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9th IEEE International Conference for Convergence in Technology, I2CT 2024

作者： Harshitha Reddy, T. Aryagopal Sai Jagadeesh, Dumpa Venkata Anand, M. Pati, Peeta Basa Bhanu Prakash, K.N. Amrita Vishwa Vidyapeetham Amrita School of Engineering Department of Computer Science And Engineering Bengaluru India A∗star Bioinformatics Institute Singapore

ISBN: (纸本)9798350394474

Parkinson's disease is a neurological disorder mostly observed in the population over the age of 60 years. Over 8.5 million people world-wide are affected by it. Early diagnosis of the disease helps take preventive and curative measures to enable the affected individuals to lead a normal life. Quality of speech is one of the key indicators for identification of the *** this study, we investigate the effectiveness of multiple machine learning algorithms on various speech related attributes to determine the existence of this disease. Additionally, we identify the crucial features which impact the model's functioning. The study employs Explainable AI (XAI) to investigate the influence of voice features on the research outcomes. The experimental findings showcase a diagnostic accuracy of 95% using Random Forest & XGBoost classifiers. We, using SHAP, identify that 6 features out of a set of 24 provide the best efficiency of diagnosis. © 2024 IEEE.

关键词： Support vector machines

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Parkinson's Disease Severity Assessment: A Comparative Study & Interpretability Analysis 5

Parkinson's Disease Severity Assessment: A Comparative Study...

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5th IEEE International Conference for Emerging Technology, INCET 2024

作者： Tiwari, Utkarsh Jahanve, P. Reddy Karna, Siwani Anand, M. Pati, Peeta Basa Prakash, Bhanu K.N. Department of Computer Science and Engineering Amrita School of Computing Bengaluru Amrita Vishwa Vidyapeetham India Bioinformatics Institute A*STAR Singapore

ISBN: (纸本)9798350361155

Parkinson's disease (PD) is a progressive neurological disorder that mainly affects people over the age of sixty. Currently, there is no such cure for PD. However, Treatments are available to help relieve the symptoms related to PD. A rating tool called MDS-UPDRS III is used to gauge the severity and progression and stages of disease severity are measured by the Hoehn and Yahr (NHY) staging system. This study performs a comparative analysis of the effectiveness of various machine learning models such as AdaBoost, XGBoost, Gradient Boosting Classifier (GBC), Decision Trees (DT), K-Nearest Neighbor (KNN), Logistic regression (LR), and Gaussian Naïve Bayes (GNB) on a dataset containing a variety of PD-related features obtained from 2861 persons. Local Interpretable Model-agnostic Explanations (LIME) is employed to perform the analysis of the strength of each feature toward the outcome prediction for various classification tasks. It is observed that the AdaBoost classifier delivers superior performance of 93.2% accuracy and 84.2% F1-Score for the dataset. © 2024 IEEE.

关键词： Adaptive boosting

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Automating life science labs at the single-cell level through precise ultrasonic liquid sample ejection:PULSE

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Microsystems & Nanoengineering 2024年第6期10卷 173-188页

作者： Peiran Zhang Zhenhua Tian Ke Jin Kaichun Yang Wesley Collyer Joseph Rufo Neil Upreti Xianjun Dong Luke P.Lee Tony Jun Huang Department of Mechanical Engineering and Materials Science Duke UniversityDurhamNC 27708USA Department of Mechanical Engineering Virginia Polytechnic Institute and State UniversityBlacksburgVA 24061USA Genomics and Bioinformatics Hub Department of NeurologyBrigham and Women’s HospitalHarvard Medical SchoolBostonMAUSA Department of Medicine Brigham and Women’s HospitalHarvard Medical SchoolBostonMAUSA Department of Bioengineering Department of Electrical Engineering and Computer ScienceUniversity of California at BerkeleyBerkeleyCAUSA Institute of Quantum Biophysics Department of BiophysicsSungkyunkwan UniversitySuwonKorea Department of Chemistry&Nanoscience Ewha Womans UniversitySeoulKorea

Laboratory automation technologies have revolutionized biomedical ***,the availability of automation solutions at the single-cell level remains scarce,primarily owing to the inherent challenges of handling cells with such small dimensions in a precise,biocompatible ***,we present a single-cell-level laboratory automation solution that configures various experiments onto standardized,microscale test-tube matrices via our precise ultrasonic liquid sample ejection technology,known as *** enables the transformation of titer plates into microdroplet arrays by printing nanodrops and single cells acoustically in a programmable,scalable,and biocompatible *** pipetting robots,PULSE enables researchers to conduct biological experiments using single cells as anchoring points(e.g.,1 cell vs.1000 cells per“tube”),achieving higher resolution and potentially more relevant data for modeling and downstream *** demonstrate the ability of PULSE to perform biofabrication,precision gating,and deterministic array barcoding via preallocated droplet-addressable *** cells can be gently printed at a speed range of 5–20 cell⋅s−1 with an accuracy of 90.5–97.7%,which can then adhere to the substrate and grow for up to 72 h while preserving cell *** the deterministic barcoding experiment,95.6%barcoding accuracy and 2.7%barcode hopping were observed by comparing the phenotypic data with known genotypic data from two types of single *** PULSE platform allows for precise and dynamic analyses by automating experiments at the single-cell level,offering researchers a powerful tool in biomedical research.

关键词： precise liquid offering

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An Experimental Evaluation of Summarisation-Based Frequent Subgraph Mining for Subgraph Searching

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SN computer science 2024年第6期5卷 1-23页

作者： Wangmo, Chimi Wiese, Lena Department of Mathematics and Computer Science Institute of Computer Science Goethe University Robert-Mayer-Str. 10 Frankfurt 60325 Germany Research Group Bioinformatics Fraunhofer ITEM Nikolai-Fuchs-Str. 1 Hannover 30625 Germany

The subgraph searching is a fundamental operation for the analysis and exploration of graphs. Nowadays, molecular databases are nearing close to one hundred million molecules. Since finding all the data graphs in a graph database that contain the query graph using subgraph isomorphism is an NP-complete problem, indexes are built and processed. Further, to assist the formulation of the query by a user, the visual exploratory subgraph query paradigm proposes a graphical user interface and leverages exploration time to reduce query processing time. However, state-of-the-art approaches need to scale better to dynamic graph databases and suffer from efficiency problems. In addition, the existing Summarisation-based frequent subgraph mining for visual exploratory subgraph searching (SuMExplorer) is lacking implementation and evaluation study for handling visual subgraph similarity search and modify operations. In this paper, we present a novel index structure, which aids the subgraph searching using the summarised-based weighted frequent subgraph mining on data graphs. By the structure-preserving, we exploit the indexes to support similarity and modify operations. We conduct extensive performance studies on both real-world and synthetic datasets to evaluate the overall performance of the extended SuMExplorer to the recent visual exploratory FERRARI and traditional subgraph search algorithms (such as the gIndex and the GRAPES-DD). Our results showed that our indexes can query up to 3 times faster in comparison to the FERRARI while reducing the storage footprint by 2 orders of magnitude. © The Author(s) 2024.

关键词： Dynamic graph database Experimental evaluation Graph indexing Visual exploratory subgraph searching

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Effects of triggers of senescence and senolysis in murine pancreatic cancer cells

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Hepatobiliary & Pancreatic Diseases International 2024年第6期23卷 628-637页

作者： Denis Revskij Aline Woitas Bianca Kölle Camilla Umstätter Dietmar Zechner Faiz M Khan Georg Fuellen Robert Jaster Department of MedicineⅡ Division of GastroenterologyRostock University Medical CenterRostockGermany Rudolf-Zenker-Institute of Experimental Surgery Rostock University Medical CenterRostockGermany Department of Systems Biology and Bioinformatics Institute of Computer ScienceUniversity of RostockRostockGermany Institute for Biostatistics and Informatics in Medicine and Ageing Research Rostock University Medical CenterRostockGermany

Background:The combination of senescence triggers with senolytic drugs is considered a promising new approach to cancer ***,we studied the efficacy of the genotoxic agent etoposide(Eto)and irradiation in inducing senescence of Panc02 pancreatic cancer cells,and the capability of the Bcl-2 inhibitor navitoclax(ABT-263;Nav)to trigger ***:Panc02 cells were treated with Eto or irradiated with 5–20 Gy before exposure to *** survival,proliferation,and senescence were assessed by trypan blue staining,quantification of DNA synthesis,and staining of senescence-associatedβ-galactosidase(SA-β-Gal)-positive cells,*** of mRNA were determined by real-time polymerase chain reaction,and protein expression was analyzed by ***02 cells were also grown as pancreatic tumors in mice,which were subsequently treated with Eto and ***:Eto and irradiation had an antiproliferative effect on Panc02 cells that was significantly or tendentially enhanced by *** vivo,Eto and Nav together,but not Eto alone,significantly reduced the proportion of proliferating *** expression of the senescence markerγH2AX and tumor infiltration with T-cells were not affected by the *** vitro,almost all Eto-exposed cells and a significant proportion of cells irradiated with 20 Gy were SA-β-*** of Nav reduced the percentage of SA-β-Gal-positive cells after irradiation but not after pretreatment with *** response to triggers of senescence,cultured Panc02 cells showed increased protein levels ofγH2AX and the autophagy marker LC3B-II,and higher mRNA levels of Cdkn1a,Mdm2,and PAI-1,while the effects of Nav were ***:In vitro and in vivo,the combination of senescence triggers with Nav inhibited tumor cell growth more effectively than the triggers *** data also provide some evidence for senolytic effects of Nav in vitro.

关键词： Pancreatic cancer Panc02 cells Etoposide Irradiation Navitoclax

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An experimental and numerical approach for optimization of internal and external corrugations with various geometries in cylindrical thin-walled concertina energy absorbers under quasi-static axial load

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Mechanics of Advanced Materials and Structures 2024年第25期31卷 6628-6642页

作者： Rahpeima, Reza Nateghi Boroujeni, Iman Nia, Ali Alavi Graduate institute of biomedical electronics and bioinformatics College of Electrical Engineering and Computer Science National Taiwan University Taipei Taiwan Department of Mechanical Engineering Tarbiat Modares University Tehran Iran Department of Mechanical Engineering Bu-Ali Sina University Hamedan Iran

Thin-walled tubes have been extensively used as energy absorbers in many engineering structures that are under dynamic or quasi-static loads. In this article, the effect of corrugation and its geometry on the collapse characteristics of aluminum concertina tubes under quasi-static axial load is investigated both experimentally and numerically. The numerical simulations were performed with the use of LS-Dyna commercial software. Then, several chosen samples were tested experimentally to verify the results of the simulation. Forty different samples with four different corrugation geometries including singly isosceles triangular corrugation, continual isosceles triangular corrugation, continual scalene triangular corrugation, and continual semi-circular corrugation, and each with 10 different size dimensions were simulated. Among all of these simulations, six of them, each with two replicates were subjected to experimental tests. Experimental examples are aluminum cylindrical thin-walled tubes with the same thickness, height, and diameter that corrugations with different geometries are applied to them by the use of the cold rolling method. Finally, to describe the findings in more theoretical terms, a comparison between our obtained results and earlier theoretical investigations is made. The results show a significant influence of corrugations application on the improvement of the collapse characteristics of the cylindrical tubes so that the collapse style of intact tubes can be controlled by applying corrugations. The results show that by increasing the amplitude and number of corrugations, the absorbed energy, and the initial maximum force decrease. It is also found that among the different corrugation geometries, the corrugations with singly isosceles triangular geometry have the highest energy absorption as well as the lowest initial maximum force. © 2023 Taylor & Francis Group, LLC.

关键词： Geometry

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Two-step model of paleohexaploidy, ancestral genome reshuffling and plasticity of heat shock response in Asteraceae

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Horticulture Research 2023年第6期10卷 82-95页

作者： Xiangming Kong Yan Zhang Ziying Wang Shoutong Bao Yishan Feng Jiaqi Wang Zijian Yu Feng Long Zejia Xiao Yanan Hao Xintong Gao Yinfeng Li Yue Ding Jianyu Wang Tianyu Lei Chuanyuan Xu Jinpeng Wang Department of Bioinformatics School of Life Sciencesand Center for Genomics and Computational BiologyNorth China University of Science and TechnologyTangshanHebei 063000China State Key Laboratory of Systematic and Evolutionary Botany Institute of BotanyChinese Academy of ScienceBeijing 100093China University of Chinese Academy of Sciences Beijing 100049China

An ancient hexaploidization event in the most but not all Asteraceae plants,may have been responsible for shaping the genomes of many horticultural,ornamental,and medicinal plants that promoting the prosperity of the largest angiosperm family on the ***,the duplication process of this hexaploidy,as well as the genomic and phenotypic diversity of extant Asteraceae plants caused by paleogenome reorganization,are still poorly *** analyzed 11 genomes from 10 genera in Asteraceae,and redated the Asteraceae common hexaploidization(ACH)event∼70.7–78.6 million years ago(Mya)and the Asteroideae specific tetraploidization(AST)event∼41.6–46.2 ***,we identified the genomic homologies generated from the ACH,AST and speciation events,and constructed a multiple genome alignment framework for ***,we revealed biased fractionations between the paleopolyploidization produced subgenomes,suggesting the ACH and AST both are allopolyplodization ***,the paleochromosome reshuffling traces provided clear evidence for the two-step duplications of ACH event in ***,we reconstructed ancestral Asteraceae karyotype(AAK)that has 9 paleochromosomes,and revealed a highly flexible reshuffling of Asteraceae *** specific significance,we explored the genetic diversity of Heat Shock Transcription Factors(Hsfs)associated with recursive whole-genome polyploidizations,gene duplications,and paleogenome reshuffling,and revealed that the expansion of Hsfs gene families enable heat shock plasticity during the genome evolution of *** study provides insights on polyploidy and paleogenome remodeling for the successful establishment of Asteraceae,and is helpful for further communication and exploration of the diversification of plant families and phenotypes.

关键词： shuffling shock plasticity

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Clinical Knowledge and Reasoning Abilities of Large Language Models in Pharmacy: A Comparative Study on the NAPLEX Exam 10

Clinical Knowledge and Reasoning Abilities of Large Language...

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10th International Conference on Social Networks Analysis, Management and Security, SNAMS 2023

作者： Angel, Mirana Patel, Anuj Alachkar, Amal Baldi, Pierre Institute for Genomics and Bioinformatics University of California Irvine Irvine United States University of California Irvine Department of Computer Science Irvine United States School of Pharmacy & Pharmaceutical Sciences University of California Irvine Irvine United States

ISBN: (纸本)9798350318906

This study aims to evaluate the capabilities and limitations of three large language models (LLMs)-GPT-3, GPT-4, and Bard, in the field of pharmacy by assessing their reasoning abilities on a sample of the North American Pharmacist Licensure Examination (NAPLEX). Additionally, we explore the potential impacts of LLMs on pharmacy education and practice. To evaluate the LLMs, we utilized the sample of the NAPLEX exam comprising 137 multiple-choice questions. These questions were presented to GPT-3, GPT-4, and Bard through their respective user interfaces, and the answers generated by the LLMs were subsequently compared with the answer key. The results reveal a notable disparity in the performance of the LLMs. GPT-4 emerged as the top performer, accurately answering 78.8% of the questions. This marked a substantial 11% and 27.7% improvement over Bard and GPT-3, respectively. However, when considering questions that required multiple selections, the performance of each LLM decreased significantly. GPT-4, GPT-3, and Bard could only correctly respond to 53.6%, 13.9%, and 21.4% of such questions, respectively. Among the three LLMs evaluated, GPT-4 was the only model capable of passing the NAPLEX exam. Nevertheless, given the continuous evolution of LLMs, it is reasonable to anticipate that future models will effortlessly excel in this context. This highlights the significant potential of LLMs to influence the field of pharmacy. Hence, we must evaluate both the positive and negative implications associated with the integration of LLMs in pharmacy education and practice. © 2023 IEEE.

关键词： User interfaces

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The Path-Label Reconciliation (PLR) Dissimilarity Measure for Gene Trees 24

The Path-Label Reconciliation (PLR) Dissimilarity Measure fo...

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24th International Workshop on Algorithms in bioinformatics, WABI 2024

作者： López Sánchez, Alitzel Ramírez-Rafael, José Antonio Flores-Lamas, Alejandro Hernández-Rosales, Maribel Lafond, Manuel Computer Science Department Université de Sherbrooke Canada Center for Research and Advanced Studies of the National Polytechnic Institute Gto. Irapuato Mexico Department of Computer Science Interdisciplinary Center for Bioinformatics University of Leipzig Germany Max Planck Institute for Mathematics in the Sciences Leipzig Germany

ISBN: (纸本)9783959773409

In this study, we investigate the problem of comparing gene trees reconciled with the same species tree using a novel semi-metric, called the Path-Label Reconciliation (PLR) dissimilarity measure. This approach not only quantifies differences in the topology of reconciled gene trees, but also considers discrepancies in predicted ancestral gene-species maps and speciation/duplication events, offering a refinement of existing metrics such as Robinson-Foulds (RF) and their labeled extensions LRF and ELRF. A tunable parameter α also allows users to adjust the balance between its species map and event labeling components. We show that PLR can be computed in linear time and that it is a semi-metric. We also discuss the diameters of reconciled gene tree measures, which are important in practice for normalization, and provide initial bounds on PLR, LRF, and ELRF. To validate PLR, we simulate reconciliations and perform comparisons with LRF and ELRF. The results show that PLR provides a more evenly distributed range of distances, making it less susceptible to overestimating differences in the presence of small topological changes, while at the same time being computationally efficient. Our findings suggest that the theoretical diameter is rarely reached in practice. The PLR measure advances phylogenetic reconciliation by combining theoretical rigor with practical applicability. Future research will refine its mathematical properties, explore its performance on different tree types, and integrate it with existing bioinformatics tools for large-scale evolutionary analyses. The open source code is available at: https://***/project/parle/. © Alitzel López Sánchez, José Antonio Ramírez-Rafael, Alejandro Flores-Lamas, Maribel Hernández-Rosales, and Manuel Lafond1

关键词： evolutionary scenarios gene trees Reconciliation species trees

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A reference-grade genome assembly for Gossypium bickii and insights into its genome evolution and formation of pigment glands and gossypol

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Plant Communications 2023年第1期4卷 13-27页

作者： Kuang Sheng Yue Sun Meng Liu Yuefen Cao Yifei Han Cheng Li Uzair Muhammad Muhammad Khan Daud Wanru Wang Huazu Li Samrana Samrana Yixuan Hui Shuijin Zhu Jinhong Chen Tianlun Zhao Institute of Crop Science College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina Novogene Bioinformatics Institute BeijingChina Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina Department of Biotechnology and Genetic Engineering Kohat University of Science and TechnologyKohatPakistan Hainan Institute Zhejiang UniversitySanyaChina

The pigment gland is a morphological characteristic of Gossypium and its related *** bickii(G_(1))is characterized by delayed pigment gland morphogenesis in the *** this study,a referencegrade genome of G_(1) was generated,and comparative genomics analysis showed that G_(1) was closest to Gossypium australe(G_(2)),followed by A-and D-genome *** large fragment translocations in chromosomes 5 and 13 were detected between the G genome and other Gossypiumgenomes and were unique to the G_(1) and G_(2) *** with the G_(2) genome,two large fragment inversions in chromosomes 12 and 13 were detected in G_(1).According to the phylogeny,divergence time,and similarity analysis of nuclear andchloroplast genomes,G_(1)was formedby hybridization between Gossypium sturtianum(C_(1))and a common ancestor of G_(2) and Gossypiumnelsonii(G_(3)).The coordinated expression patterns of pigment gland formation(GoPGF)and gossypol biosynthesis genes in G_(1) were verified to be consistent with its phenotype,and nine genes thatwere related to theprocessof pigmentgland formationwere *** gene,GbiCYP76B6,regulated by GoPGF,was found to affect gossypol *** findings offer insights into the origin and evolution of G_(1) and its mechanism of pigment gland formation and gossypol biosynthesis.

关键词： Gossypium bickii genome evolution gossypol pigment glands

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