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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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Cover Feature: Diversity Oriented Strategy (DOS) for the Efficient Synthesis of Benzofuro[2,3-b]pyridine Derivatives with Anticancer Activity (ChemMedChem 3/2025)

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ChemMedChem 2025年第3期20卷

作者： Reymark Ereje Jantana Yahuafai Theeranuch Jaroenchuensiri Patcharaporn Supakijjanusorn Sukanya Unson Borwornlak Toopradab Thanyada Rungrotmongkol Somsak Pianwanit Chanat Aonbangkhen Tanatorn Khotavivattana Center of Excellence in Natural Products Department of Chemistry Faculty of Science Chulalongkorn University Pathumwan Bangkok 10330 Thailand Department of Physical Sciences College of Science University of the Philippines Baguio Baguio City 2600 Philippines Clinical Research Section Division of Research and Academic Support National Cancer Institute Bangkok 10400 Thailand Program in Bioinformatics and Computational Biology Graduate School Chulalongkorn University Pathumwan Bangkok 10330 Thailand Center of Excellence in Computational Chemistry Department of Chemistry Faculty of Science Chulalongkorn University Pathumwan Bangkok 10330 Thailand

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Evaluation of Frequency-Dependent Effects of Deep Brain Stimulation in a Cortex-Basal Ganglia-Thalamus Network Model of Parkinson’s Disease*

Evaluation of Frequency-Dependent Effects of Deep Brain Stim...

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Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)

作者： Marcelo R. Romano Renan C. Moioli Leonardo A. Elias Neural Engineering Research Laboratory School of Electrical and Computer Engineering University of Campinas Campinas SP Brazil Graduate Program in Bioinformatics Digital Metropolis Institute Federal University of Rio Grande do Norte Natal Brazil Center for Biomedical Engineering University of Campinas Campinas SP Brazil

ISBN: (数字)9781728119908

ISBN: (纸本)9781728119915

Parkinson's disease (PD) is a chronic neurodegenerative disease whose motor symptoms are accompanied by an exaggerated power in the alpha-beta (7-35Hz) band and an increased synchronization of neurons encompassing the cortex-basal ganglia-thalamus network. Currently, deep brain stimulation (DBS) is used as an effective therapy for reducing the excessive power and synchrony observed in brain circuits, thereby ameliorating the PD symptoms. In the present study, we used a biologically plausible computational model of cortex-basal ganglia-thalamus network, which represents both healthy and PD conditions, to systematically investigate the effects of DBS frequency on the model outputs. DBS was applied to the subthalamic nucleus (STN) at different stimulation frequencies (40Hz to 300Hz). Spike train variability and spectral power in the 7-35Hz band were measured from the several nuclei represented in the model. In addition, the magnitude squared coherence between the nuclei was assessed. An increased DBS frequency tended to produce interspike intervals (ISIs) with higher variability as compared to PD condition. Also, DBS significantly reduced the alpha-beta power for almost all brain nuclei. The median of the magnitude-squared coherence matrix (which is a metric of global network synchronization) decreased significantly with the increase of DBS frequency.

关键词： Satellite broadcasting Brain modeling Neurons Computational modeling Coherence Partial discharges Synchronization

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Astrocytic Cebpd Regulates Pentraxin 3 Expression to Promote Fibrotic Scar Formation After Spinal Cord Injury

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Molecular neurobiology 2023年第4期60卷 2200-2208页

作者： Shao-Ming Wang Jung-Yu C Hsu Chiung-Yuan Ko Hsiang-En Wu Yu-Wei Hsiao Ju-Ming Wang Graduate Institute of Biomedical Sciences China Medical University Taichung 404333 Taiwan. wangs@mail.cmu.edu.tw. Neuroscience and Brain Disease Center China Medical University Taichung Taiwan. wangs@mail.cmu.edu.tw. Department of Neurology China Medical University Hospital Taichung Taiwan. wangs@mail.cmu.edu.tw. Department of Cell Biology and Anatomy College of Medicine National Cheng Kung University Tainan Taiwan. Ph.D. Program in Medical Neuroscience College of Medical Science and Technology Taipei Medical University Taipei Taiwan. TMU Research Center of Neuroscience Taipei Medical University Taipei Taiwan. TMU Research Center of Cancer Translational Medicine Taipei Taiwan. Cellular Pathobiology Section Integrative Neuroscience Research Branch Intramural Research Program National Institute on Drug Abuse NIH/DHHS Suite 3512 333 Cassell Drive Baltimore MD 21224 USA. Department of Biotechnology and Bioindustry Sciences College of Bioscience and Biotechnology National Cheng Kung University Tainan Taiwan. Department of Biotechnology and Bioindustry Sciences College of Bioscience and Biotechnology National Cheng Kung University Tainan Taiwan. yumingw@mail.ncku.edu.tw. Graduate Institute of Medical Sciences College of Medicine Taipei Medical University Taipei Taiwan. yumingw@mail.ncku.edu.tw. International Research Center for Wound Repair and Regeneration National Cheng Kung University Tainan Taiwan. yumingw@mail.ncku.edu.tw. Graduate Institute of Medicine College of Medicine Kaohsiung Medical University Kaohsiung Taiwan. yumingw@mail.ncku.edu.tw. Institute of Bioinformatics and Biosignal Transduction College of Bioscience and Biotechnology National Cheng Kung University Tainan 701 Taiwan. yumingw@mail.ncku.edu.tw.

Astroglial-fibrotic scars resulted from spinal cord injury affect motor and sensory function, leading to paralysis. In particular, the fibrotic scar is a main barrier that disrupts neuronal regeneration after spinal cord injury. However, the association between astrocytes and fibrotic scar formation is not yet understood. We have previously demonstrated that the transcriptional factor Cebpd contributes to astrogliosis, which promotes glial scar formation after spinal cord injury. Herein, we show that fibrotic scar formation was decreased in the epicenter region in Cebpd mice after contusive spinal cord injury and astrocytic Cebpd promoted fibroblast migration through secretion of Ptx3. Furthermore, the expression of Mmp3 was increased under recombinant protein Ptx3 treatment in fibroblasts by observing microarray data, resulting in fibroblast migration. In addition, regulation of Mmp3 occurs through the NFκB signaling pathway by using an irreversible inhibitor of IκBα phosphorylation in pretreated fibroblasts. Of note, we used the synthetic peptide RI37, which blocks fibroblast migration and decreases fibroblast Mmp3 expression in IL-1β-treated astrocyte conditioned media. Collectively, our data suggest that fibroblast migration can be affected by astrocytic Cebpd through the Ptx3/NFκB/Mmp3 axis pathway and that the RI37 peptide may act as a therapeutic medicine to inhibit fibrotic scar formation after spinal cord injury.

关键词： Astrocyte Cebpd Fibrotic scar Ptx3 Spinal cord injury

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Multi-stream deep learning framework to predict mild cognitive impairment with Rey Complex Figure Test

arXiv

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arXiv 2024年

作者： Park, Junyoung Seo, Eun Hyun Kim, Sunjun Yi, SangHak Lee, Kun Ho Won, Sungho Department of Neurology and Neurological Sciences Stanford University School of Medicine StanfordCA94305 United States RexSoft Inc Seoul08826 Korea Republic of Gwangju Alzheimer's & Related Dementia Cohort Research Center Chosun University Gwangju61452 Korea Republic of Premedical Science College of Medicine Chosun University Gwangju61452 Korea Republic of Neurozen Inc. Seoul06160 Korea Republic of Department of Neurology Wonkwang University Hospital Wonkwang University School of Medicine Iksan15865 Korea Republic of Department of Biomedical Science Chosun University Gwangju61452 Korea Republic of Korea Brain Research Institute Daegu41068 Korea Republic of Department of Public Health Sciences Graduate School of Public Health Seoul National University Seoul08826 Korea Republic of Interdisciplinary Program in Bioinformatics Seoul National University Seoul08826 Korea Republic of Institute of Health and Environment Seoul National University Seoul08826 Korea Republic of

Drawing tests like the Rey Complex Figure Test (RCFT) are widely used to assess cognitive functions such as visuospatial skills and memory, making them valuable tools for detecting mild cognitive impairment (MCI). Despite their utility, existing predictive models based on these tests often suffer from limitations like small sample sizes and lack of external validation, which undermine their reliability. We developed a multi-stream deep learning framework that integrates two distinct processing streams: a multi-head self-attention based spatial stream using raw RCFT images and a scoring stream employing a previously developed automated scoring system. Our model was trained on data from 1,740 subjects in the Korean cohort and validated on an external hospital dataset of 222 subjects from Korea. The proposed multi-stream model demonstrated superior performance over baseline models (AUC = 0.872, Accuracy = 0.781) in external validation. The integration of both spatial and scoring streams enables the model to capture intricate visual details from the raw images while also incorporating structured scoring data, which together enhance its ability to detect subtle cognitive impairments. This dual approach not only improves predictive accuracy but also increases the robustness of the model, making it more reliable in diverse clinical settings. Our model has practical implications for clinical settings, where it could serve as a cost-effective tool for early MCI screening. © 2024, CC BY.

关键词： Convolutional neural networks

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Sex Differences of Co-Exposures to Melamine and Phthalates and Early Renal Injury in Children

SSRN

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SSRN 2024年

作者： Wu, Ming-Tsang Tsai, Hui-Ju Wu, Chia-Fang Li, Sih-Syuan Chen, Jia-Jen Hsieh, Chia-Jung Chen, Chu-Chih Wang, Shu-Li Chen, Mei-Lien Graduate Institute of Clinical Medicine Taiwan Department of Family Medicine Kaohsiung Municipal Ta-Tung Hospital Kaohsiung Medical University Kaohsiung Taiwan Department of Family Medicine Kaohsiung Medical University Hospital Kaohsiung Medical University Kaohsiung Taiwan Department of Family Medicine School of Medicine College of Medicine Kaohsiung Medical University Kaohsiung Taiwan Research Center for Precision Environmental Medicine Kaohsiung Medical University Kaohsiung Taiwan Taipei Taiwan Ph.D. Program in Environmental and Occupational Medicine Kaohsiung Medical University Kaohsiung Taiwan Department of Public Health Tzu Chi University Hualien Taiwan Division of Biostatistics and Bioinformatics Institute of Population Health Sciences National Health Research Institutes Taiwan Institute of Environmental and Occupational Health Sciences School of Medicine National Yang Ming Chiao Tung University Taipei Taiwan National Institute of Environmental Health Sciences National Health Research Institutes Miaoli Taiwan

Studies concerning the effect of co-exposure to melamine and phthalates, two common environmental chemicals and potential nephrotoxins, on kidney function in children are rare. Thus, this study aims to examine the above-mentioned relationship, and their sex-different effect is also explored. Study children (3-7 years old) were recruited from one cohort of the Taiwan Maternal and Infant Cohort Study (TMICS) between 2016 and 2020. One-spot urine specimens were collected to simultaneously measure melamine, 11 phthalate metabolites, and two markers of renal injury, microalbumin and N-acetyl-beta-D-glucosaminidas (NAG). Daily intakes of melamine and six phthalates, including DEHP (di-2-ethylhexylphthalate), DiBP (Dibutyl phthalate), DnBP (Di-n-butyl phthalate), BBzP (Butyl benzyl phthalate), and DEP (Diethyl phthalate), were estimated using a creatinine excretion-based model. A total of 552 children (319 boys and 213 girls) were studied, with a mean age of 4 years. Although the individual effect of study chemicals on early renal injury was not significant, we did find that boys in the highest quartile of estimated melamine intake (≥ 0.68 µg/kg/day) had significantly higher urine ACR levels and in the highest quartile of estimated phthalate intake of DEHP (≥ 5.36 µg/kg/day), DEP (≥ 0.89 µg/kg/day), and DiBP (≥ 1.19 µg/kg/day) had significantly higher urine NAG levels when compared to the combined three lowest quartile ones as comparison groups. Categorizing the highest quartile of the above four significant chemicals as "1" score and summed, the higher the score of the joint effect of melamine, DEHP, DEP, or DiBP, the higher the urine ACR and NAG levels noted in study children, particularly in boys. We conclude that children with high co-exposure of melamine and certain phthalate chemicals have increased markers of early kidney injury particularly in boys. © 2024, The Authors. All rights reserved.

关键词： Metabolites

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Sex-specific interactive effect of melamine and DEHP on a marker of early kidney damage in Taiwanese adults: A national population-based study from the Taiwan Biobank

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Ecotoxicology and Environmental Safety 2023年第1期263卷 115208页

作者： Li, Sih-Syuan Chen, Jia-Jen Su, Ming-Wei Lin, Chien-Wei Chen, Chu-Chih Wang, Yin-Han Liu, Chia-Chu Tsai, Yi-Chun Hsieh, Tusty-Jiuan Wu, Ming-Tsang Wu, Chia-Fang Research Center for Precision Environmental Medicine Kaohsiung Medical University Kaohsiung Taiwan Taiwan Biobank Academia Sinica Taipei Taiwan Division of Biostatistics and Bioinformatics Institute of Population Health Sciences National Health Research Institutes Taiwan Department of Urology Kaohsiung Medical University Hospital Kaohsiung Medical University Kaohsiung Taiwan Division of Nephrology Department of Internal Medicine Kaohsiung Medical University Hospital Kaohsiung Medical University Kaohsiung Taiwan Graduate Institute of Medicine College of Medicine Kaohsiung Medical University Kaohsiung Taiwan Department of Family Medicine Kaohsiung Medical University Hospital Kaohsiung Medical University Kaohsiung Taiwan Ph.D. Program in Environmental and Occupational Medicine Kaohsiung Medical University Kaohsiung Taiwan Department of Public Health Kaohsiung Medical University Kaohsiung Taiwan International Master Program of Translational Medicine National United University Miaoli Taiwan

Taiwan had the high incidence of chronic kidney disease (CKD) worldwide. Our objective was to examine associations between daily exposure of phthalates and melamine, two common nephrotoxins, and kidney damage risk in a well-established nationwide cohort. Study subjects were from Taiwan Biobank (TWB) with existing data of questionnaire and biochemical examinations. Average daily intake (ADI) levels of melamine and seven parental phthalates, including DEHP (di-2-ethylhexylphthalate), DiBP (Dibutyl phthalate), DnBP (Di-n-butyl phthalate), BBzP (Butyl benzyl phthalate), DEP (Diethyl phthalate), and DMP (Dimethyl phthalate) were estimated using a creatinine excretion-based model from urine melamine and 10 phthalate metabolites. Urine microalbumin to creatinine ratio (ACR) was used to represent for the outcome of kidney damage. Two statistical strategies were used: First, a weighted quantile sum (WQS) regression model to select the most important exposure variables of ADI levels of phthalates and melamine associated with ACR;Second, to examine effects of those most important exposure variables on ACR in multivariable linear regression models. In total, 1153 eligible adults were left for analyses. Of them, 591 (51.3%) and 562 (48.7%) were men and women, respectively, with a median age of 49 years old. By WQS, a significant and positive association was found between ADI of melamine and phthalates and ACR (β = 0.14, p = 0.002). ADI levels of melamine had the highest weight (0.57), followed by DEHP (0.13). Next, examining the two most important exposures in association with ACR, we found that the higher the melamine and DEHP intakes, the higher the ACR levels were found. An interaction effect was also found between melamine and DEHP intakes on urine ACR (p = 0.015). This result was more prominent in men (p = 0.008) than in women (p = 0.651). Environmental co-exposure of melamine and DEHP can potentially affect ACR in the community-dwelling Taiwanese adult population. © 2023 T

关键词： Chronic kidney disease (CKD) Interactive effect Melamine Phthalates Renal dysfunction Sex

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Anomaly Detection in Climate Data Using Stacked and Densely Connected Long Short-Term Memory Model

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Journal of Computers (Taiwan) 2020年第4期31卷 42-53页

作者： Saleh Abbas, Bahtiar Wahyono, Teguh Heryadi, Yaya Soeparno, Haryono Doctor of Computer Science Binus Graduate Program Bina Nusantara University Jakarta Indonesia Faculty of Information Technology Satya Wacana Christian University Salatiga Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Department of Industrial Engineering Bina Nusantara University Jakarta Indonesia

Climate anomalies are considered as an important factor closely related to many disasters causing many human losses, such as airline crash, wildfires, drought and flooding in many areas. Many researchers have projected that the rising global temperature will increase the draught, especially in the mid-latitude areas. Taking those problems into account, studies on anomaly detection in climate are crucial. While climate prediction aims to analyze and model regular pattern of climate, climate anomaly studies aim to model climate deviation from its previous general patterns. Long Short Term Memory (LSTM) is a method employed in this research because it has been proven to work effectively in several anomaly detection studies, especially for data with similar characteristics. This paper presents empirical results of using Basic LSTM, Densely Connected (DC) LSTM, and Stacked-DC LSTM models to detect temperature anomaly as a manifestation of climate change in Semarang City. The results show that Stacked DC LSTM produced higher accuracy in detecting anomaly than the other two methods. © 2020 Computer Society of the Republic of China. All rights reserved.

关键词： Long short-term memory

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Environmental melamine exposure and adverse kidney outcomes in patients with type 2 diabetes mellitus

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Environmental Pollution 2023年第Part1期331卷 121883页

作者： Tsai, Yi-Chun Wu, Chia-Fang Hung, Wei-Wen Yu, Ping-Shaou Liu, Chia-Chu Hsieh, Tusty-Jiuan Chen, Chu-Chih Li, Sih-Syuan Chen, Jia-Jen Chiu, Yi-Wen Hwang, Shang-Jyh Wu, Ming-Tsang Division of Nephrology Department of Internal Medicine Kaohsiung Medical University Hospital Kaohsiung Medical University Kaohsiung Taiwan Division of General Medicine Department of Internal Medicine Kaohsiung Medical University Hospital Kaohsiung Medical University Kaohsiung Taiwan Center for Liquid Biopsy and Cohort Research Kaohsiung Medical University Kaohsiung Taiwan School of Medicine College of Medicine Kaohsiung Medical University Kaohsiung Taiwan International Master Program of Translational Medicine National United University Miaoli Taiwan Division of Endocrinology and Metabolism Kaohsiung Medical University Hospital Kaohsiung Medical University Kaohsiung Taiwan Kaohsiung Municipal CiJin Hospital Kaohsiung Taiwan Research Center for Precision Environmental Medicine Kaohsiung Medical University Kaohsiung Taiwan Department of Urology Kaohsiung Medical University Hospital Kaohsiung Medical University Kaohsiung Taiwan Graduate Institute of Medicine College of Medicine Kaohsiung Medical University Kaohsiung Taiwan Division of Biostatistics and Bioinformatics Institute of Population Health Sciences National Health Research Institutes Taiwan Department of Public Health College of Health Sciences Kaohsiung Medical University Kaohsiung Taiwan Department of Family Medicine Kaohsiung Medical University Hospital Kaohsiung Medical University Kaohsiung City Taiwan Program in Environmental and Occupational Medicine College of Medicine Kaohsiung Medical University Kaohsiung City Taiwan

The impact of melamine exposure on kidney outcomes in type 2 diabetes mellitus (T2D) patients remains unclear. In this prospective cohort study, 561 T2D patients during October 2016 and June 2020 were enrolled and followed until December 2021. Baseline one-spot urinary corrected melamine levels were measured by LC-MS/MS. Average daily intake (ADI) of melamine represented environmental melamine exposure in daily life, and was estimated using urinary corrected melamine level by creatinine excretion (CE)-based model. Primary kidney outcomes were defined as doubling of serum creatinine levels or end stage kidney disease (ESKD), and secondary kidney outcomes included rapid decline in kidney function as estimated glomerular filtration rate (eGFR) decline >5 ml/min/1.73 m2/year. Baseline median urinary corrected melamine levels and estimated DI of melamine were 0.8 μg/mmol and 0.3 μg/kg/day in 561 T2D patients. During 3.7 years of follow-up, urinary corrected melamine level was positively correlated with reaching composite outcomes of either doubling of serum creation levels or ESKD and rapid decline in kidney function. Those with the highest quartile of urinary corrected melamine had 2.96-fold risk of composite outcomes of either doubling of serum creation levels or ESKD and 2.47-fold risk of eGFR decline >5 ml/min/1.73 m2/year. Estimated ADI of melamine also had significant correlation with adverse kidney outcomes. Furthermore, the positive relationship between melamine exposure and rapid decline in kidney function was only found in T2D patients with male, baseline eGFR ≥60 ml/min/1.73 m2 or glycated hemoglobin ≤7%. In conclusion, melamine exposure is significantly associated with adverse kidney outcomes in T2D patients, especially in those with male, well sugar control or good baseline kidney function. © 2023 Elsevier Ltd

关键词： Melamine Kidney outcomes Type 2 diabetes mellitus

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RETRACTION: AKT3-mediated IWS1 phosphorylation promotes the proliferation of EGFR-mutant lung adenocarcinomas through cell cycle-regulated U2AF2 RNA splicing (Retraction of Vol 12, art no 4624, 2021)

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NATURE COMMUNICATIONS 2022年第1期13卷 1页

作者： Laliotis, Georgios I. Chavdoula, Evangelia Paraskevopoulou, Maria D. Kaba, Abdul La Ferlita, Alessandro Singh, Satishkumar Anastas, Vollter Nair, Keith A., II Orlacchio, Arturo Taraslia, Vasiliki Vlachos, Ioannis Capece, Marina Hatzigeorgiou, Artemis Palmieri, Dario Tsatsanis, Christos Alaimo, Salvatore Sehgal, Lalit Carbone, David P. Coppola, Vincenzo Tsichlis, Philip N. Department of Cancer Biology and Genetics The Ohio State University Columbus OH USA The Ohio State University Comprehensive Cancer Center-Arthur G. James Cancer Hospital and Richard J. Solove Research Institute Columbus OH USA School of Medicine University of Crete Heraklion Crete Greece Department of Clinical and Experimental Medicine Bioinformatics Unit University of Catania Catania Italy Tufts Graduate School of Biomedical Sciences Program in Genetics Boston MA USA Department of Medicine Division of Hematology The Ohio State University Columbus OH USA Department of Internal Medicine Division of Medical Oncology The Ohio State University Medical Center Columbus OH USA Institute of Molecular Biology and Biotechnology Foundation for Research and Technology Hellas Heraklion Crete Greece Molecular Oncology Research Institute Tufts Medical Center Boston MA USA DIANA-Lab Hellenic Pasteur Institute Athens Greece

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