Preliminary morphologic and molecular study of teh Entoloma rusticoides group (Agaricales - Basidiomycota)

Es presenta un estudi sobre el grup rusticoides del gènere Entoloma subgènere Claudopus a la Península Ibérica. L'anàlisi filogenètica, sobre la base de 48 seqüències d'ITS i 45 seqüències de LSU, entre les quals, les dels tipus de 8 dels tàxons analitzats, mostra una marcada diversitat genètica que concorda amb la notable variabilitat observada en aquest grup. D'acord amb aquest fet, es descriuen els següents nous tàxons: E. almeriense, E. graphitipes f. cystidiatum, E. halophilum, E. muscoalpinum i E. phaeocarpum. A més, es tipifiquen E. phaeocyathus i E. rusticoides. S'inclouen claus provisionals d'identificació. S'aporten descripcions macro i microscòpiques, dibuixos i fotografies de la majoria dels tàxons estudiats.A study of the Entoloma rusticoides-group (subgenus Claudopus) in the Iberian peninsula is presented. Phylogenetic inference, based on 48 nrITS and 45 28S nrLSU sequences, including those of 8 type specimens, revealed a high genetic diversity, in accordance with the observed morphological variability in this group. In addition new taxa are proposed to accomodate independent lineages (E. almeriense, E. graphitipes f. cystidiatum, E. halophilum, E. muscoalpinum and E. phaeocarpum) and the typification of E. phaeocyathus and E. rusticoides is proposed. Preliminary taxonomic keys are included to help identification. For most species macro and microscopic descriptions, drawings and photographs are presented

Preliminary morphologic and molecular study of teh Entoloma rusticoides group (Agaricales - Basidiomycota)

Es presenta un estudi sobre el grup rusticoides del gènere Entoloma subgènere Claudopus a la Península Ibérica. L'anàlisi filogenètica, sobre la base de 48 seqüències d'ITS i 45 seqüències de LSU, entre les quals, les dels tipus de 8 dels tàxons analitzats, mostra una marcada diversitat genètica que concorda amb la notable variabilitat observada en aquest grup. D'acord amb aquest fet, es descriuen els següents nous tàxons: E. almeriense, E. graphitipes f. cystidiatum, E. halophilum, E. muscoalpinum i E. phaeocarpum. A més, es tipifiquen E. phaeocyathus i E. rusticoides. S'inclouen claus provisionals d'identificació. S'aporten descripcions macro i microscòpiques, dibuixos i fotografies de la majoria dels tàxons estudiats.A study of the Entoloma rusticoides-group (subgenus Claudopus) in the Iberian peninsula is presented. Phylogenetic inference, based on 48 nrITS and 45 28S nrLSU sequences, including those of 8 type specimens, revealed a high genetic diversity, in accordance with the observed morphological variability in this group. In addition new taxa are proposed to accomodate independent lineages (E. almeriense, E. graphitipes f. cystidiatum, E. halophilum, E. muscoalpinum and E. phaeocarpum) and the typification of E. phaeocyathus and E. rusticoides is proposed. Preliminary taxonomic keys are included to help identification. For most species macro and microscopic descriptions, drawings and photographs are presented

On the nature and impact of self-similarity in real-time systems

In real-time systems with highly variable task execution times simplistic task models are insufficient to accurately model and to analyze the system. Variability can be tackled using distributions rather than a single value, but the proper charac- terization depends on the degree of variability. Self-similarity is one of the deep- est kinds of variability. It characterizes the fact that a workload is not only highly variable, but it is also bursty on many time-scales. This paper identifies in which situations this source of indeterminism can appear in a real-time system: the com- bination of variability in task inter-arrival times and execution times. Although self- similarity is not a claim for all systems with variable execution times, it is not unusual in some applications with real-time requirements, like video processing, networking and gaming. The paper shows how to properly model and to analyze self-similar task sets and how improper modeling can mask deadline misses. The paper derives an analyti- cal expression for the dependence of the deadline miss ratio on the degree of self- similarity and proofs its negative impact on real-time systems performance through system¿s modeling and simulation. This study about the nature and impact of self- similarity on soft real-time systems can help to reduce its effects, to choose the proper scheduling policies, and to avoid its causes at system design time.This work was developed under a grant from the European Union (FRESCOR-FP6/2005/IST/5-03402).Enrique Hernández-Orallo; Vila Carbó, JA. (2012). On the nature and impact of self-similarity in real-time systems. Real-Time Systems. 48(3):294-319. doi:10.1007/s11241-012-9146-0S294319483Abdelzaher TF, Sharma V, Lu C (2004) A utilization bound for aperiodic tasks and priority driven scheduling. IEEE Trans Comput 53(3):334–350Abeni L, Buttazzo G (1999) QoS guarantee using probabilistic deadlines. 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In: Proc of the 23rd IEEE real-time systems symposium, pp 289–300Erramilli A, Narayan O, Willinger W (1996) Experimental queueing analysis with long-range dependent packet traffic. IEEE/ACM Trans Netw 4(2):209–223Erramilli A, Roughan M, Veitch D, Willinger W (2002) Self-similar traffic and network dynamics. Proc IEEE 90(5):800–819Gardner M (1999) Probabilistic analysis and scheduling of critical soft real-time systems. Phd thesis, University of Illinois, Urbana-ChampaignGarrett MW, Willinger W (1994) Analysis, modeling and generation of self-similar vbr video traffic. In: ACM SIGCOMMHarchol-Balter M (2002) Task assignment with unknown duration. J ACM 49(2):260–288Harchol-Balter M (2007) Foreword: Special issue on new perspective in scheduling. SIGMETRICS Perform Eval Rev 34(4):2–3Harchol-Balter M, Downey AB (1997) Exploiting process lifetime distributions for dynamic load balancing. ACM Trans Comput Syst 15(3):253–285Hernandez-Orallo E, Vila-Carbo J (2007) Network performance analysis based on histogram workload models. In: Proceedings of the 15th international symposium on modeling, analysis, and simulation of computer and telecommunication systems (MASCOTS), pp 331–336Hernandez-Orallo E, Vila-Carbo J (2010) Analysis of self-similar workload on real-time systems. In: IEEE real-time and embedded technology and applications symposium (RTAS). IEEE Computer Society, Washington, pp 343–352Hernández-Orallo E, Vila-Carbó J (2010) Network queue and loss analysis using histogram-based traffic models. Comput Commun 33(2):190–201Hughes CJ, Kaul P, Adve SV, Jain R, Park C, Srinivasan J (2001) Variability in the execution of multimedia applications and implications for architecture. SIGARCH Comput Archit News 29(2):254–265Leland W, Ott TJ (1986) Load-balancing heuristics and process behavior. SIGMETRICS Perform Eval Rev 14(1):54–69Leland WE, Taqqu MS, Willinger W, Wilson DV (1994) On the self-similar nature of ethernet traffic (extended version). IEEE/ACM Trans Netw 2(1):1–15Liu CL, Layland JW (1973) Scheduling algorithms for multiprogramming in a hard-real-time environment. J ACM 20(1):46–61Mandelbrot B (1965) Self-similar error clusters in communication systems and the concept of conditional stationarity. IEEE Trans Commun 13(1):71–90Mandelbrot BB (1969) Long run linearity, locally Gaussian processes, h-spectra and infinite variances. Int Econ Rev 10:82–113Norros I (1994) A storage model with self-similar input. Queueing Syst 16(3):387–396Norros I (2000) Queueing behavior under fractional Brownian traffic. In: Park K, Willinger W (eds) Self-similar network traffic and performance evaluation. Willey, New York, Chap 4Park K, Willinger W (2000) Self-similar network traffic: An overview. In: Park K, Willinger W (eds) Self-similar network traffic and performance evaluation. Willey, New York, Chap 1Paxson V, Floyd S (1995) Wide area traffic: the failure of Poisson modeling. IEEE/ACM Trans Netw 3(3):226–244Rolls DA, Michailidis G, Hernández-Campos F (2005) Queueing analysis of network traffic: methodology and visualization tools. Comput Netw 48(3):447–473Rose O (1995) Statistical properties of mpeg video traffic and their impact on traffic modeling in atm systems. In: Conference on local computer networksRoy N, Hamm N, Madhukar M, Schmidt DC, Dowdy L (2009) The impact of variability on soft real-time system scheduling. In: RTCSA ’09: Proceedings of the 2009 15th IEEE international conference on embedded and real-time computing systems and applications. IEEE Computer Society, Washington, pp 527–532Sha L, Abdelzaher T, Årzén KE, Cervin A, Baker T, Burns A, Buttazzo G, Caccamo M, Lehoczky J, Mok AK (2004) Real time scheduling theory: A historical perspective. Real-Time Syst 28(2):101–155Taqqu MS, Willinger W, Sherman R (1997) Proof of a fundamental result in self-similar traffic modeling. SIGCOMM Comput Commun Rev 27(2):5–23Tia T, Deng Z, Shankar M, Storch M, Sun J, Wu L, Liu J (1995) Probabilistic performance guarantee for real-time tasks with varying computation times. In: Proc of the real-time technology and applications symposium, pp 164–173Vila-Carbó J, Hernández-Orallo E (2008) An analysis method for variable execution time tasks based on histograms. Real-Time Syst 38(1):1–37Willinger W, Taqqu M, Erramilli A (1996) A bibliographical guide to self-similar traffic and performance modeling for modern high-speed networks. In: Stochastic networks: Theory and applications, pp 339–366Willinger W, Taqqu MS, Sherman R, Wilson DV (1997) Self-similarity through high-variability: statistical analysis of ethernet lan traffic at the source level. IEEE/ACM Trans Netw 5(1):71–8

External validation of multidimensional prognostic indices (ADO, BODEx and DOSE) in a primary care international cohort (PROEPOC/COPD cohort)

Background: Due to the heterogeneous and systemic nature of the chronic obstructive pulmonary disease (COPD), the new guidelines are oriented toward individualized attention. Multidimensional scales could facilitate its proper clinical and prognostic assessment, but not all of them were validated in an international primary care cohort, different from the original ones used for model development. Therefore, our main aim is to assess the prognostic capacity of the ADO, BODEx and DOSE indices in primary care for predicting mortality in COPD patients and to validate the models obtained in subgroups of patients, classified by revised Global Initiative for Chronic Obstructive Lung Disease (2011) and updated Spanish Guideline (2014). Besides, we want to confirm that the prognostic capacity of all indices increases if the number of exacerbations is substituted by the interval between them and to assess the impact on health of the patient''s lifestyle, social network and adherence to treatment. Methods: Design: External validation of scales, open and prospective cohort study in primary care. Setting: 36 health centres in 6 European high, medium and low income countries. Subjects: 477 patients diagnosed with COPD, captured in clinical visit by their General Practitioner/Nurse. Predictors: Detailed patient history, exacerbations, lung function test and questionnaires at baseline. Outcomes: Exacerbations, all-cause mortality and specific mortality, within 5 years of recruitment. Analysis: Multivariate logistic regression and Cox regression will be used. Possible non-linear effect of the indices will be studied by using Structured Additive Regression models with penalised splines. Subsequently, we will assess different aspects of the regression models: discrimination, calibration and diagnostic precision. Clinical variables modulated in primary care and the interval between exacerbations will be considered and incorporated into the analysis. Discussion: The Research Agenda for General Practice/Family Medicine highlights that the evidence on predictive values of prognostic indices in primary care is scarce. A prospective cohort like that of PROEPOC/COPD provides good opportunities for research into COPD and make communication easier between family practitioners, nursing staff, pneumologists and other professionals, supporting a multi-disciplinary approach to the treatment of these patients. Trial registration:ISRCTN52402811. Date: 15/01/2015. Prospectively registered

Prevalence and impact of COVID-19 sequelae on treatment and survival of patients with cancer who recovered from SARS-CoV-2 infection: evidence from the OnCovid retrospective, multicentre registry study

Background: The medium-term and long-term impact of COVID-19 in patients with cancer is not yet known. In this study, we aimed to describe the prevalence of COVID-19 sequelae and their impact on the survival of patients with cancer. We also aimed to describe patterns of resumption and modifications of systemic anti-cancer therapy following recovery from SARS-CoV-2 infection. Methods: OnCovid is an active European registry study enrolling consecutive patients aged 18 years or older with a history of solid or haematological malignancy and who had a diagnosis of RT-PCR confirmed SARS-CoV-2 infection. For this retrospective study, patients were enrolled from 35 institutions across Belgium, France, Germany, Italy, Spain, and the UK. Patients who were diagnosed with SARS-CoV-2 infection between Feb 27, 2020, and Feb 14, 2021, and entered into the registry at the point of data lock (March 1, 2021), were eligible for analysis. The present analysis was focused on COVID-19 survivors who underwent clinical reassessment at each participating institution. We documented prevalence of COVID-19 sequelae and described factors associated with their development and their association with post-COVID-19 survival, which was defined as the interval from post-COVID-19 reassessment to the patients’ death or last follow-up. We also evaluated resumption of systemic anti-cancer therapy in patients treated within 4 weeks of COVID-19 diagnosis. The OnCovid study is registered in ClinicalTrials.gov, NCT04393974. Findings: 2795 patients diagnosed with SARS-CoV-2 infection between Feb 27, 2020, and Feb 14, 2021, were entered into the study by the time of the data lock on March 1, 2021. After the exclusion of ineligible patients, the final study population consisted of 2634 patients. 1557 COVID-19 survivors underwent a formal clinical reassessment after a median of 22·1 months (IQR 8·4–57·8) from cancer diagnosis and 44 days (28–329) from COVID-19 diagnosis. 234 (15·0%) patients reported COVID-19 sequelae, including respiratory symptoms (116 [49·6%]) and residual fatigue (96 [41·0%]). Sequelae were more common in men (vs women; p=0·041), patients aged 65 years or older (vs other age groups; p=0·048), patients with two or more comorbidities (vs one or none; p=0·0006), and patients with a history of smoking (vs no smoking history; p=0·0004). Sequelae were associated with hospitalisation for COVID-19 (p<0·0001), complicated COVID-19 (p<0·0001), and COVID-19 therapy (p=0·0002). With a median post-COVID-19 follow-up of 128 days (95% CI 113–148), COVID-19 sequelae were associated with an increased risk of death (hazard ratio [HR] 1·80 [95% CI 1·18–2·75]) after adjusting for time to post-COVID-19 reassessment, sex, age, comorbidity burden, tumour characteristics, anticancer therapy, and COVID-19 severity. Among 466 patients on systemic anti-cancer therapy, 70 (15·0%) permanently discontinued therapy, and 178 (38·2%) resumed treatment with a dose or regimen adjustment. Permanent treatment discontinuations were independently associated with an increased risk of death (HR 3·53 [95% CI 1·45–8·59]), but dose or regimen adjustments were not (0·84 [0·35–2·02]). Interpretation: Sequelae post-COVID-19 affect up to 15% of patients with cancer and adversely affect survival and oncological outcomes after recovery. Adjustments to systemic anti-cancer therapy can be safely pursued in treatment-eligible patients. Funding: National Institute for Health Research Imperial Biomedical Research Centre and the Cancer Treatment and Research Trust

Spread of a SARS-CoV-2 variant through Europe in the summer of 2020.

Following its emergence in late 2019, the spread of SARS-CoV-21,2 has been tracked by phylogenetic analysis of viral genome sequences in unprecedented detail3–5. Although the virus spread globally in early 2020 before borders closed, intercontinental travel has since been greatly reduced. However, travel within Europe resumed in the summer of 2020. Here we report on a SARS-CoV-2 variant, 20E (EU1), that was identified in Spain in early summer 2020 and subsequently spread across Europe. We find no evidence that this variant has increased transmissibility, but instead demonstrate how rising incidence in Spain, resumption of travel, and lack of effective screening and containment may explain the variant’s success. Despite travel restrictions, we estimate that 20E (EU1) was introduced hundreds of times to European countries by summertime travellers, which is likely to have undermined local efforts to minimize infection with SARS-CoV-2. Our results illustrate how a variant can rapidly become dominant even in the absence of a substantial transmission advantage in favourable epidemiological settings. Genomic surveillance is critical for understanding how travel can affect transmission of SARS-CoV-2, and thus for informing future containment strategies as travel resumes. © 2021, The Author(s), under exclusive licence to Springer Nature Limited

Prevalence and impact of COVID-19 sequelae on treatment and survival of patients with cancer who recovered from SARS-CoV-2 infection: evidence from the OnCovid retrospective, multicentre registry study

Background: The medium-term and long-term impact of COVID-19 in patients with cancer is not yet known. In this study, we aimed to describe the prevalence of COVID-19 sequelae and their impact on the survival of patients with cancer. We also aimed to describe patterns of resumption and modifications of systemic anti-cancer therapy following recovery from SARS-CoV-2 infection. Methods: OnCovid is an active European registry study enrolling consecutive patients aged 18 years or older with a history of solid or haematological malignancy and who had a diagnosis of RT-PCR confirmed SARS-CoV-2 infection. For this retrospective study, patients were enrolled from 35 institutions across Belgium, France, Germany, Italy, Spain, and the UK. Patients who were diagnosed with SARS-CoV-2 infection between Feb 27, 2020, and Feb 14, 2021, and entered into the registry at the point of data lock (March 1, 2021), were eligible for analysis. The present analysis was focused on COVID-19 survivors who underwent clinical reassessment at each participating institution. We documented prevalence of COVID-19 sequelae and described factors associated with their development and their association with post-COVID-19 survival, which was defined as the interval from post-COVID-19 reassessment to the patients' death or last follow-up. We also evaluated resumption of systemic anti-cancer therapy in patients treated within 4 weeks of COVID-19 diagnosis. The OnCovid study is registered in ClinicalTrials.gov, NCT04393974. Findings: 2795 patients diagnosed with SARS-CoV-2 infection between Feb 27, 2020, and Feb 14, 2021, were entered into the study by the time of the data lock on March 1, 2021. After the exclusion of ineligible patients, the final study population consisted of 2634 patients. 1557 COVID-19 survivors underwent a formal clinical reassessment after a median of 22·1 months (IQR 8·4-57·8) from cancer diagnosis and 44 days (28-329) from COVID-19 diagnosis. 234 (15·0%) patients reported COVID-19 sequelae, including respiratory symptoms (116 [49·6%]) and residual fatigue (96 [41·0%]). Sequelae were more common in men (vs women; p=0·041), patients aged 65 years or older (vs other age groups; p=0·048), patients with two or more comorbidities (vs one or none; p=0·0006), and patients with a history of smoking (vs no smoking history; p=0·0004). Sequelae were associated with hospitalisation for COVID-19 (p&lt;0·0001), complicated COVID-19 (p&lt;0·0001), and COVID-19 therapy (p=0·0002). With a median post-COVID-19 follow-up of 128 days (95% CI 113-148), COVID-19 sequelae were associated with an increased risk of death (hazard ratio [HR] 1·80 [95% CI 1·18-2·75]) after adjusting for time to post-COVID-19 reassessment, sex, age, comorbidity burden, tumour characteristics, anticancer therapy, and COVID-19 severity. Among 466 patients on systemic anti-cancer therapy, 70 (15·0%) permanently discontinued therapy, and 178 (38·2%) resumed treatment with a dose or regimen adjustment. Permanent treatment discontinuations were independently associated with an increased risk of death (HR 3·53 [95% CI 1·45-8·59]), but dose or regimen adjustments were not (0·84 [0·35-2·02]). Interpretation: Sequelae post-COVID-19 affect up to 15% of patients with cancer and adversely affect survival and oncological outcomes after recovery. Adjustments to systemic anti-cancer therapy can be safely pursued in treatment-eligible patients