37 Sweden. Science for Life Laboratory Department of Biochemistry and Biophysics Stockholm University Solna 17165 Sweden. Uppsala Genome Center Department of Immunology Genetics and Pathology Uppsala University National Genomics Infrastructure hosted by SciLifeLab Uppsala Sweden. Department of Medical Biochemistry and Microbiology Uppsala University Uppsala 752 37 Sweden. Evolutionary Biology Program Department of Ecology and Genetics (IEG) Uppsala University Uppsala SE-752 36 Sweden.

The clouded apollo (Parnassius mnemosyne) is a palearctic butterfly distributed over a large part of western Eurasia, but population declines and fragmentation have been observed in many parts of the range. The development of genomic tools can help to shed light on the genetic consequences of the decline and to make informed decisions about direct conservation actions. Here, we present a high-contiguity, chromosome-level genome assembly of a female clouded apollo butterfly and provide detailed annotations of genes and transposable elements. We find that the large genome (1.5 Gb) of the clouded apollo is extraordinarily repeat rich (73%). Despite that, the combination of sequencing techniques allowed us to assemble all chromosomes (nc = 29) to a high degree of completeness. The annotation resulted in a relatively high number of protein-coding genes (22,854) compared with other Lepidoptera, of which a large proportion (21,635) could be assigned functions based on homology with other species. A comparative analysis indicates that overall genome structure has been largely conserved, both within the genus and compared with the ancestral lepidopteran karyotype. The high-quality genome assembly and detailed annotation presented here will constitute an important tool for forthcoming efforts aimed at understanding the genetic consequences of fragmentation and decline, as well as for assessments of genetic diversity, population structure, inbreeding, and genetic load in the clouded apollo butterfly.

关键词： Parnassius mnemosyne clouded apollo butterfly gene annotation genome assembly genome size repeat annotation

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