An objective comparison of cell-tracking algorithms

We present a combined report on the results of three editions of the Cell Tracking Challenge, an ongoing initiative aimed at promoting the development and objective evaluation of cell segmentation and tracking algorithms. With 21 participating algorithms and a data repository consisting of 13 data sets from various microscopy modalities, the challenge displays today's state-of-the-art methodology in the field. We analyzed the challenge results using performance measures for segmentation and tracking that rank all participating methods. We also analyzed the performance of all of the algorithms in terms of biological measures and practical usability. Although some methods scored high in all technical aspects, none obtained fully correct solutions. We found that methods that either take prior information into account using learning strategies or analyze cells in a global spatiotemporal video context performed better than other methods under the segmentation and tracking scenarios included in the challenge

New strategies for echocardiographic evaluation of left ventricular function in a mouse model of long-term myocardial infarction

In summary, we have performed a complete characterization of LV post-infarction remodeling in a DBA/2J mouse model of MI, using parameters adapted to the particular characteristics of the model In the future, this well characterized model will be used in both investigative and pharmacological studies that require accurate quantitative monitoring of cardiac recovery after myocardial infarction

Reaching a consensus on research priorities for supporting women with autoimmune rheumatic diseases during pre-conception, pregnancy and early parenting: A Nominal Group Technique exercise with lay and professional stakeholders

Background:Women with autoimmune rheumatic diseases (ARDs) find it difficult to get information and support with family planning, pregnancy, and early parenting. A systematic approach to prioritising research is required to accelerate development and evaluation of interventions to meet the complex needs of this population. Methods:A Nominal Group Technique (NGT) exercise was carried out with lay and professional stakeholders (n=29). Stakeholders were prepared for debate through presentation of available evidence. Stakeholders completed three tasks to develop, individually rank, and reach consensus on research priorities: Task 1 – mapping challenges and services using visual timelines; Task 2 - identifying research topics; Task 3 - individually ranking research topics in priority order. Results of the ranking exercise were fed back to the group for comment. Results:The main themes emerging from Task 1 were the need for provision of information, multi-disciplinary care, and social and peer support. In Task 2, 15 research topics and 58 sub-topics were identified around addressing the challenges and gaps in care identified during Task 1. In Task 3, a consensus was reached on the ten research topics that should be given the highest priority. These were individually ranked, resulting in the following order of priorities (from 1 – highest to 10 – lowest): 1. Shared decision-making early in the care pathway; 2. Pre-conception counseling; 3. Information about medication use during pregnancy/breastfeeding; 4. Personalised care planning; 5. Support for partners/family members; 6. Information about local support/disease specific issues; 7. Shared decision-making across the care pathway; 8. Peer-support; 9. Social inequalities in care, and; 10. Guidance on holistic/alternative therapies. Conclusions:This systematic approach to identification of research priorities from a multi-disciplinary and lay perspective indicated that activities should focus on development and evaluation of interventions that increase patient involvement in clinical decision-making, multi-disciplinary models of care, and timely provision of information

GFP-tagged multimetal-tolerant bacteria and their detection in the rhizosphere of white mustard

The introduction of rhizobacteria that tolerate heavy metals is a promising approach to support plants involved in phytoextraction and phytostabilisation. In this study, soil of a metal-mine wasteland was analyzed for the presence of metal-tolerant bacterial isolates, and the tolerance patterns of the isolated strains for a number of heavy metals and antibiotics were compared. Several of the multimetal-tolerant strains were tagged with a broad host range reporter plasmid (i.e. pPROBE-NT) bearing a green fluorescent protein marker gene (gfp). Overall, the metal-tolerant isolates were predominately Gram-negative bacteria. Most of the strains showed a tolerance to five metals (Zn, Cu, Ni, Pb and Cd), but with differing tolerance patterns. From among the successfully tagged isolates, we used the transconjugant Pseudomonas putida G25 (pPROBE-NT) to inoculate white mustard seedlings. Despite a significant decrease in transconjugant abundance in the rhizosphere, the gfp-tagged cells survived on the root surfaces at a level previously reported for root colonisers

Image processing tools for the validation of CryoEM maps

The number of maps deposited in public databases (Electron Microscopy Data Bank, EMDB) determined by cryo-electron microscopy has quickly grown in recent years. With this rapid growth, it is critical to guarantee their quality. So far, map validation has primarily focused on the agreement between maps and models. From the image processing perspective, the validation has been mostly restricted to using two half-maps and the measurement of their internal consistency. In this article, we suggest that map validation can be taken much further from the point of view of image processing if 2D classes, particles, angles, coordinates, defoci, and micrographs are also provided. We present a progressive validation scheme that qualifies a result validation status from 0 to 5 and offers three optional qualifiers (A, W, and O) that can be added. The simplest validation state is 0, while the most complete would be 5AWO. This scheme has been implemented in a website https://biocomp.cnb.csic.es/EMValidationService/ to which reconstructed maps and their ESI can be uploaded

Global overview of the management of acute cholecystitis during the COVID-19 pandemic (CHOLECOVID study)

Background: This study provides a global overview of the management of patients with acute cholecystitis during the initial phase of the COVID-19 pandemic. Methods: CHOLECOVID is an international, multicentre, observational comparative study of patients admitted to hospital with acute cholecystitis during the COVID-19 pandemic. Data on management were collected for a 2-month study interval coincident with the WHO declaration of the SARS-CoV-2 pandemic and compared with an equivalent pre-pandemic time interval. Mediation analysis examined the influence of SARS-COV-2 infection on 30-day mortality. Results: This study collected data on 9783 patients with acute cholecystitis admitted to 247 hospitals across the world. The pandemic was associated with reduced availability of surgical workforce and operating facilities globally, a significant shift to worse severity of disease, and increased use of conservative management. There was a reduction (both absolute and proportionate) in the number of patients undergoing cholecystectomy from 3095 patients (56.2 per cent) pre-pandemic to 1998 patients (46.2 per cent) during the pandemic but there was no difference in 30-day all-cause mortality after cholecystectomy comparing the pre-pandemic interval with the pandemic (13 patients (0.4 per cent) pre-pandemic to 13 patients (0.6 per cent) pandemic; P = 0.355). In mediation analysis, an admission with acute cholecystitis during the pandemic was associated with a non-significant increased risk of death (OR 1.29, 95 per cent c.i. 0.93 to 1.79, P = 0.121). Conclusion: CHOLECOVID provides a unique overview of the treatment of patients with cholecystitis across the globe during the first months of the SARS-CoV-2 pandemic. The study highlights the need for system resilience in retention of elective surgical activity. Cholecystectomy was associated with a low risk of mortality and deferral of treatment results in an increase in avoidable morbidity that represents the non-COVID cost of this pandemic

Image processing tools for the validation of CryoEM maps

Documento escrito por un elevado número de autores/as, solo se referencia el/la que aparece en primer lugar y los/as autores/as pertenecientes a la UC3M.Correction: The authors regret the omission of one of the authors, Federico de Isidro Gómez, from the original manuscript. The corrected list of authors and affiliations for this paper is as shown above. The Royal Society of Chemistry apologises for these errors and any consequent inconvenience to authors and readers. (Faraday Discuss., 2022,240, 228-228. https://doi.org/10.1039/D2FD90074B)The number of maps deposited in public databases (Electron Microscopy Data Bank, EMDB) determined by cryo-electron microscopy has quickly grown in recent years. With this rapid growth, it is critical to guarantee their quality. So far, map validation has primarily focused on the agreement between maps and models. From the image processing perspective, the validation has been mostly restricted to using two half-maps and the measurement of their internal consistency. In this article, we suggest that map validation can be taken much further from the point of view of image processing if 2D classes, particles, angles, coordinates, defoci, and micrographs are also provided. We present a progressive validation scheme that qualifies a result validation status from 0 to 5 and offers three optional qualifiers (A, W, and O) that can be added. The simplest validation state is 0, while the most complete would be 5AWO. This scheme has been implemented in a website https://biocomp.cnb.csic.es/EMValidationService/ to which reconstructed maps and their ESI can be uploaded.Javier Vargas and Jordi Burguet would like to thank the Spanish Ministry of Science and Innovation for financial support through the call 2019 Proyectos de I+D+i - RTI Tipo A (PID2019108850RA-I00) and Arrate Muñoz Barrutia, PID2019-109820RB-I00, MCIN/AEI/ 10.13039/501100011033/, cofinanced by European Regional Development Fund (ERDF), A way of making Europe. The authors acknowledge the economic support from MICIN of the Instruct Image Processing Center (I2PC) as part of the Spanish participation in Instruct-ERIC, the European Strategic Infrastructure Project (ESFRI) in the area of Structural Biology, Grant PID2019-104757RB-I00 funded by MCIN/AEI/10.13039/501100011033/ and ERDF A way of making Europe, by the European Union and Grant PRE2020-093527 funded by MCIN/ AEI/ 10.13039/501100011033 and by ESF Investing in your future. We also acknowledge support from Comunidad Autónoma de Madrid through Grant: S2017/BMD-3817, Instituto de Salud Carlos III (project IMPaCT-Data, exp. IMP/ 00019), co-funded by the European Union, European Regional Development Fund (ERDF, A way to make Europe), and European Union (EU) and Horizon 2020 through grants: EOSC Life (INFRAEOSC-04-2018, Proposal: 824087), HighResCells (ERC- 2018- SyG, Proposal: 810057), IMpaCT (WIDESPREAD-03-2018Proposal: 857203), EOSC- Synergy (EINFRA-EOSC-5, Proposal: 857647), iNEXTDiscovery (Proposal: 871037), EnLaCES (H2020-MSCA-IF-2020, Proposal: 101024130)

EDTA reduces the physiological damage of lead on cardoon plants grown hydroponically

Cardoon seedlings (Cynara cardunculus L.) were grown hydroponically in nutrient solution and exposed to lead (Pb$^{2+}$: ImM) in the presence of a range of different EDTA concentrations (EDTANa$_2$: 0, 0.5, 1 or 2mM). Analyses were performed to establish whether the coordination of Pb$^{2+}$ transport by EDTA enhances the mobility of this metal within the plant and to determine the toxic effects of these treatments during a phytoextraction process. Net photosynthesis, transpiration rate and stomatal conductance decreased dramatically in plants treated with Pb$^{2+}$ or Pb-EDTA at doses below 1 mM. ln these treatments, most of the Pb$^{2+}$ accumulated in the roots, alld only a very low amount of it was translocated to the shoots. Increasing the EDTA doses up to Pb$^{2+}$ equimolarity, increased the Pb$^{2+}$ shoot content more than 10-fold without any physiological evidence of toxicity. The treatment with higher doses of EDTA (Pb$^{2+}$ 1 mM + EDTA 2 mM) did not show toxicity symptoms, but the Pb$^{2+}$ concentration in the aboveground tissues decreased when compared with the equimolar treatment. The interaction with the absorption of some essential cations such as Ca$^{2+}$ and phytotoxicity on chelated-assisted phytoextraction is discussed

The cost of care of systemic lupus erythematosus (SLE) in the UK:annual direct costs for adult SLE patients with active autoantibody-positive disease

Objectives The aim of the Systemic LUpus Erythematosus Cost of Care In Europe (LUCIE) study was to evaluate the annual direct medical costs of managing adults with active autoantibody-positive disease on medication for SLE in secondary care. This paper presents the UK analyses only. Methods A cost-of-illness study was conducted from the perspective of the National Health Service. Health resource utilization data were retrieved over a two-year period from four centres in England and unit cost data were taken from published sources. Results At baseline, 86 patients were included, 38 (44.2%) had severe SLE and 48 (55.8%) had non-severe SLE. The mean (SD) SELENA-SLEDAI score was 7.7 (5.7). The mean (SD) annual direct medical cost of was estimated at £3231 (£2333) per patient and was 2.2 times higher in patients with severe SLE compared with patients with non-severe SLE ( p &lt; 0.001). Multivariate model analyses showed that renal disease involvement ( p = 0.0016) and severe flares ( p = 0.0001) were associated with higher annual direct costs. Conclusions Improvement of the overall stability of SLE and early intervention to minimize the impact of renal disease may be two approaches to mitigate the long-term direct cost of managing SLE patients in the UK. </jats:sec