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| 2. |
- Colomé, Núria, et al.
(författare)
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Multi-laboratory experiment PME11 for the standardization of phosphoproteome analysis
- 2022
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Ingår i: Journal of Proteomics. - : Elsevier. - 1874-3919 .- 1876-7737. ; 251
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Tidskriftsartikel (refereegranskat)abstract
- Global analysis of protein phosphorylation by mass spectrometry proteomic techniques has emerged in the last decades as a powerful tool in biological and biomedical research. However, there are several factors that make the global study of the phosphoproteome more challenging than measuring non-modified proteins. The low stoichiometry of the phosphorylated species and the need to retrieve residue specific information require particular attention on sample preparation, data acquisition and processing to ensure reproducibility, qualitative and quantitative robustness and ample phosphoproteome coverage in phosphoproteomic workflows. Aiming to investigate the effect of different variables in the performance of proteome wide phosphoprotein analysis protocols, ProteoRed-ISCIII and EuPA launched the Proteomics Multicentric Experiment 11 (PME11). A reference sample consisting of a yeast protein extract spiked in with different amounts of a phosphomix standard (Sigma/Merck) was distributed to 31 laboratories around the globe. Thirty-six datasets from 23 laboratories were analyzed. Our results indicate the suitability of the PME11 reference sample to benchmark and optimize phosphoproteomics strategies, weighing the influence of different factors, as well as to rank intra and inter laboratory performance.
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| 3. |
- Fernández-Calviño, David, et al.
(författare)
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Using pine bark and mussel shell amendments to reclaim microbial functions in a Cu polluted acid mine soil
- 2018
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Ingår i: Applied Soil Ecology. - : Elsevier BV. - 0929-1393. ; 127, s. 102-111
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Tidskriftsartikel (refereegranskat)abstract
- An extremely acid mine soil polluted with Cu was amended with pine bark, crushed mussel shell or a 1:1 mixture of these two by-products. The performance of the soil microbial community was measured as the bacterial and fungal community growth, which were monitored during 2 years following the amendments. Pine bark caused significant increases of microbial growth rates, but with distinct differences between fungal and bacterial groups. Bacterial growth increased transiently at intermediate rates of pine bark applications, but returned to control rates within 2 years of application. In contrast, pine bark applications consistently increased fungal growth with effects that were maintained throughout the study period. The addition of only crushed mussel shell to the mine soil caused very delayed positive effects on the bacterial growth and almost no significant effects on the fungal growth. However, the combination of pine bark with crushed mussel shells 1:1 mixtures caused positive growth responses of both bacteria and fungi that remained persistent throughout the 2 years of study. Fungal and bacterial growth were both suppressed in the mine soil by the lack of organic matter. In addition, bacterial growth was also secondarily suppressed by acidity, and hence, when organic matter (pine bark) additions were combined with pH increases (crushed mussel shell additions), bacterial growth was additionally stimulated. In conclusion, the proposed mixture of by-products (pine bark and crushed mussel shell) is suggested as a promising reclamation strategy for acid mine soils. These results also suggest that in soils like that studied here the organic matter limitation is a more important factor than the soil pH and Cu availability for fungal and bacterial performance.
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| 4. |
- Vialas, Vital, et al.
(författare)
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A multicentric study to evaluate the use of relative retention times in targeted proteomics
- 2017
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Ingår i: Journal of Proteomics. - : Elsevier BV. - 1874-3919. ; 152, s. 138-149
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Tidskriftsartikel (refereegranskat)abstract
- Despite the maturity reached by targeted proteomic strategies, reliable and standardized protocols are urgently needed to enhance reproducibility among different laboratories and analytical platforms, facilitating a more widespread use in biomedical research. To achieve this goal, the use of dimensionless relative retention times (iRT), defined on the basis of peptide standard retention times (RT), has lately emerged as a powerful tool. The robustness, reproducibility and utility of this strategy were examined for the first time in a multicentric setting, involving 28 laboratories that included 24 of the Spanish network of proteomics laboratories (ProteoRed-ISCIII). According to the results obtained in this study, dimensionless retention time values (iRTs) demonstrated to be a useful tool for transferring and sharing peptide retention times across different chromatographic set-ups both intra- and inter-laboratories. iRT values also showed very low variability over long time periods. Furthermore, parallel quantitative analyses showed a high reproducibility despite the variety of experimental strategies used, either MRM (multiple reaction monitoring) or pseudoMRM, and the diversity of analytical platforms employed. Biological significance From the very beginning of proteomics as an analytical science there has been a growing interest in developing standardized methods and experimental procedures in order to ensure the highest quality and reproducibility of the results. In this regard, the recent (2012) introduction of the dimensionless retention time concept has been a significant advance. In our multicentric (28 laboratories) study we explore the usefulness of this concept in the context of a targeted proteomics experiment, demonstrating that dimensionless retention time values is a useful tool for transferring and sharing peptide retention times across different chromatographic set-ups.
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| 5. |
- Ferrando, Carlos, et al.
(författare)
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Effects of oxygen on post-surgical infections during an individualised perioperative open-lung ventilatory strategy : a randomised controlled trial
- 2020
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Ingår i: British Journal of Anaesthesia. - : ELSEVIER SCI LTD. - 0007-0912 .- 1471-6771. ; 124:1, s. 110-120
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Tidskriftsartikel (refereegranskat)abstract
- Background: We aimed to examine whether using a high fraction of inspired oxygen (FIO2) in the context of an individualised intra- and postoperative open-lung ventilation approach could decrease surgical site infection (SSI) in patients scheduled for abdominal surgery. Methods: We performed a multicentre, randomised controlled clinical trial in a network of 21 university hospitals from June 6, 2017 to July 19, 2018. Patients undergoing abdominal surgery were randomly assigned to receive a high (0.80) or conventional (0.3) FIO2 during the intraoperative period and during the first 3 postoperative hours. All patients were mechanically ventilated with an open-lung strategy, which included recruitment manoeuvres and individualised positive end-expiratory pressure for the best respiratory-system compliance, and individualised continuous postoperative airway pressure for adequate peripheral oxyhaemoglobin saturation. The primary outcome was the prevalence of SSI within the first 7 postoperative days. The secondary outcomes were composites of systemic complications, length of intensive care and hospital stay, and 6-month mortality. Results: We enrolled 740 subjects: 371 in the high FIO2 group and 369 in the low FIO2 group. Data from 717 subjects were available for final analysis. The rate of SSI during the first postoperative week did not differ between high (8.9%) and low (9.4%) FIO2 groups (relative risk [RR]: 0.94; 95% confidence interval [CI]: 0.59-1.50; P=0.90]). Secondary outcomes, such as atelectasis (7.7% vs 9.8%; RR: 0.77; 95% CI: 0.48-1.25; P=0.38) and myocardial ischaemia (0.6% [n=2] vs 0% [n=0]; P=0.47) did not differ between groups. Conclusions: An oxygenation strategy using high FIO2 compared with conventional FIO2 did not reduce postoperative SSIs in abdominal surgery. No differences in secondary outcomes or adverse events were found.
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| 6. |
- Gutierrez-Gutierrez, Belen, et al.
(författare)
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Propensity Score and Desirability of Outcome Ranking Analysis of Ertapenem for Treatment of Nonsevere Bacteremic Urinary Tract Infections Due to Extended-Spectrum-Beta-Lactamase-Producing Enterobacterales in Kidney Transplant Recipients
- 2021
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Ingår i: Antimicrobial Agents and Chemotherapy. - : American Society for Microbiology. - 0066-4804 .- 1098-6596. ; 65:11
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Tidskriftsartikel (refereegranskat)abstract
- There are scarce data on the efficacy of ertapenem in the treatment of bacteremia due to extended-spectrum-beta-lactamase (ESBL)-producing Enterobacterales (ESBL-E) in kidney transplant (KT) recipients. We evaluated the association between treatment with ertapenem or meropenem and clinical cure in KT recipients with nonsevere bacteremic urinary tract infections (B-UTI) caused by ESBL-E. We performed a registered, retrospective, international (29 centers in 14 countries) cohort study (INCREMENT-SOT, NCT02852902). The association between targeted therapy with ertapenem versus meropenem and clinical cure at day 14 (the principal outcome) was studied by logistic regression. Propensity score matching and desirability of outcome ranking (DOOR) analyses were also performed. A total of 201 patients were included; only 1 patient (treated with meropenem) in the cohort died. Clinical cure at day 14 was reached in 45/100 (45%) and 51/101 (50.5%) of patients treated with ertapenem and meropenem, respectively (adjusted OR 1.29; 95% CI 0.51 to 3.22; P = 0.76); the propensity score-matched cohort included 55 pairs (adjusted OR for clinical cure at day 14, 1.18; 95% CI 0.43 to 3.29; P = 0.74). In this cohort, the proportion of cases treated with ertapenem with better DOOR than with meropenem was 49.7% (95% CI, 40.4 to 59.1%) when hospital stay was considered. It ranged from 59 to 67% in different scenarios of a modified (weights-based) DOOR sensitivity analysis when potential ecological advantage or cost was considered in addition to outcome. In conclusion, targeted therapy with ertapenem appears as effective as meropenem to treat nonsevere B-UTI due to ESBL-E in KT recipients and may have some advantages.
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| 7. |
- Guzman-Parra, Jose, et al.
(författare)
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Attitudes and use of information and communication technologies in older adults with mild cognitive impairment or early stages of dementia and their caregivers : cross-sectional study
- 2020
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Ingår i: Journal of Medical Internet Research. - : JMIR Publications. - 1438-8871. ; 22:6
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Information and communication technologies are promising tools to increase the quality of life of people with dementia or mild cognitive impairment and that of their caregivers. However, there are barriers to their use associated with sociodemographic factors and negative attitudes, as well as inadequate knowledge about technologies. OBJECTIVE: The aim of this study was to analyze technophilia (attitudes toward new technologies) and the use of smartphones and tablets along with associated factors in people with dementia/mild cognitive impairment and their caregivers. METHODS: Data from the first visit of the Support Monitoring and Reminder for Mild Dementia (SMART4MD) randomized multicenter clinical trial were used for this analysis. Data were obtained from two European countries, Spain and Sweden, and from three centers: Consorci Sanitari de Terrassa (Catalonia, Spain), Servicio Andaluz de Salud (Andalusia, Spain), and the Blekinge Institute of Technology (Sweden). Participants with a score between 20 and 28 in the Mini Mental State Examination, with memory problems (for more than 6 months), and who were over the age of 55 years were included in the study, along with their caregivers. The bivariate Chi square and Mann-Whitney tests, and multivariate linear and logistic regression models were used for statistical analysis. RESULTS: A total of 1086 dyads were included (N=2172). Overall, 299 (27.53%) of people with dementia/mild cognitive impairment had a diagnosis of dementia. In addition, 588 (54.14%) of people with dementia/mild cognitive impairment reported using a smartphone almost every day, and 106 (9.76%) used specific apps or software to support their memory. Among the caregivers, 839 (77.26%) used smartphones and tablets almost every day, and 181 (16.67%) used specific apps or software to support their memory. The people with dementia/mild cognitive impairment showed a lower level of technophilia in comparison to that of their caregivers after adjusting for confounders (B=0.074, P=.02) with differences in technology enthusiasm (B=0.360, P<.001), but not in technology anxiety (B=-0.042, P=.37). Technophilia was associated with lower age (B=-0.009, P=.004), male gender (B=-0.160, P<.001), higher education level (P=.01), living arrangement (living with children vs single; B=-2.538, P=.01), country of residence (Sweden vs Spain; B=0.256, P<.001), lower depression (B=-0.046, P<.001), and better health status (B=0.004, P<.001) in people with dementia/mild cognitive impairment. Among caregivers, technophilia was associated with comparable sociodemographic factors (except for living arrangement), along with a lower caregiver burden (B=-0.005, P=.04) and better quality of life (B=0.348, P<.001). CONCLUSIONS: Technophilia was associated with a better quality of life and sociodemographic variables in people with dementia/mild cognitive impairment and caregivers, suggesting potential barriers for technological interventions. People with dementia/mild cognitive impairment frequently use smartphones and tablets, but the use of specific apps or software to support memory is limited. Interventions using these technologies are needed to overcome barriers in this population related to sociodemographic characteristics and the lack of enthusiasm for new technologies. TRIAL REGISTRATION: ClinicalTrials.gov NCT03325699; https://clinicaltrials.gov/ct2/show/NCT03325699. ©Jose Guzman-Parra, Pilar Barnestein-Fonseca, Gloria Guerrero-Pertiñez, Peter Anderberg, Luis Jimenez-Fernandez, Esperanza Valero-Moreno, Jessica Marian Goodman-Casanova, Antonio Cuesta-Vargas, Maite Garolera, Maria Quintana, Rebeca I García-Betances, Evi Lemmens, Johan Sanmartin Berglund, Fermin Mayoral-Cleries.
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| 8. |
- Mercaldo, Valentina, et al.
(författare)
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Altered striatal actin dynamics drives behavioral inflexibility in a mouse model of fragile X syndrome.
- 2023
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Ingår i: Neuron. - : Elsevier BV. - 1097-4199 .- 0896-6273.
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Tidskriftsartikel (refereegranskat)abstract
- The proteome of glutamatergic synapses is diverse across the mammalian brain and involved in neurodevelopmental disorders (NDDs). Among those is fragile X syndrome (FXS), an NDD caused by the absence of the functional RNA-binding protein FMRP. Here, we demonstrate how the brain region-specific composition of postsynaptic density (PSD) contributes to FXS. In the striatum, the FXS mouse model shows an altered association of the PSD with the actin cytoskeleton, reflecting immature dendritic spine morphology and reduced synaptic actin dynamics. Enhancing actin turnover with constitutively active RAC1 ameliorates these deficits. At the behavioral level, the FXS model displays striatal-driven inflexibility, a typical feature of FXS individuals, which is rescued by exogenous RAC1. Striatal ablation of Fmr1 is sufficient to recapitulate behavioral impairments observed in the FXS model. These results indicate that dysregulation of synaptic actin dynamics in the striatum, a region largely unexplored in FXS, contributes to the manifestation of FXS behavioral phenotypes.
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| 9. |
- Phillips, Helen R. P., et al.
(författare)
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Global distribution of earthworm diversity
- 2019
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 366:6464, s. 480-
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Tidskriftsartikel (refereegranskat)abstract
- Soil organisms, including earthworms, are a key component of terrestrial ecosystems. However, little is known about their diversity, their distribution, and the threats affecting them. We compiled a global dataset of sampled earthworm communities from 6928 sites in 57 countries as a basis for predicting patterns in earthworm diversity, abundance, and biomass. We found that local species richness and abundance typically peaked at higher latitudes, displaying patterns opposite to those observed in aboveground organisms. However, high species dissimilarity across tropical locations may cause diversity across the entirety of the tropics to be higher than elsewhere. Climate variables were found to be more important in shaping earthworm communities than soil properties or habitat cover. These findings suggest that climate change may have serious implications for earthworm communities and for the functions they provide.
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| 10. |
- Pierrotti, Ligia C., et al.
(författare)
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Efficacy of beta-lactam/beta-lactamase inhibitors to treat extended-spectrum beta-lactamase-producing Enterobacterales bacteremia secondary to urinary tract infection in kidney transplant recipients (INCREMENT-SOT Project)
- 2021
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Ingår i: Transplant Infectious Disease. - : John Wiley & Sons. - 1398-2273 .- 1399-3062. ; 23:3
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Tidskriftsartikel (refereegranskat)abstract
- Background Whether active therapy with beta-lactam/beta-lactamase inhibitors (BLBLI) is as affective as carbapenems for extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-E) bloodstream infection (BSI) secondary to urinary tract infection (UTI) in kidney transplant recipients (KTRs) remains unclear. Methods We retrospectively evaluated 306 KTR admitted to 30 centers from January 2014 to October 2016. Therapeutic failure (lack of cure or clinical improvement and/or death from any cause) at days 7 and 30 from ESBL-E BSI onset was the primary and secondary study outcomes, respectively. Results Therapeutic failure at days 7 and 30 occurred in 8.2% (25/306) and 13.4% (41/306) of patients. Hospital-acquired BSI (adjusted OR [aOR]: 4.10; 95% confidence interval [CI]: 1.50-11.20) and Pitt score (aOR: 1.47; 95% CI: 1.21-1.77) were independently associated with therapeutic failure at day 7. Age-adjusted Charlson Index (aOR: 1.25; 95% CI: 1.05-1.48), Pitt score (aOR: 1.72; 95% CI: 1.35-2.17), and lymphocyte count <= 500 cells/mu L at presentation (aOR: 3.16; 95% CI: 1.42-7.06) predicted therapeutic failure at day 30. Carbapenem monotherapy (68.6%, primarily meropenem) was the most frequent active therapy, followed by BLBLI monotherapy (10.8%, mostly piperacillin-tazobactam). Propensity score (PS)-adjusted models revealed no significant impact of the choice of active therapy (carbapenem-containing vs any other regimen, BLBLI- vs carbapenem-based monotherapy) within the first 72 hours on any of the study outcomes. Conclusions Our data suggest that active therapy based on BLBLI may be as effective as carbapenem-containing regimens for ESBL-E BSI secondary to UTI in the specific population of KTR. Potential residual confounding and unpowered sample size cannot be excluded (ClinicalTrials.gov identifier: NCT02852902).
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