Giant tortoise genomes provide insights into longevity and age-related disease

© 2018, The Author(s), under exclusive licence to Springer Nature Limited. Giant tortoises are among the longest-lived vertebrate animals and, as such, provide an excellent model to study traits like longevity and age-related diseases. However, genomic and molecular evolutionary information on giant tortoises is scarce. Here, we describe a global analysis of the genomes of Lonesome George—the iconic last member of Chelonoidis abingdonii—and the Aldabra giant tortoise (Aldabrachelys gigantea). Comparison of these genomes with those of related species, using both unsupervised and supervised analyses, led us to detect lineage-specific variants affecting DNA repair genes, inflammatory mediators and genes related to cancer development. Our study also hints at specific evolutionary strategies linked to increased lifespan, and expands our understanding of the genomic determinants of ageing. These new genome sequences also provide important resources to help the efforts for restoration of giant tortoise populations

Constraints on dark matter to dark radiation conversion in the late universe with DES-Y1 and external data

84siWe study a class of decaying dark matter models as a possible resolution to the observed discrepancies between early- and late-time probes of the universe. This class of models, dubbed DDM, characterizes the evolution of comoving dark matter density with two extra parameters. We investigate how DDM affects key cosmological observables such as the CMB temperature and matter power spectra. Combining 3x2pt data from Year 1 of the Dark Energy Survey,Planck-2018 CMB temperature and polarization data, Supernova (SN) Type Ia data from Pantheon, and BAO data from BOSS DR12, MGS and 6dFGS, we place new constraints on the amount of dark matter that has decayed and the rate with which it converts to dark radiation. The fraction of the decayed dark matter in units of the current amount of dark matter, $zeta$, is constrained at 68% confidence level to be <0.32 for DES-Y1 3x2pt data, <0.030 for CMB+SN+BAO data, and <0.037 for the combined dataset. The probability that the DES and CMB+SN+BAO datasets are concordant increases from 4% for the $Lambda$CDM model to 8% (less tension) for DDM. Moreover, tension in $S_8=sigma_8sqrt{Omega_m/0.3}$ between DES-Y1 3x2pt and CMB+SN+BAO is reduced from 2.3$sigma$ to 1.9$sigma$. We find no reduction in the Hubble tension when the combined data is compared to distance-ladder measurements in the DDM model. The maximum-posterior goodness-of-fit statistics of DDM and $Lambda$CDM are comparable, indicating no preference for the DDM cosmology over $Lambda$CDM....partially_openopenChen, Angela; Huterer, Dragan; Lee, Sujeong; Ferté, Agnès; Weaverdyck, Noah; Alonso Alves, Otavio; Leonard, C. Danielle; MacCrann, Niall; Raveri, Marco; Porredon, Anna; Di Valentino, Eleonora; Muir, Jessica; Lemos, Pablo; Liddle, Andrew; Blazek, Jonathan; Campos, Andresa; Cawthon, Ross; Choi, Ami; Dodelson, Scott; Elvin-Poole, Jack; Gruen, Daniel; Ross, Ashley; Secco, Lucas F.; Sevilla, Ignacio; Sheldon, Erin; Troxel, Michael A.; Zuntz, Joe; Abbott, Tim; Aguena, Michel; Allam, Sahar; Annis, James; Avila, Santiago; Bertin, Emmanuel; Bhargava, Sunayana; Bridle, Sarah; Brooks, David; Carnero Rosell, Aurelio; Carrasco Kind, Matias; Carretero, Jorge; Costanzi, Matteo; Crocce, Martin; da Costa, Luiz; Elidaiana da Silva Pereira, Maria; Davis, Tamara; Doel, Peter; Eifler, Tim; Ferrero, Ismael; Fosalba, Pablo; Frieman, Josh; Garcia-Bellido, Juan; Gaztanaga, Enrique; Gerdes, David; Gruendl, Robert; Gschwend, Julia; Gutierrez, Gaston; Hinton, Samuel; Hollowood, Devon L.; Honscheid, Klaus; Hoyle, Ben; James, David; Jarvis, Mike; Kuehn, Kyler; Lahav, Ofer; Maia, Marcio; Marshall, Jennifer; Menanteau, Felipe; Miquel, Ramon; Morgan, Robert; Palmese, Antonella; Paz-Chinchon, Francisco; Plazas Malagón, Andrés; Roodman, Aaron; Sanchez, Eusebio; Scarpine, Vic; Schubnell, Michael; Serrano, Santiago; Smith, Mathew; Suchyta, Eric; Tarle, Gregory; Thomas, Daniel; To, Chun-Hao; Varga, Tamas Norbert; Weller, Jochen; Wilkinson, ReeseChen, Angela; Huterer, Dragan; Lee, Sujeong; Ferté, Agnès; Weaverdyck, Noah; Alonso Alves, Otavio; Leonard, C. Danielle; Maccrann, Niall; Raveri, Marco; Porredon, Anna; Di Valentino, Eleonora; Muir, Jessica; Lemos, Pablo; Liddle, Andrew; Blazek, Jonathan; Campos, Andresa; Cawthon, Ross; Choi, Ami; Dodelson, Scott; Elvin-Poole, Jack; Gruen, Daniel; Ross, Ashley; Secco, Lucas F.; Sevilla, Ignacio; Sheldon, Erin; Troxel, Michael A.; Zuntz, Joe; Abbott, Tim; Aguena, Michel; Allam, Sahar; Annis, James; Avila, Santiago; Bertin, Emmanuel; Bhargava, Sunayana; Bridle, Sarah; Brooks, David; Carnero Rosell, Aurelio; Carrasco Kind, Matias; Carretero, Jorge; Costanzi, Matteo; Crocce, Martin; da Costa, Luiz; Elidaiana da Silva Pereira, Maria; Davis, Tamara; Doel, Peter; Eifler, Tim; Ferrero, Ismael; Fosalba, Pablo; Frieman, Josh; Garcia-Bellido, Juan; Gaztanaga, Enrique; Gerdes, David; Gruendl, Robert; Gschwend, Julia; Gutierrez, Gaston; Hinton, Samuel; Hollowood, Devon L.; Honscheid, Klaus; Hoyle, Ben; James, David; Jarvis, Mike; Kuehn, Kyler; Lahav, Ofer; Maia, Marcio; Marshall, Jennifer; Menanteau, Felipe; Miquel, Ramon; Morgan, Robert; Palmese, Antonella; Paz-Chinchon, Francisco; Plazas Malagón, Andrés; Roodman, Aaron; Sanchez, Eusebio; Scarpine, Vic; Schubnell, Michael; Serrano, Santiago; Smith, Mathew; Suchyta, Eric; Tarle, Gregory; Thomas, Daniel; Chun-Hao, To; Varga, Tamas Norbert; Weller, Jochen; Wilkinson, Rees

Pervasive gaps in Amazonian ecological research

Biodiversity loss is one of the main challenges of our time,1,2 and attempts to address it require a clear un derstanding of how ecological communities respond to environmental change across time and space.3,4 While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes,5–7 vast areas of the tropics remain understudied.8–11 In the American tropics, Amazonia stands out as the world’s most diverse rainforest and the primary source of Neotropical biodiversity,12 but it remains among the least known forests in America and is often underrepre sented in biodiversity databases.13–15 To worsen this situation, human-induced modifications16,17 may elim inate pieces of the Amazon’s biodiversity puzzle before we can use them to understand how ecological com munities are responding. To increase generalization and applicability of biodiversity knowledge,18,19 it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple or ganism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region’s vulnerability to environmental change. 15%–18% of the most ne glected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lostinfo:eu-repo/semantics/publishedVersio

Pervasive gaps in Amazonian ecological research

Biodiversity loss is one of the main challenges of our time,1,2 and attempts to address it require a clear understanding of how ecological communities respond to environmental change across time and space.3,4 While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes,5,6,7 vast areas of the tropics remain understudied.8,9,10,11 In the American tropics, Amazonia stands out as the world's most diverse rainforest and the primary source of Neotropical biodiversity,12 but it remains among the least known forests in America and is often underrepresented in biodiversity databases.13,14,15 To worsen this situation, human-induced modifications16,17 may eliminate pieces of the Amazon's biodiversity puzzle before we can use them to understand how ecological communities are responding. To increase generalization and applicability of biodiversity knowledge,18,19 it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple organism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region's vulnerability to environmental change. 15%–18% of the most neglected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lost

Mortality from gastrointestinal congenital anomalies at 264 hospitals in 74 low-income, middle-income, and high-income countries: a multicentre, international, prospective cohort study

Summary Background Congenital anomalies are the fifth leading cause of mortality in children younger than 5 years globally. Many gastrointestinal congenital anomalies are fatal without timely access to neonatal surgical care, but few studies have been done on these conditions in low-income and middle-income countries (LMICs). We compared outcomes of the seven most common gastrointestinal congenital anomalies in low-income, middle-income, and high-income countries globally, and identified factors associated with mortality. Methods We did a multicentre, international prospective cohort study of patients younger than 16 years, presenting to hospital for the first time with oesophageal atresia, congenital diaphragmatic hernia, intestinal atresia, gastroschisis, exomphalos, anorectal malformation, and Hirschsprung’s disease. Recruitment was of consecutive patients for a minimum of 1 month between October, 2018, and April, 2019. We collected data on patient demographics, clinical status, interventions, and outcomes using the REDCap platform. Patients were followed up for 30 days after primary intervention, or 30 days after admission if they did not receive an intervention. The primary outcome was all-cause, in-hospital mortality for all conditions combined and each condition individually, stratified by country income status. We did a complete case analysis. Findings We included 3849 patients with 3975 study conditions (560 with oesophageal atresia, 448 with congenital diaphragmatic hernia, 681 with intestinal atresia, 453 with gastroschisis, 325 with exomphalos, 991 with anorectal malformation, and 517 with Hirschsprung’s disease) from 264 hospitals (89 in high-income countries, 166 in middleincome countries, and nine in low-income countries) in 74 countries. Of the 3849 patients, 2231 (58·0%) were male. Median gestational age at birth was 38 weeks (IQR 36–39) and median bodyweight at presentation was 2·8 kg (2·3–3·3). Mortality among all patients was 37 (39·8%) of 93 in low-income countries, 583 (20·4%) of 2860 in middle-income countries, and 50 (5·6%) of 896 in high-income countries (p<0·0001 between all country income groups). Gastroschisis had the greatest difference in mortality between country income strata (nine [90·0%] of ten in lowincome countries, 97 [31·9%] of 304 in middle-income countries, and two [1·4%] of 139 in high-income countries; p≤0·0001 between all country income groups). Factors significantly associated with higher mortality for all patients combined included country income status (low-income vs high-income countries, risk ratio 2·78 [95% CI 1·88–4·11], p<0·0001; middle-income vs high-income countries, 2·11 [1·59–2·79], p<0·0001), sepsis at presentation (1·20 [1·04–1·40], p=0·016), higher American Society of Anesthesiologists (ASA) score at primary intervention (ASA 4–5 vs ASA 1–2, 1·82 [1·40–2·35], p<0·0001; ASA 3 vs ASA 1–2, 1·58, [1·30–1·92], p<0·0001]), surgical safety checklist not used (1·39 [1·02–1·90], p=0·035), and ventilation or parenteral nutrition unavailable when needed (ventilation 1·96, [1·41–2·71], p=0·0001; parenteral nutrition 1·35, [1·05–1·74], p=0·018). Administration of parenteral nutrition (0·61, [0·47–0·79], p=0·0002) and use of a peripherally inserted central catheter (0·65 [0·50–0·86], p=0·0024) or percutaneous central line (0·69 [0·48–1·00], p=0·049) were associated with lower mortality. Interpretation Unacceptable differences in mortality exist for gastrointestinal congenital anomalies between lowincome, middle-income, and high-income countries. Improving access to quality neonatal surgical care in LMICs will be vital to achieve Sustainable Development Goal 3.2 of ending preventable deaths in neonates and children younger than 5 years by 2030

Prevalence, associated factors and outcomes of pressure injuries in adult intensive care unit patients: the DecubICUs study

Funder: European Society of Intensive Care Medicine; doi: http://dx.doi.org/10.13039/501100013347Funder: Flemish Society for Critical Care NursesAbstract: Purpose: Intensive care unit (ICU) patients are particularly susceptible to developing pressure injuries. Epidemiologic data is however unavailable. We aimed to provide an international picture of the extent of pressure injuries and factors associated with ICU-acquired pressure injuries in adult ICU patients. Methods: International 1-day point-prevalence study; follow-up for outcome assessment until hospital discharge (maximum 12 weeks). Factors associated with ICU-acquired pressure injury and hospital mortality were assessed by generalised linear mixed-effects regression analysis. Results: Data from 13,254 patients in 1117 ICUs (90 countries) revealed 6747 pressure injuries; 3997 (59.2%) were ICU-acquired. Overall prevalence was 26.6% (95% confidence interval [CI] 25.9–27.3). ICU-acquired prevalence was 16.2% (95% CI 15.6–16.8). Sacrum (37%) and heels (19.5%) were most affected. Factors independently associated with ICU-acquired pressure injuries were older age, male sex, being underweight, emergency surgery, higher Simplified Acute Physiology Score II, Braden score 3 days, comorbidities (chronic obstructive pulmonary disease, immunodeficiency), organ support (renal replacement, mechanical ventilation on ICU admission), and being in a low or lower-middle income-economy. Gradually increasing associations with mortality were identified for increasing severity of pressure injury: stage I (odds ratio [OR] 1.5; 95% CI 1.2–1.8), stage II (OR 1.6; 95% CI 1.4–1.9), and stage III or worse (OR 2.8; 95% CI 2.3–3.3). Conclusion: Pressure injuries are common in adult ICU patients. ICU-acquired pressure injuries are associated with mainly intrinsic factors and mortality. Optimal care standards, increased awareness, appropriate resource allocation, and further research into optimal prevention are pivotal to tackle this important patient safety threat

Correction to: Prevalence, associated factors and outcomes of pressure injuries in adult intensive care unit patients: the DecubICUs study

The original version of this article unfortunately contained a mistake

Prevalence, associated factors and outcomes of pressure injuries in adult intensive care unit patients: the DecubICUs study

Funder: European Society of Intensive Care Medicine; doi: http://dx.doi.org/10.13039/501100013347Funder: Flemish Society for Critical Care NursesAbstract: Purpose: Intensive care unit (ICU) patients are particularly susceptible to developing pressure injuries. Epidemiologic data is however unavailable. We aimed to provide an international picture of the extent of pressure injuries and factors associated with ICU-acquired pressure injuries in adult ICU patients. Methods: International 1-day point-prevalence study; follow-up for outcome assessment until hospital discharge (maximum 12 weeks). Factors associated with ICU-acquired pressure injury and hospital mortality were assessed by generalised linear mixed-effects regression analysis. Results: Data from 13,254 patients in 1117 ICUs (90 countries) revealed 6747 pressure injuries; 3997 (59.2%) were ICU-acquired. Overall prevalence was 26.6% (95% confidence interval [CI] 25.9–27.3). ICU-acquired prevalence was 16.2% (95% CI 15.6–16.8). Sacrum (37%) and heels (19.5%) were most affected. Factors independently associated with ICU-acquired pressure injuries were older age, male sex, being underweight, emergency surgery, higher Simplified Acute Physiology Score II, Braden score 3 days, comorbidities (chronic obstructive pulmonary disease, immunodeficiency), organ support (renal replacement, mechanical ventilation on ICU admission), and being in a low or lower-middle income-economy. Gradually increasing associations with mortality were identified for increasing severity of pressure injury: stage I (odds ratio [OR] 1.5; 95% CI 1.2–1.8), stage II (OR 1.6; 95% CI 1.4–1.9), and stage III or worse (OR 2.8; 95% CI 2.3–3.3). Conclusion: Pressure injuries are common in adult ICU patients. ICU-acquired pressure injuries are associated with mainly intrinsic factors and mortality. Optimal care standards, increased awareness, appropriate resource allocation, and further research into optimal prevention are pivotal to tackle this important patient safety threat