A comparative analisys of i*-based agent-oriented modeling languages

Agent-oriented models are frequently used in disciplines such as requirements engineering and organizational process modelling. i* is currently one of the most widespread notations used for this purpose. Due to its strategic nature, instead of a single definition, there exist several versions and variants, often not totally defined and even contradictory. In this paper we present a comparative study of the three most widespread i* variants: Eric Yu’s seminal proposal, the Goal-oriented Requirement Language (GRL) and the language used in the TROPOS method. Next, we propose a generic conceptual model to be used as reference framework of these three variants and we show its use for generating specific models for the three mentioned variants, as well as for other existing proposals.Peer ReviewedPostprint (author’s final draft

Amino acid substitutions associated with treatment failure of hepatitis C virus infection

Trabajo presentado en el XVI Congreso Nacional de Virología, celebrado en Málaga (España) del 06 al 09 de septiembre de 2022.Despite the high sustained virological response rates achieved with current directly-acting antiviral agents (DAAs) against hepatitis C virus (HCV), around 2% to 5% of patients do not achieve such a response. Identification of amino acid substitutions associated with treatment failure requires analytical designs, such as subtype-specific ultra-deep sequencing (UDS) methods for HCV characterization and patient management. By deep sequencing analysis of 220 subtyped HCV samples from infected patients who failed therapy, collected from 39 Spanish hospitals, we determined amino acid sequences of the DAA-target proteins NS3, NS5A and NS5B, by UDS of HCV patient samples, in search of resistanceassociated substitutions (RAS). Using this procedure, we have identified six highly represented amino acid substitutions (HRSs) in NS5A and NS5B of HCV, which are not bona fide RAS. They were present frequently in basal and post-treatment virus of patients who failed therapy to different DAA-based therapies. Contrary to several RAS, HRSs belong to the acceptable subset of substitutions according to the PAM250 replacement matrix. Coherently, their mutant frequency, measured by the number of deep sequencing reads within the HCV quasispecies that encode the relevant substitutions, ranged between 90% and 100% in most cases. Also, they have limited predicted disruptive effects on the threedimensional structures of the proteins harboring them. The information on HRSs that will be gathered during sequencing should be relevant not only to help predict treatment outcomes and disease progression but also to further understand HCV population dynamics, which appears much more complex than thought prior to the introduction of deep sequencing.The work at CBMSO was supported by grants SAF2014-52400-R from MINECO, SAF2017-87846-R and BFU2017-91384-EXP MICIU, PI18/00210 from ISCIII, S2013/ABI-2906 (PLATESA) and S2018/BAA-4370 (PLATESA2) from Comunidad de Madrid/FEDER. C.P. is supported by the Miguel Servet program of the ISCIII (CP14/00121 and CPII19/00001), cofinanced by the European Regional Development Fund (ERDF). CIBERehd is funded by ISCIII. Institutional grants from the Fundación Ramón Areces and Banco Santander to the CBMSO are also acknowledged. The team at CBMSO belongs to the Global Virus Network (GVN). The work in Barcelona was supported by ISCIII, cofinanced by ERDF grant number PI19/00301 and by the Centro para el Desarrollo Tecnológico Industrial (CDTI) from the MICIU, grant number IDI20151125. Work at CAB was supported by MINECO grant BIO2016-79618R and PID2019-104903RB-I00 (funded by the EU under the FEDER program) and by the Spanish State research agency (AEI) through project number MDM-2017-0737 Unidad de Excelencia “María de Maeztu”-Centro de Astrobiología (CSIC-INTA). Work at IBMB was supported by MICIN grant BIO2017-83906-P (funded by the EU under the FEDER program). C.G.-C. is supported by predoctoral contract PRE2018-083422 from MICIU. B.M.-G. is supported by predoctoral contract PFIS FI19/00119 from Instituto de Salud Carlos III (Ministerio de Sanidad y Consumo), cofinanced by Fondo Social Europeo (FSE).Peer reviewe

Prognostic and predictive factors in recurrent and/or metastatic head and neck squamous cell carcinoma : A review of the literature

The pattern of clinical behaviour and response to treatment of recurrent and/or metastatic head and neck squamous cell carcinoma is heterogeneous. Treatment strategies that can be employed vary from potentially curative salvage surgery and re-irradiation to palliative systemic therapies and best supportive care. The advent of new therapeutic options, in terms of more sophisticated surgical approaches and techniques, highly conformal and precise radiation techniques and immunotherapy may offer improved control of disease and longer survival. Moreover, the epidemiological changes during the last decades, including the increase of human papilloma virus-related oropharyngeal primary tumors, are also reflected in the recurrent and metastatic setting. In this complex context the identification of predictive and prognostic factors is urgently needed to tailor treatment, to increase its efficacy, and to avoid unnecessary toxicities. A better knowledge of prognosis may also help the patients and caregivers in decision making on the optimal choice of care. The purpose of our review is to highlight the current evidence and shortcomings in this field.Peer reviewe

Análisis comparativo de lenguajes de modelado orientados a objetivos basados en i*

Los modelos orientados a objetivos son usados frecuentemente en disciplinas tales como la ingeniería de requisitos o el modelado de procesos en organizaciones. i* es una de las notaciones más empleadas para construir este tipo de modelos. Desafortunadamente, no existe una definición única de i* sino diferentes versiones y variantes que, con frecuencia, no están totalmente definidas dificultando su comprensión y utilización. En este artículo, se presenta un estudio comparativo de las tres variantes más utilizadas de i*: la propuesta original de Eric Yu, el lenguaje GRL y el lenguaje utilizado en el método TROPOS. A continuación, se formula un modelo conceptual genérico como marco de referencia de las variantes estudiadas, se muestra cómo a partir de este modelo genérico pueden generarse los modelos específicos de cada una, y se evidencia que también puede usarse para clasificar algunas variantes puntuales que encontramos en la literatura.Peer ReviewedPostprint (author's final draft

Is There A Role for Limited Parotid Resections for Primary Malignant Parotid Tumors?

Background: Lateral or total parotidectomy are the standard surgical treatmentsfor malignant parotid tumors. However, some authors have proposed a more limited procedure.(2) Methods: We performed a review of the literature on this topic. Studies were included that metthe following criteria: malignant parotid tumors, information about the extent of surgical resection,treated with less than a complete lateral lobectomy, and information on local control and/or survival.Nine articles fulfilled the inclusion criteria. (3) Results: Eight of the nine series reported favorableresults for the more limited approaches. Most used them for small, mobile, low-grade cancers inthe lateral parotid lobe. Most authors have used a limited partial lateral lobectomy for a presumedbenign lesion. The remaining study analyzed pediatric patients treated with enucleation with poorlocal control. (4) Conclusions: There is weak evidence for recommending less extensive proceduresthan a lateral parotid lobectomy. In the unique case of a partial lateral parotidectomy performed fora tumor initially thought to be benign but pathologically proved to be malignant, close follow-upcan be recommended for low grade T1 that has been excised with free margins and does not haveadverse prognostic factors

High-resolution hepatitis C virus subtyping using NS5B deep sequencing and phylogeny, an alternative to current methods

HepatitisCvirus(HCV)is classified into seven major genotypesand67 subtypes. Recent studies haveshownthat inHCVgenotype 1-infected patients, response rates to regimens containingdirect-acting antivirals(DAAs)are subtype dependent. Currently available genotypingmethods have limited subtyping accuracy.Wehave evaluated theperformanceof adeep-sequencing-basedHCVsubtyping assay, developed for the 454/GS-Junior platform, in comparisonwith thoseof two commercial assays (VersantHCVgenotype 2.0andAbbott Real-timeHCVGenotype II)andusingdirectNS5Bsequencing as a gold standard (direct sequencing), in 114 clinical specimenspreviously tested by first-generation hybridization assay (82 genotype 1and32 with uninterpretable results). Phylogenetic analysis of deep-sequencing reads matched subtype 1 callingbypopulation Sanger sequencing(69%1b,31%1a) in 81 specimensandidentified amixed-subtype infection (1b/3a/1a) in one sample. Similarly,amongthe 32previously indeterminate specimens, identical genotypeandsubtype results were obtained by directanddeep sequencing in all but four samples with dual infection. In contrast, both VersantHCVGenotype 2.0andAbbott Real-timeHCVGenotype II failed subtype 1 calling in 13 (16%) samples eachandwere unable to identify theHCVgenotype and/or subtype inmore than half of the nongenotype 1 samples.Weconcluded that deep sequencing ismore efficient forHCVsubtyping than currently available methodsandallows qualitative identificationofmixed infectionsandmay bemorehelpfulwith respect to informing treatment strategies withnewDAA-containing regimens across allHCVsubtypesThis study has been supported by CDTI (Centro para el Desarrollo Tecnológico Industrial), Spanish Ministry of Economics and Competitiveness (MINECO), IDI-20110115; MINECO projects SAF 2009-10403; and also by the Spanish Ministry of Health, Instituto de Salud Carlos III (FIS) projects PI10/01505, PI12/01893, and PI13/00456. CIBERehd is funded by the Instituto de Salud Carlos III, Madrid, Spain. Work at CBMSO was supported by grant MINECO-BFU2011-23604, FIPSE, and Fundación Ramón Areces. X. Forns received unrestricted grant support from Roche and has acted as advisor for MSD, Gilead, and Abbvie. M. Alvarez-Tejado, J. Gregori, and J. M. Muñoz work in Roche Diagnostic

Protective effects of the succinate/SUCNR1 axis on damaged hepatocytes in NAFLD

[Objective]: Succinate and succinate receptor 1 (SUCNR1) are linked to fibrotic remodeling in models of non-alcoholic fatty liver disease (NAFLD), but whether they have roles beyond the activation of hepatic stellate cells remains unexplored. We investigated the succinate/SUCNR1 axis in the context of NAFLD specifically in hepatocytes.[Methods]: We studied the phenotype of wild-type and Sucnr1−/− mice fed a choline-deficient high-fat diet to induce non-alcoholic steatohepatitis (NASH), and explored the function of SUCNR1 in murine primary hepatocytes and human HepG2 cells treated with palmitic acid. Lastly, plasma succinate and hepatic SUCNR1 expression were analyzed in four independent cohorts of patients in different NAFLD stages.[Results]. Sucnr1 was upregulated in murine liver and primary hepatocytes in response to diet-induced NASH. Sucnr1 deficiency provoked both beneficial (reduced fibrosis and endoplasmic reticulum stress) and detrimental (exacerbated steatosis and inflammation and reduced glycogen content) effects in the liver, and disrupted glucose homeostasis. Studies in vitro revealed that hepatocyte injury increased Sucnr1 expression, which when activated improved lipid and glycogen homeostasis in damaged hepatocytes. In humans, SUCNR1 expression was a good determinant of NAFLD progression to advanced stages. In a population at risk of NAFLD, circulating succinate was elevated in patients with a fatty liver index (FLI) ≥60. Indeed, succinate had good predictive value for steatosis diagnosed by FLI, and improved the prediction of moderate/severe steatosis through biopsy when added to an FLI algorithm.[Conclusions]. We identify hepatocytes as target cells of extracellular succinate during NAFLD progression and uncover a hitherto unknown function for SUCNR1 as a regulator of hepatocyte glucose and lipid metabolism. Our clinical data highlight the potential of succinate and hepatic SUCNR1 expression as markers to diagnose fatty liver and NASH, respectively.This study was supported by grants from MCIN/AEI/10.13039/501100011033 (SAF2015-65019-R, RTI2018-093919-B-100 and PID2021-122480OB-100 to S.F.-V.; PID2021-122766OB-100 to A.M.V; PID2021-124425OB-I00 to P.A.) co-financed by the European Regional Development Fund (ERDF) and Grupos consolidados Gobierno Vasco IT1476-22 to P.A. This research was funded by the Institute of Health “Carlos III” (ISCIII) and co-financed by ERDF (PI20/00095 to V.C.-M.; PI20/00338 to J.V. and PI20/00505 to B.R.-M.). This study was also supported by a grant from ISCIII and CIBERDEM, DEM19PI01/2019 to V.C.-M. and P.R. The project that gave rise to these results received funding from “La Caixa” Foundation (ID 100010434), under the grant agreement LCF/PR/HR20/52400013 (to S.F.-V.). This study was also supported by Rovira i Virgili University and Tarragona Provincial Council with the Talent Salut fellowship to A.R.-C. A.M.-B. is a recipient of an FPU grant (FPU20/05633) from MCIN/AEI/10.13039/501100011033. B.A. acknowledges support from the PERIS program 2016–2020 (LT017/20/000033), from Departament de Salut de la Generalitat de Catalunya. V.C.-M. acknowledges support from the Ramón y Cajal program (RYC2019-02649-I), from MCIN/AEI/10.13039/501100011033/ and the European Social Fund (ESF), “Investing in your future”. B.R.-M. acknowledges support from the Miguel Servet Type I program (CP19/00098) from the Fondo de Investigación Sanitaria, co-financed by the ERDF. SFV and JVO acknowledge support from the Agency for Management of University Research Grants of the Generalitat de Catalunya (2021 SGR 01409, 2021 SGR 0089). The study was also supported by CIBER–Consorcio Centro de Investigación Biomédica en Red (CB07708/0012), ISCIII, Ministerio de Ciencia e Innovación.Peer reviewe

Resultados de una encuesta sobre el soporte nutricional perioperatorio en la cirugía pancreática y biliar en España

Introduction: a survey on peri-operative nutritional support in pancreatic and biliary surgery among Spanish hospitals in 2007 showed that few surgical groups followed the 2006 ESPEN guidelines. Ten years later we sent a questionnaire to check the current situation. Methods: a questionnaire with 21 items sent to 38 centers, related to fasting time before and after surgery, nutritional screening use and type, time and type of peri-operative nutritional support, and number of procedures. Results: thirty-four institutions responded. The median number of pancreatic resections (head/total) was 29.5 (95% CI: 23.0-35; range, 5-68) (total, 1002); of surgeries for biliary malignancies (non-pancreatic), 9.8 (95% CI: 7.3-12.4; range, 2-30); and of main biliary resections for benign conditions, 10.4 (95% CI: 7.6-13.3; range, 2-33). Before surgery, only 41.2% of the sites used nutritional support (&lt; 50% used any nutritional screening procedure). The mean duration of preoperative fasting for solid foods was 9.3 h (range, 6-24 h); it was 6.6 h for liquids (range, 2-12). Following pancreatic surgery, 29.4% tried to use early oral feeding, but 88.2% of the surveyed teams used some nutritional support; 26.5% of respondents used TPN in 100% of cases. Different percentages of TPN and EN were used in the other centers. In malignant biliary surgery, 22.6% used TPN always, and EN in 19.3% of cases. Conclusions: TPN is the commonest nutrition approach after pancreatic head surgery. Only 29.4% of the units used early oral feeding, and 32.3% used EN; 22.6% used TPN regularly after surgery for malignant biliary tumours. The 2006 ESPEN guideline recommendations are not regularly followed 12 years after their publication in our country.Introducción: realizamos una encuesta sobre soporte nutricional perioperatorio en cirugía pancreática y biliar en hospitales españoles en 2007, que mostró que pocos grupos quirúrgicos seguían las guías de ESPEN 2006. Diez años después enviamos un cuestionario para comprobar la situación actual. Métodos: treinta y ocho centros recibieron un cuestionario con 21 preguntas sobre tiempo de ayunas antes y después de la cirugía, cribado nutricional, duración y tipo de soporte nutricional perioperatorio, y número de procedimientos. Resultados: respondieron 34 grupos. La mediana de pancreatectomías (cabeza/total) fue de 29,5 (IC 95 %: 23,0-35; rango, 5-68) (total, 1002), la de cirugías biliares malignas de 9,8 (IC 95 %: 7,3-12,4; rango, 2-30) y la de resecciones biliares por patología benigna de 10,4 (IC 95 %: 7,6-13,3; rango, 2-33). Solo el 41,2 % de los grupos utilizaban soporte nutricional antes de la cirugía (< 50 % habian efectuado un cribado nutricional). El tiempo medio de ayuno preoperatorio para sólidos fue de 9,3 h (rango, 6-24 h), y de 6,6 h para líquidos (rango, 2-12). Tras la pancreatectomía, el 29,4 % habían intentado administrar una dieta oral precoz, pero el 88,2 % de los grupos usaron algún tipo de soporte nutricional y el 26,5 % usaron NP en el 100 % de los casos. Los demás grupos usaron diferentes porcentajes de NP y NE en sus casos. En la cirugía biliar maligna, el 22,6 % utilizaron NP siempre y NE en el 19,3 % de los casos. Conclusiones: la NP es el soporte nutricional más utilizado tras la cirugía de cabeza pancreática. Solo el 29,4 % de las unidades usan nutrición oral precoz y el 32,3 % emplean la NE tras este tipo de cirugía. El 22,6 % de las instituciones usan NP habitualmente tras la cirugía de tumores biliares malignos. Las guías ESPEN 2006 no se siguen de forma habitual en nuestro país tras más de 10 años desde su publicación