A study of Machine Learning models for Clinical Coding of Medical Reports at CodiEsp 2020

The task of identifying one or more diseases associated with a patient’s clinical condition is often very complex, even for doctors and specialists. This process is usually time-consuming and has to take into account different aspects of what has occurred, including symptoms elicited and previous healthcare situations. The medical diagnosis is often provided to patients in the form of written paper without any correlation with a national or international standard. Even if the WHO (World Health Organization) released the ICD10 international glossary of diseases, almost no doctor has enough time to manually associate the patient’s clinical history with international codes. The CodiEsp task at CLEF 2020 addressed this issue by proposing the development of an automatic system to deal with this task. Our solution investigated different machine learning strategies in order to identify an approach to face that challenge. The main outcomes of the experiments showed that a strategy based on BERT for pre-filtering and one based on BiLSTMCNN-SelfAttention for classification provide valuable results. We carried out several experiments on a subset of the training set for tuning the final model submitted to the challenge. In particular, we analyzed the impact of the algorithm, the input encoding strategy, and the thresholds for multi-label classification. A set of experiments has been carried out also during a post hoc analysis. The experiments confirmed that the strategy submitted to the CodiEsp task is the best performing one among those evaluated, and it allowed us to obtain a final mean average error value on the test set equal to 0.202. To support future developments of the proposed approach and the replicability of the experiments we decided to make the source code publicly accessible

Electro-optically induced absorption in α-Si:H/α-SiCN waveguiding multistacks

Electro optical absorption in hydrogenated amorphous silicon (α-Si:H) - amorphous silicon carbonitride (α-SiCxNγ) multilayers have been studied in two different planar multistacks waveguides. The waveguides were realized by plasma enhanced chemical vapour deposition (PECVD), a technology compatible with the standard microelectronic processes. Light absorption is induced at λ = 1.55 μm through the application of an electric field which induces free carrier accumulation across the multiple insulator/ semiconductor device structure. The experimental performances have been compared to those obtained through calculations using combined two-dimensional (2-D) optical and electrical simulations. © 2008 Optical Society of America

E-Cadherin Destabilization Accounts for the Pathogenicity of Missense Mutations in Hereditary Diffuse Gastric Cancer

E-cadherin is critical for the maintenance of tissue architecture due to its role in cell-cell adhesion. E-cadherin mutations are the genetic cause of Hereditary Diffuse Gastric Cancer (HDGC) and missense mutations represent a clinical burden, due to the uncertainty of their pathogenic role. In vitro and in vivo, most mutations lead to loss-of-function, although the causal factor is unknown for the majority. We hypothesized that destabilization could account for the pathogenicity of E-cadherin missense mutations in HDGC, and tested our hypothesis using in silico and in vitro tools. FoldX algorithm was used to calculate the impact of each mutation in E-cadherin native-state stability, and the analysis was complemented with evolutionary conservation, by SIFT. Interestingly, HDGC patients harbouring germline E-cadherin destabilizing mutants present a younger age at diagnosis or death, suggesting that the loss of native-state stability of E-cadherin accounts for the disease phenotype. To elucidate the biological relevance of E-cadherin destabilization in HDGC, we investigated a group of newly identified HDGC-associated mutations (E185V, S232C and L583R), of which L583R is predicted to be destabilizing. We show that this mutation is not functional in vitro, exhibits shorter half-life and is unable to mature, due to premature proteasome-dependent degradation, a phenotype reverted by stabilization with the artificial mutation L583I (structurally tolerated). Herein we report E-cadherin structural models suitable to predict the impact of the majority of cancer-associated missense mutations and we show that E-cadherin destabilization leads to loss-of-function in vitro and increased pathogenicity in vivo

Late Pleistocene-Holocene History of Chaco-Pampa Sediments in Argentina and Paraguay

Eine erheblich verbesserte Rekonstruktion der spätpleistozänen/holozänen morphologischen und geologischen Geschichte des paraguayischen Chaco und der argentinischen Pampa Ebene wird vorgestellt. Wegen der großen Ausdehnung des Gebietes waren Satellitenbilder der Schlüssel, um frühere und neue interdisziplinäre geowissenschaftliche Ergebnisse zu einem verlässlicheren Bild zusammenzuführen. Für diesen synoptischen Überblick wurde die Interpretation von Fernerkundungsdaten durch Geländeuntersuchungen und physikalische Altersbestimmungen ergänzt. Viele Lumineszenzalter (75 IRSL und 12 TL) von Löß, lößähnlichen Sedimenten und Sanden wurden bestimmt, die bei der Rekonstruktion der Klimageschichte des Untersuchungsgebiets im Marinen Isotopen Stadium 3 bis 1 (MIS 3–1) beitragen. Lößablagerungen überwiegen in der Zeit vor MIS 2. Die numerische Alter von lakustrinen und alluvialen Sedimenten, im Löß zwischengelagert, belegen wechselnde feuchte und trockene Perioden in der Chaco/Pampa-Ebene im MIS 2 und MIS 1. Überwiegend trockene Bedingungen herrschten von 8.5 bis 3.5 ka BP (mittleres MIS 1), als Sande in Form von Dünen oder in Paläoflussbetten abgelagert wurden. Zeitlich begrenzte Phasen extrem verstärkter Paläoflussaktivität im Mittelholozän wurden auf sporadische Starkregenereignisse in den Anden zurückgeführt. Die Ursprungsgebiete des Löß, der lößartigen Sedimente und der sandigen Ablagerungen wurden in der südwestlichen Pampa, den benachbarten Andenabhängen und im Altiplano lokalisiert. Diese Sedimente wurden von dort nach Osten und später nach Nordosten transportiert, wie sich aus den morphologischen Mustern als Zeugnisse früherer äolischer Aktivität rekonstruieren ließ.researc

Analgesic effects of intravenous flunixin and intrafunicular lidocaine or their combination for castration of lambs.

Abstract Objective: To analyse the effectiveness of intrafunicular lidocaine and intravenous flunixin for reducing pain and signs of stress in lambs undergoing surgical castration. Design: Randomised controlled trial. Setting: One university teaching hospital in Italy. Participants: 30 healthy male lambs, 9-12 weeks old. Intervention: Allocation to five groups: a control group (C), undergoing general anaesthesia but not castration; a surgery group (S), undergoing orchiectomy without analgesic treatment; a surgery-lidocaine group (SL), undergoing orchiectomy and receiving intrafunicular 2 per cent lidocaine solution; a surgery-flunixin group (SF), undergoing orchiectomy and receiving intravenous flunixin; a surgery-flunixin-lidocaine group (SFL), undergoing orchiectomy and receiving both intrafunicular lidocaine and intravenous flunixin. Main outcome measures: Nociception and stress were assessed through intraoperative indicators, serum cortisol concentration, glycaemia, behaviour, immune response and clinical evaluation of the heart rate (HR), respiratory rate and rectal temperature after surgery. Results: Groups S and SL showed increased values of intraoperative HR, mean arterial pressure and postoperative cortisol concentration. In group SFL, cortisol values were similar to those of group C. No other difference could be detected. Conclusions: The combination of intravenous flunixin and intrafunicular lidocaine reduced the pain and discomfort of lambs castrated under general anaesthesia. Intrafunicular lidocaine alone did not prevent pain or discomfort associated with castration

Rtg signaling sustains mitochondrial respiratory capacity in hog1-dependent osmoadaptation

Mitochondrial RTG-dependent retrograde signaling, whose regulators have been characterized in Saccharomyces cerevisiae, plays a recognized role under various environmental stresses. Of special significance, the activity of the transcriptional complex Rtg1/3 has been shown to be modu-lated by Hog1, the master regulator of the high osmolarity glycerol pathway, in response to osmotic stress. The present work focuses on the role of RTG signaling in salt-induced osmotic stress and its interaction with HOG1. Wild-type and mutant cells, lacking HOG1 and/or RTG genes, are compared with respect to cell growth features, retrograde signaling activation and mitochondrial function in the presence and in the absence of high osmostress. We show that RTG2, the main upstream regulator of the RTG pathway, contributes to osmoadaptation in an HOG1-dependent manner and that, with RTG3, it is notably involved in a late phase of growth. Our data demonstrate that impairment of RTG signaling causes a decrease in mitochondrial respiratory capacity exclusively under os-mostress. Overall, these results suggest that HOG1 and the RTG pathway may interact sequentially in the stress signaling cascade and that the RTG pathway may play a role in inter-organellar metabolic communication for osmoadaptation

Detrital Thermochronology Reveals Major Middle Miocene Exhumation of the Eastern Flank ofthe Andes That Predates the PampeanFlat Slab (33°–33.5°S)

The Cordón del Plata and Cordón del Portillo (32.6°?33.8°S) are the portions of the FrontalCordillera that straddle the transition zone between the Pampean flat‐slab subduction segment to thenorth and the normal subduction segment to the south. A complete understanding of how the FrontalCordillera developed is necessary in order to evaluate different tectonic models for the Andes along withtheir relation to subduction dynamics and contractional upper‐crustal deformation. Detrital apatite fissiontrack thermochronology of modern river sediments that drain the eastern and western slopes of theCordón del Plata and the northern Cordón del Portillo provides constraints on regional exhumationhistories. AFT data from each catchment typically contain multiple age peaks, but all have a prominent15.3?17 Ma age peak. One catchment, the Las Tunas River has a unimodal distribution at 17.0 ± 1.1 Ma, with a confined track length distribution indicative of rapid cooling at that time. These results, combined with provenance analysis in the adjacent Cacheuta Basin, indicate significant early to middle Miocene (~16 Ma) exhumation in the Cordón del Plata and the northern sector of the Cordón del Portillo. Exhumation related to rock uplift occurred prior to the ~11 Ma onset of a flat slab eometry at these latitudes, but immediately after the main east vergent contractional event in the adjacent Principal Cordillera. Such Frontal Cordillera exhumation fits in an eastward, youngest to the foreland sequence of deformation of the different morphostructural Andean units at ~33°?34°S, arguing against the recently proposed west vergent orogenic system at these latitudes.Fil: Lossada, Ana Clara. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Estudios Andinos "Don Pablo Groeber". Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Estudios Andinos "Don Pablo Groeber"; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Geología; ArgentinaFil: Hoke, Gregory D.. Syracuse University. College Of Arts And Sciences. Department Of Earth Sciences; Estados UnidosFil: Giambiagi, Laura Beatriz. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales. Provincia de Mendoza. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales. Universidad Nacional de Cuyo. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales; ArgentinaFil: Fitzgerald, P. G.. Syracuse University. College Of Arts And Sciences. Department Of Earth Sciences; Estados UnidosFil: Mescua, Jose Francisco. Universidad Nacional de Cuyo. Facultad de Ciencias Exactas y Naturales; ArgentinaFil: Suriano, Julieta. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales. Provincia de Mendoza. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales. Universidad Nacional de Cuyo. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales; ArgentinaFil: Aguilar, A.. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales. Provincia de Mendoza. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales. Universidad Nacional de Cuyo. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales; Argentin

Ischaemic and bleeding complications with new, compared to standard, ADP-antagonist regimens in acute coronary syndromes: a meta-analysis of randomized trials

Background: Platelets play a pivotal role in the pathogenesis of acute coronary syndromes (ACS) and their inhibition remains a mainstay therapy in this setting. We aimed to perform a meta-analysis of randomized trials to evaluate the benefits of new oral antiplatelet regimens to block platelet ADPreceptors compared to standard-dose clopidogrel (300 mg loading dose followed by 75 mg/daily). Methods: We obtained results from all randomized trials enrolling patients with ACS. Primary endpoint was mortality. Secondary endpoints were myocardial infarction and definite in-stent thrombosis. Safety endpoint was the risk of major bleeding complications. We prespecified subanalyses according to new antiplatelet drugs (prasugrel/ticagrelor), high-dose clopidogrel (600 mg) and patients undergoing percutaneous coronary intervention. Results: A total of seven randomized trials were finally included in the meta-analysis (n = 58 591). We observed a significant reduction in mortality (2.9% vs. 3.4%, OR= 0.87, 95% CI 0.79–0.95, P = 0.002), recurrent myocardial infarction (4.2% vs. 5.2%, OR= 0.80, 95% CI 0.74–0.87, P < 0.0001), definite in-stent thrombosis (0.9% vs. 1.7%, OR= 0.52, 95% CI 0.43–0.63, P < 0.0001). The benefits in mortality and reinfarction were driven by the treatment with prasugrel or ticagrelor, without a significant difference in terms of major bleeding complications as compared to standarddose clopidogrel (5% vs. 4.7%, OR= 1.06 95% CI 0.96–1.17, P = 0.25). Conclusions: This meta-analysis showed that new oral antiplatelet regimens are associated with a significant reduction in mortality, reinfarction and in-stent thrombosis in ACS patients without an overall increase of major bleeding when treated with new antiplatelet drugs

Cenozoic exhumation history at the core of the Andes at 31.5°S revealed by apatite fission track thermochronology

The Andes at ~31°-32°S lie above the Chilean-Pampean flat slab zone (~27–33°S), where several morphostructural units developed resulting in a large orogenic width. The core of the Andes is composed of the La Ramada fold-and-thrust belt in Principal Cordillera and the basement blocks of Frontal Cordillera. While rock uplift of these blocks has been broadly constrained to the middle Miocene based on structural and provenance studies, thermochronologic approaches with the potential to directly constrain the timing and amount of exhumation have not been exploited until recently. Apatite fission track data from a ~1 km vertical profile collected within the Carboniferous Pico Los Sapos Batholith in the High Andes at 31.5°S places some constraints on the thermal evolution of the region since the Paleocene. The age-elevation profile combined with inverse thermal modeling and previous AHe thermochronology, indicates an episodic cooling/exhumation history. Rocks cooled rapidly in the early Cenozoic (ca. 65-55 Ma), followed by a period of relative thermal and tectonic stability when residence in an apatite partial annealing zone (PAZ) from at least ~52 Ma to ca.15 Ma, followed by final rapid cooling beginning ca. 15 Ma. We interpret early Cenozoic and middle Miocene rapid cooling events as to be related to erosional exhumation during Andean contractional phases, associated with thrust activity along the Mondaquita Fault. The age-elevation profile is partially duplicated, with upper samples being offset ~500 m due to back-thrusting since the late Miocene. The preservation of part of an exhumed PAZ indicates 3–5 km of exhumation since the onset of rapid cooling/exhumation at ~15 Ma. Although evidence for an early Cenozoic compressional phase in the High Andes at this latitude is scarce, the occurrence of a regional K-T (~65 Ma) unconformity supports our results. The Eocene Inca phase, registered north of 30°S, on the other hand, is not shown in our thermochronological data, suggesting that this tectonic phase did not affect the core of the Andes south of this latitude. Independent geological evidence both from the hinterland (structural, geochemical and thermochronological analyses) and foreland (provenance studies) corroborate our findings of a middle Miocene deformational event in the core of the Andes at 31.5°S.Fil: Lossada, Ana Clara. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Estudios Andinos "Don Pablo Groeber". Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Estudios Andinos "Don Pablo Groeber"; ArgentinaFil: Suriano, Julieta. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales. Provincia de Mendoza. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales. Universidad Nacional de Cuyo. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales; ArgentinaFil: Giambiagi, Laura Beatriz. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales. Provincia de Mendoza. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales. Universidad Nacional de Cuyo. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales; ArgentinaFil: Fitzgerald, Paul G.. Syracuse University; Estados UnidosFil: Hoke, Gregory. Syracuse University; Estados UnidosFil: Mescua, Jose Francisco. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales. Provincia de Mendoza. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales. Universidad Nacional de Cuyo. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales; Argentina. Universidad Nacional de Cuyo. Facultad de Ciencias Exactas y Naturales; ArgentinaFil: Tedesco, Ana. Secretaría de Industria y Minería. Servicio Geológico Minero Argentino; ArgentinaFil: Arzadún, Guadalupe. lA - Te Andes S.A. Laboratorio de Termocronología de Los Andes; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Bordese, Sofía. lA - Te Andes S.A. Laboratorio de Termocronología de Los Andes; Argentin

Impact of recycling and lateral sediment input on grain size fining trends – implications for reconstructing tectonic and climate forcings in ancient sedimentary systems

Grain size trends in basin stratigraphy are thought to preserve a rich record of the climatic and tectonic controls on landscape evolution. Stratigraphic models assume that over geological timescales, the downstream profile of sediment deposition is in dynamic equilibrium with the spatial distribution of tectonic subsidence in the basin, sea level and the flux and calibre of sediment supplied from mountain catchments. Here, we demonstrate that this approach in modelling stratigraphic responses to environmental change is missing a key ingredient: the dynamic geomorphology of the sediment routing system. For three large alluvial fans in the Iglesia basin, Argentine Andes we measured the grain size of modern river sediment from fan apex to toe and characterise the spatial distribution of differential subsidence for each fan by constructing a 3D model of basin stratigraphy from seismic data. We find, using a self-similar grain size fining model, that the profile of grain size fining on all three fans cannot be reproduced given the subsidence profile measured and for any sediment supply scenario. However, by adapting the self-similar model, we demonstrate that the grain size trends on each fan can be effectively reproduced when sediment is not only sourced from a single catchment at the apex of the system, but also laterally, from tributary catchments and through fan surface recycling. Without constraint on the dynamic geomorphology of these large alluvial systems, signals of tectonic and climate forcing in grain size data are masked and would be indecipherable in the geological record. This has significant implications for our ability to make sensitive, quantitative reconstructions of external boundary conditions from the sedimentary record