Hidden geometric correlations in real multiplex networks

Real networks often form interacting parts of larger and more complex systems. Examples can be found in different domains, ranging from the Internet to structural and functional brain networks. Here, we show that these multiplex systems are not random combinations of single network layers. Instead, they are organized in specific ways dictated by hidden geometric correlations between the individual layers. We find that these correlations are strong in different real multiplexes, and form a key framework for answering many important questions. Specifically, we show that these geometric correlations facilitate: (i) the definition and detection of multidimensional communities, which are sets of nodes that are simultaneously similar in multiple layers; (ii) accurate trans-layer link prediction, where connections in one layer can be predicted by observing the hidden geometric space of another layer; and (iii) efficient targeted navigation in the multilayer system using only local knowledge, which outperforms navigation in the single layers only if the geometric correlations are sufficiently strong. Our findings uncover fundamental organizing principles behind real multiplexes and can have important applications in diverse domains.Comment: Supplementary Materials available at http://www.nature.com/nphys/journal/v12/n11/extref/nphys3812-s1.pd

Programmed cell senescence during mammalian embryonic development

Cellular senescence disables proliferation in damaged cells, and it is relevant for cancer and aging. Here, we show that senescence occurs during mammalian embryonic development at multiple locations, including the mesonephros and the endolymphatic sac of the inner ear, which we have analyzed in detail. Mechanistically, senescence in both structures is strictly dependent on p21, but independent of DNA damage, p53, or other cell-cycle inhibitors, and it is regulated by the TGF-beta/SMAD and PI3K/FOXO pathways. Developmentally programmed senescence is followed by macrophage infiltration, clearance of senescent cells, and tissue remodeling. Loss of senescence due to the absence of p21 is partially compensated by apoptosis but still results in detectable developmental abnormalities. Importantly, the mesonephros and endolymphatic sac of human embryos also show evidence of senescence. We conclude that the role of developmentally programmed senescence is to promote tissue remodeling and propose that this is the evolutionary origin of damage-induced senescence

Structural insights into ring-building motif domains involved in bacterial sporulation.

Components of specialized secretion systems, which span the inner and outer membranes in Gram-negative bacteria, include ring-forming proteins whose oligomerization was proposed to be promoted by domains called RBM for "Ring-Building Motifs". During spore formation in Gram-positive bacteria, a transport system called the SpoIIIA-SpoIIQ complex also assembles in the double membrane that surrounds the forespore following its endocytosis by the mother cell. The presence of RBM domains in some of the SpoIIIA proteins led to the hypothesis that they would assemble into rings connecting the two membranes and form a conduit between the mother cell and forespore. Among them, SpoIIIAG forms homo-oligomeric rings in vitro but the oligomerization of other RBM-containing SpoIIIA proteins, including SpoIIIAH, remains to be demonstrated. In this work, we identified RBM domains in the YhcN/YlaJ family of proteins that are not related to the SpoIIIA-SpoIIQ complex. We solved the crystal structure of YhcN from Bacillus subtilis, which confirmed the presence of a RBM fold, flanked by additional secondary structures. As the protein did not show any oligomerization ability in vitro, we investigated the structural determinants of ring formation in SpoIIIAG, SpoIIIAH and YhcN. We showed that in vitro, the conserved core of RBM domains alone is not sufficient for oligomerization while the β-barrel forming region in SpoIIIAG forms rings on its own. This work suggests that some RBMs might indeed participate in the assembly of homomeric rings but others might have evolved toward other functions

Integrated fecal microbiome–metabolome signatures reflect stress and serotonin metabolism in irritable bowel syndrome

To gain insight into the complex microbiome-gut-brain axis in irritable bowel syndrome (IBS) several modalities of biological and clinical data must be combined. We aimed to identify profiles of faecal microbiota and metabolites associated with IBS and to delineate specific phenotypes of IBS that represent potential pathophysiological mechanisms. Faecal metabolites were measured using proton Nuclear Magnetic Resonance (1H-NMR) spectroscopy and gut microbiome using Shotgun Metagenomic Sequencing (MGS) in a combined dataset of 142 IBS patients and 120 healthy controls (HC) with extensive clinical, biological and phenotype information. Data were analysed using support vector classification and regression and kernel t-SNE. Microbiome and metabolome profiles could distinguish IBS and HC with an area-under-the-receiver-operator-curve (AUC) of 77.3% and 79.5%, respectively, but this could be improved by combining microbiota and metabolites to 83.6%. No significant differences in predictive ability of the microbiome-metabolome data were observed between the three classical, stool pattern-based, IBS subtypes. However, unsupervised clustering showed distinct subsets of IBS patients based on faecal microbiome-metabolome data. These clusters could be related plasma levels of serotonin and its metabolite 5-hydroxyindoleacetate, effects of psychological stress on gastrointestinal symptoms, onset of IBS after stressful events, medical history of previous abdominal surgery, dietary caloric intake and IBS symptom duration. Furthermore, pathways in metabolic reaction networks were integrated with microbiota data, that reflect the host-microbiome interactions in IBS. The identified microbiome-metabolome signatures for IBS, associated with altered serotonin metabolism and unfavourable stress-response related to gastrointestinal symptoms, support the microbiota-gut-brain link in the pathogenesis of IBS

Evaluation of a Mixed Meal Test for Diagnosis and Characterization of PancrEaTogEniC DiabeTes Secondary to Pancreatic Cancer and Chronic Pancreatitis: Rationale and Methodology for the DETECT Study From the Consortium for the Study of Chronic Pancreatitis, Diabetes, and Pancreatic Cancer

Pancreatogenic diabetes mellitus is most commonly the result of chronic pancreatitis but can also occur secondary to pancreatic cancer. The early identification of pancreatogenic diabetes and distinction from the more prevalent type 2 diabetes are clinically significant; however, currently, there is no validated method to differentiate these diabetes subtypes. We describe a study, "Evaluation of a Mixed Meal Test for Diagnosis and Characterization of PancrEaTogEniC DiabeTes Secondary to Pancreatic Cancer and Chronic Pancreatitis: the DETECT study," that seeks to address this knowledge gap. The DETECT study is a multicenter study that will examine differences in hormone and glucose excursions after a mixed meal test. The study will also create a biorepository that will be used to evaluate novel diagnostic biomarkers for differentiating these diabetes subtypes

Primary angiosarcoma of the ovary with prominent fibrosis of the ovarian stroma. Case report of an 81-year old patient

Primary angiosarcoma of the ovary (AS) is a rare entity with only 31 reported cases. The majority are pure angiosarcomas, the remainder are associated either with teratomas or conventional epithelial tumors. More than 50% of ovarian AS are disseminated at the time of diagnosis, the minority is detected in stage I. The prognosis of ovarian angiosarcoma in general is poor. Most reports refer to younger individuals, aged from 7 to 46 years, and only 2 case reports could be found for patients older than 64 years. Here we present a very unusual case of angiosarcoma in a 81-year-old patient

Uso de bebederos artificiales por el sereque centroamericano (Dasyprocta punctata) en la reserva de la biosfera de Calakmul, México

Objective: To describe the use of artificial drinking fountains by the central American Agouti (Dasyprocta punctata) in the Calakmul Biosphere Reserve. Design/methodology/approach: Eight artificial drinking fountains were monitored each one with a trap camera with the aim to estimate the relative abundance index and activity patterns of visits to the drinking fountains. The monitoring was during the dry season of 2019. The analyzes were carried out with the InfoStat and R programs. Results: From January to May 2019, with a sampling effort of 1121 days/camera, average abundance of 160.08±85.44. The pattern of visits to the drinking troughs was mainly diurnal. Limitations of the study/implications: The use of trap cameras in the artificial drinking fountains allows us to know the extent of habitat modification in the Calakmul Biosphere Reserve. Findings/conclusions: The implementation of artificial drinking fountains in the RBC during the dry season was a successful action to mitigate the effects of water scarcity. The use of the water resource by the Central American Agouti in artificial drinking fountains was constant, other species of mammals and birds were also observed making use of artificial drinking fountains.Objetivo: Describir el uso de bebederos artificiales por el sereque (Dasyprocta punctata) en la Reserva de la Biosfera de Calakmul. Diseño/metodología/aproximación: Se monitorearon ocho bebederos artificiales cada uno con una cámara trampa con la finalidad de estimar el índice de abundancia relativa y los patrones de actividad de visitas a los bebederos. El monitoreo fue durante la temporada de secas del 2019. Los análisis se realizaron con los programas R e InfoStat. Resultado: De enero a mayo de 2019, con un esfuerzo de muestreo fue de 1121 días/cámara, abundancia promedio de 160.08±85.44. El patrón de visitas a los bebederos fue principalmente diurno. Limitaciones/implicaciones: El uso de cámaras trampa en los bebederos artificiales nos permite conocer los alcances en la modificación del hábitat en la Reserva de la Biosfera de Calakmul (RBC). Hallazgos/conclusiones: La implementación de bebederos artificiales en la RBC durante la temporada de seca fue una acción de éxito para mitigar los efectos de la escases de agua. El aprovechamiento del recurso agua por el sereque en los bebederos artificiales fue constante, también se observaron otras especies de mamíferos y aves haciendo uso de los bebederos artificiales

World input-output network

Production systems, traditionally analyzed as almost independent national systems, are increasingly connected on a global scale. Only recently becoming available, the World Input-Output Database (WIOD) is one of the first efforts to construct the global multi-regional input-output (GMRIO) tables. By viewing the world input-output system as an interdependent network where the nodes are the individual industries in different economies and the edges are the monetary goods flows between industries, we analyze respectively the global, regional, and local network properties of the so-called world input-output network (WION) and document its evolution over time. At global level, we find that the industries are highly but asymmetrically connected, which implies that micro shocks can lead to macro fluctuations. At regional level, we find that the world production is still operated nationally or at most regionally as the communities detected are either individual economies or geographically well defined regions. Finally, at local level, for each industry we compare the network-based measures with the traditional methods of backward linkages. We find that the network-based measures such as PageRank centrality and community coreness measure can give valuable insights into identifying the key industries