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Intruder familiarity and not duet similarity influences the territory defense in a year-round territorial bird species

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Avian Research 2022年第2期13卷 152-158页

作者： Tihana Hamzaj Brendan Graham Katherine Bonilla Ignacio Gutiérrez Luis Sandoval Institute of Evolutionary Ecology and Conservation Genomics University of UlmUlm Gemany Laboratorio de Ecología Urbana y Comunicación Animal Escuela de BiologíaUniversidad de Costa RicaMontes de Oca CP11501-2060 Costa Rica department of Biological Sciences University of Lethbridge4401 University Dr WLethbridgeABTIK 3M4anada

To avoid unnecessary energy expenditures in territorial defense,many species(e.g.,insects,amphibians,birds,and mammals)have developed the capability to distinguish between different intruder types using visual,acoustic,and/or chemical *** the mechanism used for intruder recognition is key to understanding the dynamics of territorial *** birds that use vocalizations for territorial defense,the frequency and duration of vocalizations or the familiarity with the intruder may be the main mechanism used for intruder ***,we conducted a playback experiment with territorial White-eared Ground-sparrows(Melozone leucotis),to analyze if territorial pairs recognize intruders using frequency and duration characteristics(a bird’s response is based on how structurally similar the intruders’duets are to their own)or by familiarity with the intruders(neighbors ***-neighbors).We focused on duets because this species uses duets exclusively for territorial *** broadcasted a duet from a territorial neighbor,two duets from non-neighbors(with different frequency and duration characteristics),and a duet from a control species in 39 territorial pair from three *** playback we measured five behavioral responses:latency of the first vocalization,latency of the approach to the speaker,time spent close the speaker(within 5 m),number of individuals that approached the speaker,and the number of *** found that territorial White-eared Ground-sparrow pairs responded stronger to neighbors than non-neighbors,and this response is not influenced by duet duration or frequency *** result suggests that neighbors represent a greater territorial threat for White-eared Ground-sparrows than *** work is necessary to understand how common this observation is for tropical species that defend small territories year-round.

关键词： dear enemy Duets Neighbor-stranger discrimination Territory defense White-eared ground-sparrows

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Clinical Profiles at the Time of Diagnosis of SARS-CoV-2 Infection in costa rica During the Pre-vaccination Period Using a Machine Learning Approach

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Phenomics 2022年第5期2卷 312-322页

作者： Jose Arturo Molina-Mora Alejandra González Sergio Jiménez-Morgan Estela Cordero-Laurent Hebleen Brenes Claudio Soto-Garita Jorge Sequeira-Soto Francisco Duarte-Martínez Centro de Investigación en Enfermedades Tropicales(CIET)and Facultad de Microbiología Universidad de Costa RicaSan José2060Costa Rica Instituto costarricense de Investigación y Enseñanza en Nutrición y Salud(INCIENSA) Tres Ríos 30301Costa Rica Escuela de Medicina Universidad de Costa RicaSan José2060Costa Rica

The clinical manifestations of COVID-19,caused by the SARS-CoV-2,define a large spectrum of symptoms that are mainly dependent on the human host *** costa rica,more than 169,000 cases and 2185 deaths were reported during the year 2020,the pre-vaccination *** describe the clinical presentations at the time of diagnosis of SARS-CoV-2 infection in costa rica during the pre-vaccination period,we implemented a symptom-based clustering using machine learning to identify clusters or clinical profiles at the population level among 18,974 records of positive *** were compared based on symptoms,risk factors,viral load,and genomic features of the SARS-CoV-2 sequence.A total of 18 symptoms at time of diagnosis of SARS-CoV-2 infection were reported with a frequency>1%,and those were used to identify seven clinical profiles with a specific composition of clinical *** the comparison between clusters,a lower viral load was found for the asymptomatic group,while the risk factors and the SARS-CoV-2 genomic features were distributed among all the *** other distribution patterns were found for age,sex,vital status,and *** conclusion,during the pre-vaccination time in costa rica,the symptoms at the time of diagnosis of SARS-CoV-2 infection were described in clinical *** host co-morbidities and the SARS-CoV-2 genotypes are not specific of a particular profile,rather they are present in all the groups,including asymptomatic *** addition,this information can be used for decision-making by the local healthcare institutions(first point of contact with health professionals,case definition,or infrastructure).In further analyses,these results will be compared against the profiles of cases during the vaccination period.

关键词： COVID-19 costa rica Machine learning Diagnosis SARS-CoV-2 Clinical profiles

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A nonlinear relapse model with disaggregated contact rates:Analysis of a forward-backward bifurcation

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Infectious Disease Modelling 2023年第3期8卷 769-782页

作者： Jimmy Calvo-Monge Fabio Sanchez Juan Gabriel Calvo Dario Mena Escuela de Matematica Universidad de Costa RicaCiudad Universitaria Rodrigo FacioSan Jose11501Costa Rica Centro de Investigacion en Matematica Pura y Aplicada Universidad de Costa RicaCiudad Universitaria Rodrigo FacioSan Jose11501Costa Rica

Throughout the progress of epidemic scenarios,individuals in different health classes are expected to have different average daily contact *** contact heterogeneity has been studied in recent adaptive models and allows us to capture the inherent differences across health statuses *** with reinfection bring out more complex scenarios and offer an important application to consider contact ***,we developed a nonlinear differential equation model to explore the dynamics of relapse phenomena and contact differences across health *** incidence rate function is formulated,taking inspiration from recent adaptive *** incorporates contact behavior for individuals in each health *** use constant contact rates at each health status for our analytical results and prove conditions for different forward-backward bifurcation *** relationship between the different contact rates heavily in-fluences these *** examples highlight the effect of temporarily recov-ered individuals and initial conditions on infected population persistence.

关键词： Nonlinear relapse Nonlinear incidence MaMthematical model Backward bifurcation Adaptive behavior 2000 MSC 37N25 92B05

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In Silico Pipeline to Identify Tumor‑Specific Antigens for Cancer Immunotherapy Using Exome Sequencing Data

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Phenomics 2023年第2期3卷 130-137页

作者： Diego Morazán‑Fernández Javier Mora Jose Arturo Molina‑Mora Caja costarricense de Seguro Social San José10104Costa Rica Centro de Investigación de Enfermedades Tropicales Centro de Investigación en Cirugía y Cáncerand Facultad de MicrobiologíaUniversidad de Costa RicaSan José2060Costa Rica

Tumor-specific antigens or neoantigens are peptides that are expressed only in cancer cells and not in healthy *** of these molecules can induce an immune response,and therefore,their use in immunotherapeutic strategies based on cancer vaccines has been extensively *** based on these approaches have been triggered by the current high-throughput DNA sequencing ***,there is no universal nor straightforward bioinformatic protocol to discover neoan-tigens using DNA sequencing ***,we propose a bioinformatic protocol to detect tumor-specific antigens associated with single nucleotide variants(SNVs)or“mutations”in tumoral *** this purpose,we used publicly available data to build our model,including exome sequencing data from colorectal cancer and healthy cells obtained from a single case,as well as frequent human leukocyte antigen(HLA)class I alleles in a specific *** data from costa rican Central Valley population was selected as an *** strategy included three main steps:(1)pre-processing of sequencing data;(2)variant calling analysis to detect tumor-specific SNVs in comparison with healthy tissue;and(3)prediction and characterization of peptides(protein fragments,the tumor-specific antigens)derived from the variants,in the context of their affinity with frequent alleles of the selected *** our model data,we found 28 non-silent SNVs,present in 17 genes in chromosome *** protocol yielded 23 strong binders peptides derived from the SNVs for frequent HLA class I alleles for the costa rican *** the analyses were performed as an example to implement the pipeline,to our knowledge,this is the first study of an in silico cancer vaccine using DNA sequencing data in the context of the HLA *** is concluded that the standardized protocol was not only able to identify neoantigens in a specific but also provides a complete pipeline for the eventual design of cancer vaccines using

关键词： Neopeptide Colorectal cancer Cancer vaccine Neoantigens Human leukocyte antigen costa rica

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How two helicases work together within the TFIIH complex, a perspective from structural studies of XPB and XPD helicases

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Frontiers in Biology 2013年第4期8卷 363-368页

作者： Li FAN department of Biochemistry University of California at Riverside Riverside CA 92521 USA

Xeroderma pigmentosum group B （XPB） and D （XPD） are two DNA helicases inside the transcription factor TFIIH complex required for both transcription and DNA repair. The importance of these helicases is underscored by the fact that mutations of XPB and XPD cause diseases with extremely high sensitivity to UV-light and high risk of cancer, premature aging, etc. This mini-review focuses on recent developments in both structural and functional characterization of these XP heficases to illustrate their distinguished biological roles within the architectural restriction of the TFIIH complex. In particular, molecular mechanisms of DNA unwinding by these helicases for promoter opening during transcription initiation and bubble-creation around the lesion during DNA repair are described based on the integration of the crystal structures of XPB and XPD helicases into the architecture of the TFIIH complex.

关键词： XPB XPD TFIIH helicase DNA repair nucleotide excision repair Wanscription

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Urbanization has opposite effects on the territory size of two passerine birds

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Avian Research 2020年第2期11卷 191-199页

作者： Roselvy Juárez Eduardo Chacón‑Madrigal Luis Sandoval Escuela de Biología Universidad de Costa RicaCP:11501‑2060San PedroMontes de OcaSan JoséCosta Rica Ambientey desarrollo Universidad ZamoranoCarretera a Danlíkm 30Francisco MorazánHonduras.

Background:Urban expansion has been identified as one of the leading drivers of biodiversity change or *** birds,urbanization is specifically related to survival,breeding success,and territory *** how different birds adjust territory size in response to urbanization is essential for their conservation in urban environments and to better understand why some species are lost and others persist under this *** evaluated the effect of urbanization on the territory size of an urban avoider species,White-eared Ground-Sparrow(Melozone leucotis),and an urban adapter species,House Wren(Troglodytes aedon),at five costa rican ***:We measured the size of 30 ground-sparrow and 28 wren territories using a total of 296 h of *** followed each individual for at least 1 h per day for at least 2 days of two consecutive years,and geo-referenced their *** size was estimated using the minimum convex polygon *** measured the urban surfaces(roads,buildings,any other paved area,soccer fields,lawns,and gardens with short grass)within ***:Ground-sparrow territories were larger at the highly urbanized site than at the non-urbanized *** territories were larger at the low urbanized site than at the highly urbanized *** found a positive relationship between urban surface and territory size for the ground-sparrow,but not for the ***:Our results showed that not all birds adjust territory size in the same way in response to *** showed that urban avoiders probably need to defend larger territories in urban environments to find all the resources required to survive because urban environments may provide insufficient resources such as food or *** adapters on the other hand defend smaller territories in urban environments because even small territories may provide sufficient *** results suggest specific behavioral adaptations developed by Neotropical birds inha

关键词： House Wren Melozone leucotis Troglodytes aedon Urban adapter Urban avoider Urban-rural gradient Territory size White‑eared Ground‑Sparrow

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Catalytic performance of zinc-supported copper and nickel catalysts in the glycerol hydrogenolysis

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Journal of Energy Chemistry 2020年第3期29卷 185-194页

作者： R.J.Chimentao B.C.Miranda D.Ruiz F.Gispert-Guirado F.Medina J.Llorca J.B.O.Santos Physical Chemistry department Faculty of Chemical SciencesUniversity of ConcepcionCasilla 160-CConcepcionChile Chemical Engineering School Universidad de Costa Ric1San Jose 2060Costa Rica Scientific Resources Service Universitat Rovira i VirgiliTarragona 43007Spain department of Chemical Engineering Universitat Rovira i VirgiliTarragona 43007Spain department of Chemical Engineering Barcelona Research Center in Multiscale Science and EngineeringInstitute of Energy TechnologiesUniversitat Politècnica de Cataluny1EEBE08019 Barcelon1Spain department of Chemical Engineering Universidade Federal de Sao Carlos(UFSCAR)Sao CarlosBrazil

Gas-phase catalytic conversion of glycerol to value added chemicals was investigated over zinc-supported copper and nickel *** addition of aluminum in the support was also investigated in glycerol conversion and the results indicate an increase in the acidity and adsorption capacity for both copper and nickel *** and XRD analysis revealed Ni Zn alloy formation in the Ni/ZnO *** XRD patterns of the prepared Zn Al mixed oxide catalysts show the presence of Gahanite phase(ZnAl2O4).In addition,H2 chemisorption and TPR results suggest a strong metal-support interactions(SMSI)effect between Ni and Zn O *** supports Zn O and ZnAl(Zn/Al=0.5)were investigated in the glycerol conversion and they did not present *** supported on ZnO and ZnAl mixed oxide(Zn/Al=0.5)was active towards hydroxyacetone *** was active in the hydrogenolysis of glycerol both for C–C and C–O bonds cleavage of glycerol producing *** metal-support interactions(SMSI)between Ni and ZnO has a remarkable suppression effect on the methanation activity during the glycerol conversion.

关键词： Glycerol Hydrogenolysis dehydration Hydroxyacetone Copper Nickel Catalyst

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Myxomycete colonization on translocated and non-translocated dead leaves from temperate and tropical forests

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Studies in Fungi 2020年第1期5卷 462-470页

作者： Rojas C Stephenson SL Rojas PA Finca Experimental Interdisciplinaria de Modelos Agroecológicos University of Costa RicaTurrialba30502-Costa Rica Engineering Research Institute University of Costa RicaSan Pedro de Montes de Oca11501-Costa Rica department of Biological Sciences University of ArkansasFayettevilleAR 72701USA

Samples of dead leaves on the forest floor were collected from a locality in central costa rica and another locality in northwest Arkansas in the United States and then were placed in fine-mesh nylon bags,autoclaved and left out in the field for four *** of the bags prepared with sterile material from each country were placed out in the country where they were collected,and the other half were placed in the other country.A characterization of forest structure and ground leaf chemistry was carried out for both localities and both leaf *** recollected,all samples were processed for myxomycetes with the use of the moist chamber culture *** cultures yielded a total of 156 records of myxomycetes representing 16 species,but only 13 records and six species were isolated from the samples left out in costa *** hundred percent of cultures placed out in Arkansas produced myxomycetes,whereas only 68%of those placed out in costa rica were positive for these *** in species richness and number of records were observed across forests where the samples were placed out,and no differences were observed based on the origin of the *** suggested that myxomycete colonization in the studied areas is primarily affected by the dynamics of the forest type and secondarily by substrate *** myxomycete species recorded on leaves with poorer chemical values are also consistent with field *** the present study,the more open character of the temperate forest in Arkansas without a film of water layer covering the leaves on the ground seemed to have played a role in the establishment of myxomycete propagules in the sterile material during the time of the investigation.

关键词： Arkansas costa rica myxogastrids Pea Ridge slime molds Turrialba

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Physical and chemical changes of rapeseed meal proteins during toasting and their effects on in vitro digestibility

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Journal of Animal Science and Biotechnology 2017年第2期8卷 417-427页

作者： Sergio Salazar-Villanea Erik M.A.M.Bruininx Harry Gruppen Wouter H.Hendriks Patrick Carré Alain Quinsac Antonius F.B.van der Poel Wageningen Livestock Research P.O.Box 3386700 AH WageningenThe Netherlands Animal Nutrition Group Wageningen University&ResearchP.O.Box 3386700 AH WageningenThe Netherlands Agfifirm Innovation Center Royal Dutch Agrifirm GroupP.O.Box 200187302 HA ApeldoornThe Netherlands Laboratory of Food Chemistry Wageningen University&ResearchP.O.Box 176700 AA WageningenThe Netherlands CREOL/OLEAD 11 rue MongeParc Industriel33600 PessacFrance Terres Inovia 11 rue MongeParc Industriel33600 PessacFrance

Background： Toasting during the production of rapeseed meal（RSM） decreases ileal crude protein（CP） and amino acid（AA） digestibility. The mechanisms that determine the decrease in digestibility have not been fully elucidated. A high protein quality, low-denatured, RSM was produced and toasted up to 120 min, with samples taken every 20 min. The aim of this study was to characterize secondary structure and chemical changes of proteins and glucosinolates occurring during toasting of RSM and the effects on its in vitro CP ***： The decrease in protein solubility and the increase of intermolecular β-sheets with increasing toasting time were indications of protein aggregation. The contents of NDF and ADIN increased with increasing toasting *** of arginine, lysine and O-methylisourea reactive lysine（OMIU-RL） linearly decreased with increasing toasting time, with a larger decrease of OMIU-RL than lysine. First-order reactions calculated from the measured parameters show that glucosinolates were degraded faster than lysine, OMIU-RL and arginine and that physical changes to proteins seem to occur before chemical changes during toasting. despite the drastic physical and chemical changes noticed on the proteins, the coefficient of in vitro CP digestibility ranged from 0.776 to 0.750 and there were no effects on the extent of protein hydrolysis after 120 min. In contrast, the rate of protein hydrolysis linearly decreased with increasing toasting time, which was largely correlated to the decrease in protein solubility, lysine and OMIU-RL observed. Rate of protein hydrolysis was more than 2-fold higher for the untoasted RSM compared to the 120 min toasted ***： Increasing the toasting time for the production of RSM causes physical and chemical changes to the proteins that decrease the rate of protein hydrolysis. The observed decrease in the rate of protein hydrolysis could impact protein digestion and utilization.

关键词： Hydrolysis rate In vitro protein digestibility Rapeseed meal Reactive lysine Secondary structure

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Automated Synthesis of Wideband Bandpass Filters Based on Slow-Wave EBG Structures

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Computers, Materials & Continua 2016年第6期52卷 159-174页

作者： Marco Orellana Jordi Selga Paris Vélez Marc Sans Ana Rodríguez Vicente Boria Ferran Martín GEMMA/CIMITEC Departament d’Enginyeria ElectrònicaUniversitat Autònoma de Barcelona08193 Bellaterra(Barcelona)Spain departamento de Comunicaciones-iTEAM Universitat Politècnica de València46022 ValenciaSpain

This paper is focused on the automated synthesis of wideband bandpass filters operating at microwave frequencies and based on electromagnetic bandgap(EBG)*** classical counterpart of such filter consists of a combination of transmission line sections and shunt-connected grounded stubs placed at equidistant *** replacing the transmission line sections with capacitively-loaded lines(a kind of EBG-based lines)exhibiting the same phase shift at the lower cutoff frequency and the same characteristic(actually Bloch)impedance,filter size is reduced and the spurious pass bands can be efficiently *** practice,the loading capacitances are implemented by means of patches,in order to achieve a fully planar filter *** presence of the patches reduces the effective phase velocity of the capacitively-loaded lines,thus providing a slow-wave effect useful for filter ***,due to periodicity,such EBG-based lines exhibit wide stop bands,which are used for spurious *** though such EBGbased filters were previously reported by some of the authors,a systematic synthesis method was not applied for filter *** this paper,the main aim is to demonstrate the potential of aggressive space mapping(ASM)for that purpose,and it will be shown that such filters can be automatically synthesized.

关键词： Electromagnetic bandgaps(EBG) microwave filters slow-wave transmission lines space mapping.

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