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Phylogenetic framework for coevolutionary studies： a compass for exploring jungles of tangled trees

Current Zoology 2016年第4期62卷 393-403页

作者： andres MARTiNEZ-AQUINO Division Zoologfa Invertebrados Museo de La Plata FCNyM UNLP Paseo del Bosque s/n 1900 La Plata Argentina

Phylogenetics is used to detect past evolutionary events, from how species originated to how their ecological interactions with other species arose, which can mirror cophylogenetic patterns. Cophylogenetic reconstructions uncover past ecological relationships between taxa through inferred coevolutionary events on trees, for example, codivergence, duplication, host-switching, and loss. These events can be detected by cophylogenetic analyses based on nodes and the length and branching pattern of the phylogenetic trees of symbiotic associations, for example, host-parasite. In the past 2 decades, algorithms have been developed for cophylogetenic analyses and implemented in different software, for ex ample, statistical congruence index and event-based methods. Based on the combination of these approaches, it is possible to integrate temporal information into cophylogenetical inference, such as es- timates of lineage divergence times between 2 taxa, for example, hosts and parasites. Additionally, the advances in phylogenetic biogeography applying methods based on parametric process models and combined Bayesian approaches, can be useful for interpreting coevolutionary histories in a scenario of biogeographical area connectivity through time. This article briefly reviews the basics of parasitology and provides an overview of software packages in cophylogenetic methods. Thus, the objective here is to present a phylogenetic framework for coevolutionary studies, with special emphasis on groups of parasitic organisms. Researchers wishing to undertake phylogeny-based coevolutionary studies can use this review as a ＂compass＂ when ＂walking＂ through jungles of tangled phylogenetic trees.

关键词： coevolution cophylogenetic analyses host-parasite molecular systematics parametric biogeography symbiosis.

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Effect of BaF2 addition on luminescence properties of Er3+/Yb3+ co-doped phosphate glasses

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Journal of Rare Earths 2018年第1期36卷 58-63页

作者： K.Linganna R.Narro-García P.Manasa H.Desirena E.De la rosa C.K.Jayasankar Department of Physics Sri Venkateswara University Centro de Investigaciones en Optica Advanced Optical Lens Research Center Korea Photonics Technology Institute (KOPTI) Centro de Física Aplicada y Tecnología Avanzada UNAM

Er/Ybco-doped phosphate glasses(PO-AlO-BaO-BaF-KO-ErO-YbO) with varying BaFcontent,were prepared by a conventional melt quenching technique and their spectroscopic properties were examined through the Raman, absorption, emission and decay measurements. Raman spectra(350-1400 cm) of the Er/Ybco-doped phosphate glasses with varying BaFcontent, were recorded upon laser excitation at 785 nm. Near infrared luminescence spectra were measured in the1400-1600 nm region under 970 nm diode laser excitation and characteristic band was observed at1533 nm corresponding to ~4Ⅰ→~4Ⅰtransition of Erion. The decay curves for the ~4Ⅰlevel of Erion, were measured and the lifetime is found to decrease from 7.94 to 7.70 ms when BaFcontent increases from 0 to 8 mol% and then increases up to 7.83 ms with further increase in BaFcontent(12 mol%). The emission *** and figure of merit for the ~4Ⅰ→~4Ⅰtransition of Erion were evaluated and compared to the other host matrices. The upconversion luminescence was measured and intense red emission was observed for all the studied samples.

关键词： Er3+/Yb3+co-doped phosphate glasses Raman spectra Absorption and emission cross-sections Lifetime Rare earths

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Hepatitis B vaccine in celiac disease:Yesterday,today and tomorrow

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World Journal of Gastroenterology 2013年第6期19卷 838-845页

作者： Giovanna Vitaliti Andrea Domenico Praticò Carla Cimino Giovanna Di Dio Elena Lionetti Mario la rosa Salvatore Leonardi Department of Pediatrics University of Catania

Some studies showed that in celiac patients the immunological response to vaccination is similar to that one found in general population except for vaccine against hepatitis B virus (HBV).The non-responsiveness to HBV vaccine has also been described in healthy people,nevertheless the number of non-responders has been demonstrated to be higher in celiac disease (CD) patients than in healthy *** hypothesis explaining this higher rate of unresponsiveness to HBV vaccine in CD patients have been described,such as the genetic hypothesis,according with CD patients carrying the disease-specific haplotype Hla-B8,DR3,and DQ2,show a lower response to HBV vaccine both in clinical expressed CD patients and in healthy people carrying the same *** the other hand,it has been demonstrated that the gluten intake during the vaccination seems to influence the response to the same ***,it has been demonstrated a possible genetic predisposition to hepatitis B vaccine nonresponsiveness likely due to the presence of specific human leukocyte antigen haplotypes and specific single nucleotide polymorphism in genes of cytokine/cytokinereceptors and toll like receptors,but the pathogenic mechanism responsible for this low responsiveness still remains *** aim of this review is to focus on the possible pathogenic causes of unresponsiveness to HBV vaccine in CD patients and to propose an alternative vaccination schedule in order to improve the responsiveness to HBV vaccine in this at-risk patients.

关键词： Celiac disease Non responders Hepatitis B vaccine Vaccination schedules

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Hepatitis B vaccine by intradermal route in non responder patients:An update

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World Journal of Gastroenterology 2014年第30期20卷 10383-10394页

作者： Martina Filippelli Elena Lionetti Alessia Gennaro Angela lanzafame Teresa Arrigo Carmelo Salpietro Mario la rosa Salvatore Leonardi Department of Medical and Pediatric Science University of Catania95100 CataniaItaly Department of Pediatric Sciences University of Messina98100 MessinaItaly

Vaccination is the main prophylactic measure to reduce the mortality caused by hepatitis B virus (HBV) infection in healthy subjects since the immune response to hepatitis B recombinant vaccination occurs in over 90% of general population. Individuals who develop an anti-HBs titer less than 10 mIU/mL after primary vaccination cycle are defined “no responders”. Many factors could cause a non response to the HBV vaccination, such as administration of the vaccine in buttocks, impaired vaccine storage conditions, drug abuse, smoking, infections and obesity. Moreover there are some diseases, like chronic kidney disease, human immunodeficiency virus infection, chronic liver disease, celiac disease, thalassaemia, type I diabetes mellitus, down’s syndrome and other forms of mental retardation that are characterized by a poorer response to HBV vaccination than healthy subjects. To date it is still unclear how to treat this group of patients at high risk of hepatitis B infection. Recent studies seem to indicate that the administration of HBV recombinant vaccine by the intradermal route is very effective and could represent a more useful strategy than intramuscular route. This review focuses on the use of anti hepatitis B vaccine by intradermal route as alternative to conventional intramuscular vaccine in all non responder patients. A comprehensive review of the literature using PubMed database, with appropriate terms, was undertaken for articles in English published since 1983. The literature search was undertaken in September 2013.

关键词： Hepatitis B virus Vaccine Intradermal route Non responders Update

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The Iberian Roma Population Variant Server(IRPVS)

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Journal of Genetics and Genomics 2024年第7期51卷 769-773页

作者： Fabiola Mavillard Javier Perez-Florido Francisco M.Ortuño Amador Valladares Miren L.Álvarez-Villegas Gema Roldán rosario Carmona Manuel Soriano Santiago Susarte Pilar Fuentes Daniel López-López Ana María Nuñez-Negrillo Alejandra Carvajal Yolanda Morgado Daniel Arteaga rosa Ufano Pablo Mir Juan F.Gamella Joaquín Dopazo Carmen Paradas Macarena Cabrera-Serrano Instituto de Biomedicina de Sevilla(IBiS) Hospital Universitario Virgen del Rocío/CSIC/Universidad de SevillaSevillaSpain Centro Investigación Biomédica en Red Enfermedades Neurodegenerativas(CIBERNED) Instituto de Salud CarlosⅢSevillaSpain Plataforma Andaluza de Medicina Computacional Fundación Progreso y Salud(FPS)Hospital Virgen del RocíoSevillaSpain Grupo de medicina computacional de sistemas Instituto de Biomedicina de Sevilla(IBiS)Hospital Virgen del RocíoSevillaSpain Nodo de Genómica Funcional (INB-ELIXIR-es)Fundación Progreso y Salud(FPS)Hospital Virgen del RocíoSevilla 41013Spain Bioinformática en Enfermedades raras(BiER) Centro de Investigación Biomédica en Red de Enfermedades Raras(CIBERER)Instituto de salud CarlosⅢSevillaSpain Departamento de Ingeniería de Computadores Automática y RobóticaUniversidad de GranadaGranadaSpain Servicio de Urgencias de Atención Primaria Distrito SevillaSevillaSpain Centro de Servicios Sociales Negociado de Servicios EspecializadosAyuntamiento de SevillaSevillaSpain Departamento de Enfermería Facultad de Ciencias de la SaludUniversidad de GranadaGranadaSpain Departamento de Neurología Hospital Virgen de las NievesGranadaSpain Departamento de Neurología Hospital Virgen de ValmeSevillaSpain Centro de Salud Utrera Sur SevillaSpain Centro de Salud Polígono Sur SevillaSpain Unidad de Trastornos del Movimiento Servicio de Neurología y Neurofisiología ClínicaHospital Universitario Virgen del RocíoSevillaSpain Departamento de Medicina Facultad de MedicinaUniversidad de SevillaSevilleSpain Departamento de Antropología Social Universidad de GranadaSpain Unidad Enfermedades Neuromusculares Servicio de Neurología y Neurofisiología ClínicaHospital Universitario Virgen del RocíoSevillaSpain

In recent years,the number of known disease genes has exponentially grown due to the widespread adoption of cost-effective massive parallel *** identify new disease variants,especially in monogenic disorders,a frequen... 详细信息

关键词： Server filtering massive

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Fetkin-hydro,a new thermo-hydrological algorithm for low-temperature thermochronological modeling

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Geoscience Frontiers 2021年第3期12卷 186-200页

作者： Francisco Sánchez andres Barrea Federico M.Dávila andres Mora Centro de Investigaciones en Ciencias de la Tierra(CICTERRA) CONICET-UNCFCEFyNCiudad UniversitariaAv.Vélez Sarsfield 16115000 CórdobaArgentina Facultad de Matemática AstronomíaFísica y Computación(FAMAF)Ciudad UniversitariaAv.Medida Allende 21445000 CórdobaArgentina Ecopetrol BotafogoRio de JaneiroBrazil

Despite two decades of major advances in the field of thermochronological modeling,state-of-the-art numerical implementations still rely mostly on burial and exhumation processes to explain radiometric *** though such an approach has proved valuable,failing to account for other first-order geological variables has led to misinterpretations and therefore,calls for a *** this study a new version of the Fetkin(finite element temperature kinematics,Ecopetrol)program is *** new algorithm couples time-dependent hydrological and thermal calculations,thus rendering thermochronological ages that,instead of being solely dependent on the kinematical evolution of a system,conditioning by the fluid flow is also *** contrast with previous thermochronological models,this work considers the influence of effective stress on rock properties(porosity and permeability)and therefore,in thermal *** analyses addressing relevant geological questions show not only the versatility of the code but also,new perspectives on forward low-temperature thermochronological *** circulation through pure-sandstone settings produce colder thermal architectures than those obtained in impermeable *** in cooling ages from models with and without fluid circulation are up to 5 Myr.A 4-fold variation in thrusting rates(0.5 km/Myr to 2 km/Myr)produces a 15-Myr difference in cooling ages in models with fluid flow,which contrasts to much lower differences,only 2 Myr,in domains without(or minimal)fluid circulation.2D thermal solutions in fold-bend-fold thrust belts composed of sandstones remain static despite substantial relief development by kinematic folding.A case-study from Western Argentina,in the Andean Precordillera,confirms the plausibility of the numerical algorithm here posed and raises new questions on the first-order thermal controls in settings under deformation.

关键词： Thermochronology Hydrogeology Fluid flow Numerical modeling

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Prevalence and associated factors of obesity in inflammatory bowel disease:A case-control study

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World Journal of Gastroenterology 2020年第47期26卷 7528-7537页

作者： Giuseppe Losurdo rosa Federica la Fortezza Andrea Iannone Antonella Contaldo Michele Barone Enzo Ierardi Alfredo Di Leo Mariabeatrice Principi Section of Gastroenterology Department of Emergency and Organ TransplantationUniversity of BariBari 70124Italy

BACKGROUND In recent years,an increasing prevalence of obesity in inflammatory bowel disease(IBD)has been ***,moreover,has been directly correlated with a more severe clinical course and loss of response to *** To assess the prevalence and associated factors of obesity in *** We collected data about IBD disease pattern and activity,drugs and laboratory investigations in our *** measures were retrieved and obesity defined as a body mass index(BMI)>***,we compared characteristics of obese vs non obese patients,and Chi-squared test and Student’s t test were used for discrete and continuous variables,respectively,at univariate *** multivariate analysis,we used binomial logistic regression and estimated odd ratios(OR)and 95%confidence intervals(CI)to ascertain factors associated with *** We enrolled 807 patients with IBD,either ulcerative colitis(UC)or Crohn’s disease(CD).Four hundred seventy-four patients were male(58.7%);the average age was 46.2±13.2 years;438(54.2%)patients had CD and 369(45.8%)*** enrolled 378 controls,who were comparable to IBD group for age,sex,BMI,obesity,diabetes and abdominal circumference,while more smokers and more subjects with hypertension were observed among *** prevalence of obesity was 6.9%in IBD and 7.9%in controls(not statistically different;P=0.38).In the comparison of obese IBD patients and obese controls,we did not find any difference regarding diabetes and hypertension prevalence,nor in sex or smoking *** IBD patients were younger than obese controls(51.2±14.9 years vs 60.7±12.1 years,P=0.03).At univariate analysis,obese IBD were older than normal weight ones(51.2±14.9 vs 44.5±15.8,P=0.002).IBD onset age was earlier in obese population(44.8±13.6 vs 35.6±15.6,P=0.004).We did not detect any difference in disease *** subjects had consumed more frequently long course of systemic steroids(66.6%vs 12.5%,P=0.02)as well as antibiotics s

关键词： Inflammatory bowel disease Obesity Body mass index Antibiotics Risk factor Corticosteroids

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Liver transplantation is beneficial regardless of cirrhosis stage or acute-on-chronic liver failure grade:A single-center experience

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World Journal of Gastroenterology 2022年第40期28卷 5881-5892页

作者： Eduardo Cervantes-Alvarez Mario Vilatoba Nathaly Limon-de la rosa Osvely Mendez-Guerrero David Kershenobich Aldo Torre Nalu Navarro-Alvarez PECEM Facultad de MedicinaUniversidad Nacional Autónoma de MéxicoMexico City 14080Mexico Department of Gastroenterology Instituto Nacional de Ciencias Médicas y Nutrición Salvador ZubiránMexico City 14080Mexico Department of Trasplant Instituto Nacional de Ciencias Médicas y Nutrición Salvador ZubiránMexico City 14080Mexico Department of Molecular Biology Universidad Panamericana School of MedicineMexico City 03920Mexico Department of Surgery University of Colorado Anschutz Medical CampusDenverCO 80045United States

BACKGROUND Liver transplantation for the most critically ill remains controversial;however,it is currently the only curative treatment *** To assess immediate posttransplant outcomes and compare the short(1 year)and long-term(6 years)posttransplant survival among cirrhotic patients stratified by disease *** We included cirrhotic patients undergoing liver transplantation between 2015 and 2019 and categorized them into compensated cirrhosis(CC),decompensated cirrhosis(DC),and acute-on-chronic liver failure(ACLF).ACLF was further divided into severity *** primary outcomes of interest were total days of intensive care unit(ICU)and hospital stay,development of complications and posttransplant survival at 1 and 6 *** 235 patients underwent liver transplantation(CC=11,DC=129 and ACLF=95).Patients with ACLF had a significantly longer hospital stay[8.0(6.0-13.0)vs CC,6.0(3.0-7.0),and DC 7.0(4.5-10.0);P=0.01]and developed more infection-related complications[47(49.5%),vs CC,1(9.1%)and DC,38(29.5%);Plant survival at 1-and 6-years was similar among groups(P=0.60 and P=0.90,respectively).ACLF patients stratified according to ACLF grade[ACLF-1 n=40(42.1%),ACLF-2 n=33(34.7%)and ACLF-3 n=22(23.2%)],had similar ICU and hospital stay length(P=0.68,P=0.54),as well as comparable frequencies of overall and infectious posttransplant complications(P=0.58,P=0.80).There was no survival difference between ACLF grades at 1 year and 6 years(P=0.40 and P=0.15).CONCLUSION Patients may benefit from liver transplantation regardless of the cirrhosis *** patients have a longer hospital stay and frequency of infectious complications;however,excellent,and comparable 1 and 6-year survival rates support their enlisting and transplantation including those with ACLF-3.

关键词： Liver transplantation Acute-on-chronic liver failure Prognosis Survival analysis Critical care

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The Gut Microbiota and Atherosclerosis:The State of the Art and Novel Perspectives

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Cardiovascular Innovations and Applications 2016年第B9期1卷 433-442页

作者： Giulio la rosa Luigi Marzio Biasucci Department of Cardiovascular Sciences Catholic University of Sacred HeartLargo Agostino Gemelli 800168 RomeItaly

The human gut microbiota is composed of more than 100 trillion *** communities are dominated by species belonging to the phyla Bacteroidetes,Firmicutes,Actinobacteria,Proteobacteria,and *** ora-derived short-chain fatty acids play a pivotal role in the framework of insulin resistance,obesity,and metabolic *** are an important energy source and are involved in several pathways,with proatherogenic and antiatherogenic *** increased gut microbiota lipopolysaccharide levels(defi ned as“metabolic endotoxemia”)induce a state of low-grade infl ammation and are involved in atherosclerotic disease through Toll-like receptor *** important infl ammatory trigger in gut microbiota–mediated atherosclerotic promotion is trimethylamine *** the other hand,protocatechuic acid was found to promote cholesterol effl ux from macrophages,showing an antiatherogenic *** studies to clarify specifi c gut composition involved in cardiometabolic syndrome and atherogenesis are needed for greater use of targeted approaches.

关键词： gut microbiota atherosclerosis metabolic syndrome

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Biaxial versus uniaxial strain tuning of single-layer MoS_(2)

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Nano Materials Science 2022年第1期4卷 44-51页

作者： Felix Carrascoso Riccardo Frisenda andres Castellanos-Gomez Materials Science Factory Instituto de Ciencia de Materiales de Madrid(ICMM-CSIC)28049Madrid Spain

Strain engineering has arisen as a powerful technique to tune the electronic and optical properties of twod imensional semiconductors like molybdenum disulfide(MoS_(2)).Although several theoretical works predicted that biaxial strain would be more effective than uniaxial strain to tune the band structure of MoS_(2),a direct experimental verification is still missing in the *** we implemented a simple experimental setup that allows to apply biaxial strain through the bending of a cruciform polymer *** used the setup to study the effect of biaxial strain on the differential reflectance spectra of 12 single-layer MoS_(2)flakes finding a redshift of the excitonic features at a rate between-40 meV/%and-110 meV/%of biaxial *** also directly compare the effect of biaxi al and uniaxial strain on the same single-layer MoS_(2)finding that the biaxial strain gauge factor is 2.3 times larger than the uniaxial strain one.

关键词： finding layer gauge

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