Modelos de redes neuronales para identificar entidades en documentos.

Este trabajo surge a raíz de un periodo de prácticas realizado en la empresa NTT DATA. Concre- tamente en el departamento de AI Assest Development Center en el equipo de Dolffia. Dolffia es una plataforma de procesamiento de documentos basada en IA, que extrae y clasifica información de ma- nera rápida y precisa. El objetivo del trabajo es crear una herramienta capaz de identificar las distintas entidades estructurales de un documento. Para ello tuve que aprender sobre NLP (Natural Language Processing) y descubrir los diferentes algoritmos usados en el machine learning.El propósito del trabajo es conseguir un modelo capaz de resolver la tarea mencionada de manera eficaz. Para llegar a ese modelo primero hay que entender unos fundamentos teóricos y el problema que hemos de resolver.En el primer capítulo del trabajo se hace una aproximación al mundo de la Inteligencia Artificial, más concretamente al aprendizaje automático. Diferenciando entre aprendizaje supervisado y no supervisado, se explican algoritmos como la regresión lineal, el gradiente descendiente o la detección de anomalías. A continuación se desarrolla en detalle la definición y conceptos básicos de una red neuronal. Finalmente se hace breve inciso en los modelos habitualmente usados en el NLP, es decir, en el procesamiento del lenguaje natural.En el segundo capítulo se introduce el problema de identificación de entidades en documentos. Pri- mero se explican sus bases y se comentan dificultades que nos van a surgir al resolverlo. Seguidamente se analizan métodos tradicionales para resolverlo, cómo son los métodos lingüísticos, los métodos basados en diccionarios y los métodos basados en aprendizaje automático. Por último, y de manera extendida, se explica cómo se puede resolver el problema usando redes neuronales convolucionales y la novedosa arquitectura conocida como Transformers.En el tercer capítulo comienza la parte realmente práctica del trabajo. En primer lugar se explica la forma elegida de resolver el problema: vamos a hacer un fine-tuning de un modelo de la biblioteca Transformers 1 de Hugging Face 2. El modelo elegido es LayoutLMv2. En la primera sección se explica en detalle y se compara con su predecesor. En la siguiente sección se hace una explicación exhaustiva de DocLayNet, el conjunto de datos elegido para hacer el fine-tuning, y cómo lo hemos preprocesado.Finalmente, en el cuarto y último capítulo se explica cómo se ha realizado el entrenamiento del modelo LayoutLMv2 con el dataset DocLayNet, a continuación se analizan los resultados obtenidos. Para acabar se comentan brevemente posibles mejoras a realizar sobre nuestro modelo en un futuro.<br /

Aeciospore ejection in the rust pathogen Puccinia graminis is driven by moisture ingress

Fungi have evolved an array of spore discharge and dispersal processes. Here, we developed a theoretical model that explains the ejection mechanics of aeciospore liberation in the stem rust pathogen Puccinia graminis. Aeciospores are released from cluster cups formed on its Berberis host, spreading early-season inoculum into neighboring small-grain crops. Our model illustrates that during dew or rainfall, changes in aeciospore turgidity exerts substantial force on neighboring aeciospores in cluster cups whilst gaps between spores become perfused with water. This perfusion coats aeciospores with a lubrication film that facilitates expulsion, with single aeciospores reaching speeds of 0.053 to 0.754 m·s−1. We also used aeciospore source strength estimates to simulate the aeciospore dispersal gradient and incorporated this into a publicly available web interface. This aids farmers and legislators to assess current local risk of dispersal and facilitates development of sophisticated epidemiological models to potentially curtail stem rust epidemics originating on Berberis

Potential for re-emergence of wheat stem rust in the United Kingdom

Wheat stem rust, a devastating disease of wheat and barley caused by the fungal pathogen Puccinia graminis f. sp. tritici, was largely eradicated in Western Europe during the mid-to-late twentieth century. However, isolated outbreaks have occurred in recent years. Here we investigate whether a lack of resistance in modern European varieties, increased presence of its alternate host barberry and changes in climatic conditions could be facilitating its resurgence. We report the first wheat stem rust occurrence in the United Kingdom in nearly 60 years, with only 20% of UK wheat varieties resistant to this strain. Climate changes over the past 25 years also suggest increasingly conducive conditions for infection. Furthermore, we document the first occurrence in decades of P. graminis on barberry in the UK. Our data illustrate that wheat stem rust does occur in the UK and, when climatic conditions are conducive, could severely harm wheat and barley production.</p

Mortality and pulmonary complications in patients undergoing surgery with perioperative SARS-CoV-2 infection: an international cohort study

Background: The impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on postoperative recovery needs to be understood to inform clinical decision making during and after the COVID-19 pandemic. This study reports 30-day mortality and pulmonary complication rates in patients with perioperative SARS-CoV-2 infection. Methods: This international, multicentre, cohort study at 235 hospitals in 24 countries included all patients undergoing surgery who had SARS-CoV-2 infection confirmed within 7 days before or 30 days after surgery. The primary outcome measure was 30-day postoperative mortality and was assessed in all enrolled patients. The main secondary outcome measure was pulmonary complications, defined as pneumonia, acute respiratory distress syndrome, or unexpected postoperative ventilation. Findings: This analysis includes 1128 patients who had surgery between Jan 1 and March 31, 2020, of whom 835 (74·0%) had emergency surgery and 280 (24·8%) had elective surgery. SARS-CoV-2 infection was confirmed preoperatively in 294 (26·1%) patients. 30-day mortality was 23·8% (268 of 1128). Pulmonary complications occurred in 577 (51·2%) of 1128 patients; 30-day mortality in these patients was 38·0% (219 of 577), accounting for 81·7% (219 of 268) of all deaths. In adjusted analyses, 30-day mortality was associated with male sex (odds ratio 1·75 [95% CI 1·28–2·40], p\textless0·0001), age 70 years or older versus younger than 70 years (2·30 [1·65–3·22], p\textless0·0001), American Society of Anesthesiologists grades 3–5 versus grades 1–2 (2·35 [1·57–3·53], p\textless0·0001), malignant versus benign or obstetric diagnosis (1·55 [1·01–2·39], p=0·046), emergency versus elective surgery (1·67 [1·06–2·63], p=0·026), and major versus minor surgery (1·52 [1·01–2·31], p=0·047). Interpretation: Postoperative pulmonary complications occur in half of patients with perioperative SARS-CoV-2 infection and are associated with high mortality. Thresholds for surgery during the COVID-19 pandemic should be higher than during normal practice, particularly in men aged 70 years and older. Consideration should be given for postponing non-urgent procedures and promoting non-operative treatment to delay or avoid the need for surgery. Funding: National Institute for Health Research (NIHR), Association of Coloproctology of Great Britain and Ireland, Bowel and Cancer Research, Bowel Disease Research Foundation, Association of Upper Gastrointestinal Surgeons, British Association of Surgical Oncology, British Gynaecological Cancer Society, European Society of Coloproctology, NIHR Academy, Sarcoma UK, Vascular Society for Great Britain and Ireland, and Yorkshire Cancer Research

Modelling aeciospore release, dispersal and disease transmission to inform wheat rust management

Wheat rust pathogens have been threatening agriculture all through history and they currently cause big economic loses every year. Investigating how these pathogens are able to spread and the key aspects of host-pathogen dynamics is vital for the design of appropriate control strategies. Two of the most damaging pathogens that require more careful monitoring are Puccinia graminis tritici (Pgt), that causes wheat stem rust, and Puccinia striiformis f. sp. tritici (Pst), cause of wheat yellow rust. Here, I have studied the process of aeciospore dispersal for Pgt, beginning with aeciospore release. Aeciospore release was recorded using high-speed videography and the velocity of ejection was estimated. Aeciospores are observed to release in clusters to achieve greater distances and their ejection is not affected by the temperatures tested here (5-37oC). Humidity is the key factor in aeciospore release, and it leads to their increase in volume, which was also measured in this thesis. A model of how this occurs is also proposed here. The dispersal process of Pgt aeciospores is also investigated, by evaluating the number of aeciospores that can be produced in barberry bushes. A Gaussian Plume model is used to predict how far aeciospores can travel, including real-time weather data gather using an API. This model was included into a user-friendly website to make the model accessible to the widest demographic. This tool can help identify the barberry bushes that present a higher risk and thus prioritise them for careful monitoring. Finally, the dynamics of Pst population in the UK at a field level is studied here. To do so, I developed a quick method for genotyping Pst-infected wheat samples collected from the field to determine which race they belong to. Using this method, I analysed samples collected all through the wheat growing season (December-June) for two consecutive years (2015-16 and 2016-17). Results indicate that one race (Warrior -) has become predominant in the UK and that seasonality for different races is observed. However, the presence of Pst races in one season was not indicative of prevalence of the same race in following seasons. In summary, this thesis provides tools to improve wheat rust management, both for stem and yellow rust at different levels. First, by trying to predict Pgt aeciospore release and dispersal to avoid future epidemics and secondly, with a quick genotyping method that can lower the costs of yellow rust surveillance

Ensamblaje de genoma usando técnicas de optimización cuánticas.

La computación cuántica, una tecnología en auge, promete revolucionar la resolución de problemas en diversos campos e industrias. Aprovechando la potencia de los qubits, los ordenadores cuánticos tienen la capacidad de codificar múltiples valores simultáneamente, superando con creces las limitaciones de la computación clásica. En el campo de la bioinformática, la computación cuántica es muy prometedora y en este trabajo se ha aplicado para resolver el problema del ensamblaje del genoma de-novo. El ensamblaje de genoma es una tarea compleja en genómica, y la computación cuántica puede proporcionar métodos más precisos y eficientes para su resolución. Hemos desarrollado e implementado un algoritmo para resolver el problema del ensamblaje del genoma utilizando técnicas de teoría de grafos y optimización combinatoria. Hemos ejecutado este algoritmo en un simulador de computación cuántica y en un dispositivo de computación cuántica real, y hemos validado su rendimiento en comparación con los enfoques clásicos en términos de velocidad, precisión y escalabilidad en conjuntos de datos sintéticos simulados. Esta memoria resume nuestros resultados y analiza el potencial, los retos y las limitaciones de la computación cuántica para resolver problemas como éste, que superan rápidamente las capacidades de la computación clásica.<br /

Maintenance of A/P body regions in planarians by TCEN49, a putative cystine-knot neurotrophin.

In freshwater planarians, the protein TCEN49 has been linked to the regional specification of the central body region, which includes the pharynx

RNA interference: a new and powerful tool for functional genomic analysis.

In many species, the introduction of double-stranded RNA induces potent and specific gene silencing, referred to as RNA interference. This phenomenon, which is based on targeted degradation of mRNAs and occurs in almost any eukaryote, from trypanosomes to mice including plants and fungi, has sparked general interest from both applied and fundamental standpoints. RNA interference, which is currently used to investigate gene function in a variety of systems, is linked to natural resistance to viruses and transposon silencing, as if it were a primitive immune system involved in genome surveillance. Here, we review the mechanism of RNA interference in post-transcriptional gene silencing, its function in nature, its value for functional genomic analysis, and the modifications and improvements that may make it more efficient and inheritable. We also discuss the future directions of this versatile technique in both fundamental and applied science

Maintenance of A/P body regions in planarians by TCEN49, a putative cystine-knot neurotrophin.

In freshwater planarians, the protein TCEN49 has been linked to the regional specification of the central body region, which includes the pharynx

RNA interference: a new powerful tool for functional genomic analysis

En moltes espècies, la introducció de RNAs de doble cadena indueix un silenciament gènic molt específic i potent, anomenat interferència induïda per RNA. Aquest fenomen, basat en la degradació dirigida de mRNAs, es produeix en gairebé tots els eucariotes, des de tripanosomes a ratolins, incloent-hi fongs i plantes. Les seves possibles aplicacions en ciència bàsica i aplicada han despertat un interès general. La interferència induïda per RNA, que actualment s'empra per investigar la funció gènica en sistemes molt diversos, està relacionada amb la resistència natural a virus i al silenciament de transposons, com si fos un sistema immunitari primitiu implicat en la vigilància i control del genoma. En aquest article, fem una revisió dels mecanismes d'actuació del silenciament gènic postranscripcional induït per la interferència de RNA, de la seva funció a la natura, de la importància que té la seva aplicació en estudis de genòmica funcional i de les modificacions i millores que el fan més efectiu i heretable, i discutim les perspectives de futur d'aquesta tècnica tan versàtil en ciència bàsica i aplicada.In many species, the introduction of double-stranded RNA induces potent and specific gene silencing, referred to as RNA interference. This phenomenon, which is based on targeted degradation of mRNAs and occurs in almost any eukaryote, from trypanosomes to mice including plants and fungi, has sparked general interest from both applied and fundamental standpoints. RNA interference, which is currently used to investigate gene function in a variety of systems, is linked to natural resistance to viruses and transposon silencing, as if it were a primitive immune system involved in genome surveillance. Here, we review the mechanism of RNA interference in post-transcriptional gene silencing, its function in nature, its value for functional genomic analysis, and the modifications and improvements that may make it more efficient and inheritable. We also discuss the future directions of this versatile technique in both fundamental and applied science