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Basophile:Accurate Fragment Charge State Prediction Improves Peptide Identification Rates

Genomics, Proteomics & Bioinformatics 2013年第2期11卷 86-95页

作者： Dong Wang Surendra Dasari Matthew C.Chambers jerry D.Holman Kan Chen daniel C.Liebler daniel j.orton Samuel O.Purvine Matthew E.Monroe Chang Y.Chung Kristie L.Rose David L.Tabb Department of Biomedical Informatics Vanderbilt University Medical Center Division of Biomedical Statistics and Informatics Mayo Clinic Department of Biochemistry Vanderbilt University Medical Center Biological Sciences Division and Environmental Molecular Sciences Laboratory Pacific Northwest National Laboratory Department of Pharmacology Vanderbilt University Medical Center Vanderbilt-Ingram Cancer Center Vanderbilt University School of Medicine

In shotgun proteomics, database search algorithms rely on fragmentation models to pre- dict fragment ions that should be observed for a given peptide sequence. The most widely used strat- egy （Naive model） is oversimplified, cleaving all peptide bonds with equal probability to produce fragments of all charges below that of the precursor ion. More accurate models, based on fragmen- tation simulation, are too computationally intensive for on-the-fly use in database search algorithms. We have created an ordinal-regression-based model called Basophile that takes fragment size and basic residue distribution into account when determining the charge retention during CID/higher- energy collision induced dissociation （HCD） of charged peptides. This model improves the accuracy of predictions by reducing the number of unnecessary fragments that are routinely predicted for highly-charged precursors. Basophile increased the identification rates by 26% （on average） over the Naive model, when analyzing triply-charged precursors from ion trap data. Basophile achieves simplicity and speed by solving the prediction problem with an ordinal regression equation, which can be incorporated into any database search software for shotgun proteomic identification.

关键词： Fragmentation Basicity Fragment size Ordinal regression

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Iron regulatory protein 1: the deadly switch of ferroptosis

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Neural Regeneration Research 2024年第3期19卷 477-478页

作者： daniel A.Bórquez Pamela j.Urrutia Center for Biomedical Research Faculty of MedicineUniversidad Diego PortalesSantiagoChile Institute of Nutrition&Food Technology(INTA) Universidad de ChileSantiagoChile Geroscience Center for Brain Health and Metabolism SantiagoChile

Ferroptosis,an iron-dependent cell death:Ferroptosis is a type of regulated necrosis,characterized by redox-active iron accumulation and increased free radical production derived by Fenton chemistry,that triggers oxidation of polyunsaturated fatty acids in phospholipids,loss of cellular membranes integrity,and leakage of intracellular contents.

关键词： integrity switch Iron

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Distributed Secondary Control Based on Dynamic Diffusion Algorithm for Current Sharing and Average Voltage Regulation in DC Microgrids

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journal of Modern Power Systems and Clean Energy 2024年第2期12卷 597-607页

作者： Dawei Liao Fei Gao daniel j.Rogers Wentao Huang Dong Liu Houjun Tang Department of Electrical Engineering Shanghai Jiao Tong UniversityShanghaiChina Department of Engineering Science University of OxfordOxford OX12JDU.K. IEEE

This paper introduces a distributed secondary control scheme for achieving current sharing and average voltage regulation objectives in a DC *** proposed scheme employs a dynamic diffusion algorithm(DDA)instead of the consensus algorithm to enable distributed communication among *** help understand DDA,the relation of DDA and other diffusion algorithms is discussed in detail and its superiority is shown by comparison with diffusion and consensus ***,considering the discrete nature and different sampling time of the digital controller and communication network,a z-domain model of the entire DC microgrid is *** influence of communication and secondary control parameters on the system stability is *** on the established model,the tolerable communication rates are ***-time simulations conducted on the OPAL-RT platform validate the effectiveness of the proposed scheme,showcasing its advantages in terms of convergence speed and stability.

关键词： Cooperative control DC microgrid diffusion algorithm discrete-time modeling distributed secondary control

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Dominance of transposable element‑related satDNAs results in great complexity of“satDNA library”and invokes the extension towards“repetitive DNA library”

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Marine Life Science & Technology 2024年第2期6卷 236-251页

作者： Monika Tunjić‑Cvitanić daniel García‑Souto juan j.Pasantes EvaŠatović‑Vukšić Division of Molecular Biology Ruđer BoškovićInstitute10000 ZagrebCroatia Genomes and Disease Centre for Research in Molecular Medicine and Chronic Diseases(CIMUS)Universidade de Santiago de Compostela15706 Santiago de CompostelaSpain Department of Zoology Genetics and Physical AnthropologyUniversidade de Santiago de Compostela15706 Santiago de CompostelaSpain Centro de Investigación Mariña Dpto de BioquímicaXenética e InmunoloxíaUniversidade de Vigo36310 VigoSpain

Research on bivalves is fast-growing,including genome-wide analyses and genome *** characteristics qualify oysters as a valuable model to explore repetitive DNA sequences and their genome *** we char-acterize the satellitomes of five species in the family Ostreidae(Crassostrea angulata,***,***,***,Ostrea edulis),revealing a substantial number of satellite DNAs(satDNAs)per genome(ranging between 33 and 61)and peculiarities in the composition of their *** satDNAs were either associated to or derived from transposable elements,displaying a scarcity of transposable element-unrelated satDNAs in these *** to the non-conventional satellitome constitution and dominance of Helitron-associated satDNAs,comparative satellitomics demanded more in-depth analyses than standardly *** analyses(including ***,the first bivalve species with a defined satellitome)revealed that 13 satDNAs occur in all six oyster genomes,with Cg170/HindIII satDNA being the most abundant in all of *** the“satDNA library model”highlighted the necessity to adjust this term when studying tandem repeat evolution in organisms with such *** repetitive sequences with potential variation in the organizational form and repeat-type affiliation are examined across related species,the introduction of the terms“TE library”and“repetitive DNA library”becomes essential.

关键词： Satellitome Comparative satellitomics Helitron Bivalves “Dark matter of the genome”

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Determining minimum sample size for the conditioned Latin hypercube sampling algorithm

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Pedosphere 2024年第3期34卷 530-539页

作者： daniel D.SAURETTE Asim BISWAS Richard j.HECK Adam W.GILLESPIE Aaron A.BERG School of Environmental Sciences University of Guelph50 Stone Rd EastGuelph ON N1G 2W1(Canada) Ontario Ministry of Agriculture Food and Rural Affairs1 Stone Rd WestGuelph ON N1G 2Y4(Canada) Geography Environment&GeomaticsUniversity of Guelph50 Stone Rd EastGuelph ON N1G 2W1(Canada)

In digital soil mapping(DSM),a fundamental assumption is that the spatial variability of the target variable can be explained by the predictors or environmental *** to adequately sample the predictors have been well documented,with the conditioned Latin hypercube sampling(cLHS)algorithm receiving the most attention in the DSM *** advances in sampling design,a critical gap remains in determining the number of samples required for DSM *** propose a simple workflow and function coded in R language to determine the minimum sample size for the cLHS algorithm based on histograms of the predictor variables using the Freedman-Diaconis rule for determining optimal bin *** preprocessing was included to correct for multimodal and non-normally distributed data,as these can affect sample size determination from the *** on a user-selected quantile range(QR)for the sample plan,the densities of the histogram bins at the upper and lower bounds of the QR were used as a scaling factor to determine minimum sample *** technique was applied to a field-scale set of environmental covariates for a well-sampled agricultural study site near Guelph,Ontario,Canada,and tested across a range of *** results showed increasing minimum sample size with an increase in the QR *** sample size increased from 44 to 83 when the QR increased from 50% to 95% and then increased exponentially to 194 for the 99%*** technique provides an estimate of minimum sample size that can be used as an input to the cLHS algorithm.

关键词： bin width digital soil mapping normal distribution quantile range sampling design

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Anneal-free ultra-low loss silicon nitride integrated photonics

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Light(Science & Applications) 2024年第8期13卷 1565-1577页

作者： Debapam Bose Mark W.Harrington Andrei Isichenko Kaikai Liu jiawei Wang Nitesh Chauhan Zachary L.Newman daniel j.Blumenthal Department of Electrical and Computer Engineering University of California Santa BarbaraSanta BarbaraCA 93106USA Octave Photonics LouisvilleCO 80027USA

Heterogeneous and monolithic integration of the versatile low-loss silicon nitride platform with low-temperature materials such as silicon electronics and photonics,III–V compound semiconductors,lithium niobate,organics,and glasses has been inhibited by the need for high-temperature annealing as well as the need for different process flows for thin and thick *** techniques are needed to maintain the state-of-the-art losses,nonlinear properties,and CMOS-compatible processes while enabling this next generation of 3D silicon nitride *** report a significant advance in silicon nitride integrated photonics,demonstrating the lowest losses to date for an anneal-free process at a maximum temperature 250℃,with the same deuterated silane based fabrication flow,for nitride and oxide,for an order of magnitude range in nitride thickness without requiring stress mitigation or *** report record low anneal-free losses for both nitride core and oxide cladding,enabling 1.77 dBm^(-1) loss and 14.9 million Q for 80 nm nitride core waveguides,more than half an order magnitude lower loss than previously reported sub 300℃ *** 800 nm-thick nitride,we achieve as good as 8.66 dBm^(-1) loss and 4.03 million Q,the highest reported Q for a low temperature processed resonator with equivalent device area,with a median of loss and Q of 13.9 dBm^(-1) and 2.59 million each *** demonstrate laser stabilization with over 4 orders of magnitude frequency noise reduction using a thin nitride reference cavity,and using a thick nitride micro-resonator we demonstrate OPO,over two octave supercontinuum generation,and four-wave mixing and parametric gain with the lowest reported optical parametric oscillation threshold per unit resonator *** results represent a significant step towards a uniform ultra-low loss silicon nitride homogeneous and heterogeneous platform for both thin and thick waveguides capable of linear and nonlinear photonic circuits and

关键词： resonator thick free

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Floristic composition and edaphic relationships in ferruginous campo rupestre reference ecosystems

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journal of Mountain Science 2024年第3期21卷 719-733页

作者： G.Wilson FERNANDES Letícia RAMOS Dario C.PAIVA jéssica CUNHA-BLUM Vanessa Matos GOMES daniel NEGREIROS Ecologia Evolutiva&Biodiversidade Departamento de GenéticaEcologia e Evolução/ICBUniversidade Federal de Minas Gerais31270-901Belo HorizonteMGBrazil Knowledge Center for Biodiversity 31270-901Belo HorizonteMGBrazil Department of Biological Sciences Institute of EnvironmentFlorida International UniversityMiamiFL 33199USA Programa de Pós Graduação em Biodiversidade e Uso dos Recursos Naturais Universidade Estadual de Montes ClarosMontes ClarosMGBrazil Laboratório de Estudo das Relações Solo-Planta Departamento de SolosUniversidade Federal Rural do Rio de JaneiroSeropédicaRGBrazil

Land use change and occupation have led to modifications in the environment causing loss of biodiversity and ecosystem services throughout the *** environments with high economic relevance,such as the ferruginous campo rupestre(rupestrian grassland known as Canga in Brazil),are even more susceptible to severe impacts due to their extreme habitat conditions and low *** determination of reference ecosystems based on the intrinsic characteristics of the ecosystem is essential for conservation as well as to the implementation of ecological *** proposed the reference ecosystem of the three main types of habitats of the ferruginous campo rupestre based on their floristic *** described the floristic composition of each habitat and evaluated the physicochemical properties of the soils and the relationship between plants and *** three habitats showed high diversity of plant species and many endemic species,such as Chamaecrista choriophylla,Cuphea pseudovaccinium,Lychnophora pinaster,and Vellozia *** distribution of vegetation was strongly related with the edaphic characteristics,with a set of species more adapted to high concentration of base saturation,fine sand,organic carbon,and iron,while another set of species succeeded in more acidic soils with higher S and silt *** provide support for the contention that the ferruginous campo rupestre is a mosaic of different habitats shaped by intrinsic local *** to recognize the floristic composition of each particular habitat can lead to inappropriate restoration,increased habitat homogenization and increased loss of biodiversity and ecosystem *** study also advances the knowledge base for building the reference ecosystem for the different types of ferruginous campo rupestre habitats,as well as a key database for highlighting those species contribute most to community assembly in this diverse and threatened tropical mountain ecosystem.

关键词： Canga Ecological restoration Extreme ecosystem Non-forest ecosystems Rupestrian grassland Taxon environment relationships

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Predicting Chemical Immunotoxicity through Data-Driven QSAR Modeling of Aryl Hydrocarbon Receptor Agonism and Related Toxicity Mechanisms

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Environment & Health 2024年第7期2卷 474-485页

作者： Nada j.Daood daniel P.Russo Elena Chung Xuebin Qin Hao Zhu Predicting Chemical Immunotoxicity through Data-Driven QSAR Modeling of Aryl Hydrocarbon Receptor Agonism and Related Toxicity Mechanisms Department of Chemistry and Biochemistry Rowan UniversityGlassboroNew Jersey 08028United States Center for Biomedical Informatics and Genomics Tulane University School of MedicineNew OrleansLouisiana 70112United States Tulane National Primate Research Center Tulane University School of MedicineCovingtonLouisiana 70433United States

Computational modeling has emerged as a time-saving and cost-effective alternative to traditional animal testing for assessing chemicals for their potential ***,few computational modeling studies for immunotoxicity were reported,with few models available for predicting toxicants due to the lack of training data and the complex mechanisms of *** this study,we employed a data-driven quantitative structure–activity relationship(QSAR)modeling workflow to extensively enlarge the limited training data by revealing multiple targets involved in *** this end,a probe data set of 6,341 chemicals was obtained from a high-throughput screening(HTS)assay testing for the activation of the aryl hydrocarbon receptor(AhR)signaling pathway,a key event leading to *** this probe data set against PubChem yielded 3,183 assays with testing results for varying proportions of these 6,341 compounds.100 assays were selected to develop QSAR models based on their correlations to AhR *** individual QSAR models were built for each assay using combinations of four machine-learning algorithms and three molecular fingerprints.5-fold cross-validation of the resulting models showed good predictivity(average CCR=0.73).A total of 20 assays were further selected based on QSAR model performance,and their resulting QSAR models showed good predictivity of potential immunotoxicants from external *** study provides a computational modeling strategy that can utilize large public toxicity data sets for modeling immunotoxicity and other toxicity endpoints,which have limited training data and complicated toxicity mechanisms.

关键词： Immunotoxicity QSAR Machine learning Aryl hydrocarbon receptor Data mining

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Feeding ecology and interactions with mammal hosts in a symbiotic genus of birds(Buphagus spp.)in Namibia

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Avian Research 2024年第3期15卷 336-344页

作者： Michael S.Lukubwe daniel Velarde-Garcéz Fernando Sequeira Susana Lopes Adrian j.F.K.Craig Vanessa A.Mata Department of Zoology and Entomology Rhodes UniversityMakhandaSouth Africa Department of Wildlife Management and Tourism Studies University of NamibiaKatima Mulilo CampusNamibia Departamento de Biologia Faculdade de CiênciasUniversidade do PortoPortoPortugal CIBIO Centro de Investigação em Biodiversidade e Recursos GenéticosInBIO Laboratório AssociadoCampus de VairãoVairãoPortugal BIOPOLIS Program in Genomics Biodiversity and Land PlanningCIBIOCampus de VairãoVairãoPortugal

As the sole obligate symbiotic birds in Africa,oxpeckers offer a unique model for studying symbiotic *** to the multitrophic level they occupy and the context dependent foraging behavior they exhibit,the type of symbiotic relationship can be *** addition to providing a cleaning service to the host by removing ticks,oxpeckers frequently feed on blood,mucus,and saliva,inflicting potential damage on the ***,we used DNA metabarcoding on faecal samples to analyze the taxonomic composition of the trophic interactions of the Yellow-billed Oxpecker(Buphagus africanus)and Red-billed Oxpecker(***)in northeastern *** contrast to conventional methods,DNA metabarcoding allows for a detailed identification of dietary resources encompassing both mammal hosts and consumed arthropods within the same *** this information,we examined differences in the diet composition between oxpecker species and localities,as well as the co-occurrence between host and arthropod *** findings revealed that oxpeckers predominantly source their diet from mammals,ticks,and flies;however,ticks and flies rarely co-occur in the diet of an *** observed variability among individuals in their feeding ecology,which is strongly correlated with locality and,to a lesser extent,with the mammal *** noted a high degree of mobility between hosts within relatively short periods,with 32%of the samples showing traces of at least two mammal *** study illustrates the dynamic foraging behavior of these specialized symbiotic birds,shedding light on their potential role in pest control services and disease transmission.

关键词： Commensalism Diet DNA metabarcoding Oxpeckers Parasitism Trophic ecology

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Efficiency and effectiveness of systems for the treatment of domestic wastewater based on subsurface flow constructed wetlands in jarabacoa, Dominican Republic

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Water Science and Engineering 2024年第2期17卷 118-128页

作者： Yvelisse Pérez Enmanuel Vargas daniel Garcia-Cortes William Hernandez Humberto Checo Ulises jauregui-Haza Area de Ciencias Basicas y Ambientales Instituto Tecnologico de Santo Domingo(INTEC)Avenida de Los Proceres 49Los Jardines del NorteSanto Domingo 10602Dominican Republic Ministry of Environment and Natural Resources Calle Cayetano Germosen esq.Ave.LuperonEl PedregalSanto Domingo 11107Dominican Republic Plan Yaque Calle Estela Geraldino 14 AltosJarabacoa 41000Dominican Republic Institute of Technologies and Applied Sciences University of HavanaHavana 10400Cuba

Constructed wetlands(CwW)are well known nature-based systems for water *** study evaluated the efficiency and effectiveness of seven domestic wastewater treatment systems based on horizontal flow CWs in jarabacoa,the Dominican *** results showed that the CWs were efficient in reducing the degree of contamination of wastewater to levels below the Dominican wastewater discharge standards for parameters such as the 5-day biochemical oxygen demand(BOD5)and chemical oxygen demand,but not for the removal of phosphorus and fecal *** addition,a horizontal flow subsurface wetland in the peri-urban area El Dorado was evaluated in terms of the performance of wastewater treatment in tropical climatic *** concentrations of heavy metals,such as zinc,copper,chromium,and iron,were found to decrease in the effluent of the wetland,and the concentrations for nickel and manganese tended to *** levels of heavy metals in the effluent were lower than the limit values of the Dominican wastewater discharge *** construction cost of these facilities was around 200 USD per population equivalent,similar to the cost in other countries in the same *** study suggested some solutions to the improved performance of CWs:selection of a microbial flora that guarantees the reduction of nitrates and nitrites to molecular nitrogen,use of endemic plants that bioaccumulate heavy metals,combination of constructed wetlands with filtration on activated carbon,and inclusion of water purification processes that allow to evaluate the reuse of treated water.

关键词： Domestic wastewater Constructed wetland BOD COD Pathogens Heavy metals

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