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simplifyEnrichment:A Bioconductor Package for Clustering and Visualizing Functional Enrichment Results

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Genomics, Proteomics & Bioinformatics 2023年第1期21卷 190-202页

作者： Zuguang Gu daniel.Hübschmann Molecular Precision Oncology Program National Center for Tumor Diseases(NCT)HeidelbergD-69120 HeidelbergGermany Heidelberg Institute of Stem Cell Technology and Experimental Medicine(HI-STEM) D-69120 HeidelbergGermany German Cancer Consortium(DKTK) D-69120 HeidelbergGermany Department of Pediatric Immunology Hematology and OncologyUniversity Hospital HeidelbergD-69120 HeidelbergGermany

Functional enrichment analysis or gene set enrichment analysis is a basic bioinformatics method that evaluates the biological importance of a list of genes of ***,it may produce a long list of significant terms with highly redundant information that is difficult to *** tools to simplify enrichment results by clustering them into groups either still produce redundancy between clusters or do not retain consistent term similarities within *** propose a new method named binary cut for clustering similarity matrices of functional *** comprehensive benchmarks on both simulated and real-world datasets,we demonstrated that binary cut could efficiently cluster functional terms into groups where terms showed consistent similarities within groups and were mutually exclusive between *** compared binary cut clustering on the similarity matrices obtained from different similarity measures and found that semantic similarity worked well with binary cut,while similarity matrices based on gene overlap showed less consistent *** implemented the binary cut algorithm in the R package simplifyEnrichment,which additionally provides functionalities for visualizing,summarizing,and comparing the *** simplifyEnrichment package and the documentation are available at https://***/packages/simplifyEnrichment/.

关键词： Functional enrichment Simplify enrichment Clustering R/Bioconductor Software Visualization

New developments in the treatment of castration resistant prostate cancer

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Asian Journal of Andrology 2014年第4期16卷 555-560页

作者： Roxanne Wadia daniel.P Petrylak Department of Medicine Smilow Cancer Center Yale University School of Medicine Yale Comprehensive Cancer Center New Haven Connecticut USA

In the past 5 years, the treatment and understanding of metastatic castrate resistant prostate cancer （CRPC） have improved dramatically. Our understanding of the mechanisms of castration resistance has allowed for the development of new drugs to target prostate cancer, and our understanding of genetic mutations may give us new tools with which to more accurately diagnose and be able to predict the course of this heterogeneous disease. This article summarizes the recent advances in the understanding of the development of CRPC, as well as the new drugs and targets, which have evolved from this basic research.

关键词： castration resistant prostate cancer abiraterone enzalutamide chemotherapy docetaxel cabazitaxel PSMA antibody

Integrated management of cardiac failure:the cardiac failure clinic

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Frontiers of Medicine 2011年第1期5卷 20-25页

作者： daniel.LOISANCE La Pitie Hospital Paris 75013France

The prevalence of the risk factors and the risk of cardiac failure are both increasing in *** might be the consequence of the changes of the life conditions(emigration to the urban areas,changes in the diet and life style,lack of physical exercise,etc.).The wide range of clinical presentations of cardiac failure(acute or chronic)and of therapeutic approaches(medical or surgical)makes necessary the integration within the same structure of the various experts involved in the diagnosis and the treatment of cardiac *** and human resources required to offer all the options represent a multifaceted commitment which should be focused optimally in dedicated *** these centers,collaboration should replace competition between the medical and the surgical cardiac *** of team work should permit to optimize the cost efficacy of the *** of all,such a structure will facilitate the translation of innovative therapies between the research centers and clinical facilities.

关键词： cardiac failure cardiac transplantation mechanical circulatory support

It takes two to tango: Unraveling a new post-translational modification involved in SnRK2.6 activation

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Molecular Plant 2021年第11期14卷 1779-1781页

作者： Miguel daniel.Mozo Armando Albert Instituto de Quimica Ffsica Rocasolano Consejo Superior de Investigaciones Cientificas(IQFR-CSIC)Calle Serrano 11928006 MadridSpain

Protein kinases are a conserved superfamily of proteins that play an essential role in signal transduction by attaching a phosphoryl group to serine,threonine,or tyrosine residues of a protein,hence converting them to *** process,which can be reversed by protein phosphatases,regulates vital cellular processes in plants,including metabolism,proliferation,and *** is also key to trigger response mechanisms to drought,increased salinity,and other abiotic stresses(Zhu,2016).

关键词： hence reversed translational

DNMT1-dependent regulation of cortical interneuron function and survival

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Neural Regeneration Research 2021年第12期16卷 2405-2406页

作者： daniel.Pensold Geraldine Zimmer-Bensch RWTH Aachen University Institute for Biology IIDepartment of Functional Epigenetics in the Animal ModelAachenGermany

Increased occurrence of age-associated disabilities and neurodegenerative diseases is the price we pay for the tremendous elevation in life expectancy in our modern *** comes along with structural,neurochemical and physiological alterations in the brain that cause memory decline and cognitive impairments(Rozycka and Liguz-Lecznar,2017).Numerous factors contribute to cognitive aging including hormonal,metabolic,and immune dysregulation,elevated oxidative stress and inflammation,changes in neurotransmission,and diminished neurotrophic support of neurons(Rozycka and Liguz-Lecznar,2017).

关键词： alterations elevated function

Semen analysis and sperm function testing

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Asian Journal of Andrology 2012年第1期14卷 6-13,174页

作者： daniel.R Franken Sergio Oehninger Department of Obstetrics and Gynaecology Tygerberg Hospita Tygerberg Cape Town 7505 South Africa Department of Obstetrics and Gynaecology Eastern Virginia Medical School Jones Institute for Reproductive Medicine Norfolk VA 23507 USA

Despite controversy regarding the clinical value of semen analysis, male fertility investigation still relies on a standardized analysis of the semen parameters. This is especially true for infertility clinics in both developing and developed countries. Other optional tests or sophisticated technologies have not been widely applied. The current review addresses important changes in the analysis of semen as described in the new World Health Organization （WHO） manual for semen analysis. The most important change in the manual is the use of evidence-based publications as references to determine cutoff values for normality. Apart from the above mentioned changes, the initial evaluation and handling methods remain, in most instances, the same as in previous editions. Furthermore, the review evaluates the importance of quality control in andrology with emphasis on the evaluation of sperm morphology. WHO sperm morphology training programmes for Sub-Saharan countries were initiated at Tygerberg Hospital in 1995. The external qualitY control programme has ensured that the majority of participants have maintained their morphological reading skills acquired during initial training. This review reports on current sperm functional tests, such as the induced acrosome reaction, and sperm-zona pellucida binding assays, as well as the impact of sperm quality in terms of DNA integrity, and the relationship of sperm function tests to sperm morphology.

关键词： male infertility quality assurance semen analysis spermatozoa sperm concentration sperm function sperm morphology sperm motility

Avalonia,get bent!–Paleomagnetism from SW Iberia confirms the Greater Cantabrian Orocline

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Geoscience Frontiers 2021年第2期12卷 805-825页

作者： Bruno daniel.Leite Mendes daniel.Pastor-Galan Mark J.Dekkers Wout Krijgsman Paleomagnetic Laboratory Fort Hoofddijk Department of Earth SciencesUtrecht UniversityBudapestlaan 173584CDthe Netherlands Frontier Research Institute for Interdisciplinary Sciences Tohoku UniversityJapan Department Earth Science Tohoku UniversityJapan Center for North East Asia Studies Tohoku University980-857641 KawauchiAoba-kuSendaiMiyagiJapan

The amalgamation of Pangea formed the contorted Variscan-Alleghanian orogen,suturing Gondwana and Laurussia during the *** all swirls of this orogen,a double curve in Iberia stands out,the coupled Cantabrian Orocline and Central Iberian *** Cantabrian Orocline formed at ca.315–290 Ma subsequent to the Variscan *** formation mechanism of the Cantabrian Orocline is disputed,the most commonly proposed mechanisms include either(1)that south-westernmost Iberia would be an Avalonian(Laurussian)indenter or(2)that the stress field changed,buckling the *** contrast,the geometry and kinematics of the Central Iberian curve are largely *** some authors defend both curvatures are genetically linked,others support they are distinct and formed at different *** uncertainty adds an extra layer of complexity to our understanding of the final stages of Pangea’s *** solve these issues,we study the late Carboniferous–early Permian vertical-axis rotations of SW Iberia with *** results show up to 70counterclockwise vertical-axis rotations during late Carboniferous times,concurring with the anticipated kinematics if SW Iberia was part of the southern limb of the Cantabrian *** results do not allow the necessary penecontemporaneous clockwise rotations in Central Iberia to support a concomitant formation of both Cantabrian and Central Iberian *** coherent rotation of both Gondwanan and Avalonian pieces of SW Iberia discards the Laurussian indenter hypothesis as a formation mechanism of the Cantabrian Orocline and confirms the Greater Cantabrian Orocline *** Greater Cantabrian Orocline likely formed as a consequence of a change in the stress field during the late Carboniferous and extended beyond the Rheic Ocean suture affecting the margins of both Laurussia and Gondwana.

关键词： Pangea Variscan orogeny Greater Cantabrian Orocline Paleomagnetism Central Iberian curve

Utilizing semantic-level computer vision for fracture trace characterization of hard rock pillars in underground space

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Geoscience Frontiers 2024年第2期15卷 366-391页

作者： Chuanqi Li Jian Zhou daniel.Dias Laboratory 3SR CNRS UMR 5521Grenoble Alpes UniversityGrenoble 38000France School of Resources and Safety Engineering Central South UniversityChangsha 410083China

This study utilizes a semantic-level computer vision-based detection to characterize fracture traces of hard rock pillars in underground *** trace images captured by photogrammetry are used to establish the database for training two convolutional neural network(CNN)-based models,i.e.,U-Net(University of Freiburg,Germany)and DeepLabV3+(Google,USA)*** code technology,polyline approximation algorithm,and the circular window scanning approach are combined to quantify the main characteristics of fracture traces on flat and uneven surfaces,including trace length,dip angle,density,and *** extraction results indicate that the CNN-based models have better performances than the edge detection methods-based Canny and Sobel operators for extracting the trace and reducing noise,especially the DeepLabV3+***,the quantization results further prove the reliability of extracting the fracture *** a result,a case study with two types of traces(i.e.,on flat and uneven surfaces)demonstrates that the applied semantic-level computer vision detection is an accurate and efficient approach for characterizing the fracture trace of hard rock pillars.

关键词： Fracture trace Hard rock pillar Semantic-level computer vision Convolutional neural network(CNN) Underground space

The Roper resonance in a finite volume

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Communications in Theoretical Physics 2020年第7期72卷 49-59页

作者： daniel.Severt Ulf-G Meiβner Helmholtz-Institut für Strahlen-und Kernphysik and Bethe Center for Theoretical Physics Universitat BonnD-53115 BonnGermany Institute for Advanced Simulation Institut für Kernphysik and Jülich Center for Hadron PhysicsForschungszentrum JülichD-52425 JiilichGermany Tbilisi State University 0186 TbilisiGeorgia

We calculate the energy levels corresponding to the Roper resonance based on a two-flavor chiral effective Lagrangian for pions,nucleons,deltas,and the Roper resonance at the leading one-loop *** show that the Roper m... 详细信息

关键词： Lattice QCD Roper resonance finite volume methods