A deep learning approach to halo merger tree construction

A key ingredient for semi-analytic models of galaxy formation is the mass assembly history of haloes, encoded in a tree structure. The most commonly used method to construct halo merger histories is based on the outcomes of high-resolution, computationally intensive N-body simulations. We show that machine learning (ML) techniques, in particular Generative Adversarial Networks (GANs), are a promising new tool to tackle this problem with a modest computational cost and retaining the best features of merger trees from simulations. We train our GAN model with a limited sample of merger trees from the Evolution and Assembly of GaLaxies and their Environments (EAGLE) simulation suite, constructed using two halo finders-tree builder algorithms: SUBFIND-D-TREES and ROCKSTAR-ConsistentTrees. Our GAN model successfully learns to generate well-constructed merger tree structures with high temporal resolution, and to reproduce the statistical features of the sample of merger trees used for training, when considering up to three variables in the training process. These inputs, whose representations are also learned by our GAN model, are mass of the halo progenitors and the final descendant, progenitor type (main halo or satellite), and distance of a progenitor to that in the main branch. The inclusion of the latter two inputs greatly improves the final learned representation of the halo mass growth history, especially for SUBFIND-like ML trees. When comparing equally sized samples of ML merger trees with those of the EAGLE simulation, we find better agreement for SUBFIND-like ML trees. Finally, our GAN-based framework can be utilized to construct merger histories of low-and intermediate-mass haloes, the most abundant in cosmological simulations.Fil: Robles, Sandra. Universidad Autónoma de Madrid; España. Kings College London (kcl); . University of Melbourne; AustraliaFil: Gómez, Jonathan S. Universidad Católica de Chile; Chile. Universidad Autónoma de Madrid; España. Pontificia Universidad Católica de Chile; ChileFil: Ramírez Rivera, Adín. University of Oslo; NoruegaFil: Padilla, Nelson David. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Astronomía Teórica y Experimental. Universidad Nacional de Córdoba. Observatorio Astronómico de Córdoba. Instituto de Astronomía Teórica y Experimental; ArgentinaFil: Dujovne, Diego. Universidad Diego Portales; Chil

A comparative analysis of lung function and spirometry parameters in genotype-controlled natives living at low and high altitude

Background: The reference values for lung function are associated to anatomical and lung morphology parameters, but anthropometry it is not the only influencing factor: altitude and genetics are two important agents affecting respiratory physiology. Altitude and its influence on respiratory function has been studied independently of genetics, considering early and long-term acclimatization. Objective: The objective of this study is to evaluate lung function through a spirometry study in autochthonous Kichwas permanently living at low and high-altitude. Methodology: A cross-sectional study of spirometry differences between genetically matched lowland Kichwas from Limoncocha (230 m) at Amazonian basin and high-altitude Kichwas from Oyacachi (3,180 m) in Andean highlands. Chi-square method was used to analyze association or independence of categorical variables, while Student's t test was applied to comparison of means within quantitative variables. ANOVA, or in the case that the variables didn't meet the criteria of normality, Kruskal Wallis test were used to compare more than two groups. Results: People from Oyacachi (high altitude) showed a higher predicted values than those from Limonocha (low altitude). The FVC and the FEV1 were significantly greater among highlanders than lowlanders (p value < 0.001). The FEV1/FVC was significantly higher among lowlanders than highlanders for men and women. A restrictive pattern was found in 12.9% of the participants. Conclusion: Residents of Oyacachi had greater lung capacity than their peers from Limoncocha, a finding physiologically plausible according to published literature. When analyzing the spirometric patterns obtained in these populations, it was evident that no person had an obstructive pattern, while on the other hand, the restrictive pattern appeared in Limoncocha and Oyacachi populations in 12.9% although it is clear that there is a predominance of this in the individuals belonging to Limoncocha

Hematological parameters, lipid profile and cardiovascular risk analysis among genotype-controlled indigenous Kichwa men and women living at low and high altitudes

Introduction: Human adaptation to high-altitude is due to characteristic adjustments at every physiological level. Differences in lipid profile and cardiovascular risk factors in altitude dwellers have been previously explored, nevertheless there are no reports available on genotype-controlled matches among different altitude adapted indigenous populations. Objective: To explore the possible differences in plasma lipid profile and cardiovascular risk among autochthonous Kiwcha people inhabitants of low and high-altitude locations. Methodology: A cross-sectional analysis of plasmatic lipid profiles and cardiovascular risk factors in lowland Kiwchas from Limoncocha (230 m) and high-altitude Kiwchas from Oyacachi (3,800 m). Results: In the low altitude group, 66% were women (n=78) and 34% (n=40) were men, while at high altitude, 59% (n=56) were women and 41% (n=41%) were men. We found the proportion of overweight and obese individuals to be higher among low altitude dwellers (p<0.05). Red blood cells (RBC), Hemoglobin concentration and SpO2% were higher among high altitude dwellers and erythrocyte's size was found to be smaller at high altitude .The group located at low altitude showed also lower levels of plasma cholesterol, LDL and HDL but most of these differences are not influenced by gender or elevation. Conclusions: Living at altitude elicits well-known adaptive physiological changes such as erythrocyte count, hemoglobin concentration, hematocrit, and serum glucose. We report also clinical differences in the plasma lipid profile, with higher levels of cholesterol and high density and low-density lipoproteins in Andes Mountain inhabitants versus their Amazonian basin peers. Despite we found altered underlying physiological pathways between the populations, this does not allow in a different cardiovascular risk

Dietary antioxidant intake is inversely associated with 2,3-dinor oxylipin metabolites, the major excreted oxylipins in overweight and obese subjects

Cardiometabolic disease risk factors, including obesity, insulin resistance, high blood pressure, and dyslipidemia, are associated with elevated oxidative stress biomarkers like oxylipins. Increased adiposity by itself induces various isomers of this oxidized lipid family, while dietary polyphenols show benefits in its regulation. Previously, we showed that specific co-abundant microorganisms characterized the gut microbiota of Colombians and associated differentially with diet, lifestyle, obesity, and cardiometabolic health status, which led us to hypothesize that urinary oxylipins would reflect the intensity of oxidative metabolism linked to gut microbiota dysbiosis. Thus, we selected a convenience sample of 105 participants (age: 40.2 ± 11.9 years, 47.6% women), grouped according to microbiota, cardiometabolic health status, and body mass index (BMI); and evaluated 33 urinary oxylipins by HPLC-QqQ-MS/MS (e.g., isoprostanes, prostaglandins, and metabolites), paired with anthropometry and blood chemistry information and dietary antioxidants estimated from a 24-h food recall. In general, oxylipins did not show differences among individuals who differed in gut microbiota. While the unmetabolized oxylipin levels were not associated with BMI, the total content of oxylipin metabolites was highest in obese and cardiometabolically abnormal subjects (e.g., insulin resistant), mainly by prostaglandin-D (2,3-dinor-11β-PGF) and 15-F-IsoPs (2,3-dinor-15-F-IsoP and 2,3-dinor-15-epi-15-F-IsoP) metabolites. The total polyphenol intake in this cohort was 1070 ± 627 mg/day. After adjusting for body weight, the polyphenol intake was significantly higher in lean than overweight and showed an inverse association with dinor-oxylipin levels in principal component analysis. These results suggest that the 2,3-dinor-oxylipins could be more specific biomarkers associated with BMI than their parent oxylipins and that are sensitive to be regulated by dietary antioxidants.The authors thank the volunteers who agreed to participate in this study, the Colombian Ministry of science, technology, and innovation (Minciencias; grant number 832-2018), and Grupo Empresarial Nutresa. They also thank the Ibero-American Programme for Science, Technology and Development (CYTED) – Action 112RT0460 CORNUCOPIA networ

Comprehensive comparative analysis of RNA sequencing methods for degraded or low input samples

RNA-Seq is an effective method to study the transcriptome, but can be difficult to apply to scarce or degraded RNA from fixed clinical samples, rare cell populations, or cadavers. Recent studies have proposed several methods for RNA-Seq of low quality and/or low quantity samples, but their relative merits have not been systematically analyzed. Here, we compare five such methods using metrics relevant to transcriptome annotation, transcript discovery, and gene expression. Using a single human RNA sample, we constructed and sequenced ten libraries with these methods and two control libraries. We find that the RNase H method performed best for low quality RNA, and confirmed this with actual degraded samples. RNase H can even effectively replace oligo (dT) based methods for standard RNA-Seq. SMART and NuGEN had distinct strengths for low quantity RNA. Our analysis allows biologists to select the most suitable methods and provides a benchmark for future method development

A Neptune-mass Planet Orbiting the Nearby G Dwarf HD16417

Precision Doppler measurements from an intensive 48 night "Rocky Planet Search" observing campaign on the Anglo-Australian Telescope (AAT) have revealed the presence of a low-mass exoplanet orbiting the G1 dwarf HD16417. Subsequent Doppler observations with the AAT, as well as independent observations obtained by the Keck Planet Search, have confirmed this initial detection and refine the orbital parameters to period 17.24+/-0.01 d, eccentricity 0.20+/-0.09, orbital semi-major axis 0.14+/-0.01 AU and minimum planet mass 22.1+/-2.0 Mearth. HD 16417 raises the number of published exoplanets with minimum masses of less than 25 Mearth to eighteen. Interestingly, the distribution of detected sub-25 Mearth planets over the spectral types G, K and M is almost uniform. The detection of HD 16417b by an intensive observing campaign clearly demonstrates the need for extended and contiguous observing campaigns when aiming to detect low-amplitude Doppler planets in short period orbits. Perhaps most critically it demonstrates that the search for low-mass Doppler planets will eventually require these traditional "bright-time" projects to extend throughout dark lunations.Comment: To appear in Ap

The Anglo-Australian Planet Search. XXII. Two New Multi-Planet Systems

We report the detection of two new planets from the Anglo-Australian Planet Search. These planets orbit two stars each previously known to host one planet. The new planet orbiting HD 142 has a period of 6005\pm427 days, and a minimum mass of 5.3M_Jup. HD142c is thus a new Jupiter analog: a gas-giant planet with a long period and low eccentricity (e = 0.21 \pm 0.07). The second planet in the HD 159868 system has a period of 352.3\pm1.3 days, and m sin i=0.73\pm0.05 M_Jup. In both of these systems, including the additional planets in the fitting process significantly reduced the eccentricity of the original planet. These systems are thus examples of how multiple-planet systems can masquerade as moderately eccentric single-planet systems.Comment: 31 pages, 8 figures, accepted for publication in Ap

Amphibians in Zootaxa: 20 years documenting the global diversity of frogs, salamanders, and caecilians

Zootaxa is a mega-journal that since its inception, 20 years ago, has contributed to the documentation of the planet?s biodiversity. Its role concerning terrestrial vertebrates has been crucial especially for amphibians, which are the most threatened class of vertebrates. As current editors of the Amphibia section, we reviewed the state of knowledge of taxonomic publications on amphibians over the last two decades (from 2001 to 2020). Our review reveals that 2,533 frogs, 259 salamanders, and 55 caecilians have been named in these 20 years, mainly in the tropical regions of South America, Asia, and Africa. More than half (57%) of these species descriptions were published in only 10 journals. At least 827 species of the new amphibians (29% of the total) were described in Zootaxa. This mega-journal has served also as a place of publication for monographs and systematic reviews, in addition to short articles documenting the vocalizations of anurans and the morphology of embryos and larvae. Its efficient evaluation process, the freedom of manuscript length, including full-color figures, and free of cost for the authors, has made Zootaxa a favorite for amphibian researchers. In an era of accelerating rates of biodiversity loss, documenting, describing, naming, and proposing evolutionary scenarios for species is, more than ever, an urgent task.Fil: Rivera Correa, Mauricio. Universidad de Antioquia; ColombiaFil: Baldo, Juan Diego. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas | Universidad Nacional de Misiones. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas; ArgentinaFil: Vera Candioti, María Florencia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico - Tucumán. Unidad Ejecutora Lillo; ArgentinaFil: Goyannes Dill Orrico, Victor. Universidade Estadual de Santa Cruz; BrasilFil: Blackburn, David C.. University Of Florida. Florida Museum Of History; Estados UnidosFil: Castroviejo Fisher, Santiago. Pontificia Universidade Católica do Rio Grande do Sul; BrasilFil: Chan, Kin Onn. National University of Singapore; SingapurFil: Gambale, Priscilla. Universidade Federal de Goiás; BrasilFil: Gower, David J.. Natural History Museum; Reino UnidoFil: Quah, Evan S. H.. National University of Singapore; SingapurFil: Rowley, Jodi J. L.. University of New South Wales; AustraliaFil: Twomey, Evan. Goethe Universitat Frankfurt; AlemaniaFil: Vences, Miguel. Technische Universitat Carolo Wilhelmina Zu Braunschweig.; Alemani