检索结果-内蒙古大学图书馆

arXiv 2023年

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

While numerous methods have been proposed for computing distances between probability distributions in Euclidean space, relatively little attention has been given to computing such distances for distributions on graphs. However, there has been a marked increase in data that either lies on graph (such as protein interaction networks) or can be modeled as a graph (single cell data), particularly in the biomedical sciences. Thus, it becomes important to find ways to compare signals defined on such graphs. Here, we propose Graph Fourier MMD (GFMMD), a novel distance between distributions and signals on graphs. GFMMD is defined via an optimal witness function that is both smooth on the graph and maximizes difference in expectation between the pair of distributions on the graph. We find an analytical solution to this optimization problem as well as an embedding of distributions that results from this method. We also prove several properties of this method including scale invariance and applicability to disconnected graphs. We showcase it on graph benchmark datasets as well on single cell RNA-sequencing data analysis. In the latter, we use the GFMMD-based gene embeddings to find meaningful gene clusters. We also propose a novel type of score for gene selection called gene localization score which helps select genes for cellular state space characterization. Copyright © 2023, The Authors. All rights reserved.

关键词： Genes

来源：评论

学校读者我要写书评

暂无评论

Towards Fabrication of Next-Generation Physical Sensors Through Integrating Suspended Sub-Micron Silicon Nanowires with Microelectromechanical Systems

Towards Fabrication of Next-Generation Physical Sensors Thro...

引用

IEEE SENSORS

作者： Basit Ali Mehdi Bostan Shirin Muhammad Muzammil Ege Nacarkucuk Sina Zare Pakzad Umut Kerimzade B. Erdem Alaca Department of Mechanical Engineering Koç University Istanbul Turkey Computational Sciences and Engineering Program Koç University Istanbul Turkey Institute of Sensor and Actuator Systems TU Wien Austria Christian Doppler Laboratory for Piezoelectric Silicon MEMS with Enhanced Sensitivity and Responsivity Institute of Sensor and Actuator Systems TU Wien Austria nSTAR-Koç University Nanofabrication and Nanocharacterization Center for Scientific and Technological Advanced Research Koç University Istanbul Turkey Surface Science and Technology Center (KUYTAM) Koç University Istanbul Turkey

ISBN: (数字)9798350363517

ISBN: (纸本)9798350363524

Silicon nanowires possess superior mechanical, electrical, and optical properties, making them ideal for next-generation sensors. This study presents a scalable technology for monolithic fabrication of sub-micron silicon nanowires with micro electromechanical systems, achieving integration of suspended sub-micron silicon nanowires within microelectromechanical systems up to 80 μm thick on Si substrates, with high yield and repeatability. The technological approach is validated on silicon-on-insulator substrates, followed by electromechanical characterization via electrical probe measurements and vibrational testing for performance validation. The presented technology is promising for the potential development of next-generation high-performance physical sensors such as accelerometers and gyroscopes.

关键词： Microelectromechanical systems Sensor phenomena and characterization Vibration measurement Silicon Sensor systems Nanowires Optical sensors Next generation networking Substrates Electromechanical sensors

来源：评论

学校读者我要写书评

暂无评论

Phase-engineered heterostructures of Mo2C by plasma-assisted selenization and sulfurization processes toward excellent hydrogen evolution reaction

引用

Nano Energy 2024年 122卷

作者： Kimbulapitiya, K.M.M.D.K. Rehman, Bushra Wani, Sumayah Shakil Chen, Chieh-Ting Cyu, Ruei-Hong Manikandan, Arumugam Date, Manisha Kondiba Peng, Yu-Ren Kumara, R.J.G.L.R. Chuang, Feng-Chuan Chueh, Yu-Lun Department of Physics National Sun Yat-sen University Kaohsiung80424 Taiwan Department of Materials Science and Engineering National Tsing-Hua University Hsinchu Taiwan College of Semiconductor Research National Tsing-Hua University Hsinchu30013 Taiwan Center for Nanotechnology Materials Science and Microsystem National Tsing-Hua University Hsinchu Taiwan Ph.D. Program in Prospective Functional Materials Industry National Tsing Hua University Hsinchu30013 Taiwan Physics Division National Center for Theoretical Sciences Hsinchu30013 Taiwan Center for Theoretical and Computational Physics National Sun Yat-Sen University Kaohsiung80424 Taiwan Department of Physics National Tsing Hua University Hsinchu30013 Taiwan

Due to the outstanding semiconducting and metallic properties, 2D materials such as Transition Metal dichalcogenides (TMDs) and Transition Metal Carbides (TMCs) appear to be promising candidate for Nano-scale electronics devices. Among them, 2D - Mo2C (Molybdenum carbide) has attracted attention as a new member of the MXene group, owing to its potential applications for superconductors, electronics devices, and catalysts for Hydrogen evolution Reactions (HER). Structural modification toward the creation of novel heterostructures with phase engineering opens new pathways for different applications. Herein, we prepared a large area Mo2C film by chemical vapor deposition method. The upper region of Mo2C layers can be oxidized to create Mo2C/MoOx heterostructures. Furthermore, those oxide layers were further transformed into MoSe2 and MoS2 by plasma-assisted selenization and sulfurization processes at different temperatures with a fixed plasma power of 150 W. The heterostructures demonstrated outstanding electrocatalytic activity for HER due to an existed metallic phase and active sites present after plasma-assisted selenization and sulfurization processes at the low temperature. The performance of the HER decreases at high temperatures owing to their semiconducting phase. The pristine Mo2C showed a Tafel slope of 72 mV dec−1 and an overpotential of 276 mV at 10 mA/cm2, while the Mo2C/MoSe2 heterostructure synthesized at 350 °C350 °exhibited an improved Tafel slope of 66 mV dec−1 and overpotential of 257 mV at 10 mA/ cm2. Additionally, the Mo2C/MoS2 heterostructure prepared at 350 °C also demonstrated a 263 mV improvement in overpotential at 10 mA/cm2. All the heterostructures showed excellent stability over a period of 10 h except Mo2C/MoOx. This work opens new strategies to fabricate high-quality MXene and TMDs heterostructures with metal-semiconductor interface. © 2024

关键词： Molybdenum compounds

来源：评论

学校读者我要写书评

暂无评论

Liquid-Liquid Transition in Water from First Principles

引用

Physical Review Letters 2022年第25期129卷 255702-255702页

作者： Thomas E. Gartner, III Pablo M. Piaggi Roberto Car Athanassios Z. Panagiotopoulos Pablo G. Debenedetti Department of Chemistry Princeton University Princeton New Jersey 08544 USA Department of Physics Princeton University Princeton New Jersey 08544 USA Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA Princeton Institute for the Science and Technology of Materials Princeton University Princeton New Jersey 08544 USA Department of Chemical and Biological Engineering Princeton University Princeton New Jersey 08544 USA

A long-standing question in water research is the possibility that supercooled liquid water can undergo a liquid-liquid phase transition (LLT) into high- and low-density liquids. We used several complementary molecular simulation techniques to evaluate the possibility of an LLT in an ab initio neural network model of water trained on density functional theory calculations with the SCAN exchange correlation functional. We conclusively show the existence of a first-order LLT and an associated critical point in the SCAN description of water, representing the first definitive computational evidence for an LLT in water from first principles.

关键词： Classical statistical mechanics First order phase transitions First-principles calculations Liquid-liquid phase transition Phase transitions Thermodynamics Deep learning Density functional theory Molecular dynamics

来源：评论

学校读者我要写书评

暂无评论

A Variational Approach to Bayesian Phylogenetic Inference

arXiv

引用

arXiv 2022年

作者： Zhang, Cheng Matsen, Frederick A. School of Mathematical Sciences Center for Statistical Science Peking University Beijing100871 China Howard Hughes Medical Institute Computational Biology Program Fred Hutchinson Cancer Research Center SeattleWA98109 United States Department of Genome Sciences Department of Statistics University of Washington SeattleWA98195 United States

Bayesian phylogenetic inference is currently done via Markov chain Monte Carlo (MCMC) with simple proposal mechanisms. This hinders exploration efficiency and often requires long runs to deliver accurate posterior estimates. In this paper, we present an alternative approach: a variational framework for Bayesian phylogenetic analysis. We propose combining subsplit Bayesian networks, an expressive graphical model for tree topology distributions, and a structured amortization of the branch lengths over tree topologies for a suitable variational family of distributions. We train the variational approximation via stochastic gradient ascent and adopt gradient estimators for continuous and discrete variational parameters separately to deal with the composite latent space of phylogenetic models. We show that our variational approach provides competitive performance to MCMC, while requiring much fewer (though more costly) iterations due to a more efficient exploration mechanism enabled by variational inference. Experiments on a benchmark of challenging real data Bayesian phylogenetic inference problems demonstrate the effectiveness and efficiency of our methods. © 2022, CC BY.

关键词： Bayesian networks

来源：评论

学校读者我要写书评

暂无评论

Local Order Metrics for Two-Phase Media Across Length Scales

arXiv

引用

arXiv 2022年

作者： Torquato, Salvatore Skolnick, Murray Kim, Jaeuk Department of Chemistry Department of Physics Princeton Institute for the Science and Technology of Materials Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States Department of Chemistry Princeton University PrincetonNJ08544 United States McKetta Department of Chemical Engineering University of Texas at Austin AustinTX78712 United States

The capacity to devise order metrics for microstructures of multiphase heterogeneous media is a highly challenging task, given the richness of the possible geometries and topologies of the phases that can arise. This investigation initiates a program to formulate order metrics to characterize the degree of order/disorder of the microstructures of two-phase media in d-dimensional Euclidean space Rd across length scales. In particular, we propose the use of the local volume-fraction variance σV2 (R) associated with a spherical window of radius R as an order metric. We determine σV2 (R) as a function of R for 22 different models across the first three space dimensions, including both hyperuniform and nonhyperuniform systems with varying degrees of short- and long-range order. We find that the local volume-fraction variance as well as asymptotic coefficients and integral measures derived from it provide reasonably robust and sensitive order metrics to categorize disordered and ordered two-phase media across all length scales. © 2022, CC BY-SA.

关键词： Volume fraction

来源：评论

学校读者我要写书评

暂无评论

Robocop: Multivariate state space model integrating epigenomic accessibility data to elucidate genome-wide chromatin occupancy 24th

Robocop: Multivariate state space model integrating epigenom...

引用

24th Annual Conference on Research in computational Molecular Biology, RECOMB 2020

作者： Mitra, Sneha Zhong, Jianling MacAlpine, David M. Hartemink, Alexander J. Department of Computer Science Duke University DurhamNC27708 United States Program in Computational Biology and Bioinformatics Duke University DurhamNC27708 United States Department of Pharmacology and Cancer Biology Duke University Medical Center DurhamNC27710 United States Center for Genomic and Computational Biology Duke University DurhamNC27708 United States

ISBN: (纸本)9783030452568

Chromatin is the tightly packaged structure of DNA and protein within the nucleus of a cell. The arrangement of different protein complexes along the DNA modulates and is modulated by gene expression. Measuring the binding locations and level of occupancy of different transcription factors (TFs) and nucleosomes is therefore crucial to understanding gene regulation. Antibody-based methods for assaying chromatin occupancy are capable of identifying the binding sites of specific DNA binding factors, but only one factor at a time. On the other hand, epigenomic accessibility data like ATAC-seq, DNase-seq, and MNase-seq provide insight into the chromatin landscape of all factors bound along the genome, but with minimal insight into the identities of those factors. Here, we present RoboCOP, a multivariate state space model that integrates chromatin information from epigenomic accessibility data with nucleotide sequence to compute genome-wide probabilistic scores of nucleosome and TF occupancy, for hundreds of different factors at once. RoboCOP can be applied to any epigenomic dataset that provides quantitative insight into chromatin accessibility in any organism, but here we apply it to MNase-seq data to elucidate the protein-binding landscape of nucleosomes and 150 TFs across the yeast genome. Using available protein-binding datasets from the literature, we show that our model more accurately predicts the binding of these factors genome-wide. © Springer Nature Switzerland AG 2020.

关键词： Hidden Markov models

来源：评论

学校读者我要写书评

暂无评论

Narrowing of the Racial Disparities Gap in Survival of Patients With Mycosis Fungoides: A Longitudinal Analysis of the SEER Database

引用

Clinical Lymphoma, Myeloma and Leukemia 2025年第7期25卷 e501-e506页

作者： Le, Britney Soror, Noha Ismail, Hamid D. Baker, Mohammed Shetayyah, Salman Abu Chung, Catherine G. William, Basem M. Ohio University Heritage College of Osteopathic Medicine Dublin OH The University of Oklahoma College of Medicine Oklahoma City OK United States Department of Computational Data Science and Engineering North Carolina Agricultural and Technical State University Greensboro NC United States Faculty of Medicine Jordan University of Science and Technology Irbid Jordan The Ohio State University Comprehensive Cancer Center: Arthur G. James Cancer Hospital and Richard J. Solove Research Institute Division of Dermatology Columbus OH Ohio Health Blood and Marrow Transplant Program Columbus OH

Background: Mycosis fungoides (MF) is the commonest subtype of cutaneous T-cell lymphoma. In the United States, prior studies reported that African Americans (AA) with MF had poor outcomes. Data characterizing differences in racial disparity outcomes over time are limited. Patients and Methods: We collected data from the United States Surveillance, Epidemiology, and End Results (SEER) database to investigate the survival patterns of patients with MF from 1988 to 2011. Cases were divided into 3 cohorts based on the year of diagnosis. Univariable and multivariable analysis were conducted to assess for factors associated with overall survival (OS). Results: 2896 cases of MF were detected, with a median follow-up duration of 60 months. The disparity in survival between the years 1988-1995 and 2004-2011 was significant (P = .05). The parameter estimates of the Cox proportional hazards model for the 1988-1995 period (using the 2004-2011 period as a reference) was also significant (P = .024). Patients diagnosed between 1988 and 1995 were 1.4 times more likely to die from the disease than those diagnosed between 2004 and 2011. The survival gap between AA and white patients narrowed in 1996-2003 and 2004-2011 in comparison to 1988-1995. This indicates improvements in the survival of AA patients over time. Conversely, the survival rates of white patients remained relatively stable over time. Conclusions: Our study demonstrates that AA with MF have reduced survival. Despite the persistent pattern of lower survival across all periods, the gap in survival between white and AA seems to be narrowing over time. © 2025 Elsevier Inc.

关键词： Cutaneous lymphoma Mycosis fungoides Outcome research Racial disparity SEER database

来源：评论

学校读者我要写书评

暂无评论

A Path Analysis Model for Explaining Factors That Influence the Use of Masker among Commuting Workers Using KRL Commuter Line Bogor Jakarta

Research Square

引用

Research Square 2021年

作者： Kusmawan, David Andari, Shofi Indri Hapsari, S. Faculty Medicine and Health Science Universitas Jambi Indonesia Bioinformatics and Computational Biology Graduate Program Iowa State University United States Occupational Health and Safety Department Faculty of Public Health Universitas Indonesia Indonesia

Jakarta is one of the most air polluted cities in the world, it can increase the risk of healthy of commuting worker. As one of the most air polluted cities in the world, Jakarta is at high risk of its commuting worker’s health. They are at risk of being exposed to pollutant. This study aims to determine the factors influencing directly and indirectly to healthy behavior (using masker) for commuting workers who use the KRL Commuterline Bogor - Jakarta. A total of 155 respondents participated in the study and the collected data were then analyzed using descriptive and path analysis. Commuters are aware of the hazard potential related to air pollution during commuting were 137 people (88.4%). Commuters with good perception of pollution were 104 people (67.1%). Commuters used masker during commuting was 125 people (80.6%). Healthy behavior (using masker) in commuting worker using KRL Commuter Line were affected by some factors both directly and indirectly. Knowledge and commuting experience toward healthy behavior using masker were two variables with a significant direct influence on healthy behavior using masker, and knowledge was also the only mediated variable with a significant indirect effect of education to healthy behavior (using masker). © 2021, CC BY.

关键词： Pollution

来源：评论

学校读者我要写书评

暂无评论

An efficient linear mixed model framework for meta-analytic Association studies across multiple contexts 21

An efficient linear mixed model framework for meta-analytic ...

引用

21st International Workshop on Algorithms in Bioinformatics, WABI 2021

作者： Jew, Brandon Li, Jiajin Sankararaman, Sriram Sul, Jae Hoon Bioinformatics Interdepartmental Program University of California Los AngelesCA United States Department of Human Genetics University of California Los AngelesCA United States Department of Computer Science University of California Los AngelesCA United States Department of Computational Medicine University of California Los AngelesCA United States Department of Psychiatry and Biobehavioral Sciences University of California Los AngelesCA United States

ISBN: (纸本)9783959772006

Linear mixed models (LMMs) can be applied in the meta-analyses of responses from individuals across multiple contexts, increasing power to detect associations while accounting for confounding effects arising from within-individual variation. However, traditional approaches to fitting these models can be computationally intractable. Here, we describe an efficient and exact method for fitting a multiple-context linear mixed model. Whereas existing exact methods may be cubic in their time complexity with respect to the number of individuals, our approach for multiple-context LMMs (mcLMM) is linear. These improvements allow for large-scale analyses requiring computing time and memory magnitudes of order less than existing methods. As examples, we apply our approach to identify expression quantitative trait loci from large-scale gene expression data measured across multiple tissues as well as joint analyses of multiple phenotypes in genome-wide association studies at biobank scale. © Brandon Jew, Jiajin Li, Sriram Sankararaman, and Jae Hoon Sul;licensed under Creative Commons License CC-BY 4.0 21st International Workshop on Algorithms in Bioinformatics (WABI 2021).

关键词： Bioinformatics

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：