检索结果-内蒙古大学图书馆

Count time series modelling of Twitter data topic modelling: A case of Indonesia flood events

AIP Conference Proceedings 2023年第1期2594卷

作者： A. A. Hidayat B Pardamean Bioinformatics & 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

Twitter data provide rich and powerful information to leverage the dynamics of public perception to establish situational awareness and disaster mitigation strategies during critical times. In this paper, we perform topic modeling via Latent Dirichlet Allocation to extract topics from a collection of tweets related to Indonesia flood events in February 2021 with the query: “banjir”. The extracted topics are used as one of the features to build a generalized linear count time series model with Negative Binomial distribution. We find seven major topics from the model in which tweets containing a topic about the government’s role in handling the situation dominate the conversation. Taking into account a simple intervention analysis, we demonstrate a statistically significant change in the users’ behavior before and after the severe Jakarta flood on 20 February 2021. Moreover, a metric evaluation demonstrates that a covariate that describes the turning point of the Jakarta flood event is convenient to build a more accurate count time series model of the tweets.

关键词：

来源：评论

学校读者我要写书评

暂无评论

A VARIANT IN STK24 ACHIEVES GENOME-WIDE SIGNIFICANCE IN AFRICAN AMERICANS USING A LIABILITY MODEL

引用

Alzheimer's & Dementia 2014年第4期10卷 P481-P481页

作者： Jesse Mez Jaeyoon Chung Matthew Schu Logue Mark Gyungah Jun Kathryn Lunetta Lindsay A. Farrer Boston University School of Medicine Boston Massachusetts United States Boston University Bioinformatics Graduate Program Boston Massachusetts United States Boston University School of Public Health Boston Massachusetts United States

来源：评论

学校读者我要写书评

暂无评论

Moving beyond gene expression: identification of lung-disease-associated novel transcripts and alternative splicing by RNA sequencing

引用

BMC Proceedings 2012年第6期6卷 1-2页

作者： John Brothers II Paola Sebastiani Marc Lenburg Avrum Spira Rebecca Kusko Yuriy Alekesyev Gang Liu Lingqi Luo Jennifer Beane Brenda Juan Guardela John Tedrow Frank Sciurba Naftali Kaminski Ivana V Yang David A Schwartz Mick Correll John Quackenbush Mark Geraci Bioinformatics Program Boston University Boston MA 02115 USA Genetics and Genomics Graduate Program Boston University School of Medicine Boston MA 02118 USA Department of Medicine Boston University School of Medicine Section of Computational Biomedicine Boston MA 02118 USA Department of Pathology and Laboratory Medicine Boston University School of Medicine Boston MA 02118 USA Simmons Center for Interstitial Lung Disease and Department of Medicine University of Pittsburgh Medical Center Pittsburgh PA 15213 USA Center for Genes Environment and Health and Department of Medicine National Jewish Health Denver CO 80206 USA Dana-Farber Cancer Institute and Harvard School of Public Health Boston MA 02115 USA Department of Medicine University of Colorado School of Medicine Aurora CO 80045 USA

来源：评论

学校读者我要写书评

暂无评论

Structural basis of water-mediated cis Watson-Crick/Hoogsteen base-pair formation in non-CpG methylation

引用

Nucleic acids research 2024年第14期52卷 8566-8579页

作者： Shan-Meng Lin Hsiang-Ti Huang Pei-Ju Fang Chi-Fon Chang Roshan Satange Chung-Ke Chang Shan-Ho Chou Stephen Neidle Ming-Hon Hou Graduate Institute of Genomics and Bioinformatics National Chung Hsing University Taichung 402 Taiwan. Genomics Research Center Academia Sinica Taipei 115 Taiwan. Taiwan Biobank Institute of Biomedical Sciences Academia Sinica Taipei 115 Taiwan. Institute of Biochemistry National Chung Hsing University Taichung 402 Taiwan. School of Pharmacy University College London London WC1N 1AX UK. Doctoral Program in Medical Biotechnology National Chung Hsing University Taichung 402 Taiwan. Graduate Institute of Biotechnology National Chung Hsing University Taichung 402 Taiwan. Department of Life Sciences National Chung Hsing University Taichung 402 Taiwan. Biotechnology Center National Chung Hsing University Taichung 402 Taiwan.

Non-CpG methylation is associated with several cellular processes, especially neuronal development and cancer, while its effect on DNA structure remains unclear. We have determined the crystal structures of DNA duplexes containing -CGCCG- regions as CCG repeat motifs that comprise a non-CpG site with or without cytosine methylation. Crystal structure analyses have revealed that the mC:G base-pair can simultaneously form two alternative conformations arising from non-CpG methylation, including a unique water-mediated cis Watson-Crick/Hoogsteen, (w)cWH, and Watson-Crick (WC) geometries, with partial occupancies of 0.1 and 0.9, respectively. NMR studies showed that an alternative conformation of methylated mC:G base-pair at non-CpG step exhibits characteristics of cWH with a syn-guanosine conformation in solution. DNA duplexes complexed with the DNA binding drug echinomycin result in increased occupancy of the (w)cWH geometry in the methylated base-pair (from 0.1 to 0.3). Our structural results demonstrated that cytosine methylation at a non-CpG step leads to an anti→syntransition of its complementary guanosine residue toward the (w)cWH geometry as a partial population of WC, in both drug-bound and naked mC:G base pairs. This particular geometry is specific to non-CpG methylated dinucleotide sites in B-form DNA. Overall, the current study provides new insights into DNA conformation during epigenetic regulation.

关键词：

来源：评论

学校读者我要写书评

暂无评论

Prognostic Impacts and Dynamic Changes of Cohesin Complex Gene Mutations in De Novo Acute Myeloid Leukemia

引用

BLOOD 2017年 130卷 2582-2582页

作者： Tsai, Cheng-Hong Hou, Hsin-An Tang, Jih-Luh Kuo, Yuan-Yeh Chiu, Yu-Chiao Lin, Chien-Chin Lin, Liang-In Yao, Ming Li, Chi-Cheng Huang, Shang-Yi Ko, Bor-Sheng Hsu, Szu Chun Lin, Chien-Ting Wu, Shang-Ju Chen, Chien-Yuan Tsai, Woei Chou, Wen-Chien Tien, Hwei-Fang Tai-Cheng Stem Cell Therapy Center National Taiwan University Taipei Taiwan Division of Hematology Department of Internal Medicine National Taiwan University Hospital Taipei Taiwan Genome and Systems Biology Degree Program National Taiwan University Taipei Taiwan Graduate Institute of Oncology National Taiwan University Taipei Taiwan Graduate institute of Biomedical Electronics and Bioinformatics National Taiwan University Taipei Taiwan Department of Clinical Laboratory Sciences and Medical Biotechnology National Taiwan University Taipei Taiwan Department of Laboratory Medicine National Taiwan University Hospital Taipei Taiwan Division of Hematology Department of Laboratory Medicine National Taiwan University Hospital Taipei Taiwan

2582

关键词：

来源：评论

学校读者我要写书评

暂无评论

Void distributions reveal structural link between jammed packings and protein cores

arXiv

引用

arXiv 2018年

作者： Treado, John D. Mei, Zhe Regan, Lynne O'Hern, Corey S. Department of Mechanical Engineering & Materials Science Yale University New HavenCT06520 United States Integrated Graduate Program in Physical & Engineering Biology Yale University New HavenCT06520 United States Department of Chemistry Yale University New HavenCT06520 United States Department of Molecular Biophysics & Biochemistry Yale University New HavenCT06520 United States Department of Physics Yale University New HavenCT06520 United States Department of Applied Physics Yale University New HavenCT06520 United States Program in Computational Biology and Bioinformatics Yale University New HavenCT06520 United States

Dense packing of hydrophobic residues in the cores of globular proteins determines their stability. Recently, we have shown that protein cores possess packing fraction φ ≈ 0.56, which is the same as dense, random packing of amino acid-shaped particles. In this article, we compare the structural properties of protein cores and jammed packings of amino acid-shaped particles in much greater depth by measuring their local and connected void regions. We find that the distributions of surface Voronoi cell volumes and local porosities obey similar statistics in both systems. We also measure the probability that accessible, connected void regions percolate as a function of the size of a spherical probe particle and show that both systems possess the same critical probe size. By measuring the critical exponent τ that characterizes the size distribution of connected void clusters at the onset of percolation, we show that void percolation in packings of amino acid-shaped particles and protein cores belong to the same universality class, which is different from that for void percolation in jammed sphere packings. We propose that the connected void regions of proteins are a defining feature of proteins and can be used to differentiate experimentally observed proteins from decoy structures that are generated using computational protein design software. This work emphasizes that jammed packings of amino acid-shaped particles can serve as structural and mechanical analogs of protein cores, and could therefore be useful in modeling the response of protein cores to cavity-expanding and -reducing mutations. Copyright © 2018, The Authors. All rights reserved.

关键词： Amino acids

来源：评论

学校读者我要写书评

暂无评论

Characterizing the small RNA transcriptome associated with COPD and ILD using next-generation sequencing

引用

BMC Proceedings 2012年第6期6卷 1-2页

作者： Joshua D Campbell Joseph Gerrein Marc E Lenburg Avrum Spira Lingqi Luo Gang Liu Ji Xiao Jennifer Beane Brenda J Guardela John Tedrow Frank Sciurba Naftali Kaminski Yuriy O Aleksyev Ivana V Yang David A Schwartz Mick Correll John Quackenbush Mark Geraci Bioinformatics Graduate Program Boston University Boston MA USA Section of Computational Biomedicine Boston University Boston MA USA Department of Pathology and Laboratory Medicine Boston University School of Medicine Boston MA USA Simmons Center for Interstitial Lung Disease and Department of Medicine University of Pittsburgh Medical Center Pittsburgh PA USA Center for Genes Environment and Health and Department of Medicine National Jewish Health Denver CO USA Dana-Farber Cancer Institute and Harvard School of Public Health Boston MA USA Department of Medicine University of Colorado School of Medicine Aurora CO USA

来源：评论

学校读者我要写书评

暂无评论

Application for sugarcane plantation: Manpower and transportation planning

引用

AIP Conference Proceedings 2023年第1期2594卷

作者： H. G. Mawandha D. Sudigyo T. Suparyanto B. Pardamean Department of Agrotechnology Institute of Agriculture STIPER Yogyakarta Indonesia 55281 Bioinformatics & Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Program Bina Nusantara University Jakarta Indonesia 11480

Sugarcane plantations in Indonesia are still managed in a labor-intensive manner, especially plantation-owned by farmers. Labor intensive means that every stage of work in sugarcane plantation management still uses manpower. One of the jobs in sugarcane plantations that requires a lot of labor is sugar cane harvesting. Trend changing in the workforce gender would affect the quantity and quality of jobs, which is determined by the workforce's capacity and the workload of the work performed. The result of this research was a sugarcane agricultural calculator that made it simple for farmers to measure manpower and transportation requirements in estimating harvest costs. Manpower and transportation of harvested sugarcane commodities were estimated through the workload approach, namely, crop production and manpower's ability to carry a load. These two components helped sugarcane farmers to determine manpower and transportation during the harvest. The final yield produced by the projected harvest labor cost would be known immediately.

关键词：

来源：评论

学校读者我要写书评

暂无评论

Determination of Macro- And Microelements in the Inflorescences of Banana Tree Using ICP OES: Evaluation of the Daily Recommendations of Intake for Humans

引用

Scientific World Journal 2020年第1期2020卷 8383612页

作者： Rosa, Rafaela Henriques Ribeiro Fernandes, Melina De Pádua Melo, Elaine Silva Granja Arakaki, Daniela De Lima, Nayara Vieira Santos Leite, Luana Carolina Espindola, Paulo Renato De Souza, Igor Domingos Do Nascimento, Valdir Aragão Saldanha Tschinkel, Paula Fabiana La Flor Ziegler Sanches, Fabiane Do Nascimento, Valter Aragão Group of Spectroscopy and Bioinformatics Applied Biodiversity and Health (GEBABS) Graduate Program on Health and Development in West Central Region School of Medicine Federal University of Mato Grosso Do Sul UFMS Campo Grande 79070-900 Brazil Institute of Physics Federal University of Mato Grosso Do sul Campo Grande Mato Grosso do Sul Brazil Faculty of Pharmaceutical Sciences Food and Nutrition Federal University of Mato Grosso Do sul Campo Grande 79070-900 Brazil

The inflorescence of Musa paradisiaca, known as "banana heart"is a structure that includes flowers and bracts of banana, commonly used as food source worldwide. The aims of this study were (1) to determine the mineral components of Musa paradisiaca and (2) to compare the obtained results with previously reported data of Recommendation Dietary Allowances (RDAs) and edible plant permissible limits set by FAO/WHO. The samples were digested using microwave-assisted equipment, while elemental contents were determined by inductively coupled plasma optical emission spectroscopy (ICP OES). Metal (Mg, Ca, Cr, Ni, Cu, Fe, and Zn) and nonmetal (S and P) contents were detected. According to RDA, the inflorescences could be excellent sources of Mg, P, Cr, Cu, Zn, and Fe for females, males, and pregnant women, all age 31-50 y, as well as children (4-8 y). Bracts are good source of Zn for male and pregnant women and good source of Fe for children. All the samples contained considerable amounts of Mg, Ca, P, Ni, Cu, Zn, and Fe, which were quite low to induce deleterious effects (UL). FAO/WHO limits for edible plants have not yet been established for S, P, Mg, and Ca, but Ni and Zn are below of those limit values. However, Cr and Cu concentrations are higher than the values established for edible plants and may pose a threat to human health. Farmers should be encouraged by government agencies, not only for sustainability of production but also to ensure the storage and trade of banana tree inflorescence. © 2020 Rafaela Henriques Rosa et al.

关键词：

来源：评论

学校读者我要写书评

暂无评论

Evaluation of GPT and BERT-based models on identifying protein-protein interactions in biomedical text

arXiv

引用

arXiv 2023年

作者： Rehana, Hasin Çam, Nur Bengisu Basmaci, Mert Zheng, Jie Jemiyo, Christianah He, Yongqun Özgür, Arzucan Hur, Junguk Computer Science Graduate Program University of North Dakota Grand ForksND58202 United States Department of Computer Engineering Bogazici University Istanbul34342 Turkey Unit for Laboratory Animal Medicine Department of Microbiology and Immunology University of Michigan Ann ArborMI48109 United States Department of Biomedical Sciences University of North Dakota School of Medicine and Health Sciences Grand ForksND58202 United States Center for Computational Medicine and Bioinformatics University of Michigan Ann ArborMI48109 United States

Detecting protein-protein interactions (PPIs) is crucial for understanding genetic mechanisms, disease pathogenesis, and drug design. However, with the fast-paced growth of biomedical literature, there is a growing need for automated and accurate extraction of PPIs to facilitate scientific knowledge discovery. Pre-trained language models, such as generative pre-trained transformers (GPT) and bidirectional encoder representations from transformers (BERT), have shown promising results in natural language processing (NLP) tasks. We evaluated the performance of PPI identification of multiple GPT and BERT models using three manually curated gold-standard corpora: Learning Language in Logic (LLL) with 164 PPIs in 77 sentences, Human Protein Reference Database with 163 PPIs in 145 sentences, and Interaction Extraction Performance Assessment with 335 PPIs in 486 sentences. BERT-based models achieved the best overall performance, with BioBERT achieving the highest recall (91.95%) and F1-score (86.84%) and PubMedBERT achieving the highest precision (85.25%). Interestingly, despite not being explicitly trained for biomedical texts, GPT-4 achieved commendable performance, comparable to the top-performing BERT models. It achieved a precision of 88.37%, a recall of 85.14%, and an F1-score of 86.49% on the LLL dataset. These results suggest that GPT models can effectively detect PPIs from text data, offering promising avenues for application in biomedical literature mining. Further research could explore how these models might be fine-tuned for even more specialized tasks within the biomedical domain. © 2023, CC BY.

关键词： Extraction

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：