Towards Orthographic and Grammatical Clinical Text Correction: a First Approach

Akats Gramatikalen Zuzenketa (GEC, ingelesetik, Grammatical Error Analysis) Hizkuntza Naturalaren Prozesamenduaren azpieremu bat da, ortogra a, puntuazio edo gramatika akatsak dituzten testuak automatikoki zuzentzea helburu duena. Orain arte, bigarren hizkuntzako ikasleek ekoitzitako testuetara bideratu da gehien bat, ingelesez idatzitako testuetara batez ere. Master-Tesi honetan gaztelaniaz idatzitako mediku-txostenetarako Akats Gramatikalen Zuzenketa lantzen da. Arlo espezi ko hau ez da asko esploratu orain arte, ez gaztelaniarako zentzu orokorrean, ezta domeinu klinikorako konkretuki ere. Hasteko, IMEC (gaztelaniatik, Informes Médicos en Español Corregidos) corpusa aurkezten da, eskuz zuzendutako mediku-txosten elektronikoen bilduma paralelo berria. Corpusa automatikoki etiketatu da zeregin honetarako egokitutako ERRANT tresna erabiliz. Horrez gain, hainbat esperimentu deskribatzen dira, zeintzuetan sare neuronaletan oinarritutako sistemak ataza honetarako diseinatutako baseline sistema batekin alderatzen diren.Grammatical Error Correction (GEC) is a sub field of Natural Language Processing that aims to automatically correct texts that include errors related to spelling, punctuation or grammar. So far, it has mainly focused on texts produced by second language learners, mostly in English. This Master's Thesis describes a first approach to Grammatical Error Correction for Spanish health records. This specific field has not been explored much until now, nor in Spanish in a general sense nor for the clinical domain specifically. For this purpose, the corpus IMEC (Informes Médicos en Español Corregidos) ---a manually-corrected parallel collection of Electronic Health Records--- is introduced. This corpus has been automatically annotated using the toolkit ERRANT, specialized in the automatic annotation of GEC parallel corpora, which was adapted to Spanish for this task. Furthermore, some experiments using neural networks and data augmentation are shown and compared with a baseline system also created specifically for this task

Reasons for deciding to die in hospital or at home. The vision of professionals

Objetivo: Conocer las razones que llevan a decidir que los pacientes terminales mueran en el hospital o en su domicilio, desde la perspectiva de los/las profesionales. Método: Estudio cualitativo fenomenológico. Muestreo intencionado. Se realizaron cuatro grupos focales multidisciplinarios: dos en hospitales y dos en centros de Atención Primaria de Salud (APS) de Sevilla.Participaron 29 profesionales con al menos 2 años de experiencia con pacientes terminales, siguiendo el criterio de saturación teórica. Resultados: Las respuestas obtenidas del guion inicial se agruparon en tres categorías centrales: paciente y familia, profesionales y proceso asistencial. No suele consultarse al paciente sobre sus preferencias respecto al lugar donde quiere morir, y si además la familia las desconoce, no se puede realizar una planificación anticipada de cuidados. La familia elige el hospital por inseguridad respecto a la posibilidad de seguimiento y recursos en APS. Los/las profesionales poseen formación para abordar la muerte, pero no se sienten preparados, focalizando la atención en aspectos clínicos o administrativos. El proceso asistencial favorece a los pacientes oncológicos, pues es más sencillo identificar su terminalidad. No hay equidad en los recursos y es mejorable la comunicación interniveles. No se facilita la integración de la familia en el proceso que interfiere en su toma de decisiones. Conclusiones: Se debe fomentar la planificación anticipada de cuidados y usar el documento de voluntades anticipadas, la comunicación y la coordinación interniveles, dotar de recursos, especialmente a APS, y formar y preparar a los/las profesionales para abordar la muerte. Hay que implicar a la familia en el proceso, aportándole el apoyo necesario

Overview of BioASQ 2023: The eleventh BioASQ challenge on Large-Scale Biomedical Semantic Indexing and Question Answering

This is an overview of the eleventh edition of the BioASQ challenge in the context of the Conference and Labs of the Evaluation Forum (CLEF) 2023. BioASQ is a series of international challenges promoting advances in large-scale biomedical semantic indexing and question answering. This year, BioASQ consisted of new editions of the two established tasks b and Synergy, and a new task (MedProcNER) on semantic annotation of clinical content in Spanish with medical procedures, which have a critical role in medical practice. In this edition of BioASQ, 28 competing teams submitted the results of more than 150 distinct systems in total for the three different shared tasks of the challenge. Similarly to previous editions, most of the participating systems achieved competitive performance, suggesting the continuous advancement of the state-of-the-art in the field.Comment: 24 pages, 12 tables, 3 figures. CLEF2023. arXiv admin note: text overlap with arXiv:2210.0685

Work factors, spirituality, social support and their relationship with the consumption of alcohol in workers

El consumo de alcohol es un problema de salud pública que afecta los espacios laborales. El propósito del estudio es conocer la relación entre los factores laborales (el clima laboral, incertidumbre laboral, estrés laboral, espiri-tualidad, apoyo social) y el consumo de alcohol en los operarios de la industria maquiladora. Estudio correlacional en 307 trabajadores obreros. Los resultados indicaron relación positiva y significativa entre el clima laboral y el consumo de alcohol (rs=.25,p=.001); relación positiva y significativa de incertidumbre laboral con el consumo de alcohol (rs=.164,p=.004); relación negativa y significativa entre estrés laboral y apoyo social (rs=-.185,p=.001), se encontró relación negativa y significativa entre estrés laboral y espiritualidad (rs=-.124, p=.030). Se encontró relación positiva y significativa entre apoyo social y espiritualidad (rs=.191, p=.001). El Modelo de Regresión Lineal Múltiple fue significativo y explicó el 34.7% de la varianza. Conclusión: El consumo de alcohol es una conducta observada en población trabajadora, el clima laboral y la incertidumbre influyen positivamente en el consumo de alcohol. El apoyo social y la espiritualidad mostraron relación negativa y significativa con estrés laboral y pueden actuar como factores protectores del consumo de alcohol.Alcohol consumption is a public health problem that affects work spaces. The purpose of the study is to know the relationship between labor factors (work environment, work uncertainty, work stress, spirituality, social support) and alcohol consumption in workers in the maquiladora industry. Correlational study in 307 blue-collar workers. The data were analyzed, the results indicated a positive and significant relationship between the work environment and alcohol consumption (rs = .25, p = .001); positive and significant relationship between job uncertainty and alcohol consumption (rs = .164, p = .004); Negative and significant relationship between work stress and social support (rs = -. 185, p = .001), a negative and significant relationship was found between work stress and spirituality (rs = -. 124, p = .030). A positive and significant relationship was found between social support and spirituality (rs = .191, p = .001). The Multiple Linear Regression Model was significant and explained 34.7% of the variance. Conclusion: Alcohol consumption is a behavior observed in the working population, the work environment and uncertainty positively influence alcohol consumption. Social support and spirituality showed a negative and significant relationship with work stress and can act as protective factors against alcohol consumptio

Findings of the WMT 2022 Biomedical Translation Shared Task: Monolingual Clinical Case Reports

International audienceIn the seventh edition of the WMT Biomedical Task, we addressed a total of seven language pairs, namely English/German, English/French, English/Spanish, English/Portuguese, English/Chinese, English/Russian, English/Italian. This year’s test sets covered three types of biomedical text genre. In addition to scientific abstracts and terminology items used in previ- ous editions, we released test sets of clinical cases. The evaluation of clinical cases translations were given special attention by involving clinicians in the preparation of reference translations and manual evaluation. For the main MEDLINE test sets, we received a total of 609 submissions from 37 teams. For the ClinSpEn sub-task, we had the participation of five teams

J-PLUS: The javalambre photometric local universe survey

ABSTRACT: TheJavalambrePhotometric Local UniverseSurvey (J-PLUS )isanongoing 12-band photometricopticalsurvey, observingthousands of squaredegrees of theNorthernHemispherefromthededicated JAST/T80 telescope at the Observatorio Astrofísico de Javalambre (OAJ). The T80Cam is a camera with a field of view of 2 deg2 mountedon a telescopewith a diameter of 83 cm, and isequippedwith a uniquesystem of filtersspanningtheentireopticalrange (3500–10 000 Å). Thisfiltersystemis a combination of broad-, medium-, and narrow-band filters, optimallydesigned to extracttherest-framespectralfeatures (the 3700–4000 Å Balmer break region, Hδ, Ca H+K, the G band, and the Mg b and Ca triplets) that are key to characterizingstellartypes and delivering a low-resolutionphotospectrumforeach pixel of theobservedsky. With a typicaldepth of AB ∼21.25 mag per band, thisfilter set thusallowsforanunbiased and accuratecharacterization of thestellarpopulation in our Galaxy, itprovidesanunprecedented 2D photospectralinformationforall resolved galaxies in the local Universe, as well as accuratephoto-z estimates (at the δ z/(1 + z)∼0.005–0.03 precisionlevel) formoderatelybright (up to r ∼ 20 mag) extragalacticsources. Whilesomenarrow-band filters are designedforthestudy of particular emissionfeatures ([O II]/λ3727, Hα/λ6563) up to z < 0.017, theyalsoprovidewell-definedwindowsfortheanalysis of otheremissionlines at higherredshifts. As a result, J-PLUS has thepotential to contribute to a widerange of fields in Astrophysics, both in thenearbyUniverse (MilkyWaystructure, globular clusters, 2D IFU-likestudies, stellarpopulations of nearby and moderate-redshiftgalaxies, clusters of galaxies) and at highredshifts (emission-line galaxies at z ≈ 0.77, 2.2, and 4.4, quasi-stellarobjects, etc.). Withthispaper, wereleasethefirst∼1000 deg2 of J-PLUS data, containingabout 4.3 millionstars and 3.0 milliongalaxies at r <  21mag. With a goal of 8500 deg2 forthe total J-PLUS footprint, thesenumbers are expected to rise to about 35 millionstars and 24 milliongalaxiesbytheend of thesurvey.Funding for the J-PLUS Project has been provided by the Governments of Spain and Aragón through the Fondo de Inversiones de Teruel, the Spanish Ministry of Economy and Competitiveness (MINECO; under grants AYA2017-86274-P, AYA2016-77846-P, AYA2016-77237-C3-1-P, AYA2015-66211-C2-1-P, AYA2015-66211-C2-2, AYA2012-30789, AGAUR grant SGR-661/2017, and ICTS-2009-14), and European FEDER funding (FCDD10-4E-867, FCDD13-4E-2685

Treatment with tocilizumab or corticosteroids for COVID-19 patients with hyperinflammatory state: a multicentre cohort study (SAM-COVID-19)

Objectives: The objective of this study was to estimate the association between tocilizumab or corticosteroids and the risk of intubation or death in patients with coronavirus disease 19 (COVID-19) with a hyperinflammatory state according to clinical and laboratory parameters. Methods: A cohort study was performed in 60 Spanish hospitals including 778 patients with COVID-19 and clinical and laboratory data indicative of a hyperinflammatory state. Treatment was mainly with tocilizumab, an intermediate-high dose of corticosteroids (IHDC), a pulse dose of corticosteroids (PDC), combination therapy, or no treatment. Primary outcome was intubation or death; follow-up was 21 days. Propensity score-adjusted estimations using Cox regression (logistic regression if needed) were calculated. Propensity scores were used as confounders, matching variables and for the inverse probability of treatment weights (IPTWs). Results: In all, 88, 117, 78 and 151 patients treated with tocilizumab, IHDC, PDC, and combination therapy, respectively, were compared with 344 untreated patients. The primary endpoint occurred in 10 (11.4%), 27 (23.1%), 12 (15.4%), 40 (25.6%) and 69 (21.1%), respectively. The IPTW-based hazard ratios (odds ratio for combination therapy) for the primary endpoint were 0.32 (95%CI 0.22-0.47; p < 0.001) for tocilizumab, 0.82 (0.71-1.30; p 0.82) for IHDC, 0.61 (0.43-0.86; p 0.006) for PDC, and 1.17 (0.86-1.58; p 0.30) for combination therapy. Other applications of the propensity score provided similar results, but were not significant for PDC. Tocilizumab was also associated with lower hazard of death alone in IPTW analysis (0.07; 0.02-0.17; p < 0.001). Conclusions: Tocilizumab might be useful in COVID-19 patients with a hyperinflammatory state and should be prioritized for randomized trials in this situatio

MAMMALS IN PORTUGAL : A data set of terrestrial, volant, and marine mammal occurrences in P ortugal

Mammals are threatened worldwide, with 26% of all species being includedin the IUCN threatened categories. This overall pattern is primarily associatedwith habitat loss or degradation, and human persecution for terrestrial mam-mals, and pollution, open net fishing, climate change, and prey depletion formarine mammals. Mammals play a key role in maintaining ecosystems func-tionality and resilience, and therefore information on their distribution is cru-cial to delineate and support conservation actions. MAMMALS INPORTUGAL is a publicly available data set compiling unpublishedgeoreferenced occurrence records of 92 terrestrial, volant, and marine mam-mals in mainland Portugal and archipelagos of the Azores and Madeira thatincludes 105,026 data entries between 1873 and 2021 (72% of the data occur-ring in 2000 and 2021). The methods used to collect the data were: live obser-vations/captures (43%), sign surveys (35%), camera trapping (16%),bioacoustics surveys (4%) and radiotracking, and inquiries that represent lessthan 1% of the records. The data set includes 13 types of records: (1) burrowsjsoil moundsjtunnel, (2) capture, (3) colony, (4) dead animaljhairjskullsjjaws, (5) genetic confirmation, (6) inquiries, (7) observation of live animal (8),observation in shelters, (9) photo trappingjvideo, (10) predators dietjpelletsjpine cones/nuts, (11) scatjtrackjditch, (12) telemetry and (13) vocalizationjecholocation. The spatial uncertainty of most records ranges between 0 and100 m (76%). Rodentia (n=31,573) has the highest number of records followedby Chiroptera (n=18,857), Carnivora (n=18,594), Lagomorpha (n=17,496),Cetartiodactyla (n=11,568) and Eulipotyphla (n=7008). The data setincludes records of species classified by the IUCN as threatened(e.g.,Oryctolagus cuniculus[n=12,159],Monachus monachus[n=1,512],andLynx pardinus[n=197]). We believe that this data set may stimulate thepublication of other European countries data sets that would certainly contrib-ute to ecology and conservation-related research, and therefore assisting onthe development of more accurate and tailored conservation managementstrategies for each species. There are no copyright restrictions; please cite thisdata paper when the data are used in publications.info:eu-repo/semantics/publishedVersio

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure fl ux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defi ned as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium ) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the fi eld understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation it is imperative to delete or knock down more than one autophagy-related gene. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways so not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field

Outcomes from elective colorectal cancer surgery during the SARS-CoV-2 pandemic

This study aimed to describe the change in surgical practice and the impact of SARS-CoV-2 on mortality after surgical resection of colorectal cancer during the initial phases of the SARS-CoV-2 pandemic