Recombination between heterologous human acrocentric chromosomes

The short arms of the human acrocentric chromosomes 13, 14, 15, 21 and 22 (SAACs) share large homologous regions, including ribosomal DNA repeats and extended segmental duplications1,2. Although the resolution of these regions in the first complete assembly of a human genome—the Telomere-to-Telomere Consortium’s CHM13 assembly (T2T-CHM13)—provided a model of their homology3, it remained unclear whether these patterns were ancestral or maintained by ongoing recombination exchange. Here we show that acrocentric chromosomes contain pseudo-homologous regions (PHRs) indicative of recombination between non-homologous sequences. Utilizing an all-to-all comparison of the human pangenome from the Human Pangenome Reference Consortium4 (HPRC), we find that contigs from all of the SAACs form a community. A variation graph5 constructed from centromere-spanning acrocentric contigs indicates the presence of regions in which most contigs appear nearly identical between heterologous acrocentric chromosomes in T2T-CHM13. Except on chromosome 15, we observe faster decay of linkage disequilibrium in the pseudo-homologous regions than in the corresponding short and long arms, indicating higher rates of recombination6,7. The pseudo-homologous regions include sequences that have previously been shown to lie at the breakpoint of Robertsonian translocations8, and their arrangement is compatible with crossover in inverted duplications on chromosomes 13, 14 and 21. The ubiquity of signals of recombination between heterologous acrocentric chromosomes seen in the HPRC draft pangenome suggests that these shared sequences form the basis for recurrent Robertsonian translocations, providing sequence and population-based confirmation of hypotheses first developed from cytogenetic studies 50 years ago9.Our work depends on the HPRC draft human pangenome resource established in the accompanying Article4, and we thank the production and assembly groups for their efforts in establishing this resource. This work used the computational resources of the UTHSC Octopus cluster and NIH HPC Biowulf cluster. We acknowledge support in maintaining these systems that was critical to our analyses. The authors thank M. Miller for the development of a graphical synopsis of our study (Fig. 5); and R. Williams and N. Soranzo for support and guidance in the design and discussion of our work. This work was supported, in part, by National Institutes of Health/NIDA U01DA047638 (E.G.), National Institutes of Health/NIGMS R01GM123489 (E.G.), NSF PPoSS Award no. 2118709 (E.G. and C.F.), the Tennessee Governor’s Chairs programme (C.F. and E.G.), National Institutes of Health/NCI R01CA266339 (T.P., L.G.d.L. and J.L.G.), and the Intramural Research Program of the National Human Genome Research Institute, National Institutes of Health (A.R., S.K. and A.M.P.). We acknowledge support from Human Technopole (A.G.), Consiglio Nazionale delle Ricerche, Italy (S.B. and V.C.), and Stowers Institute for Medical Research (T.P., L.G.d.L., B.R. and J.L.G.).Peer Reviewed"Article signat per 13 autors/es: Andrea Guarracino, Silvia Buonaiuto, Leonardo Gomes de Lima, Tamara Potapova, Arang Rhie, Sergey Koren, Boris Rubinstein, Christian Fischer, Human Pangenome Reference Consortium, Jennifer L. Gerton, Adam M. Phillippy, Vincenza Colonna & Erik Garrison " Human Pangenome Reference Consortium: "Haley J. Abel, Lucinda L. Antonacci-Fulton, Mobin Asri, Gunjan Baid, Carl A. Baker, Anastasiya Belyaeva, Konstantinos Billis, Guillaume Bourque, Silvia Buonaiuto, Andrew Carroll, Mark J. P. Chaisson, Pi-Chuan Chang, Xian H. Chang, Haoyu Cheng, Justin Chu, Sarah Cody, Vincenza Colonna, Daniel E. Cook, Robert M. Cook-Deegan, Omar E. Cornejo, Mark Diekhans, Daniel Doerr, Peter Ebert, Jana Ebler, Evan E. Eichler, Jordan M. Eizenga, Susan Fairley, Olivier Fedrigo, Adam L. Felsenfeld, Xiaowen Feng, Christian Fischer, Paul Flicek, Giulio Formenti, Adam Frankish, Robert S. Fulton, Yan Gao, Shilpa Garg, Erik Garrison, Nanibaa’ A. Garrison, Carlos Garcia Giron, Richard E. Green, Cristian Groza, Andrea Guarracino, Leanne Haggerty, Ira Hall, William T. Harvey, Marina Haukness, David Haussler, Simon Heumos, Glenn Hickey, Kendra Hoekzema, Thibaut Hourlier, Kerstin Howe, Miten Jain, Erich D. Jarvis, Hanlee P. Ji, Eimear E. Kenny, Barbara A. Koenig, Alexey Kolesnikov, Jan O. Korbel, Jennifer Kordosky, Sergey Koren, HoJoon Lee, Alexandra P. Lewis, Heng Li, Wen-Wei Liao, Shuangjia Lu, Tsung-Yu Lu, Julian K. Lucas, Hugo Magalhães, Santiago Marco-Sola, Pierre Marijon, Charles Markello, Tobias Marschall, Fergal J. Martin, Ann McCartney, Jennifer McDaniel, Karen H. Miga, Matthew W. Mitchell, Jean Monlong, Jacquelyn Mountcastle, Katherine M. Munson, Moses Njagi Mwaniki, Maria Nattestad, Adam M. Novak, Sergey Nurk, Hugh E. Olsen, Nathan D. Olson, Benedict Paten, Trevor Pesout, Adam M. Phillippy, Alice B. Popejoy, David Porubsky, Pjotr Prins, Daniela Puiu, Mikko Rautiainen, Allison A. Regier, Arang Rhie, Samuel Sacco, Ashley D. Sanders, Valerie A. Schneider, Baergen I. Schultz, Kishwar Shafin, Jonas A. Sibbesen, Jouni Sirén, Michael W. Smith, Heidi J. Sofia, Ahmad N. Abou Tayoun, Françoise Thibaud-Nissen, Chad Tomlinson, Francesca Floriana Tricomi, Flavia Villani, Mitchell R. Vollger, Justin Wagner, Brian Walenz, Ting Wang, Jonathan M. D. Wood, Aleksey V. Zimin & Justin M. Zook"Postprint (published version

Relative Information Gain: Shannon entropy-based measure of the relative structural conservation in RNA alignments

Structural characterization of RNAs is a dynamic field, offeringmanymodelling possibilities. RNA secondary structure models are usually characterized by an encoding that depicts structural information of the molecule through string representations or graphs. In this work, we provide a generalization of the BEAR encoding (a context-aware structural encoding we previously developed) by expanding the set of alignments used for the construction of substitution matrices and then applying it to secondary structure encodings ranging from fine-grained to more coarse-grained representations. We also introduce a re-interpretation of the Shannon Information applied on RNA alignments, proposing a new scoring metric, the Relative Information Gain (RIG). The RIG score is available for any position in an alignment, showing how different levels of detail encoded in the RNA representation can contribute differently to convey structural information. The approaches presented in this study can be used alongside state-ofthe-art tools to synergistically gain insights into the structural elements that RNAs and RNA families are composed of. This additional information could potentially contribute to their improvement or increase the degree of confidence in the secondary structure of families and any set of aligned RNAs

Estimación de las variaciones de almacenamiento de agua en los esteros del Iberá a partir de datos gravimétricos satelitales

Los Esteros del Iberá, provincia de Corrientes, Argentina, conforman un humedal de aproximadamente 12.900 km2, donde la escasa densidad geográfica de los registros hidrométricos y piezométricos limita la aplicación de métodos convencionales para la estimación de las variaciones del almacenamiento de agua y las componentes del balance hídrico. La misión espacial Gravity Recovery and Climate Experiment (GRACE) provee una novedosa técnica de cálculo basada en mediciones de las variaciones espacio-temporales del campo de gravedad terrestre a escala regional. El objetivo del presente trabajo es analizar la aplicabilidad de GRACE para estimar las variaciones de las reservas de agua en los esteros del Iberá. Se compararon series temporales de los datos de GRACE, convertidos a alturas equivalentes de agua, con series de alturas hidrométricas en lagunas de la región. La correlación de las series muestra un buen ajuste, con un coeficiente de correlación lineal con valores entre 0,77 y 0,87.The Ibera wetlands, Corrientes Province, Argentina, extend for approximately 12,900 km2. Reduced areal density of hydrometric and piezometric records limits the application of conventional methods for estimating changes in water storage and water balance components. The space mission Gravity Recovery and Climate Experiment (GRACE) provides an inventive calculation technique based on measurements of the spatial/temporal variations of the Earth's gravity field at regional scale. The aim of this paper is to analyse the applicability of GRACE to estimate water storage changes in the Iberá wetlands. In order to analyse the validity of this technique time series of GRACE data, converted to equivalent water heights, were compared with hydrometric heights series recorded at lagoons within the wetland. The correlation between both types of data shows a good fit, with a linear correlation coefficient between 0.77 and 0.87.Universidad Nacional de La Plat

BRIO: a web server for RNA sequence and structure motif scan

The interaction between RNA and RNA-binding proteins (RBPs) has a key role in the regulation of gene expression, in RNA stability, and in many other biological processes. RBPs accomplish these functions by binding target RNA molecules through specific sequence and structure motifs. The identification of these binding motifs is therefore fundamental to improve our knowledge of the cellular processes and how they are regulated. Here, we present BRIO (BEAM RNA Interaction mOtifs), a new web server designed for the identification of sequence and structure RNA-binding motifs in one or more RNA molecules of interest. BRIO enables the user to scan over 2508 sequence motifs and 2296 secondary structure motifs identified in Homo sapiens and Mus musculus, in three different types of experiments (PAR-CLIP, eCLIP, HITS). The motifs are associated with the binding of 186 RBPs and 69 protein domains. The web server is freely available at http://brio.bio.uniroma2.it

The role of beta-blocker drugs in critically ill patients: a SIAARTI expert consensus statement

Background: The role of β-blockers in the critically ill has been studied, and data on the protective effects of these drugs on critically ill patients have been repeatedly reported in the literature over the last two decades. However, consensus and guidelines by scientific societies on the use of β-blockers in critically ill patients are still lacking. The purpose of this document is to support the clinical decision-making process regarding the use of β-blockers in critically ill patients. The recipients of this document are physicians, nurses, healthcare personnel, and other professionals involved in the patient's care process. Methods: The Italian Society of Anesthesia, Analgesia, Resuscitation and Intensive Care (SIAARTI) selected a panel of experts and asked them to define key aspects underlying the use of β-blockers in critically ill adult patients. The methodology followed by the experts during this process was in line with principles of modified Delphi and RAND-UCLA methods. The experts developed statements and supportive rationales in the form of informative text. The overall list of statements was subjected to blind votes for consensus. Results: The literature search suggests that adrenergic stress and increased heart rate in critically ill patients are associated with organ dysfunction and increased mortality. Heart rate control thus seems to be critical in the management of the critically ill patient, requiring careful clinical evaluation aimed at both the differential diagnosis to treat secondary tachycardia and the treatment of rhythm disturbance. In addition, the use of β-blockers for the treatment of persistent tachycardia may be considered in patients with septic shock once hypovolemia has been ruled out. Intravenous application should be the preferred route of administration. Conclusion: β-blockers protective effects in critically ill patients have been repeatedly reported in the literature. Their use in the acute treatment of increased heart rate requires understanding of the pathophysiology and careful differential diagnosis, as all causes of tachycardia should be ruled out and addressed first

Levosimendan beyond inotropy and acute heart failure: Evidence of pleiotropic effects on the heart and other organs: An expert panel position paper

Peer reviewe

European Association of Cardiothoracic Anesthesiology and Intensive Care (EACTAIC) Fellowship Curriculum: Second Edition.

International audienceThis document represents the first update of the Cardiothoracic and Vascular Anaesthesia Fellowship Curriculum of the European Association of Cardiothoracic Anaesthesiology and Intensive Care. After obtaining feedback from exit interviews with fellows in training, graduate fellows, and program directors, 2 modified online Delphi procedures with questionnaires were conducted. A consensus was reached when two-thirds of responding committee members gave green or yellow ratings on a traffic light system, and >70% indicated strong agreement or agreement on a 5-point Likert scale. The new regulations include the following: (1) more flexibility in the fellows` rotation, as long as the total number of days, rotations, and cases are completed during the training year; (2) recommendation for strict compliance with national working-time guidelines; (3) no extension of fellowship training to compensate for annual and/or sick leave, unless the required minimum number of cases and rotations are not reached; (4) interruption of fellowship training for >12 months is allowed for personal or medical reasons; (5) introduction of a checklist for quantitative assessment of standard clinical skills; (6) recommendations for a uniform structure of exit interviews; (7) possibility of a 1-month training rotation in a postanesthesia care unit instead of an intensive care unit; and (8) provided all other requirements have been met, the allowance of progression from the basic training year to the advanced fellowship training year without first passing the transesophageal echocardiography examination

European Association of Cardiothoracic Anesthesiology and Intensive Care Pediatric Cardiac Anesthesia Fellowship Curriculum:First Edition

International audiencePediatric cardiac anesthesia is a subspecialty of cardiac and pediatric anesthesiology dedicated to the perioperative care of patients with congenital heart disease. Members of the Congenital and Education Subcommittees of the European Association of Cardiothoracic Anaesthesiology and Intensive Care (EACTAIC) agreed on the necessity to develop an EACTAIC pediatric cardiac anesthesia fellowship curriculum. This manuscript represents a consensus on the composition and the design of the EACTAIC Pediatric Cardiac Anesthesia Fellowship program. This curriculum provides a basis for the training of future pediatric cardiac anesthesiologists by clearly defining the theoretical and practical requirements for fellows and host centers

Landiolol in patients with septic shock resident in an intensive care unit (LANDI-SEP): study protocol for a randomized controlled trial

In patients with septic shock, the presence of an elevated heart rate (HR) after fluid resuscitation marks a subgroup of patients with a particularly poor prognosis. Several studies have shown that HR control in this population is safe and can potentially improve outcomes. However, all were conducted in a single-center setting. The aim of this multicenter study is to demonstrate that administration of the highly beta1-selective and ultrashort-acting beta blocker landiolol in patients with septic shock and persistent tachycardia (HR ae 95 beats per minute [bpm]) is effective in reducing and maintaining HR without increasing vasopressor requirements. A phase IV, multicenter, prospective, randomized, open-label, controlled study is being conducted. The study will enroll a total of 200 patients with septic shock as defined by The Third International Consensus Definitions for Sepsis and Septic Shock criteria and tachycardia (HR ae 95 bpm) despite a hemodynamic optimization period of 24-36 h. Patients are randomized (1:1) to receive either standard treatment (according to the Surviving Sepsis Campaign Guidelines 2016) and continuous landiolol infusion to reach a target HR of 80-94 bpm or standard treatment alone. The primary endpoint is HR response (HR 80-94 bpm), the maintenance thereof, and the absence of increased vasopressor requirements during the first 24 h after initiating treatment. Despite recent studies, the role of beta blockers in the treatment of patients with septic shock remains unclear. This study will investigate whether HR control using landiolol is safe, feasible, and effective, and further enhance the understanding of beta blockade in patients with septic shock

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