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Generating barcodes for nanopore sequencing data with PRO

Fundamental research 2024年第4期4卷 785-794页

作者： Ting Yu Zitong Ren Xin Gao Guojun Li Renmin Han research center for mathematics and Interdisciplinary Sciences Frontiers Science Center for Nonlinear Expectations(Ministry of Education)Shandong UniversityShandong 266000China Computer Electrical and Mathematical Sciences and Engineering Division&Computational Bioscience Research CenterKing Abdullah University of Science and TechnologyThuwal 23955Saudi Arabia

DNA barcodes,short and unique DNA sequences,play a crucial role in sample identification when processing many samples simultaneously,which helps reduce experimental ***,the low quality of long-read sequencing makes it difficult to identify barcodes accurately,which poses significant challenges for the design of barcodes for large numbers of samples in a single sequencing ***,we present a comprehensive study of the generation of barcodes and develop a tool,PRO,that can be used for selecting optimal barcode sets and *** formulate the barcode design problem as a combinatorial problem and prove that finding the optimal largest barcode set in a given DNA sequence space in which all sequences have the same length is theoretically *** practical applications,we developed the novel method PRO by introducing the probability divergence between two DNA sequences to expand the capacity of barcode kits while ensuring demultiplexing ***,the maximum size of the barcode kits designed by PRO is 2,292,which keeps the length of barcodes the same as that of the official ones used by Oxford Nanopore Technologies(ONT).We validated the performance of PRO on a simulated nanopore dataset with high error *** demultiplexing accuracy of PRO reached 98.29%for a barcode kit of size 2,922,4.31%higher than that of Guppy,the official demultiplexing *** the size of the barcode kit generated by PRO is the same as the official size provided by ONT,both tools show superior and comparable demultiplexing accuracy.

关键词： Third-generation sequencing Nanopore sequencing DNA barcode Farthest point sampling algorithm High throughput

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Conformally symmetric wormhole solutions supported by non-commutative geometry in f(Q,T)gravity

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Communications in Theoretical Physics 2024年第2期76卷 111-124页

作者： Chaitra Chooda Chalavadi V Venkatesha N S Kavya S V Divya Rashmi Department of P.G.Studies and research in mathematics Kuvempu UniversityShankaraghattaShivamogga 577451KarnatakaIndia Department of mathematics Vidyavardhaka College of EngineeringMysuru—570002India

This paper investigates wormhole solutions within the framework of extended symmetric teleparallel gravity,incorporating non-commutative geometry,and conformal *** achieve this,we examine the linear wormhole model with anisotropic fluid under Gaussian and Lorentzian *** primary objective is to derive wormhole solutions while considering the influence of the shape function on model parameters under Gaussian and Lorentzian *** resulting shape function satisfies all the necessary conditions for a traversable ***,we analyze the characteristics of the energy conditions and provide a detailed graphical discussion of the matter contents via energy ***,we explore the effect of anisotropy under Gaussian and Lorentzian ***,we present our conclusions based on the obtained results.

关键词： traversable wormhole f(Q T)gravity energy conditions non-commutative geometry conformal motion

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PERIODIC SYSTEMS WITH TIME DEPENDENT MAXIMAL MONOTONE OPERATORS

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Acta Mathematica Scientia 2024年第4期44卷 1280-1300页

作者： Zhenhai LIU Nikolaos S.PAPAGEORGIOU center for Applied mathematics of Guangri Yulin Normal UniversityYulin 537000China Guangri Key Laboratory of Universities Optimization Control and Engineering Calculation College of Mathematics and PhysicsGuangri Minzu UniversityNanning 530006China Department of mathematics National Technical UniversityZografou Campus15780 AthensGreece

We consider a first order periodic system in R^(N),involving a time dependent maximal monotone operator which need not have a full domain and a multivalued *** prove the existence theorems for both the convex and nonconvex *** also show the existence of extremal periodic solutions and provide a strong relaxation ***,we provide an application to nonlinear periodic control systems.

关键词： periodic boundary condition time-dependent maximal monotone operator convex and nonconvex problems extremal solutions strong relaxation

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Einstein Hybrid Structure of q-Rung Orthopair Fuzzy Soft Set and Its Application for Diagnosis of Waterborne Infectious Disease

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Computer Modeling in Engineering & Sciences 2024年第5期139卷 1863-1892页

作者： Rana Muhammad Zulqarnain Hafiz Khalil ur Rehman Imran Siddique HijazAhmad Sameh Askar Shahid Hussain Gurmani School of Mathematical Sciences Zhejiang Normal UniversityJinhua321004China Department of mathematics Government College UniversityFaisalabad38000Pakistan Department of mathematics University of SargodhaSargodha40100Pakistan Section of mathematics International Telematic University UninettunoCorso Vittorio Emanuele IIRoma3900186Italy Near East university Operational Research Center in HealthcareNear East BoulevardNicosia/Mersin 1099138Turkey Department of Statistics and Operations research College of ScienceKing Saud UniversityPO Box 2455Riyadh11451Saudi Arabia

This research is devoted to diagnosing water-borne infectious diseases caused by floods employing a novel diagnosis approach,the Einstein hybrid structure of q-rung orthopair fuzzy soft *** approach integrates parts of fuzzy logic and soft set theory to develop a robust alternative for disease detection in stressful situations,especially in areas affected by *** to the traditional intuitionistic fuzzy soft set and Pythagorean fuzzy soft set,the q-rung orthopair fuzzy soft set(q-ROFSS)adequately incorporates unclear and indeterminate *** major objective of this investigation is to formulate the q-rung orthopair fuzzy soft Einstein hybrid weighted average(q-ROFSEHWA)operator and its specific ***,our stated operator is implementing intelligentmulti-criteria group decision-making(MCGDM)*** are severe natural catastrophes that raise the risk of diseases and epidemics,particularly those caused by contaminants in the water,such as gastrointestinal diseases,respiratory infections,vector-borne diseases,skin infections,and water-borne *** designed MCGDM strategy tackles the prevalence of certain conditions in flood-affected patients.A comparative investigation determined that the suggested method for detecting water-borne infectious disease due to floods is more effective and productive than conventional methods because of its logical structure.

关键词： q-rung orthopair fuzzy soft set q-ROFSEHWA operator MCGDM environmental disaster water-born infection disease

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NORMALIZED SOLUTIONS FOR THE GENERAL KIRCHHOFF TYPE EQUATIONS

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Acta Mathematica Scientia 2024年第5期44卷 1886-1902页

作者： Wenmin LIU Xuexiu ZHONG Jinfang ZHOU School of Mathematical Sciences South China Normal UniversityGuangzhou510631China South China research center for Applied mathematics and Interdisciplinary Studies&School of Mathematical Sciences South China Normal UniversityGuangzhou510631China

In the present paper,we prove the existence,non-existence and multiplicity of positive normalized solutions(λ_(c),u_(c))∈ℝ×H^(1)(ℝ^(N))to the general Kirchhoff problem-M\left(\int_{\mathbb{R}^N}\vert\nabla u\vert^2{\rm d}x\right)\Delta u+\lambda u=g(u)~\hbox{in}~\mathbb{R}^N,u\in H^1(\mathbb{R}^N),N\geq 1,satisfying the normalization constraint\int_{\mathbb{R}^N}u^2{\rm d}x=c,where M∈C([0,∞))is a given function satisfying some suitable *** argument is not by the classical variational method,but by a global branch approach developed by Jeanjean et al.[J Math Pures Appl,2024,183:44–75]and a direct correspondence,so we can handle in a unified way the nonlinearities g(s),which are either mass subcritical,mass critical or mass supercritical.

关键词： normalized solution Kirchhoff type equations general nonlinearities asymptotic behavior

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Extreme Antarctic Cold of Late Winter 2023

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Advances in Atmospheric Sciences 2024年第10期41卷 1873-1880页

作者： Anastasia J.TOMANEK David E.MIKOLAJCZYK Matthew A.LAZZARA Stefano DI BATTISTA Minghu DING Mariana FONTOLAN LITELL David H.BROMWICH Taylor P.NORTON Linda M.KELLER Lee J.WELHOUSE Antarctic Meteorological research and Data center Space Science and Engineering CenterUniversity of Wisconsin-Madison Department of Physical Sciences School of Engineering Science and MathematicsMadison Area Technical College Meteogiornale State Key Laboratory of Severe Weather Chinese Academy of Meteorological Sciences Byrd Polar and Climate research center The Ohio State University Department of Geography The Ohio State University

Extreme cold temperatures were observed in July and August 2023, coinciding with the WINFLY(winter fly-in)period of mid to late August into September 2023, meaning aircraft operations into Mc Murdo Station and Phoenix Airfield were adversely impacted. Specifically, with temperatures below-50℃, safe flight operation was not possible because of the risk of failing hydraulics and fuel turning to gel onboard the aircraft. The cold temperatures were measured across a broad area of the Antarctic, from East Antarctica toward the Ross Ice Shelf, and stretching across West Antarctica to the Antarctic Peninsula. A review of automatic weather station measurements and staffed station observations revealed a series of sites recording new record low temperatures. Four separate cold phases were identified, each a few days in duration and occurring from mid-July to the end of August 2023. A brief analysis of 500-hPa geopotential height anomalies shows how the mid-tropospheric atmospheric environment evolves in relation to these extreme cold temperatures. The monthly 500-hPa geopotential height anomalies show strong negative anomalies in August. Examination of composite geopotential height anomalies during each of the four cold phases suggests various factors leading to cold temperatures, including both southerly off-content flow and calm atmospheric conditions. Understanding the atmospheric environment that leads to such extreme cold temperatures can improve prediction of such events and benefit Antarctic operations and the study of Antarctic meteorology and climatology.

关键词： Antarctica extreme cold temperature automatic weather station networks

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Thermal analysis of the Rindler-Schwarzschild black hole via corrected entropy

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Communications in Theoretical Physics 2024年第9期76卷 95-106页

作者： Allah Ditta Xia Tiecheng Riasat Ali AliÖvgün Department of mathematics Shanghai University and Newtouch Center for Mathematics of Shanghai UniversityShanghai200444China Physics Department Eastern Mediterranean UniversityFamagusta99628 North Cyprus via Mersin 10Turkiye

In this study,we investigate the thermodynamic characteristics of the Rindler–Schwarzschild black hole *** analysis encompasses the examination of energy emission,Gibbs free energy,and thermal *** calculate various quantities such as the Hawking temperature,geometric mass,and heat capacity to assess the local and global thermodynamic *** temperature of the black hole is determined using the first law of thermodynamics,while the energy emission rate is evaluated as *** computing the Gibbs free energy,we explore the phase transition behavior exhibited by Rindler–Schwarzschild black hole,specifically examining the swallowing ***,we derive the corrected entropy to investigate the influence of thermal fluctuations on small and large black ***,we compare the impact of correction terms on the thermodynamic system by comparing the results obtained for large black holes and small black holes.

关键词： black holes thermodynamics thermal fluctuations heat capacity Gibbs free energy energy emission Rindler–Schwarzschild black hole

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APPROXIMATELY ARTINIAN （NOETHERIAN） C*-ALGEBRAS

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Acta Mathematica Scientia 2024年第6期44卷 2485-2497页

作者： Mohammad ROUZBEHANI Massoud AMINI Mohammad B.ASADI School of mathematics Statistics and Computer ScienceCollege of ScienceUniversity of Tehran Department of mathematics Faculty of Mathematical SciencesTarbiat Modares University School of mathematics Institute for Research in Fundamental Sciences (IPM)

In this article,we introduce and study the class of approximately Artinian（Noetherian） C*-algebras,called AR-algebras（AN-algebras）,which is a simultaneous generalization of Artinian（Noetherian） C*-algebras and *** study properties such as the ideal property and topological dimension zero for *** particular,we show that a faithful AR or AN algebra is strongly purely infinite iff it is purely infinite iff it is weakly purely *** extends the Kirchberg's O∞-absorption theorem,and implies that a weakly purely infinite C*-algebra is Noetherian iff every its ideal has a full projection.

关键词： (weakly) purely infinite 46L05 46L80 Artinian C*-algebra graph C*-algebra ideal property inductive limit Noetherian

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Reconstruct recent multi-population migration history by using identical-by-descent sharing

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Journal of Genetics and Genomics 2024年第6期51卷 642-651页

作者： Wenxiao Zhang Kai Yuan Ru Wen Haifang Li Xumin Ni School of mathematics and Statistics Beijing Jiaotong UniversityBeijing 100044China The Stanley center for Psychiatric research Broad Institute of MIT and HarvardCambridgeMA 02142USA Baidu Incorporated Beijing 100085China

Identical-by-descent(IBD)is a fundamental genomic characteristic in population genetics and has been widely used for population history ***,limited by the nature of IBD,which could only capture the relationship between two individuals/haplotypes,existing IBD-based history inference is constrained to two *** this study,we propose a framework by leveraging IBD sharing in multipopulation and develop a method,MatrixiBD,to reconstruct recent multi-population migration ***,we employ the structured coalescent theory to precisely model the genealogical process and then estimate the IBD sharing across multiple *** our model,we establish a theoretical connection between migration history and IBD *** method is rigorously evaluated through simulations,revealing its remarkable accuracy and ***,we apply MatrixiBD to Central and South Asia in the Human Genome Diversity Project and successfully reconstruct the recent migration history of three closely related populations in South *** taking into account the IBD sharing across multiple populations simultaneously,MatrixlBD enables us to attain clearer and more comprehensive insights into the history of regions characterized by complex migration dynamics,providing a holistic perspective on intricate patterns embedded within the recent population migration history.

关键词： Population genetics IBD sharing Migration history Structured coalescent theory Gene flow

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A discussion about the limitations of the Eurocode’s high-speed load model for railway bridges

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Railway Engineering Science 2024年第2期32卷 211-228页

作者： Gonçalo Ferreira Pedro Montenegro JoséRui Pinto António Abel Henriques Rui Calçada CONSTRUCT-LESE Faculty of EngineeringUniversity of PortoRua Dr.Roberto Frias4200-465 PortoPortugal CONSTRUCT-LABEST Faculty of EngineeringUniversity of PortoRua Dr.Roberto Frias4200-465 PortoPortugal

High-speed railway bridges are subjected to normative limitations concerning maximum permissible deck *** the design of these structures,the European norm EN 1991-2 introduces the high-speed load model(HSLM)—a set of point loads intended to include the effects of existing high-speed ***,the evolution of current trains and the recent development of new load models motivate a discussion regarding the limits of validity of the *** this study,a large number of randomly generated load models of articulated,conventional,and regular trains are tested and compared with the envelope of HSLM *** each type of train,two sets of 100,000 load models are considered:one abiding by the limits of the EN 1991-2 and another considering wider *** comparison is achieved using both a bridge-independent metric(train signatures)and dynamic analyses on a case study bridge(the Canelas bridge of the Portuguese Railway Network).For the latter,a methodology to decrease the computational cost of moving loads analysis is *** show that some theoretical load models constructed within the stipulated limits of the norm can lead to effects not covered by the *** is especially noted in conventional trains,where there is a relation with larger distances between centres of adjacent vehicle bogies.

关键词： High-speed load model Dynamic analysis High-speed railways Train signature Railway bridges Deck acceleration

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