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

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 interest.however,it may produce a long list of significant terms with highly redundant information that is difficult to summarize.Current tools to simplify enrichment results by clustering them into groups either still produce redundancy between clusters or do not retain consistent term similarities within clusters.We propose a new method named binary cut for clustering similarity matrices of functional terms.Through 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 groups.We 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 patterns.We implemented the binary cut algorithm in the R package simplifyEnrichment,which additionally provides functionalities for visualizing,summarizing,and comparing the clustering.The simplifyEnrichment package and the documentation are available at https://***/packages/simplifyEnrichment/.

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

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Parkland trees on smallholder farms ameliorate soil physical-chemical properties in the semi-arid area of Tigray,Ethiopia

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Journal of Arid Land 2024年第1期16卷 1-13页

作者： Selam LJALEM Emiru BIRhANE Kassa TEKA daniel h BERhE Department of Land Resources Management and Environmental Protection College of Dryland Agriculture and Natural ResourcesMekelle UniversityMekelle 231Ethiopia Institute of Climate and Society Mekelle UniversityMekelle 231Ethiopia Faculty of Environmental Sciences and Natural Resource Management Norwegian University of Life Sciences(NMBU)Ås 1432Norway Department of Natural Resources Management Adigrat UniversityAdigrat 50Ethiopia

Proposed agroforestry options should begin with the species that farmers are most familiar with,which would be the native multipurpose trees that have evolved under smallholder farms and socioeconomic conditions.The African birch(Anogeissus leiocarpa(DC.)Guill.&Perr.)and pink jacaranda(Stereospermum kunthianum Cham.)trees are the dominant species in the agroforestry parkland system in the drylands of Tigray,Ethiopia.Smallholder farmers highly value these trees for their multifunctional uses including timber,firewood,charcoal,medicine,etc.These trees also could improve soil fertility.however,the amount of soil physical and chemical properties enhanced by the two species must be determined to maintain the sustainable conservation of the species in the parklands and to scale up to similar agroecological systems.hence,we selected twelve isolated trees,six from each species that had similar dendrometric characteristics and were growing in similar environmental conditions.We divided the canopy cover of each tree into three radial distances:mid-canopy,canopy edge,and canopy gap(control).At each distance,we took soil samples from three different depths.We collected 216 soil samples(half disturbed and the other half undisturbed)from each canopy position and soil depth.Bulk density(BD),soil moisture content(SMC),soil organic carbon(SOC),total nitrogen(TN),available phosphorus(AP),available potassium(AK),p h,electrical conductivity(EC),and cation exchange capacity(CEC)were analysed.Results revealed that soil physical and chemical properties significantly improved except for soil texture and EC under both species,CEC under A.leiocarpus,and soil p h under S.kunthianum,all the studied soils were improved under both species canopy as compared with canopy gap.SMC,TN,AP,and AK under canopy of these trees were respectively 24.1%,11.1%,55.0%,and 9.3% higher than those soils under control.The two parkland agroforestry species significantly enhanced soil fertility near the canopy of topsoil through improving soil physical and chemica

关键词： agroforestry bulk density carbon stock dispersed tree soil texture tree canopy

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World Journal of Otorhinolaryngology-head and Neck Surgery 2024年第2期10卷 97-104页

作者： Mihai A.Bentan Evan R.Reiter Richard M.Costanzo daniel h.Coelho Department of Otolaryngology-head&Neck Surgery Virginia Commonwealth University School of MedicineRichmondVirginiaUSA

Objective:The aim of this study was to review findings from a large prospective national database of chemosensory disturbances associated with coronavirus disease 2019(COVID-19)infection.Data Sources:The Virginia Commonwealth University Smell and Taste Center national database of COVID-19 chemosensory disturbances.Methods:A series of online surveys,first opened on April 10,2020,was made accessible nationwide to any adult with sudden chemosensory dysfunction since January 2020.Participants received subsequent follow-up surveys 14 days,1 month,3 months,and 6 months after enrollment.An additional survey was sent to all participants on May 28,2022 to assess long-term outcomes.Information pertaining to demographics,symptoms,comorbidities,treatments,and life impact was collected.Results:Of 363 participants who reported complete smell recovery,51.2%recovered within 1 month,70%within 3 months,and 79%within 6 months,while 8.8%took over 1 year to completely recover.Among all participants,7.5%had no smell recovery.Positive predictors of recovery included agehe presence of nasal congestion.Negative predictors included difficulty breathing and prior head injury.Many participants reported a decrease in quality of life and the presence of potential safety hazards associated with decreased smell loss.Conclusions:Most subjects with COVID-19-related chemosensory dysfunction recover,with the majority noting complete recovery within weeks of infection.Those aged over 40 years and female gender were associated with lower rates of recovery.A considerable number of participants reported significant impact on quality of life and safety.

关键词： anosmia COVID-19 smell

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Foam rolling and stretching do not provide superior acute flexibility and stiffness improvements compared to any other warm-up intervention: A systematic review with meta-analysis

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Journal of Sport and health Science 2024年第4期13卷 509-520页

作者： Konstantin Warneke Gerit Plöschberger Lars h.Lohmann Eric Lichtenstein daniel Jochum Stanislav D.Siegel Astrid Zech David G.Behm Institute of Sport Science University of KlagenfurtKlagenfurt am Wörthersee 9020Austria Department of human Motion Science and Exercise Physiology Friedrich Schiller UniversityJena 07749Germany Department Sport Exercise and HealthUniversity of BaselBasel 4052Switzerland Department of health Sciences and Technology ETH ZurichZurich 8092Switzerland School of human Kinetics and Recreation Memorial University of NewfoundlandSt.JohnsNL A1C 5S7Canada

Background:Acute improvement in range of motion(ROM)is a widely reported effect of stretching and foam rolling,which is commonly explained by changes in pain threshold and/or musculotendinous stiffness.Interestingly,these effects were also reported in response to various other active and passive interventions that induce responses such as enhanced muscle temperature.Therefore,we hypothesized that acute ROM enhancements could be induced by a wide variety of interventions other than stretching or foam rolling that promote an increase in muscle temperature.Methods:After a systematic search in PubMed,Web of Science,and SPORTDiscus databases,38 studies comparing the effects of stretching and foam rolling with several other interventions on ROM and passive properties were included.These studies had 1134 participants in total,and the data analysis resulted in 140 effect sizes(ESs).ES calculations were performed using robust variance estimation model with R-package.Results:Study quality of the included studies was classified as fair(PEDro score=4.58)with low to moderate certainty of evidence.Results showed no significant differences in ROM(ES=0.01,p=0.88),stiffness(ES=0.09,p=0.67),or passive peak torque(ES=-0.30,p=0.14)between stretching or foam rolling and the other identified activities.Funnel plots revealed no publication bias.Conclusion:Based on current literature,our results challenge the established view on stretching and foam rolling as a recommended component of warm-up programs.The lack of significant difference between interventions suggests there is no need to emphasize stretching or foam rolling to induce acute ROM,passive peak torque increases,or stiffness reductions.

关键词： Range of motion Passive properties Muscletendon unit Muscle tissue

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Assessment of scale interactions associated with wake meandering using bispectral analysis methodologies

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Theoretical & Applied Mechanics Letters 2024年第2期14卷 65-75页

作者： Dinesh Kumar Kinjangi daniel Foti Department of Mechanical Engineering University of MemphisMemphisTennesseeUSA

Large atmospheric boundary layer fluctuations and smaller turbine-scale vorticity dynamics are separately hypothesized to initiate the wind turbine wake meandering phenomenon,a coherent,dynamic,turbine-scale oscillation of the far wake.Triadic interactions,the mechanism of energy transfers between scales,manifest as triples of wavenumbers or frequencies and can be characterized through bispectral analyses.The bispectrum,which correlates the two frequencies to their sum,is calculated by two recently developed multi-dimensional modal decomposition methods:scale-specific energy transfer method and bispectral mode decomposition.Large-eddy simulation of a utility-scale wind turbine in an atmospheric boundary layer with a broad range of large length-scales is used to acquire instantaneous velocity snapshots.The bispectrum from both methods identifies prominent upwind and wake meandering interactions that create a broad range of energy scales including the wake meandering scale.The coherent kinetic energy associated with the interactions shows strong correlation between upwind scales and wake meandering.

关键词： Wind turbine wake Mode decomposition Bispectral analysis

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Comprehensive review of hepatocellular carcinoma with portal vein tumor thrombus:State of art and future perspectives

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hepatobiliary & Pancreatic Diseases International 2024年第3期23卷 221-227页

作者： Paschalis Gavriilidis Timothy M Pawlik daniel Azoulay Department of Surgery Colchester General HospitalTurner RoadColchester CO45JLUK Department of Surgery The Ohio State Wexner Medical CenterJames Comprehensive Cancer CenterColumbusOHUSA Department of hepato-Biliary and Liver Transplantation surgery Paul Brousse University HospitalParis-Saclay UniversityVillejuif 94800France

Background:Despite advances in the diagnosis of patients with hepatocellular carcinoma(hCC),70%-80%of patients are diagnosed with advanced stage disease.Portal vein tumor thrombus(PVTT)is among the most ominous signs of advanced stage disease and has been associated with poor survival if untreated.Data sources:A systematic search of MEDLINE(PubMed),Embase,Cochrane Library and Database for Systematic Reviews(CDSR),Google Scholar,and National Institute for health and Clinical Excellence(NICE)databases until December 2022 was conducted using free text and MeSh terms:hepatocellular carcinoma,portal vein tumor thrombus,portal vein thrombosis,vascular invasion,liver and/or hepatic resection,liver transplantation,and systematic review.Results:Centers of surgical excellence have reported promising results related to the individualized surgical management of portal thrombus versus arterial chemoembolization or systemic chemotherapy.Critical elements to the individualized surgical management of hCC and portal thrombus include precise classification of the portal vein tumor thrombus,accurate identification of the subgroups of patients who may benefit from resection,as well as meticulous surgical technique.This review addressed five specific areas:(a)formation of PVTT;(b)classifications of PVTT;(c)controversies related to clinical guidelines;(d)surgical treatments versus non-surgical approaches;and(e)characterization of surgical techniques correlated with classifications of PVTT.Conclusions:Current evidence from Chinese and Japanese high-volume centers demonstrated that patients with hCC and associated PVTT can be managed with surgical resection with acceptable results.

关键词： hepatectomy Liver surgery Liver neoplasms Portal vein tumor thrombus

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Testing and modelling of transient adhesion phenomena in rolling-sliding contacts

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Friction 2024年第5期12卷 1016-1027页

作者： daniel KVARDA Alexander MEIERhOFER Klaus SIX Faculty of Mechanical Engineering Brno University of TechnologyBrno61669Czech Republic Virtual Vehicle Research Gmbh Graz8010Austria

Transient adhesion effects in rolling–sliding contacts influence all aspects of train–track interaction.This is of high importance specifically when these effects result in critically low adhesion,which poses a risk to traction and braking of railway vehicles.This study presents a model that can replicate the transient changes of the coefficient of adhesion with tested water and solid particle mix.The experimental data for the model are measured using a commercial ball-on-disc tribometer.The experimental results showed a liquid reservoir in front of the contact area that slowly reduces in size.This observation was used in the modelling approach to divide the calculation into two stages where the reservoir is present and when it disappears.The model was able to reproduce the occurrence of low adhesion region seen in experimental results with different particle concentrations.

关键词： coefficient of adhesion tribology transient effects wheel-rail contact

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Rapid growth in a large Cambrian apex predator

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National Science Review 2024年第3期11卷 128-136页

作者：吴雨 Stephen Pates daniel Pauly 张兴亮傅东静 State Key Laboratory of Continental Dynamics and Shaanxi Key Laboratory of Early Life and Environment Department of Geology Northwest University Department of Zoology University of Cambridge Institute for the Oceans and Fisheries University of British Columbia Nanjing Institute of Geology and Palaeontology Chinese Academy of Sciences

Despite the importance of ontogenetic data on early diverging euarthropods to our understanding of the ecology and evolution of past life, the data are distinctly lacking, as reconstructing life histories of fossil animals is often challenging. here we report the growth trajectory of frontal appendages of the apex predator Amplectobelua symbrachiata, one of the most common radiodont arthropods from the early Cambrian Chengjiang biota(c. 520 Ma) of China. Analysis of 432 specimens(9.1–137.1 mm length; 1.3–25.6 mm height) reveals that appendages grew isometrically, with an estimated maximum size of the whole animal of c. 90 cm. Individuals grew rapidly compared to extant arthropods, as assessed using the electronic length-frequency analysis(ELEFAN) approach. Therefore, we show that the Cambrian apex predator A. symbrachiata was an extremely fast-growing arthropod, with an unusual life history strategy that formed as part of the escalatory ‘arms race’ that shaped the Cambrian explosion over 500 Ma.

关键词： stem-group Euarthropoda Radiodonta post-embryonic development growth dynamics Cambrian Explosion

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Diagnosing upper tract urothelial carcinoma: A review of the role of diagnostic ureteroscopy and novel developments over last two decades

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Asian Journal of Urology 2024年第2期11卷 242-252页

作者： Paul Gravestock daniel Cullum Bhaskar Somani Rajan Veeratterapillay Urology Department Freeman HospitalNewcastle Upon TyneUK Department of Urology University Hospital SouthamptonSouthamptonUK

Objective: The role of ureteroscopy in the diagnosis of upper tract urothelial carcinoma is yet to be fully determined. We aimed to provide an up to date evaluation of its role and the emerging technologies in the field.Methods: A literature search of the last two decades (from 24th May, 2001 to 24th May, 2021) was carried out identifying 147 papers for potential inclusion within this narrative review.Results: Diagnostic ureteroscopy is undeniably useful in its ability to visualise and biopsy indeterminate lesions, and to risk stratify malignant lesions that may be suitable for kidney sparing surgery. however, an increased risk of intravesical recurrence following nephroureterectomy when a prior diagnostic ureteroscopy has been performed, inadequate sampling at biopsy, complications from the procedure, and difficult ureteric access are all potential drawbacks. Furthermore, whilst generally an accurate diagnostic procedure, it risks missing carcinoma in-situ lesions. Despite this, evidence shows that routine use of ureteroscopy changes the management of patients in a large proportion of cases, preventing unnecessary surgery or facilitating kidney sparing surgery. The overall rate of complications is low, and improved biopsy techniques and the use of tissue biomarkers for improved staging and grading are encouraging. The risks of delays to definitive management and post-ureteroscopy intravesical recurrence do not seem to affect survival, and trials are in progress to determine whether intravesical therapy can mitigate the latter. Further promising techniques are being investigated to improve shortcomings, particularly in relation to improved diagnosis of carcinoma in situ and preoperative staging.Conclusion: Ureteroscopy has a role in the diagnosis of upper tract malignancy, though whether it should be used routinely is yet to be determined.

关键词： Ureteroscopy Carcinoma Transitional cell Ureteralneoplasms Urinary bladder neoplasms Carcinomainsitu Biopsy

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Online Demand Response Characterization Based on Variability in Customer Behavior

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Journal of Modern Power Systems and Clean Energy 2024年第3期12卷 936-946页

作者： Lester Marrero daniel Sbárbaro Luis García-Santander the Department of Electrical Engineering University of Concepción IEEE

This paper proposes an online framework to characterize demand response(DR) over time. The proposed framework facilitates obtaining and updating the daily consumption patterns of customers. The essential concept of response profile class(RPC) is introduced for characterization and complemented by the measure of the variability in customer behavior. This paper uses a modified version of the incremental clustering by fast search and find of density peaks(CFSFDP) algorithm for daily profiles, considering the multivariate normal kernel density estimator and incremental forms of the Davies-Bouldin(i DB) and Xie-Beni(i XB) validity indices. Case studies conducted using real-world and simulated daily profiles of residential and commercial Chilean end-users have demonstrated how the proposed framework can continuously characterize DR. The proposed framework is proven to achieve realistic customer models for effective energy management by estimating the customer response to price signals at the distribution system operator(DSO) level.

关键词： Clustering algorithms Behavioral sciences Streams Pricing Feature extraction Monitoring Kernel

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