Autoadaptive Algorithm for the Stacking-Level Estimation of Membranes in TEM Images

International audienceThis paper introduces an original algorithm for the labeling of the regions of a partitioned image according to the stacking level of membranes in transmission electron microscopy (TEM) images. Image analysis of membrane protein TEM images represents a particular challenging task because of the important noise and heterogeneity present in these images. The proposed algorithm adapts automatically to fluctuations and gray level ranges characterizing each membrane stacking level. Some information about the organization of the objects in the images is introduced as prior knowledge. Three types of qualitative and quantitative experiments have been specifically devised and implemented to assess the algorithm

Understanding Conformational Dynamics of Complex Lipid Mixtures Relevant to Biology

This is a perspective article entitled “Frontiers in computational biophysics: understanding conformational dynamics of complex lipid mixtures relevant to biology” which is following a CECAM meeting with the same name.Fil: Friedman, Ran. Linnæus University; ArgentinaFil: Khalid, Syma. University of Southampton; Reino UnidoFil: Aponte Santamaría, Camilo. Ruprecht-Karls-Universität Heidelberg; Alemania. Universidad de los Andes; ColombiaFil: Arutyunova, Elena. University of Alberta; CanadáFil: Becker, Marlon. Westfälische Wilhelms Universität; AlemaniaFil: Boyd, Kevin J.. University of Connecticut; Estados UnidosFil: Christensen, Mikkel. University Aarhus; DinamarcaFil: Coimbra, João T. S.. Universidad de Porto; PortugalFil: Concilio, Simona. Universita di Salerno; ItaliaFil: Daday, Csaba. Heidelberg Institute for Theoretical Studies; AlemaniaFil: Eerden, Floris J. van. University of Groningen; Países BajosFil: Fernandes, Pedro A.. Universidad de Porto; PortugalFil: Gräter, Frauke. Heidelberg University; Alemania. Heidelberg Institute for Theoretical Studies; AlemaniaFil: Hakobyan, Davit. Westfälische Wilhelms Universität; AlemaniaFil: Heuer, Andreas. Westfälische Wilhelms Universität; AlemaniaFil: Karathanou, Konstantina. Freie Universität Berlin; AlemaniaFil: Keller, Fabian. Westfälische Wilhelms Universität; AlemaniaFil: Lemieux, M. Joanne. University of Alberta; CanadáFil: Marrink, Siewert J.. University of Groningen; Países BajosFil: May, Eric R.. University of Connecticut; Estados UnidosFil: Mazumdar, Antara. University of Groningen; Países BajosFil: Naftalin, Richard. Colegio Universitario de Londres; Reino UnidoFil: Pickholz, Mónica Andrea. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Física de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Física de Buenos Aires; ArgentinaFil: Piotto, Stefano. Universita di Salerno; ItaliaFil: Pohl, Peter. Johannes Kepler University; AustriaFil: Quinn, Peter. Colegio Universitario de Londres; Reino UnidoFil: Ramos, Maria J.. Universidad de Porto; PortugalFil: Schiøtt, Birgit. University Aarhus; DinamarcaFil: Sengupta, Durba. National Chemical Laboratory India; IndiaFil: Sessa, Lucia. Universita di Salerno; ItaliaFil: Vanni, Stefano. University Of Fribourg;Fil: Zeppelin, Talia. University Aarhus; DinamarcaFil: Zoni, Valeria. University of Fribourg; SuizaFil: Bondar, Ana-Nicoleta. Freie Universität Berlin; AlemaniaFil: Domene, Carmen. University of Oxford; Reino Unido. University of Bath; Reino Unid

Triticum timopheevii s.l. (‘new glume wheat’) finds in regions of southern and eastern Europe across space and time

Triticum timopheevii sensu lato (‘new glume wheat’, NGW) was first recognised as a distinct prehistoric cereal crop through work on archaeobotanical finds from Neolithic and Bronze Age sites in northern Greece. This was later followed by its identification in archaeobotanical assemblages from other parts of Europe. This paper provides an overview of the currently known archaeobotanical finds of Timopheev’s wheat in southeastern and eastern Europe and observes their temporal span and spatial distribution. To date, there are 89 prehistoric sites with these finds, located in different parts of the study region and dated from the Neolithic to the very late Iron Age. Their latest recorded presence in the region is in the last centuries BCE. For assemblages from the site as a whole containing at least 30 grain and/or chaff remains of Timopheev’s wheat, we take a brief look at the overall relative proportions of Triticum monococcum (einkorn), T. dicoccum (emmer) and T. timopheevii s.l. (Timopheev’s wheat), the three most common glume wheats in our study region in prehistory. We highlight several sites where the overall proportions of Timopheev’s wheat might be taken to suggest it was a minor component of a mixed crop (maslin), or an unmonitored inclusion in einkorn or emmer fields. At the same sites, however, there are also discrete contexts where this wheat is strongly predominant, pointing to its cultivation as a pure crop. We therefore emphasise the need to evaluate the relative representation of Timopheev’s wheat at the level of individual samples or contexts before making inferences on its cultivation status. We also encourage re-examination of prehistoric and historic cereal assemblages for its remains

Epidemiology of intra-abdominal infection and sepsis in critically ill patients: “AbSeS”, a multinational observational cohort study and ESICM Trials Group Project

Purpose: To describe the epidemiology of intra-abdominal infection in an international cohort of ICU patients according to a new system that classifies cases according to setting of infection acquisition (community-acquired, early onset hospital-acquired, and late-onset hospital-acquired), anatomical disruption (absent or present with localized or diffuse peritonitis), and severity of disease expression (infection, sepsis, and septic shock). Methods: We performed a multicenter (n = 309), observational, epidemiological study including adult ICU patients diagnosed with intra-abdominal infection. Risk factors for mortality were assessed by logistic regression analysis. Results: The cohort included 2621 patients. Setting of infection acquisition was community-acquired in 31.6%, early onset hospital-acquired in 25%, and late-onset hospital-acquired in 43.4% of patients. Overall prevalence of antimicrobial resistance was 26.3% and difficult-to-treat resistant Gram-negative bacteria 4.3%, with great variation according to geographic region. No difference in prevalence of antimicrobial resistance was observed according to setting of infection acquisition. Overall mortality was 29.1%. Independent risk factors for mortality included late-onset hospital-acquired infection, diffuse peritonitis, sepsis, septic shock, older age, malnutrition, liver failure, congestive heart failure, antimicrobial resistance (either methicillin-resistant Staphylococcus aureus, vancomycin-resistant enterococci, extended-spectrum beta-lactamase-producing Gram-negative bacteria, or carbapenem-resistant Gram-negative bacteria) and source control failure evidenced by either the need for surgical revision or persistent inflammation. Conclusion: This multinational, heterogeneous cohort of ICU patients with intra-abdominal infection revealed that setting of infection acquisition, anatomical disruption, and severity of disease expression are disease-specific phenotypic characteristics associated with outcome, irrespective of the type of infection. Antimicrobial resistance is equally common in community-acquired as in hospital-acquired infection

A bottom-up view of food surplus: using stable carbon and nitrogen isotope analysis to investigate agricultural strategies and diet at Bronze Age Archontiko and Thessaloniki Toumba, northern Greece

We use stable isotope analysis of crop, faunal and human remains to investigate agricultural strategies and diet at EBA-LBA Archontiko and MBA-LBA Thessaloniki Toumba. Crop production strategies varied between settlements, phases and species; flexibility is also apparent within the crop stores of individual houses. Escalating manuring intensity at LBA Thessaloniki Toumba coincides with large co-residential ‘blocks’ geared towards hoarding of agricultural surpluses, spectacularly preserved by fire at nearby LBA Assiros Toumba. Faunal isotope values reflect a range of feeding strategies, including probable herding of cattle on C4-rich coastal salt marshes, evident at Archontiko through to the LBA alongside bulk cockle harvesting. Palaeodietary analysis of LBA humans at Thessaloniki Toumba indicates that C3 crops represent the only plausible staples. Millet was a minor food but may have played a particular role in the sub-adult diet. Meat probably featured in supra-household food sharing and hospitality, associated with Mycenaean-style tableware in the LBA

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

NanoCrystal: A Web-Based Crystallographic Tool for the Construction of Nanoparticles Based on Their Crystal Habit

Modeling of nanoparticles is an essential first step to assess their capacities for different uses such as energy storage and drug delivery. However, creating an initial starting conformation for modeling and simulation is tedious because every crystalline material grows with a different crystal habit. In this application note, we describe NanoCrystal, a novel web-based crystallographic tool that creates nanoparticle models from any crystal structure guided by their preferred equilibrium shape under standard conditions according to the Wulff morphology (crystal habit). Users can upload a cif file, define the Miller indices and their corresponding minimum surface energies according to the Wulff construction of a particular crystal, and specify the size of the nanocrystal. As a result, the nanoparticle is constructed and visualized, and the coordinates of the atoms are output to the user. NanoCrystal can be accessed at http://nanocrystal.vi-seem.edu/. © 2018 American Chemical Society

Greek Traditional Dance as a Practice for Managing Stress and Anxiety in Cancer Patients

Stress and anxiety levels in cancer patients tend to decrease by performing bodily-kinesthetic and musical activities. The hypothesis of the present study is that attending lessons in Greek traditional dance is an effective method for managing anxiety and stress in patients diagnosed with cancer of any type both during and after treatment. The study was conducted on 300 cancer patients (150 experimental subjects, 150 controls) selected by Attica hospitals and nonprofit cancer patients’ organizations. Each patient in the experimental group attended an 8-week Greek traditional dance lesson program. Lessons were held twice per week, lasting 60 min each. A similar group of cancer patients not participating in any organized physical activity during the same time period served as a control group. Data were collected using the Depression Anxiety Stress Scale 21 (Dass-21) questionnaire and subjected to reliability analysis (Cronbach’s alpha) and deviation-dependent analysis (one-way repeated). Both stress and anxiety values decreased significantly in the experimental group (stress value: initial mean = 16.27, second mean = 2.58, final mean = 6.77, p < 0.001; anxiety value: initial mean = 15.59, second mean = 2.81, final mean = 5.35, p < 0.001). In contrast, no significant fluctuation was observed in the control group. Thus, there was a significant decrease in stress and anxiety values in cancer patients who attended Greek traditional dances lessons with important psychotherapeutic significance. © 2020, American Association for Cancer Education