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| 2. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Journal article (peer-reviewed)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 3. |
- Caronna, Edoardo, et al.
(author)
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Redefining migraine prevention: early treatment with anti-CGRP monoclonal antibodies enhances response in the real world
- 2024
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In: JOURNAL OF NEUROLOGY NEUROSURGERY AND PSYCHIATRY. - 0022-3050 .- 1468-330X.
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Journal article (peer-reviewed)abstract
- Background Anti-CGRP monoclonal antibodies (anti-CGRP MAbs) are approved and available treatments for migraine prevention. Patients do not respond alike and many countries have reimbursement policies, which hinder treatments to those who might respond. This study aimed to investigate clinical factors associated with good and excellent response to anti-CGRP MAbs at 6 months. Methods European multicentre, prospective, real-world study, including high-frequency episodic or chronic migraine (CM) patients treated since March 2018 with anti-CGRP MAbs. We defined good and excellent responses as >= 50% and >= 75% reduction in monthly headache days (MHD) at 6 months, respectively. Generalised mixed-effect regression models (GLMMs) were used to identify variables independently associated with treatment response. Results Of the 5818 included patients, 82.3% were females and the median age was 48.0 (40.0-55.0) years. At baseline, the median of MHD was 20.0 (14.0-28.0) days/months and 72.2% had a diagnosis of CM. At 6 months (n=4963), 56.5% (2804/4963) were good responders and 26.7% (1324/4963) were excellent responders. In the GLMM model, older age (1.08 (95% CI 1.02 to 1.15), p=0.016), the presence of unilateral pain (1.39 (95% CI 1.21 to 1.60), p<0.001), the absence of depression (0.840 (95% CI 0.731 to 0.966), p=0.014), less monthly migraine days (0.923 (95% CI 0.862 to 0.989), p=0.023) and lower Migraine Disability Assessment at baseline (0.874 (95% CI 0.819 to 0.932), p<0.001) were predictors of good response (AUC of 0.648 (95% CI 0.616 to 0.680)). These variables were also significant predictors of excellent response (AUC of 0.691 (95% CI 0.651 to 0.731)). Sex was not significant in the GLMM models. Conclusions This is the largest real-world study of migraine patients treated with anti-CGRP MAbs. It provides evidence that higher migraine frequency and greater disability at baseline reduce the likelihood of responding to anti-CGRP MAbs, informing physicians and policy-makers on the need for an earlier treatment in order to offer the best chance of treatment success.
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| 4. |
- Cruz, Raquel, et al.
(author)
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Novel genes and sex differences in COVID-19 severity
- 2022
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In: Human Molecular Genetics. - : Oxford University Press. - 0964-6906 .- 1460-2083. ; 31:22, s. 3789-3806
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Journal article (peer-reviewed)abstract
- Here, we describe the results of a genome-wide study conducted in 11 939 coronavirus disease 2019 (COVID-19) positive cases with an extensive clinical information that were recruited from 34 hospitals across Spain (SCOURGE consortium). In sex-disaggregated genome-wide association studies for COVID-19 hospitalization, genome-wide significance (P < 5 × 10−8) was crossed for variants in 3p21.31 and 21q22.11 loci only among males (P = 1.3 × 10−22 and P = 8.1 × 10−12, respectively), and for variants in 9q21.32 near TLE1 only among females (P = 4.4 × 10−8). In a second phase, results were combined with an independent Spanish cohort (1598 COVID-19 cases and 1068 population controls), revealing in the overall analysis two novel risk loci in 9p13.3 and 19q13.12, with fine-mapping prioritized variants functionally associated with AQP3 (P = 2.7 × 10−8) and ARHGAP33 (P = 1.3 × 10−8), respectively. The meta-analysis of both phases with four European studies stratified by sex from the Host Genetics Initiative (HGI) confirmed the association of the 3p21.31 and 21q22.11 loci predominantly in males and replicated a recently reported variant in 11p13 (ELF5, P = 4.1 × 10−8). Six of the COVID-19 HGI discovered loci were replicated and an HGI-based genetic risk score predicted the severity strata in SCOURGE. We also found more SNP-heritability and larger heritability differences by age (<60 or ≥60 years) among males than among females. Parallel genome-wide screening of inbreeding depression in SCOURGE also showed an effect of homozygosity in COVID-19 hospitalization and severity and this effect was stronger among older males. In summary, new candidate genes for COVID-19 severity and evidence supporting genetic disparities among sexes are provided.
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| 5. |
- Ari Noriega, Jorge, et al.
(author)
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Does ecotourism impact biodiversity? : An assessment using dung beetles (Coleoptera: Scarabaeinae) as bioindicators in a tropical dry forest natural park
- 2020
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In: Ecological Indicators. - : Elsevier. - 1470-160X .- 1872-7034. ; 117
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Journal article (peer-reviewed)abstract
- Ecotourism can be defined as an environmental activity that takes place in well-preserved areas for recreation and with the responsibility of promoting their conservation. Nowadays, ecotourism is seen as a friendly pastime, but it can potentially affect negatively community diversity and structure by a number of processes such as soil compaction, erosion, and habitat alteration, among many others. Nonetheless, there is hardly any information on the impact of ecotourism in the Tropical Dry Forests and protected areas of the Neotropical region. In an attempt to fill this knowledge gap, the effect of ecotourism was evaluated in a study of a Tropical Dry Forest in the Tayrona National Natural Park of Colombia using dung beetles as bioindicators. A large-scale sampling of three sites with different levels of tourism intensity (no tourism - NT, low tourism - LT, and high tourism - HT) was performed using pitfall tramps baited with human/pig dung during two climatic seasons (rainy and dry). A total of 3238 individuals belonging to nine genera and 15 species were collected. Significant differences in abun-dances, richness, and the Shannon Wiener diversity index were observed between areas with tourism and those without. These differences disappeared during the dry season in response to the strong reduction in species abundance and richness associated to that time of year. All areas maintained a homogeneous beetle structure in terms of functional groups present irrelevant of the intensity level of tourism. Beta diversity analysis shows that the dung beetle assemblage has a nested structure, indicating that the pressure exerted by tourism entails the loss of particular species. Our results advocate that it is necessary to implement conservation strategies in order to reduce the negative impact of tourism on the National Park's biodiversity.
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| 6. |
- Barredo, José I., et al.
(author)
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Mapping and assessment of forest ecosystems and their services : Applications and guidance for decision making in the framework of MAES
- 2015
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Reports (other academic/artistic)abstract
- The aim of this report is to illustrate by means of a series of case studies the implementation of mapping and assessment of forest ecosystem services in different contexts and geographical levels. Methodological aspects, data issues, approaches, limitations, gaps and further steps for improvement are analysed for providing good practices and decision making guidance. The EU initiative on Mappingand Assessment of Ecosystems and their Services (MAES), with the support of all Member States, contributes to improve the knowledge on ecosystem services. MAES is one of the building-block initiatives supporting the EU Biodiversity Strategy to 2020.
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| 7. |
- Commowick, Olivier, et al.
(author)
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Objective Evaluation of Multiple Sclerosis Lesion Segmentation using a Data Management and Processing Infrastructure
- 2018
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In: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 8
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Journal article (peer-reviewed)abstract
- We present a study of multiple sclerosis segmentation algorithms conducted at the international MICCAI 2016 challenge. This challenge was operated using a new open-science computing infrastructure. This allowed for the automatic and independent evaluation of a large range of algorithms in a fair and completely automatic manner. This computing infrastructure was used to evaluate thirteen methods of MS lesions segmentation, exploring a broad range of state-of-theart algorithms, against a high-quality database of 53 MS cases coming from four centers following a common definition of the acquisition protocol. Each case was annotated manually by an unprecedented number of seven different experts. Results of the challenge highlighted that automatic algorithms, including the recent machine learning methods (random forests, deep learning,.), are still trailing human expertise on both detection and delineation criteria. In addition, we demonstrate that computing a statistically robust consensus of the algorithms performs closer to human expertise on one score (segmentation) although still trailing on detection scores.
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| 8. |
- Pardo-Camacho, Cristina, et al.
(author)
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Mucosal Plasma Cell Activation and Proximity to Nerve Fibres Are Associated with Glycocalyx Reduction in Diarrhoea-Predominant Irritable Bowel Syndrome : Jejunal Barrier Alterations Underlying Clinical Manifestations
- 2022
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In: Cells. - Basel : MDPI. - 2073-4409. ; 11:13
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Journal article (peer-reviewed)abstract
- Irritable bowel syndrome (IBS) is a disorder of brain-gut interaction characterised by abdominal pain and changes in bowel habits. In the diarrhoea subtype (IBS-D), altered epithelial barrier and mucosal immune activation are associated with clinical manifestations. We aimed to further evaluate plasma cells and epithelial integrity to gain understanding of IBS-D pathophysiology. One mucosal jejunal biopsy and one stool sample were obtained from healthy controls and IBS-D patients. Gastrointestinal symptoms, stress, and depression scores were recorded. In the jejunal mucosa, RNAseq and gene set enrichment analyses were performed. A morphometric analysis by electron microscopy quantified plasma cell activation and proximity to enteric nerves and glycocalyx thickness. Immunoglobulins concentration was assessed in the stool. IBS-D patients showed differential expression of humoral pathways compared to controls. Activation and proximity of plasma cells to nerves and IgG concentration were also higher in IBS-D. Glycocalyx thickness was lower in IBS-D compared to controls, and this reduction correlated with plasma cell activation, proximity to nerves, and clinical symptoms. These results support humoral activity and loss of epithelial integrity as important contributors to gut dysfunction and clinical manifestations in IBS-D. Additional studies are needed to identify the triggers of these alterations to better define IBS-D pathophysiology.
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| 9. |
- Serrano Zueras, Clara, et al.
(author)
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Safety and efficacy evaluation of the automatic stepwise recruitment maneuver in the neonatal population : An in vivo interventional study. Can anesthesiologists safely perform automatic lung recruitment maneuvers in neonates?
- 2021
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In: Pediatric Anaesthesia. - : John Wiley & Sons. - 1155-5645 .- 1460-9592. ; 31:9, s. 1003-1010
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Journal article (peer-reviewed)abstract
- BackgroundA new software has recently been incorporated in almost all new anesthesia machines to enable automatic lung recruitment maneuvers. To date, no studies have assessed the safety and efficacy of these automatic software programs in the neonatal population.AimsWe aimed to evaluate the safety and efficacy of the lung recruitment maneuver performed using the automatic stepwise recruitment maneuver software of the FLOW-i 4.3 Anesthesia System® in a healthy and live neonatal model.MethodsEight male newborn piglets were included in the study. The lung recruitment maneuver was performed in pressure-controlled ventilation with a constant driving pressure (15 cmH2O) in a stepwise increasing positive end-expiratory pressure (PEEP) model. The target peak inspiratory pressure (PIP) was 30 cmH2O and PEEP was 15 cmH2O. The maneuver lasted for 39 seconds. The hemodynamic variables were monitored using the PICCO® system. The following respiratory parameters were monitored: oxygen saturation, fraction of inspired oxygen, partial pressure of oxygen and carbon dioxide in the arterial blood, end-tidal carbon dioxide pressure, PIP, plateau pressure, PEEP, static compliance (Cstat), and dynamic compliance (Cdyn).Safety was evaluated by assessing the accuracy of the software, need for not interrupting the maneuver, hemodynamic stability, and absence of adverse respiratory events with the lung recruitment maneuver. Efficacy was evaluated by improvement in Cstat and Cdyn after performing the lung recruitment maneuver.ResultsAll lung recruitment maneuvers were safely performed as scheduled without any interruptions. No pneumothorax or other side effects were observed. Hemodynamic stability was maintained during the lung recruitment maneuver. We observed an improvement of 33% in Cdyn and 24% in Cstat after the maneuver.ConclusionsThe automatic stepwise recruitment maneuver software of the FLOW-i 4.3 Anesthesia System® is safe and efficacious in a healthy neonatal model. We did not observe any adverse respiratory or hemodynamic events during the implementation of the lung recruitment maneuver in the pressure-controlled ventilation mode using a stepwise increasing PEEP (30/15 cmH2O) approach.
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| 10. |
- Zamora, Juan Carlos, et al.
(author)
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Considerations and consequences of allowing DNA sequence data as types of fungal taxa
- 2018
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In: IMA Fungus. - : INT MYCOLOGICAL ASSOC. - 2210-6340 .- 2210-6359. ; 9:1, s. 167-185
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Journal article (peer-reviewed)abstract
- Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
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