On sparsity, power-law and clustering properties of graphex processes

This paper investigates properties of the class of graphs based on exchangeable point processes. We provide asymptotic expressions for the number of edges, number of nodes and degree distributions, identifying four regimes: (i) a dense regime, (ii) a sparse almost dense regime, (iii) a sparse regime with power-law behaviour, and (iv) an almost extremely sparse regime. We show that under mild assumptions, both the global and local clustering coefficients converge to constants which may or may not be the same. We also derive a central limit theorem for the number of nodes. Finally, we propose a class of models within this framework where one can separately control the latent structure and the global sparsity/power-law properties of the graph

Bayesian nonparametrics for Sparse Dynamic Networks

We propose a Bayesian nonparametric prior for time-varying networks. To each node of the network is associated a positive parameter, modeling the sociability of that node. Sociabilities are assumed to evolve over time, and are modeled via a dynamic point process model. The model is able to (a) capture smooth evolution of the interaction between nodes, allowing edges to appear/disappear over time (b) capture long term evolution of the sociabilities of the nodes (c) and yield sparse graphs, where the number of edges grows subquadratically with the number of nodes. The evolution of the sociabilities is described by a tractable time-varying gamma process. We provide some theoretical insights into the model and apply it to three real world datasets.Comment: 10 pages, 8 figure

Asymptotic Analysis of Statistical Estimators related to MultiGraphex Processes under Misspecification

This article studies the asymptotic properties of Bayesian or frequentist estimators of a vector of parameters related to structural properties of sequences of graphs. The estimators studied originate from a particular class of graphex model introduced by Caron and Fox. The analysis is however performed here under very weak assumptions on the underlying data generating process, which may be different from the model of Caron and Fox or from a graphex model. In particular, we consider generic sparse graph models, with unbounded degree, whose degree distribution satisfies some assumptions. We show that one can relate the limit of the estimator of one of the parameters to the sparsity constant of the true graph generating process. When taking a Bayesian approach, we also show that the posterior distribution is asymptotically normal. We discuss situations where classical random graphs models such as configuration models, sparse graphon models, edge exchangeable models or graphon processes satisfy our assumptions

Clinical behavior and outcomes of breast cancer in young women with germline BRCA pathogenic variants

Càncer de mama; Genètica del càncerCáncer de mama; Genética del cáncerBreast cancer; Cancer geneticsYoung breast cancer (BC) patients carrying a germline BRCA pathogenic variant (mBRCA) have similar outcomes as non-carriers. However, the impact of the type of gene (BRCA1 vs. BRCA2) and hormone receptor status (positive [HR+] vs. negative [HR−]) on clinical behavior and outcomes of mBRCA BC remains largely unknown. This is an international, multicenter, hospital-based, retrospective cohort study that included mBRCA patients diagnosed, between January 2000 and December 2012, with stage I–III invasive early BC at age ≤40 years. From 30 centers worldwide, 1236 young mBRCA BC patients were included. Among 808 and 428 patients with mBRCA1 or mBRCA2, 191 (23.6%) and 356 (83.2%) had HR+tumors, respectively (P < 0.001). Median follow-up was 7.9 years. Second primary BC (P = 0.009) and non-BC malignancies (P = 0.02) were more frequent among mBRCA1 patients while distant recurrences were less frequent (P = 0.02). Irrespective of hormone receptor status, mBRCA1 patients had worse disease-free survival (DFS; adjusted HR = 0.76, 95% CI = 0.60–0.96), with no difference in distant recurrence-free interval (DRFI) and overall survival (OS). Patients with HR+ disease had more frequent distant recurrences (P < 0.001) and less frequent second primary malignancies (BC: P = 0.005; non-BC: P = 0.18). No differences in DFS and OS were observed according to hormone receptor status, with a tendency for worse DRFI (adjusted HR = 1.39, 95% CI = 0.94–2.05) in patients with HR+ BC. Type of mBRCA gene and hormone receptor status strongly impact BC clinical behavior and outcomes in mBRCA young patients. These results provide important information for patients’ counseling on treatment, prevention, and surveillance strategies.This study received partial financial support by grants from the Italian Ministry of Health - 5 × 1000 funds 2017 (no grant number), the Italian Association for Cancer Research (AIRC; MFAG 2020 ID 24698), and “Les Amis de l’Institut Bordet” foundation (no grant number). The funders had no role in the design and conduct of the study; collection, management, analysis, and interpretation of the data; preparation, review, or approval of the manuscript; and decision to submit the manuscript for publication. M.L. acknowledges the support from the European Society for Medical Oncology (ESMO) for a Translational Research Fellowship at the Institut Jules Bordet in Brussels (Belgium) at the time of study conduction. K.P. acknowledges the support from a predoctoral clinical ‘KOOR’ mandate from the University Hospitals Leuven (Leuven, Belgium). F.P.D. acknowledges the support for a postdoctoral clinical mandate (2017-034) from the not-for-profit organization ‘Foundation Against Cancer’ (Brussels, Belgium). A.H.P. acknowledges the support from Susan G. Komen and Breast Cancer Research Foundation (BCRF). J.H. acknowledges the support from the Carlos III National Health Institute funded by FEDER funds—a way to build Europe (PI16/11363). This research was presented in the Poster Spotlight session at the 2020 San Antonio Breast Cancer Symposium (SABCS), San Antonio, TX, United States of America, on 8–12 December 2020

Botany, Genetics and Ethnobotany: A Crossed Investigation on the Elusive Tapir's Diet in French Guiana

While the populations of large herbivores are being depleted in many tropical rainforests, the importance of their trophic role in the ecological functioning and biodiversity of these ecosystems is still not well evaluated. This is due to the outstanding plant diversity that they feed upon and the inherent difficulties involved in observing their elusive behaviour. Classically, the diet of elusive tropical herbivores is studied through the observation of browsing signs and macroscopic analysis of faeces or stomach contents. In this study, we illustrate that the original coupling of classic methods with genetic and ethnobotanical approaches yields information both about the diet diversity, the foraging modalities and the potential impact on vegetation of the largest terrestrial mammal of Amazonia, the lowland tapir. The study was conducted in the Guianan shield, where the ecology of tapirs has been less investigated. We identified 92 new species, 51 new genera and 13 new families of plants eaten by tapirs. We discuss the relative contribution of our different approaches, notably the contribution of genetic barcoding, used for the first time to investigate the diet of a large tropical mammal, and how local traditional ecological knowledge is accredited and valuable for research on the ecology of elusive animals

Feminizing care pathways: Mixed‐methods study of reproductive options, decision making, pregnancy, post‐natal care and parenting amongst women with kidney disease

Aims: To identify the needs, experiences and preferences of women with kidney disease in relation to their reproductive health to inform development of shared decision‐making interventions. Design: UK‐wide mixed‐methods convergent design (Sep 20–Aug 21). Methods: Online questionnaire (n = 431) with validated components. Purposively sampled semi‐structured interviews (n = 30). Patient and public input throughout. Findings: Kidney disease was associated with defeminization, negatively affecting current (sexual) relationships and perceptions of future life goals. There was little evidence that shared decision making was taking place. Unplanned pregnancies were common, sometimes influenced by poor care and support and complicated systems. Reasons for (not) wanting children varied. Complicated pregnancies and miscarriages were common. Women often felt that it was more important to be a “good mother” than to address their health needs, which were often unmet and unrecognized. Impacts of pregnancy on disease and options for alternates to pregnancy were not well understood. Conclusion: The needs and reproductive priorities of women are frequently overshadowed by their kidney disease. High‐quality shared decision‐making interventions need to be embedded as routine in a feminized care pathway that includes reproductive health. Research is needed in parallel to examine the effectiveness of interventions and address inequalities. Impact: We do not fully understand the expectations, needs, experiences and preferences of women with kidney disease for planning and starting a family or deciding not to have children. Women lack the knowledge, resources and opportunities to have high‐quality conversations with their healthcare professionals. Decisions are highly personal and related to a number of health, social and cultural factors; individualized approaches to care are essential. Healthcare services need to be redesigned to ensure that women are able to make informed choices about pregnancy and alternative routes to becoming a parent. Patient or Public Contribution: The original proposal for this research came from listening to the experiences of women in clinic who reported unmet needs and detailed experiences of their pregnancies (positive and negative). A patient group was involved in developing the funding application and helped to refine the objectives by sharing their experiences. Two women who are mothers living with kidney disease were co‐opted as core members of the research team. We hosted an interim findings event and invited patients and wider support services (adoption, fertility, surrogacy, education and maternal chronic kidney disease clinics) from across the UK to attend. We followed the UK national standards for patient and public involvement throughout

SPINK7 expression changes accompanied by HER2, P53 and RB1 can be relevant in predicting oral squamous cell carcinoma at a molecular level

The oral squamous cell carcinoma (OSCC), which has a high morbidity rate, affects patients worldwide. Changes in SPINK7 in precancerous lesions could promote oncogenesis. Our aim was to evaluate SPINK7 as a potential molecular biomarker which predicts OSCC stages, compared to: HER2, TP53, RB1, NFKB and CYP4B1. This study used oral biopsies from three patient groups: dysplasia (n = 33), less invasive (n = 28) and highly invasive OSCC (n = 18). The control group consisted of clinically suspicious cases later to be confirmed as normal mucosa (n = 20). Gene levels of SPINK7, P53, RB, NFKB and CYP4B1 were quantified by qPCR. SPINK7 levels were correlated with a cohort of 330 patients from the TCGA. Also, SPINK7, HER2, TP53, and RB1, were evaluated by immunohistofluorescence. One-way Kruskal–Wallis test and Dunn's post-hoc with a p < 0.05 significance was used to analyze data. In OSCC, the SPINK7 expression had down regulated while P53, RB, NFKB and CYP4B1 had up regulated (p < 0.001). SPINK7 had also diminished in TCGA patients (p = 2.10e-6). In less invasive OSCC, SPINK7 and HER2 proteins had decreased while TP53 and RB1 had increased with respect to the other groups (p < 0.05). The changes of SPINK7 accompanied by HER2, P53 and RB1 can be used to classify the molecular stage of OSCC lesions allowing a diagnosis at molecular and histopathological levels.Fil: Pennacchiotti, Graciela Laura. Universidad de Chile; ChileFil: Valdes Garrido, Fabio. Instituto Nacional del Cáncer; ChileFil: González Arriaga, Wilfredo Alejandro. Universidad de Valparaíso; ChileFil: Montes, Héctor Federico. Universidad Nacional de Cuyo. Facultad de Odontologia; ArgentinaFil: Parra, Judith Maria Roxana. Universidad Nacional de Cuyo. Facultad de Odontologia; ArgentinaFil: Guida, Valeria Andrea. Universidad Nacional de Cuyo. Facultad de Odontologia; ArgentinaFil: Gomez, Silvina Esther. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Medicina y Biología Experimental de Cuyo; ArgentinaFil: Guerrero Gimenez, Martin Eduardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Medicina y Biología Experimental de Cuyo; ArgentinaFil: Fernandez Muñoz, Juan Manuel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Medicina y Biología Experimental de Cuyo; ArgentinaFil: Zoppino, Felipe Carlos Martin. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Medicina y Biología Experimental de Cuyo; ArgentinaFil: Caron, Ruben Walter. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Medicina y Biología Experimental de Cuyo; ArgentinaFil: Ezquer, Marcelo Eduardo. Universidad del Desarrollo; ChileFil: Ramires Fernández, Ricardo. Universidad Mayor; ChileFil: Bruna, Flavia Alejandra. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Medicina y Biología Experimental de Cuyo; Argentina. Universidad Nacional de Cuyo. Facultad de Odontologia; Argentin