50 research outputs found

    FlowDiv: A new pipeline for analyzing flow cytometric diversity

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    Background: Flow cytometry (FCM) is one of the most commonly used technologies for analysis of numerous biological systems at the cellular level, from cancer cells to microbial communities. Its high potential and wide applicability led to the development of various analytical protocols, which are often not interchangeable between fields of expertise. Environmental science in particular faces difficulty in adapting to non-specific protocols, mainly because of the highly heterogeneous nature of environmental samples. This variety, although it is intrinsic to environmental studies, makes it difficult to adjust analytical protocols to maintain both mathematical formalism and comprehensible biological interpretations, principally for questions that rely on the evaluation of differences between cytograms, an approach also termed cytometric diversity. Despite the availability of promising bioinformatic tools conceived for or adapted to cytometric diversity, most of them still cannot deal with common technical issues such as the integration of differently acquired datasets, the optimal number of bins, and the effective correlation of bins to previously known cytometric populations. Results: To address these and other questions, we have developed flowDiv, an R language pipeline for analysis of environmental flow cytometry data. Here, we present the rationale for flowDiv and apply the method to a real dataset from 31 freshwater lakes in Patagonia, Argentina, to reveal significant aspects of their cytometric diversities. Conclusions: flowDiv provides a rather intuitive way of proceeding with FCM analysis, as it combines formal mathematical solutions and biological rationales in an intuitive framework specifically designed to explore cytometric diversity.Fil: Wanderley, Bruno M. S.. Universidade Federal do Rio Grande do Norte; BrasilFil: AraĂșjo, Daniel S.. Universidade Federal do Rio Grande do Norte; BrasilFil: Quiroga, MarĂ­a Victoria. Consejo Nacional de Investigaciones CientĂ­ficas y TĂ©cnicas. Centro CientĂ­fico TecnolĂłgico Conicet - La Plata. Instituto de Investigaciones BiotecnolĂłgicas. Instituto de Investigaciones BiotecnolĂłgicas "Dr. RaĂșl AlfonsĂ­n" (sede ChascomĂșs). Universidad Nacional de San MartĂ­n. Instituto de Investigaciones BiotecnolĂłgicas. Instituto de Investigaciones BiotecnolĂłgicas "Dr. RaĂșl AlfonsĂ­n" (sede ChascomĂșs); ArgentinaFil: Amado, AndrĂ© M.. Universidade Federal do Rio Grande do Norte; Brasil. Universidade Federal de Juiz de Fora; BrasilFil: Neto, AdriĂŁo D. D.. Universidade Federal do Rio Grande do Norte; BrasilFil: Sarmento, Hugo. Universidade Federal do SĂŁo Carlos; BrasilFil: Metz, SebastiĂĄn DarĂ­o. Consejo Nacional de Investigaciones CientĂ­ficas y TĂ©cnicas. Centro CientĂ­fico TecnolĂłgico Conicet - La Plata. Instituto de Investigaciones BiotecnolĂłgicas. Instituto de Investigaciones BiotecnolĂłgicas "Dr. RaĂșl AlfonsĂ­n" (sede ChascomĂșs). Universidad Nacional de San MartĂ­n. Instituto de Investigaciones BiotecnolĂłgicas. Instituto de Investigaciones BiotecnolĂłgicas "Dr. RaĂșl AlfonsĂ­n" (sede ChascomĂșs); ArgentinaFil: Unrein, Fernando. Consejo Nacional de Investigaciones CientĂ­ficas y TĂ©cnicas. Centro CientĂ­fico TecnolĂłgico Conicet - La Plata. Instituto de Investigaciones BiotecnolĂłgicas. Instituto de Investigaciones BiotecnolĂłgicas "Dr. RaĂșl AlfonsĂ­n" (sede ChascomĂșs). Universidad Nacional de San MartĂ­n. Instituto de Investigaciones BiotecnolĂłgicas. Instituto de Investigaciones BiotecnolĂłgicas "Dr. RaĂșl AlfonsĂ­n" (sede ChascomĂșs); Argentin

    A Digital Repository and Execution Platform for Interactive Scholarly Publications in Neuroscience

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    The CARMEN Virtual Laboratory (VL) is a cloud-based platform which allows neuroscientists to store, share, develop, execute, reproduce and publicise their work. This paper describes new functionality in the CARMEN VL: an interactive publications repository. This new facility allows users to link data and software to publications. This enables other users to examine data and software associated with the publication and execute the associated software within the VL using the same data as the authors used in the publication. The cloud-based architecture and SaaS (Software as a Service) framework allows vast data sets to be uploaded and analysed using software services. Thus, this new interactive publications facility allows others to build on research results through reuse. This aligns with recent developments by funding agencies, institutions, and publishers with a move to open access research. Open access provides reproducibility and verification of research resources and results. Publications and their associated data and software will be assured of long-term preservation and curation in the repository. Further, analysing research data and the evaluations described in publications frequently requires a number of execution stages many of which are iterative. The VL provides a scientific workflow environment to combine software services into a processing tree. These workflows can also be associated with publications and executed by users. The VL also provides a secure environment where users can decide the access rights for each resource to ensure copyright and privacy restrictions are met

    Impact of SARS-Cov-2 infection in patients with hypertrophic cardiomyopathy : results of an international multicentre registry

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    To describe the natural history of SARS-CoV-2 infection in patients with hypertrophic cardiomyopathy (HCM) compared with a control group and to identify predictors of adverse events. Three hundred and five patients [age 56.6 ± 16.9 years old, 191 (62.6%) male patients] with HCM and SARS-Cov-2 infection were enrolled. The control group consisted of 91 131 infected individuals. Endpoints were (i) SARS-CoV-2 related mortality and (ii) severe clinical course [death or intensive care unit (ICU) admission]. New onset of atrial fibrillation, ventricular arrhythmias, shock, stroke, and cardiac arrest were also recorded. Sixty-nine (22.9%) HCM patients were hospitalized for non-ICU level care, and 21 (7.0%) required ICU care. Seventeen (5.6%) died: eight (2.6%) of respiratory failure, four (1.3%) of heart failure, two (0.7%) suddenly, and three (1.0%) due to other SARS-CoV-2-related complications. Covariates associated with mortality in the multivariable were age {odds ratio (OR) per 10 year increase 2.25 [95% confidence interval (CI): 1.12-4.51], P = 0.0229}, baseline New York Heart Association class [OR per one-unit increase 4.01 (95%CI: 1.75-9.20), P = 0.0011], presence of left ventricular outflow tract obstruction [OR 5.59 (95%CI: 1.16-26.92), P = 0.0317], and left ventricular systolic impairment [OR 7.72 (95%CI: 1.20-49.79), P = 0.0316]. Controlling for age and sex and comparing HCM patients with a community-based SARS-CoV-2 cohort, the presence of HCM was associated with a borderline significant increased risk of mortality OR 1.70 (95%CI: 0.98-2.91, P = 0.0600). Over one-fourth of HCM patients infected with SARS-Cov-2 required hospitalization, including 6% in an ICU setting. Age and cardiac features related to HCM, including baseline functional class, left ventricular outflow tract obstruction, and systolic impairment, conveyed increased risk of mortality

    Worldwide trends in underweight and obesity from 1990 to 2022: a pooled analysis of 3663 population-representative studies with 222 million children, adolescents, and adults

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    Background Underweight and obesity are associated with adverse health outcomes throughout the life course. We estimated the individual and combined prevalence of underweight or thinness and obesity, and their changes, from 1990 to 2022 for adults and school-aged children and adolescents in 200 countries and territories. Methods We used data from 3663 population-based studies with 222 million participants that measured height and weight in representative samples of the general population. We used a Bayesian hierarchical model to estimate trends in the prevalence of different BMI categories, separately for adults (age ≄20 years) and school-aged children and adolescents (age 5–19 years), from 1990 to 2022 for 200 countries and territories. For adults, we report the individual and combined prevalence of underweight (BMI <18·5 kg/m2) and obesity (BMI ≄30 kg/m2). For schoolaged children and adolescents, we report thinness (BMI <2 SD below the median of the WHO growth reference) and obesity (BMI >2 SD above the median). Findings From 1990 to 2022, the combined prevalence of underweight and obesity in adults decreased in 11 countries (6%) for women and 17 (9%) for men with a posterior probability of at least 0·80 that the observed changes were true decreases. The combined prevalence increased in 162 countries (81%) for women and 140 countries (70%) for men with a posterior probability of at least 0·80. In 2022, the combined prevalence of underweight and obesity was highest in island nations in the Caribbean and Polynesia and Micronesia, and countries in the Middle East and north Africa. Obesity prevalence was higher than underweight with posterior probability of at least 0·80 in 177 countries (89%) for women and 145 (73%) for men in 2022, whereas the converse was true in 16 countries (8%) for women, and 39 (20%) for men. From 1990 to 2022, the combined prevalence of thinness and obesity decreased among girls in five countries (3%) and among boys in 15 countries (8%) with a posterior probability of at least 0·80, and increased among girls in 140 countries (70%) and boys in 137 countries (69%) with a posterior probability of at least 0·80. The countries with highest combined prevalence of thinness and obesity in school-aged children and adolescents in 2022 were in Polynesia and Micronesia and the Caribbean for both sexes, and Chile and Qatar for boys. Combined prevalence was also high in some countries in south Asia, such as India and Pakistan, where thinness remained prevalent despite having declined. In 2022, obesity in school-aged children and adolescents was more prevalent than thinness with a posterior probability of at least 0·80 among girls in 133 countries (67%) and boys in 125 countries (63%), whereas the converse was true in 35 countries (18%) and 42 countries (21%), respectively. In almost all countries for both adults and school-aged children and adolescents, the increases in double burden were driven by increases in obesity, and decreases in double burden by declining underweight or thinness. Interpretation The combined burden of underweight and obesity has increased in most countries, driven by an increase in obesity, while underweight and thinness remain prevalent in south Asia and parts of Africa. A healthy nutrition transition that enhances access to nutritious foods is needed to address the remaining burden of underweight while curbing and reversing the increase in obesit

    Impact of opioid-free analgesia on pain severity and patient satisfaction after discharge from surgery: multispecialty, prospective cohort study in 25 countries

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    Background: Balancing opioid stewardship and the need for adequate analgesia following discharge after surgery is challenging. This study aimed to compare the outcomes for patients discharged with opioid versus opioid-free analgesia after common surgical procedures.Methods: This international, multicentre, prospective cohort study collected data from patients undergoing common acute and elective general surgical, urological, gynaecological, and orthopaedic procedures. The primary outcomes were patient-reported time in severe pain measured on a numerical analogue scale from 0 to 100% and patient-reported satisfaction with pain relief during the first week following discharge. Data were collected by in-hospital chart review and patient telephone interview 1 week after discharge.Results: The study recruited 4273 patients from 144 centres in 25 countries; 1311 patients (30.7%) were prescribed opioid analgesia at discharge. Patients reported being in severe pain for 10 (i.q.r. 1-30)% of the first week after discharge and rated satisfaction with analgesia as 90 (i.q.r. 80-100) of 100. After adjustment for confounders, opioid analgesia on discharge was independently associated with increased pain severity (risk ratio 1.52, 95% c.i. 1.31 to 1.76; P < 0.001) and re-presentation to healthcare providers owing to side-effects of medication (OR 2.38, 95% c.i. 1.36 to 4.17; P = 0.004), but not with satisfaction with analgesia (beta coefficient 0.92, 95% c.i. -1.52 to 3.36; P = 0.468) compared with opioid-free analgesia. Although opioid prescribing varied greatly between high-income and low- and middle-income countries, patient-reported outcomes did not.Conclusion: Opioid analgesia prescription on surgical discharge is associated with a higher risk of re-presentation owing to side-effects of medication and increased patient-reported pain, but not with changes in patient-reported satisfaction. Opioid-free discharge analgesia should be adopted routinely

    Unforeseen plant phenotypic diversity in a dry and grazed world

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    23 pĂĄginas..- 4 figuras y 7 figuras.- 50 referencias y 90 referenciasEarth harbours an extraordinary plant phenotypic diversity1 that is at risk from ongoing global changes2,3. However, it remains unknown how increasing aridity and livestock grazing pressure—two major drivers of global change4,5,6—shape the trait covariation that underlies plant phenotypic diversity1,7. Here we assessed how covariation among 20 chemical and morphological traits responds to aridity and grazing pressure within global drylands. Our analysis involved 133,769 trait measurements spanning 1,347 observations of 301 perennial plant species surveyed across 326 plots from 6 continents. Crossing an aridity threshold of approximately 0.7 (close to the transition between semi-arid and arid zones) led to an unexpected 88% increase in trait diversity. This threshold appeared in the presence of grazers, and moved toward lower aridity levels with increasing grazing pressure. Moreover, 57% of observed trait diversity occurred only in the most arid and grazed drylands, highlighting the phenotypic uniqueness of these extreme environments. Our work indicates that drylands act as a global reservoir of plant phenotypic diversity and challenge the pervasive view that harsh environmental conditions reduce plant trait diversity8,9,10. They also highlight that many alternative strategies may enable plants to cope with increases in environmental stress induced by climate change and land-use intensification.This research was funded by the European Research Council (ERC Grant agreement 647038 1004 [BIODESERT]) and Generalitat Valenciana (CIDEGENT/2018/041). N.G. was supported by CAP 20–25 (16-IDEX-0001) and the AgreenSkills+ fellowship programme which has received funding from the European Union’s Seventh Framework Programme under grant agreement FP7-609398 (AgreenSkills+ contract). F.T.M. acknowledges support from the King Abdullah University of Science and Technology (KAUST), the KAUST Climate and Livability Initiative, the University of Alicante (UADIF22-74 and VIGROB22-350), the Spanish Ministry of Science and Innovation (PID2020-116578RB-I00), and the Synthesis Center (sDiv) of the German Centre for Integrative Biodiversity Research Halle–Jena–Leipzig (iDiv). Y.L.B.-P. was supported by a Marie Sklodowska-Curie Actions Individual Fellowship (MSCA-1018 IF) within the European Program Horizon 2020 (DRYFUN Project 656035). H.S. is supported by a MarĂ­a Zambrano fellowship funded by the Ministry of Universities and European Union-Next Generation plan. L.W. acknowledges support from the US National Science Foundation (EAR 1554894). G.M.W. acknowledges support from the Australian Research Council (DP210102593) and TERN. M.B is supported by a RamĂłn y Cajal grant from Spanish Ministry of Science (RYC2021-031797-I). L.v.d.B. and K.T. were supported by the German Research Foundation (DFG) Priority Program SPP-1803 (TI388/14-1). A.F. acknowledges the financial support from ANID PIA/BASAL FB210006 and Millenium Science Initiative Program NCN2021-050. A.J. was supported by the Bavarian Research Alliance for travel and field work (BayIntAn UBT 2017 61). A.L. and L.K. acknowledge support from the German Research Foundation, DFG (grant CRC TRR228) and German Federal Government for Science and Education, BMBF (grants 01LL1802C and 01LC1821A). B.B. and S.U. were supported by the Taylor Family-Asia Foundation Endowed Chair in Ecology and Conservation Biology. P.J.R. and A.J.M. acknowledge support from Fondo Europeo de Desarrollo Regional through the FEDER AndalucĂ­a operative programme, FEDER-UJA 1261180 project. E.M.-J. and C.P. acknowledge support from the Spanish Ministry of Science and Innovation (PID2020-116578RB-I00). D.J.E. was supported by the Hermon Slade Foundation. J.D. and A.RodrĂ­guez acknowledge support from the FCT (2020.03670.CEECIND and SFRH/BDP/108913/2015, respectively), as well as from the MCTES, FSE, UE and the CFE (UIDB/04004/2021) research unit financed by FCT/MCTES through national funds (PIDDAC). S.C.R. acknowledges support from the US Department of Energy (DE-SC-0008168), US Department of Defense (RC18-1322), and the US Geological Survey Ecosystems Mission Area. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the US government. E.H.-S. acknowledges support from Mexican National Science and Technology Council (CONACYT PN 5036 and 319059). A.N. and C. Branquinho. acknowledge the support from FCT—Fundação para a CiĂȘncia e a Tecnologia (CEECIND/02453/2018/CP1534/CT0001, PTDC/ASP-SIL/7743/ 2020, UIDB/00329/2020), from AdaptForGrazing project (PRR-C05-i03-I-000035) and from LTsER Montado platform (LTER_EU_PT_001). Field work of G.P. and J.M.Z. was supported by UNRN (PI 40-C-873).Peer reviewe

    Hotspots of biogeochemical activity linked to aridity and plant traits across global drylands

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    14 páginas.- 4 figuras.- 67 referencias.- The online version contains supplementary material available at https://doi.org/10.1038/s41477-024-01670-7Perennial plants create productive and biodiverse hotspots, known as fertile islands, beneath their canopies. These hotspots largely determine the structure and functioning of drylands worldwide. Despite their ubiquity, the factors controlling fertile islands under conditions of contrasting grazing by livestock, the most prevalent land use in drylands, remain virtually unknown. Here we evaluated the relative importance of grazing pressure and herbivore type, climate and plant functional traits on 24 soil physical and chemical attributes that represent proxies of key ecosystem services related to decomposition, soil fertility, and soil and water conservation. To do this, we conducted a standardized global survey of 288 plots at 88 sites in 25 countries worldwide. We show that aridity and plant traits are the major factors associated with the magnitude of plant effects on fertile islands in grazed drylands worldwide. Grazing pressure had little influence on the capacity of plants to support fertile islands. Taller and wider shrubs and grasses supported stronger island effects. Stable and functional soils tended to be linked to species-rich sites with taller plants. Together, our findings dispel the notion that grazing pressure or herbivore type are linked to the formation or intensification of fertile islands in drylands. Rather, our study suggests that changes in aridity, and processes that alter island identity and therefore plant traits, will have marked effects on how perennial plants support and maintain the functioning of drylands in a more arid and grazed world.This research was supported by the European Research Council (ERC grant 647038 (BIODESERT) awarded to F.T.M.) and Generalitat Valenciana (CIDEGENT/2018/041). D.J.E. was supported by the Hermon Slade Foundation (HSF21040). J. Ding was supported by the National Natural Science Foundation of China Project (41991232) and the Fundamental Research Funds for the Central Universities of China. M.D.-B. acknowledges support from TED2021-130908B-C41/AEI/10.13039/501100011033/Unión Europea Next Generation EU/PRTR and the Spanish Ministry of Science and Innovation for the I + D + i project PID2020-115813RA-I00 funded by MCIN/AEI/10.13039/501100011033. O.S. was supported by US National Science Foundation (Grants DEB 1754106, 20-25166), and Y.L.B.-P. by a Marie Sklodowska-Curie Actions Individual Fellowship (MSCA-1018 IF) within the European Program Horizon 2020 (DRYFUN Project 656035). K.G. and N.B. acknowledge support from the German Federal Ministry of Education and Research (BMBF) SPACES projects OPTIMASS (FKZ: 01LL1302A) and ORYCS (FKZ: FKZ01LL1804A). B.B. was supported by the Taylor Family-Asia Foundation Endowed Chair in Ecology and Conservation Biology, and M. Bowker by funding from the School of Forestry, Northern Arizona University. C.B. acknowledges funding from the National Natural Science Foundation of China (41971131). D.B. acknowledges support from the Hungarian Research, Development and Innovation Office (NKFI KKP 144096), and A. Fajardo support from ANID PIA/BASAL FB 210006 and the Millennium Science Initiative Program NCN2021-050. M.F. and H.E. received funding from Ferdowsi University of Mashhad (grant 39843). A.N. and M.K. acknowledge support from FCT (CEECIND/02453/2018/CP1534/CT0001, SFRH/BD/130274/2017, PTDC/ASP-SIL/7743/2020, UIDB/00329/2020), EEA (10/CALL#5), AdaptForGrazing (PRR-C05-i03-I-000035) and LTsER Montado platform (LTER_EU_PT_001) grants. O.V. acknowledges support from the Hungarian Research, Development and Innovation Office (NKFI KKP 144096). L.W. was supported by the US National Science Foundation (EAR 1554894). Y.Z. and X.Z. were supported by the National Natural Science Foundation of China (U2003214). H.S. is supported by a María Zambrano fellowship funded by the Ministry of Universities and European Union-Next Generation plan. The use of any trade, firm or product names does not imply endorsement by any agency, institution or government. Finally, we thank the many people who assisted with field work and the landowners, corporations and national bodies that allowed us access to their land.Peer reviewe

    La renovaciĂłn de la palabra en el bicentenario de la Argentina : los colores de la mirada lingĂŒĂ­stica

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    El libro reĂșne trabajos en los que se exponen resultados de investigaciones presentadas por investigadores de Argentina, Chile, Brasil, España, Italia y Alemania en el XII Congreso de la Sociedad Argentina de LingĂŒĂ­stica (SAL), Bicentenario: la renovaciĂłn de la palabra, realizado en Mendoza, Argentina, entre el 6 y el 9 de abril de 2010. Las temĂĄticas abordadas en los 167 capĂ­tulos muestran las grandes lĂ­neas de investigaciĂłn que se desarrollan fundamentalmente en nuestro paĂ­s, pero tambiĂ©n en los otros paĂ­ses mencionados arriba, y señalan ademĂĄs las ĂĄreas que reciĂ©n se inician, con poca tradiciĂłn en nuestro paĂ­s y que deberĂ­an fomentarse. Los trabajos aquĂ­ publicados se enmarcan dentro de las siguientes disciplinas y/o campos de investigaciĂłn: FonologĂ­a, Sintaxis, SemĂĄntica y PragmĂĄtica, LingĂŒĂ­stica Cognitiva, AnĂĄlisis del Discurso, PsicolingĂŒĂ­stica, AdquisiciĂłn de la Lengua, SociolingĂŒĂ­stica y DialectologĂ­a, DidĂĄctica de la lengua, LingĂŒĂ­stica Aplicada, LingĂŒĂ­stica Computacional, Historia de la Lengua y la LingĂŒĂ­stica, Lenguas AborĂ­genes, FilosofĂ­a del Lenguaje, LexicologĂ­a y TerminologĂ­a

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

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    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
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