A Foundation LAnguage-Image model of the Retina (FLAIR): Encoding expert knowledge in text supervision

Foundation vision-language models are currently transforming computer vision, and are on the rise in medical imaging fueled by their very promising generalization capabilities. However, the initial attempts to transfer this new paradigm to medical imaging have shown less impressive performances than those observed in other domains, due to the significant domain shift and the complex, expert domain knowledge inherent to medical-imaging tasks. Motivated by the need for domain-expert foundation models, we present FLAIR, a pre-trained vision-language model for universal retinal fundus image understanding. To this end, we compiled 37 open-access, mostly categorical fundus imaging datasets from various sources, with up to 97 different target conditions and 284,660 images. We integrate the expert's domain knowledge in the form of descriptive textual prompts, during both pre-training and zero-shot inference, enhancing the less-informative categorical supervision of the data. Such a textual expert's knowledge, which we compiled from the relevant clinical literature and community standards, describes the fine-grained features of the pathologies as well as the hierarchies and dependencies between them. We report comprehensive evaluations, which illustrate the benefit of integrating expert knowledge and the strong generalization capabilities of FLAIR under difficult scenarios with domain shifts or unseen categories. When adapted with a lightweight linear probe, FLAIR outperforms fully-trained, dataset-focused models, more so in the few-shot regimes. Interestingly, FLAIR outperforms by a large margin more generalist, larger-scale image-language models, which emphasizes the potential of embedding experts' domain knowledge and the limitations of generalist models in medical imaging.Comment: The pre-trained model is available at: https://github.com/jusiro/FLAI

DOT: A flexible multi-objective optimization framework for transferring features across single-cell and spatial omics

Single-cell RNA sequencing (scRNA-seq) and spatially-resolved imaging/sequencing technologies have revolutionized biomedical research. On one hand, scRNA-seq provides information about a large portion of the transcriptome for individual cells, but lacks the spatial context. On the other hand, spatially-resolved measurements come with a trade-off between resolution and gene coverage. Combining scRNA-seq with different spatially-resolved technologies can thus provide a more complete map of tissues with enhanced cellular resolution and gene coverage. Here, we propose DOT, a novel multi-objective optimization framework for transferring cellular features across these data modalities. DOT is flexible and can be used to infer categorical (cell type or cell state) or continuous features (gene expression) in different types of spatial omics. Our optimization model combines practical aspects related to tissue composition, technical effects, and integration of prior knowledge, thereby providing flexibility to combine scRNA-seq and both low- and high-resolution spatial data. Our fast implementation based on the Frank-Wolfe algorithm achieves state-of-the-art or improved performance in localizing cell features in high- and low-resolution spatial data and estimating the expression of unmeasured genes in low-coverage spatial data across different tissues. DOT is freely available and can be deployed efficiently without large computational resources; typical cases-studies can be run on a laptop, facilitating its use.Comment: 36 pages, 6 figure

Comparison of Mechanical and Structural Properties of Nickel-titanium Alloy with Titanium-molybdenum Alloy and Titanium-niobium Alloy as Potential Metals for Endodontic Files

Introduction: The objective of this study was to compare the mechanical and structural properties of the nickel-titanium (Ni-Ti) alloy already used in endodontics with titanium-molybdenum (Ti-Mo) and titanium-niobium (Ti-Nb) alloys to determine if these can be suggested in the manufacture of endodontic files. Methods and Materials: Orthodontic wires made of the different alloys were used. The previously mentioned alloys were characterized by energy-dispersive X-ray spectroscopy (EDX), X-ray diffraction (XRD) and torsion tests. Cyclic fatigue tests were performed on a simulated canal with a curvature of 86° to 375 rpm. The fractured surfaces of the wires were observed by means of scanning electron microscopy (SEM). A Kruskal-Wallis test and U Mann Whitney test were used to determine significant differences in cyclic fatigue between groups. Results: In the mechanical tests, similar values of torsion were found for the three alloys. In XRD, the Ti-Nb showed less structural changes. In the cyclic fatigue test, Ti-Nb was found to be significantly more resistant with respect to Ni-Ti and Ti-Mo. Conclusion: Based on our in vitro study, Ti-Nb is suggested as a possible alloy for the manufacture of rotary files due to its impressive properties

The impact of the crisis in the external policy of Brazil

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Antibióticos empíricos para la neumonía adquirida en la comunidad en pacientes adultos: Una revisión sistemática y un metaanálisis en red

Objetivo: El objetivo principal de este metaanálisis en red es identificar el antibiótico empírico (Em-ATB) con mayor probabilidad de ser el mejor (HPBB) en términos de (1) tasa de curación y (2) tasa de mortalidad en pacientes hospitalizados con neumonía adquirida en la comunidad (NAC) . Método: Criterios de inclusión: (1) pacientes adultos (>16 años) diagnosticados de NAC que requirieron hospitalización; (2) aleatorizados a al menos dos Em-ATB diferentes, (3) que informen de la tasa de curación y (4) que estén escritos en inglés o español. Criterios de exclusión: (1) protocolo de antibióticos ambiguo y (2) publicados exclusivamente en formato resumen o carta. Fuentes de datos: Medline, Embase, Cochrane y revisiones de citas desde el 1 de enero de 2000 hasta el 31 de diciembre de 2018. Riesgo de sesgo: Herramienta de Cochrane. Calidad de la revisión sistemática (RS): A MeaSurement Tool to Assess systematic Reviews-2. Certeza de la evidencia: Grading of Recommendations Assessment, Development and Evaluation. Análisis estadísticos: método frecuentista realizado con la biblioteca 'netmeta', paquete R. Resultados: se incluyeron 27 ensayos controlados aleatorizados (ECA) de las 41.307 citas seleccionadas inicialmente. En cuanto al riesgo de sesgo, más de una cuarta parte de los estudios presentaron riesgo bajo y ningún estudio presentó riesgo alto en todos los dominios. La calidad de la RS es moderada. Para la curación, se construyeron dos redes. Así, dos Em-ATB tienen la HPBB: cetarolina 600 mg (dos veces al día) y piperacilina 2000 mg (dos veces al día). Para la mortalidad, se construyeron tres redes. Así, tres Em-ATB tienen la HPBB: ceftriaxona 2000 mg (una vez al día) más levofloxacino 500 (dos veces al día), ertapenem 1000 mg (dos veces al día) y amikacina 250 mg (dos veces al día) más claritromicina 500 mg (dos veces al día). La certeza de la evidencia para cada resultado es moderada. Conclusiones: Para la tasa de curación, ceftarolina y piperacilina son las opciones con la HPBB. Sin embargo, para la tasa de mortalidad, las opciones son ceftriaxona más levofloxacino, ertapenem y amikacina más claritromicina. Parece necesario realizar un ECA que compare los tratamientos con el HPBB para cada evento (curación o mortalidad) (CRD42017060692).Objective: The main aim of this network meta-analysis is to identify the empiric antibiotic (Em-ATB) with the highest probability of being the best (HPBB) in terms of (1) cure rate and (2) mortality rate in hospitalised patients with community acquired pneumonia (CAP) . Method: Inclusion criteria: (1) adult patients (>16 years old) diagnosed with CAP that required hospitalisation; (2) randomised to at least two different Em-ATBs, (3) that report cure rate and (4) are written in English or Spanish. Exclusion criteria: (1) ambiguous antibiotics protocol and (2) published exclusively in abstract or letter format. Data sources: Medline, Embase, Cochrane and citation reviews from 1 January 2000 to 31 December 2018. Risk of bias: Cochrane's tool. Quality of the systematic review (SR): A MeaSurement Tool to Assess systematic Reviews-2. Certainity of the evidence: Grading of Recommendations Assessment, Development and Evaluation. Statistical analyses: frequentist method performed with the 'netmeta' library, R package. Results: 27 randomised controlled trials (RCTs) from the initial 41 307 screened citations were included. Regarding the risk of bias, more than one quarter of the studies presented low risk and no study presented high risk in all domains. The SR quality is moderate. For cure, two networks were constructed. Thus, two Em-ATBs have the HPBB: cetaroline 600 mg (two times a day) and piperacillin 2000 mg (two times a day). For mortality, three networks were constructed. Thus, three Em-ATBs have the HPBB: ceftriaxone 2000 mg (once a day) plus levofloxacin 500 (two times a day), ertapenem 1000 mg (two times a day) and amikacin 250 mg (two times a day) plus clarithromycin 500 mg (two times a day). The certainity of evidence for each results is moderate. Conclusion: For cure rate, ceftaroline and piperaciline are the options with the HPBB. However, for mortality rate, the options are ceftriaxone plus levofloxacin, ertapenem and amikacin plus clarithromycin. It seems necessary to conduct an RCT that compares treatments with the HPBB for each event (cure or mortality) (CRD42017060692)

Chromosomal evidence for a putative cryptic species in the Gymnotus carapo species-complex (Gymnotiformes, Gymnotidae)

<p>Abstract</p> <p>Background</p> <p>In this study we examined the karyotypes of morphologically indistinguishable populations of the electric knifefish <it>Gymnotus carapo sensu stricto </it>from the Eastern Amazon of Brazil. These were identified unambiguously on the basis of external morphology, meristics, and pigmentation.</p> <p>Results</p> <p>Specimens from one of five localities exhibited a karyotype previously not documented for <it>Gymnotus </it>species in the Amazon basin: 2n = 40 (34M/SM+6ST/A). Samples from the other four localities exhibited a different karyotype: 2n = 42 (30M/SM+12ST/A), which we had previously described. Specimens from all five localities presented constitutive heterochromatin in the centromeric region of almost all chromosomes, including in the distal and interstitial regions. Staining with 4'6-Diamidino-2-phenylindole revealed C-positive banding. In both karyotypes the Nucleolar Organizer Region (NOR) was located on the short arm of pair 20, and Chromomycin A₃stained the NORs. Fluorescent <it>in situ </it>hybridization with telomeric probes showed an Interstitial Telomeric Sequence (ITS) in the proximal short arm of a metacentric pair in the 2n = 40 karyotype.</p> <p>Conclusion</p> <p>The difference between the two karyotypes on the diploid number and chromosome morphology can be explained by rearrangements of the fusion-fission type and also by pericentric inversions. The presence of ITS in a metacentric pair of the 2n = 40 karyotype suggests that the difference in the diploid number of the karyotypes results from a fusion. The consistent 2n = 42 karyotype at four localities suggests an interbreeding population. However, because fusion-fission and pericentric inversions of this nature typically result in reproductive isolation, we speculate that the form with the 2n = 40 karyotype is a different species to that of the 2n = 42 form. Nonetheless, we did not observe evident differences in external morphology, meristics and pigmentation between the two forms, which suggest that they represent cryptic sympatric species in the <it>G. carapo </it>species complex. We speculate that the chromosomal speciation occurred recently, allowing insufficient time for the fixation of other differences following post-zygotic isolation.</p

Utilidad del score SOFA en la predicción de muerte materna en la UCI materna del INMP

Objective: &nbsp;To compare the SOFA score at admission and 24 hours and evaluate its usefulness in predicting maternal death. Materials and methods: A cross-sectional descriptive study of patients admitted to the Maternal ICU of the INMP was carried out from August 2014 to July 2019. Parametric and non-parametric tests were applied according to a previous evaluation of normality and a statistical significance p&lt;0.05. Statistical analysis was performed using the statistical package STATA version 13.&nbsp;Results: The mean age corresponds to 28.32 years. The mean gestational age corresponded to 31.33 weeks; The mean hospital stay was 4.52 days. The area under the curve for SOFA at entry was 0.8818 and the area under the curve for SOFA at 24 hours was 0.9755.&nbsp;&nbsp;&nbsp;&nbsp; P=0.1225. No significant differences were found between them. It was determined that the best cut-off point corresponds to a Score of 6 with a sensitivity that corresponds to 89.29% and a specificity of 79.13%. Conclusions: The SOFA Score adapts well to obstetric patients admitted to Maternal Intensive Care settings, maintaining a cut-off of 6 for admission SOFA with good sensitivity and specificity. (89.29%, 79.13%). The SOFA score is useful in maternal ICU environments and it should be used in our country.Objetivo: Comparar el score SOFA al ingreso y a las 24horas, y evaluar su utilidad en la predicción de la muerte materna. Materiales y métodos: Se realizó un estudio descriptivo de tipo transversal de las pacientes admitidas a la UCI Materna del INMP desde agosto del 2014 a Julio del 2019. Se aplicaron pruebas paramétricas o no paramétricas según evaluación previa de normalidad y se usó una significación estadística p&lt;0.05. El análisis estadístico se realizó utilizando el paquete estadístico STATA versión 13. Resultados: La media de la edad corresponde a 28.32 años. La media de la edad gestacional correspondió a 31.33 semanas; La media de la estancia hospitalaria fue de 4.52 días. El area bajo la curva para el SOFA al ingreso fue de 0.8818 y el area bajo la curva del SOFA a las 24horas fue de 0.9755. P=0.1225. No se encontraron diferencias significativas entre ellas. Se determinó que el mejor punto de corte corresponde a un Score de 6 con una sensibilidad que corresponde a 89.29% y una especificidad de 79.13%. Conclusiones: El Score SOFA se adapta bien a las pacientes obstétricas admitidas en los ambientes de Cuidados Intensivos Materno, manteniendo un corte de 6 para el SOFA de ingreso con una buena sensibilidad y especificidad. (89.29%, 79.13%). El Score SOFA es útil para ser usado en ambientes de UCI y además debe sugerirse su uso en toda UCI obstétrica de nuestro país

Toward sustainable environmental quality: Identifying priority research questions for Latin America

The Global Horizon Scanning Project (GHSP) is an innovative initiative that aims to identify important global environmental quality research needs. Here we report 20 key research questionsfrom LatinAmerica (LA).Members of the Society of Environmental Toxicology and Chemistry (SETAC) LA and other scientistsfrom LA were asked to submit research questions that would represent priority needs to address in the region. One hundred questions were received, then partitioned among categories, examined, and some rearranged during a workshop in Buenos Aires,Argentina. Twenty priority research questions were subsequently identified. These research questions included developing, improving, and harmonizing across LA countries methods for 1) identifying contaminants and degradation products in complex matrices (including biota); 2) advancing prediction of contaminant risks and effects in ecosystems, addressing lab-to-field extrapolation challenges, and understanding complexities of multiple stressors (including chemicals and climate change); and 3) improving management and regulatory tools toward achieving sustainable development. Whereas environmental contaminants frequently identified in these key questions were pesticides, pharmaceuticals, endocrine disruptors or modulators, plastics, and nanomaterials, commonly identified environmental challenges were related to agriculture, urban effluents, solid wastes, pulp and paper mills, and natural extraction activities. Several interesting research topics included assessing and preventing pollution impacts on conservation protected areas, integrating environment and health assessments, and developing strategiesfor identification, substitution, and design of less hazardous chemicals (e.g., green chemistry). Finally, a recurrent research need included developing an understanding of differential sensitivity of regional species and ecosystems to environmental contaminants and other stressors. Addressing these critical questions will support development of long-term strategic research efforts to advance more sustainable environmental quality and protect public health and the environment in LA.Centro de Investigaciones del Medioambient

A survey of the clinicopathological and molecular characteristics of patients with suspected Lynch syndrome in Latin America

Background: Genetic counselling and testing for Lynch syndrome (LS) have recently been introduced in several Latin America countries. We aimed to characterize the clinical, molecular and mismatch repair (MMR) variants spectrum of patients with suspected LS in Latin America. Methods: Eleven LS hereditary cancer registries and 34 published LS databases were used to identify unrelated families that fulfilled the Amsterdam II (AMSII) criteria and/or the Bethesda guidelines or suggestive of a dominant colorectal (CRC) inheritance syndrome. Results: We performed a thorough investigation of 15 countries and identified 6 countries where germline genetic testing for LS is available and 3 countries where tumor testing is used in the LS diagnosis. The spectrum of pathogenic MMR variants included MLH1 up to 54%, MSH2 up to 43%, MSH6 up to 10%, PMS2 up to 3% and EPCAM up to 0.8%. The Latin America MMR spectrum is broad with a total of 220 different variants which 80% were private and 20% were recurrent. Frequent regions included exons 11 of MLH1 (15%), exon 3 and 7 of MSH2 (17 and 15%, respectively), exon 4 of MSH6 (65%), exons 11 and 13 of PMS2 (31% and 23%, respectively). Sixteen international founder variants in MLH1, MSH2 and MSH6 were identified and 41 (19%) variants have not previously been reported, thus representing novel genetic variants in the MMR genes. The AMSII criteria was the most used clinical criteria to identify pathogenic MMR carriers although microsatellite instability, immunohistochemistry and family history are still the primary methods in several countries where no genetic testing for LS is available yet. Conclusion: The Latin America LS pathogenic MMR variants spectrum included new variants, frequently altered genetic regions and potential founder effects, emphasizing the relevance implementing Lynch syndrome genetic testing and counseling in all of Latin America countries.Radium Hospital Foundation (Oslo, Norway) in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript, Helse Sør-Øst (Norway) in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript, the French Association Recherche contre le Cancer (ARC) in the analysis, and interpretation of data, the Groupement des Entreprises Françaises dans la Lutte contre le Cancer (Gefluc) in the analysis, and interpretation of data, the Association Nationale de la Recherche et de la Technologie (ANRT, CIFRE PhD fellowship to H.T.) in the analysis, and interpretation of data and by the OpenHealth Institute in the analysis, and interpretation of data. Barretos Cancer Hospital received financial support by FINEP-CT-INFRA (02/2010)info:eu-repo/semantics/publishedVersio

Expansion of Signal Transduction Pathways in Fungi by Extensive Genome Duplication

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