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Information system model for maize research to anticipate the impact of climate change on Indonesian food security

AIP Conference Proceedings 2023年第1期2594卷

作者： A. S. Perbangsa F. A. Munawwar M. B. Pabendon B. Pardamean Information Systems Department School of Information Systems Bina Nusantara University Jakarta 11480 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta 11480 Indonesia Indonesia Cereals Research Institute Maros South Sulawesi 90514 Indonesia Computer Science Department BINUS Graduate Program Master of Computer Science Bina Nusantara University Jakarta 11480 Indonesia

As a rich country in genetic resources, Indonesia has the potential for strengthening food security. Maize is one of the commodities that greatly affect food security in Indonesia. Maize is also widely used as animal feed. The high demand for maize requires efforts to increase the productivity of sustainable cultivation. Various research efforts that have been carried out require the support of a comprehensive information system. This study aimed to build a research model for maize genetic resource information systems that can help search for superior varieties. The data collection method used was collecting genotype, phenotype, climate data and interviewing the maize breeders or researchers. As for the design of the model, this study used the Object-Oriented Analysis & Design (OOAD) method with notation from Unified Modelling Language (UML). The result of this research was a web-based model of information systems for maize research.

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Antimicrobial activity of flower extracts against wound pathogens and fungi

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Current Research in Green and Sustainable Chemistry 2021年 4卷

作者： Abirami, S. Jabesta, J. Renitta, R. Emilin Anand, D. Alex Samrot, Antony V. Department of Microbiology Kamaraj College of Arts and Science Thoothukudi Tamil Nadu India Department of Food Processing Technology Karunya Institute of Technology and Sciences Karunya Nagar Coimbatore 641 114 Tamil Nadu India Department of Bioinformatics and the Centre for Molecular Data Science and Systems Biology Sathyabama Institute of Science and Technology Chennai 600119 India School of Bioscience Faculty of Medicine Bioscience and Nursing MAHSA University Jenjarom 42610 Selangor Malaysia

Since ages, the use of flowers as medicine throughout world is well known. This paper deals the antimicrobial screening of flowers of some medicinal plants against a few post-operative wound pathogens. Aqueous, ethanol and butyl alcohol extracts of flowers were subjected for antibacterial activity against the pathogens. Among the flower extracts tested, ethanol flower extract of Pedalium murex L. was having the highest antibacterial activity against pathogens. Thus, ethanol extract of P. murex (L) flower was subjected for further characterization study including GC-MS analysis. Ethanol flower extract of P. murex of 100 μg/ml showed 67.47 % free radical scavenging activity. © 2021 The Author(s)

关键词： Antimicrobial activity Extraction Pedalium murex Postoperative wound pathogens

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Gene knockout inference with variational graph autoencoder learning single-cell gene regulatory networks

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Nucleic acids research 2023年第13期51卷 6578-6592页

作者： Yongjian Yang Guanxun Li Yan Zhong Qian Xu Bo-Jia Chen Yu-Te Lin Robert S Chapkin James J Cai Department of Electrical and Computer Engineering Texas A&M University College Station TX 77843 USA. Department of Statistics Texas A&M University College Station TX 77843 USA. Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE School of Statistics East China Normal University 3663 North Zhongshan Road Shanghai 200062 China. Department of Veterinary Integrative Biosciences Texas A&M University College Station TX 77843 USA. Graduate Institute of Microbiology and Public Health College of Veterinary Medicine National Chung Hsing University Taichung 402 Taiwan. Graduate Institute of Biomedical Electronics and Bioinformatics National Taiwan University Taipei Taiwan. Program in Integrative & Complex Diseases Department of Nutrition Texas A&M University College Station TX 77843 USA. Interdisciplinary Program of Genetics Texas A&M University College Station TX 77843 USA.

In this paper, we introduce Gene Knockout Inference (GenKI), a virtual knockout (KO) tool for gene function prediction using single-cell RNA sequencing (scRNA-seq) data in the absence of KO samples when only wild-type (WT) samples are available. Without using any information from real KO samples, GenKI is designed to capture shifting patterns in gene regulation caused by the KO perturbation in an unsupervised manner and provide a robust and scalable framework for gene function studies. To achieve this goal, GenKI adapts a variational graph autoencoder (VGAE) model to learn latent representations of genes and interactions between genes from the input WT scRNA-seq data and a derived single-cell gene regulatory network (scGRN). The virtual KO data is then generated by computationally removing all edges of the KO gene-the gene to be knocked out for functional study-from the scGRN. The differences between WT and virtual KO data are discerned by using their corresponding latent parameters derived from the trained VGAE model. Our simulations show that GenKI accurately approximates the perturbation profiles upon gene KO and outperforms the state-of-the-art under a series of evaluation conditions. Using publicly available scRNA-seq data sets, we demonstrate that GenKI recapitulates discoveries of real-animal KO experiments and accurately predicts cell type-specific functions of KO genes. Thus, GenKI provides an in-silico alternative to KO experiments that may partially replace the need for genetically modified animals or other genetically perturbed systems.

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ProHap Explorer: Visualizing Haplotypes in Proteogenomic datasets

arXiv

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arXiv 2025年

作者： Vašíček, Jakub Skiadopoulou, Dafni Kuznetsova, Ksenia G. Käll, Lukas Vaudel, Marc Bruckner, Stefan Mohn Center for Diabetes Precision Medicine Department of Clinical Science University of Bergen Bergen Norway Computational Biology Unit Department of Informatics University of Bergen Bergen Norway Metabolism Program Broad Institute of MIT and Harvard CambridgeMA United States Science for Life Laboratory Department of Gene Technology KTH - Royal Institute of Technology Stockholm Sweden Department of Genetics and Bioinformatics Health Data and Digitalization Norwegian Institute of Public Health Oslo Norway Institute for Visual and Analytic Computing University of Rostock Rostock Germany

In mass spectrometry-based proteomics, experts usually project data onto a single set of reference sequences, overlooking the influence of common haplotypes (combinations of genetic variants inherited together from a parent). We recently introduced ProHap, a tool for generating customized protein haplotype databases. Here, we present ProHap Explorer, a visualization interface designed to investigate the influence of common haplotypes on the human proteome. It enables users to explore haplotypes, their effects on protein sequences, and the identification of non-canonical peptides in public mass spectrometry datasets. The design builds on well-established representations in biological sequence analysis, ensuring familiarity for domain experts while integrating novel interactive elements tailored to proteogenomic data exploration. User interviews with proteomics experts confirmed the tool's utility, highlighting its ability to reveal whether haplotypes affect proteins of interest. By facilitating the intuitive exploration of proteogenomic variation, ProHap Explorer supports research in personalized medicine and the development of targeted therapies. © 2025, CC BY.

关键词： Proteomics

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Novel strategy for disease risk prediction incorporating predicted gene expression and DNA methylation data:a multi-phased study of prostate cancer

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Cancer Communications 2021年第12期41卷 1387-1397页

作者： Chong Wu Jingjing Zhu Austin King Xiaoran Tong Qing Lu Jong Y.Park Liang Wang Guimin Gao Hong-Wen Deng Yaohua Yang Karen E.Knudsen Timothy R.Rebbeck Jirong Long Wei Zheng Wei Pan David V.Conti Christopher A Haiman Lang Wu Department of Statistics Florida State UniversityTallahasseeFL 32304USA Cancer Epidemiology Division Population Sciences in the Pacific ProgramUniversity of Hawaii Cancer CenterUniversity of Hawaii at ManoaHonoluluHI 96813USA Department of Epidemiology and Biostatistics Michigan State UniversityEast LansingMI 48824USA Department of Biostatistics University of FloridaGainesvilleFL 32603USA Department of Cancer Epidemiology H.Lee Moffitt Cancer Center and Research InstituteTampaFL 33612USA Department of Tumor Biology H.Lee Moffitt Cancer Center and Research InstituteTampaFL 33612USA Department of Public Health Sciences University of ChicagoChicagoIL 60637USA Center of Bioinformatics and Genomics Department of Global Biostatistics and Data ScienceTulane UniversityNew OrleansLA 70112USA Division of Epidemiology Department of MedicineVanderbilt Epidemiology CenterVanderbilt-Ingram Cancer CenterVanderbilt University Medical CenterNashvilleTN 37203USA Department of Cancer Biology Sidney Kimmel Cancer CenterThomas Jefferson UniversityPhiladelphiaPA 19107USA Department of Medical Oncology Dana-Farber Cancer InstituteBostonMA 02215USA Department of Epidemiology Harvard TH Chan School of Public HealthBostonMA 02115USA Division of Biostatistics University of MinnesotaMinneapolisMN 55455USA Department of Preventive Medicine Keck School of MedicineUniversity of Southern California/Norris Comprehensive Cancer CenterLos AngelesCA 90033USA

Background:DNA methylation and gene expression are known to play important roles in the etiology of human diseases such as prostate cancer(PCa).However,it has not yet been possible to incorporate information of DNA methylation and gene expression into polygenic risk scores(PRSs).Here,we aimed to develop and validate an improved PRS for PCa risk by incorporating genetically predicted gene expression and DNA methylation,and other genomic information using an integrative ***:Using data from the PRACTICAL consortium,we derived multiple sets of genetic scores,including those based on available single-nucleotide polymorphisms through widely used methods of pruning and thresholding,LDpred,LDpred-funt,AnnoPred,and EBPRS,as well as PRS constructed using the genetically predicted gene expression and DNA methylation through a revised pruning and thresholding *** the tuning step,using the UK Biobank data(1458 prevalent cases and 1467 controls),we selected PRSs with the best *** an independent set of data from the UK Biobank,we developed an integrative PRS combining information from individual ***,in the testing step,we tested the performance of the integrative PRS in another independent set of UK Biobank data of incident cases and ***:Our constructed PRS had improved performance(C statistics:76.1%)over PRSs constructed by individual benchmark methods(from 69.6%to 74.7%).Furthermore,our new PRS had much higher risk assessment power than family *** overall net reclassification improvement was 69.0%by adding PRS to the baseline model compared with 12.5%by adding family ***:We developed and validated a new PRS which may improve the utility in predicting the risk of developing *** innovative method can also be applied to other human diseases to improve risk prediction across multiple outcomes.

关键词： risk prediction polygenic risk scores predicted gene expression predicted DNA methylation integrative models prostate cancer

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STATISTICAL DESIGN AND RATIONALE OF THE BIOMARKERS FOR EVALUATING SPINE TREATMENTS (BEST) TRIAL

arXiv

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arXiv 2025年

作者： Sperger, John Kidwell, Kelley M. Mauck, Matthew C. Zhao, Beibo Anstrom, Kevin J. Batorsky, Anna Carey, Timothy S. Clauw, Daniel J. Freeman, Nikki L.B. Greco, Carol M. Ivanova, Anastasia Berkeley, Sara Jones McLean, Samuel A. Psioda, Matthew A. Rowland, Bryce Sowa, Gwendolyn A. Wasan, Ajay D. Zitovsky, Joshua P. Kosorok, Michael R. Department of Biostatistics Gillings School of Global Public Health University of North Carolina Chapel Hill United States Department of Biostatistics School of Public Health University of Michigan United States Department of Anesthesiology University of North Carolina Chapel Hill United States Collaborative Studies Coordinating Center Department of Biostatistics Gillings School of Global Public Health University of North Carolina Chapel Hill United States Department of Medicine University of North Carolina Chapel Hill United States Department of Anesthesiology Chronic Pain & Fatigue Research Center University of Michigan Ann Arbor United States Department of Biostatistics and Bioinformatics Duke University United States Department of Psychiatry University of Pittsburgh School of Medicine United States Department of Epidemiology Gillings School of Global Public Health University of North Carolina Chapel Hill United States Department of Psychiatry University of North Carolina Chapel Hill United States Statistics and Data Science Innovation Hub Biostatistics GSK Department of Physical Medicine and Rehabilitation University of Pittsburgh School of Medicine United States Departments of Anesthesiology and Perioperative Medicine and Psychiatry University of Pittsburgh School of Medicine United States Amazon Postdoctoral Scientist United States Ferguson Laboratory for Orthopaedic and Spine Research Bethel Musculoskeletal Research Center Department of Orthopaedic Surgery University of Pittsburgh School of Medicine United States Department of Bioengineering University of Pittsburgh Swanson School of Engineering United States Clinical and Translational Science Institute University of Pittsburgh United States Carolina Pragmatic Trials Laboratory North Carolina Translational and Clinical Sciences Institute UNC School of Medicine United States Duke Clinical Research Institute United States

Background/Aims: Chronic low back pain (cLBP) is a widely prevalent condition with potentially severe impacts on day-to-day functioning and quality of life. A variety of evidence-based treatment modalities exist, but all approaches have modest average treatment effects—potentially due to individual variation in treatment response and the diverse etiologies of cLBP. The Biomarkers for Evaluating Spine Treatments (BEST) trial was designed to investigate the potential for using patient features including biomarkers and phenotypic measurements to inform cLBP treatment. Methods: We provide an overview of the BEST trial and detail the statistical rationale for key study design decisions. We discuss the salient features of the scientific and clinical context of cLBP treatment that motivated the study design and planned analysis, describe modifications to existing methods that were needed because of the setting, and present simulation studies that were used to inform the study design. Results: The BEST trial was designed as a multi-site sequential, multiple-assignment randomized trial (SMART) of four cLBP treatment modalities. The primary objective was to inform a precision medicine approach to the treatment of cLBP by estimating the optimal treatment or combination of treatments based on patient features and individual patient’s response to the initial treatment. The primary analysis includes estimating an interpretable dynamic treatment regime for recommending treatments based on patient features and investigating the subgroups that respond best to each one of the treatment modalities. The trial aimed to enroll 630 protocol completers. Broad eligibility criteria were used to improve the generalizability of study results. Notably, participants could be excluded from one of the four interventions and still be eligible for the study. We modified the minimization method for reducing covariate imbalance to allow for these exclusions. Conclusion: The BEST trial may pave the way

关键词： Patient treatment

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U1 snRNP regulates alternative promoter activity by inhibiting premature polyadenylation

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Molecular Cell 2025年第10期85卷 1968-1981.e7页

作者： Kim, GyeungYun Carroll, Christine L. Wakefield, Zachary Peters Tuncay, Mustafa Fiszbein, Ana Biology Department Boston University Boston 02215 United States Graduate Program in Molecular Biology Cell Biology & Biochemistry Boston University Boston 02215 United States Graduate Program in Cell and Molecular Biology Boston University Boston 02215 United States Bioinformatics Program Faculty of Computing and Data Science Boston University Boston 02215 United States Center for Computing & Data Sciences Boston University Boston 02215 United States

Emerging evidence indicates that splicing factors mediate the close link between transcription and splicing. However, the mechanisms underlying this coupling remain unclear. U1 small nuclear ribonucleoprotein particle (U1 snRNP) not only initiates splicing but also plays a crucial role in preventing premature cleavage and polyadenylation, facilitating long-distance transcriptional elongation. Here, we show that U1 snRNP regulates alternative promoter activity in human cells by inhibiting premature polyadenylation. In genes carrying premature polyadenylation sites between two promoters, U1 snRNP inhibition with antisense oligonucleotides leads to a significant decrease in downstream promoter activity. Conversely, restoring U1 snRNP activity or inhibiting premature polyadenylation rescues downstream promoter activity. Mechanistically, U1 snRNP inhibition correlates with reduced chromatin accessibility, decreased RNA polymerase II serine 5 phosphorylation, and increased promoter-proximal pause at downstream promoters. Our findings support a model in which U1 snRNP favors productive elongation from upstream promoters, triggering downstream promoter activation by destabilizing nucleosomes and promoting promoter escape. © 2025 The Author(s)

关键词： alternative promoters dowsntream promoters promoter-proximal pause splicing factors splicing transcription transcription cooperativity transcription initiation transcription interfierence transcription start sites U1 snRNP

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Real-time Weed Identification Using Machine Learning and Image Processing in Oil Palm Plantations

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IOP Conference Series: Earth and Environmental science 2022年第1期998卷

作者： Erick Firmansyah Teddy Suparyanto Alam Ahmad Hidayat Bens Pardamean Agricultural Engineering Department Institute of Agricultural STIPER Yogyakarta 55282 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program – Master of Computer Science Bina Nusantara University Jakarta Indonesia 11480

The effectiveness and efficiency of the operation of oil palm plantations are considered to be the most crucial factor to develop the productivity and profitability of the palm oil business. One of the major obstacles for the plants to optimally produce crops based on their capacity is caused by the presence of noxious weeds in the plantation area. However, weed control via chemical processes may potentially harm the surrounding environment if it is not properly managed. Therefore, an automatic system to assist the farmers to identify and control the weeds is required to minimize harmful impacts on the environment. Machine Learning (ML) and Artificial Intelligence (AI)-based systems provide powerful tools to perform such tasks. In this work, we aim for an ML-based system design to perform an automatic weed recognition task. The methodology can provide an effort for environmental sustainability in oil palm plantations. The weed identification involves the description, the local names, and tolerance class of the weeds as well as suggestions to control them. The flow of this work consists of weed and herbicide data acquisition, data labeling, model configurations, and data training. Further, the proposed system can be adopted as an android-based application in mobile devices that can deploy the trained model to predict weed category in both real-time and non-real-time tasks.

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Single-cell landscape of innate and acquired drug resistance in acute myeloid leukemia

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Nature Communications 2024年第1期15卷 9402-9402页

作者： Wegmann, Rebekka Bonilla, Ximena Casanova, Ruben Chevrier, Stéphane Coelho, Ricardo Esposito, Cinzia Ficek-Pascual, Joanna Goetze, Sandra Gut, Gabriele Jacob, Francis Jacobs, Andrea Kuipers, Jack Lischetti, Ulrike Mena, Julien Milani, Emanuela S. Prummer, Michael Del Castillo, Jacobo Sarabia Singer, Franziska Sivapatham, Sujana Toussaint, Nora C. Vilinovszki, Oliver Wildschut, Mattheus H. E. Thavayogarajah, Tharshika Malani, Disha Zuend, Gregor Zoche, Martin Zimmermann, Marc Ziegler, Johanna Yu, Shuqing Wey, Norbert Wendt, Fabian Weller, Michael Weber, Walter P. Weber, Sandra Vlajnic, Tatjana Vetter, Marcus Van Drogen, Audrey Tusup, Marina Tuncel, Mustafa A. Tosevski, Vinko Tolnay, Markus Thomas, Tinu M. Tanna, Tanmay Stekhoven, Daniel J. Stark, Stefan Sreedharan, Vipin T. Sobottka, Bettina Snijder, Berend Shao, Wenguang Senti, Gabriela Schär, Tobias Schwan, Severin Schwalie, Petra C. Schlenker, Ramona Santacroce, Natascha Rätsch, Gunnar Rosano-González, María L. Rommel, Christian Ritter, Mathilde Rimmer, Natalie Prélot, Laurie Piscuoglio, Salvatore Pelkmans, Lucas Pedrioli, Patrick G. A. Lopez, Monica Nunez Nowak, Marta Nicolet, Stefan Ng, Charlotte K. Y. Murri, Riccardo Muenst, Simone Moch, Holger Miglino, Nicola Metzler, Julian M. Mehnert, Martin Markolin, Philipp Maass, Gerd Lugert, Sebastian Lombardo, Flavio C. Levesque, Mitchell Lehmann, Kjong-Van Kurzeder, Christian Kunze, Christian P. Kuebler, Werner Koelzer, Viktor H. Kahraman, Abdullah Kahles, André Jermann, Philip M. James, Alva R. Jahn, Katharina Jaeger, Tim M. Irmisch, Anja Immer, Alexander Huesser, Tamara Holtackers, Rene Herter, Sylvia Heinzelmann-Schwarz, Viola Haeuptle, Pirmin Günther, Detlef Grob, Linda Frey, Bruno Frei, Anja L. Ferreira, Pedro F. Fedier, André Eschbach, Katja Erkens, Martin Engler, Stefanie Dummer, Reinhard Drăgan, Monica-Andreea Davidson, Natalie R. Danenberg, Esther D’Costa, Maya Chicherova, Natalia Calgua, Byron Bosshard, Lars Bodenmiller, Bernd Bertolini, Anne Bernasconi, Lara Beisel, Christian Beerenwinkel, Niko Beck-Schim Institute of Molecular Systems Biology Department of Biology ETH Zurich Zurich Switzerland Department of Computer Science ETH Zurich Zurich Switzerland Department of Quantitative Biomedicine University of Zurich Zurich Switzerland Department of Biomedicine University Hospital Basel and University of Basel Basel Switzerland Institute of Molecular Life Sciences University of Zurich Zurich Switzerland Department of Health Sciences and Technology ETH Zurich Zurich Switzerland ETH PHRT Swiss Multi-Omics Center (SMOC) Lausanne Switzerland SIB Swiss Institute of Bioinformatics Lausanne Switzerland Department of Biosystems Science and Engineering ETH Zurich Zurich Switzerland NEXUS Personalized Health Technologies ETH Zurich Zurich Switzerland Swiss Data Science Center ETH Zürich Zurich Switzerland Department of Medical Oncology and Hematology University Hospital Zurich Zurich Switzerland Harvard Medical School and Dana-Farber Cancer Institute Boston United States Roche Pharmaceutical Research and Early Development Roche Innovation Center Zurich Zurich Switzerland Department of Pathology and Molecular Pathology University Hospital Zurich Zurich Switzerland University of Zurich Faculty of Medicine Zurich Switzerland Department of Dermatology University Hospital Zurich Zurich Switzerland AI Center at ETH Zurich Zurich Switzerland Institute of Medical Genetics and Pathology University Hospital Basel Basel Switzerland

Deep single-cell multi-omic profiling offers a promising approach to understand and overcome drug resistance in relapsed or refractory (rr) acute myeloid leukemia (AML). Here, we combine single-cell ex vivo drug profiling (pharmacoscopy) with single-cell and bulk DNA, RNA, and protein analyses, alongside clinical data from 21 rrAML patients. Unsupervised data integration reveals reduced ex vivo response to the Bcl-2 inhibitor venetoclax (VEN) in patients treated with both a hypomethylating agent (HMA) and VEN, compared to those pre-exposed to chemotherapy or HMA alone. Integrative analysis identifies both known and unreported mechanisms of innate and treatment-related VEN resistance and suggests alternative treatments, like targeting increased proliferation with the PLK inhibitor volasertib. Additionally, high CD36 expression in VEN-resistant blasts associates with sensitivity to CD36-targeted antibody treatment ex vivo. This study demonstrates how single-cell multi-omic profiling can uncover drug resistance mechanisms and treatment vulnerabilities, providing a valuable resource for future AML research. © 2024. The Author(s).

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Smart IoT CPO Storage Tank

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IOP Conference Series: Earth and Environmental science 2022年第1期998卷

作者： Rengga Arnalis Renjani Hermantoro Prima Okta Adi Nugraha Kartika Purwandari Teddy Suparyanto Bens Pardamean Department of Agricultural Engineering Institute of Agriculture STIPER Yogyakarta Indonesia 55281 Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta Indonesia 11480

Indonesia's crude palm oil (CPO) production from year to year continues to increase, at the end of 2020 it reached 17.35 million tons, up 3.6% from the previous year. Increasing production will result in more CPO stock and require good storage. The storage process that occurs is to maintain the temperature of the CPO so that the quality is not damaged. This temperature regulation is still done manually and raises the risk of work accidents. The purpose of this research is to create a temperature control system and automatic volume measurement that can be monitored from a smartphone. The manufacture of a control system used ESP8266 NodeMCu microcontroller, temperature sensor, proximity sensor, and 1000-Watt heater. Programming used the Arduino IDE and C++. The result of this study was an IoT CPO Storage Tank design equipped with sensors and microcontrollers. The temperature was measured with the DS18B20 sensor had a data accuracy of 99.19% while the volume measured with the HC-SR04 sensor had an accuracy of 99.78%. data obtained from the sensor could be seen through the Thingspeak application from a computer or smartphone.

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