Hackathon in teaching: Machine Learning applied to Life Sciences

La programación ha sido tradicionalmente una competencia perteneciente a las ingenierías, que recientemente está adquiriendo una importancia significativa en áreas como Ciencias de la Vida, donde resulta fundamental para la resolución de problemas de análisis de datos. Este trabajo es un caso de estudio enmarcado en la necesidad de mejorar las habilidades, sobre análisis de datos en el alumnado de Ciencias de la Vida y de la base temática en los estudiantes de ingeniería. Mediante la herramienta del hackathon y el trabajo en equipo, se combinó al alumnado de ambas disciplinas y se le enfrentó a una serie de problemas de análisis de datos. Se establecieron equipos de trabajo que recibieron una formación previa al comienzo de la competición. De cada equipo, se valoró la metodología empleada para la obtención de los datos, su análisis, interpretación de resultados, y exposición de las diversas tareas. Se hizo un análisis descriptivo de los resultados del Proyecto mediante encuestas al alumnado, así como su percepción sobre las actividades realizadas. El Proyecto ha conseguido que el alumnado resuelva los problemas planteados, difícilmente abordables con equipos unidisciplinares, generando un aprendizaje común y una experiencia multidisciplinar altamente satisfactoria tanto para el alumnado como para el profesorado.Programming has traditionally been an engineering competence, but recently it is acquiring significant importance in several areas, such as Life Sciences, which is considered essential for problem-solving based on data analysis. This work is a case study framed within the need to improve not only the data analysis skills of life science students, but also the biological background concerning the given issue of engineering students. Using hackathon and teamwork-based tools, students from both disciplines have been made and challenged with a series of problems in the area of Life Sciences. To solve these problems, we established work teams trained before the competition's beginning. Their results were assessed concerning the approach to obtain the data, perform the analysis, and finally interpret and present the results to solve the challenges. The project outcomes were assessed using structured surveys for students and their overall perception. The project succeeded, meaning students solved the proposed problems and achieved the activity's goals. These goals would have been difficult to address with teams composed of students from the same field of study. The hackathon succeeded in generating a shared learning and a multidisciplinary experience for their professional training, being highly rewarding for both students and faculty members

Deciding finiteness of petri nets up to bisimulation

Abstract We study the following problems for strong and weak bisimulation equivalence: given a labelled Petri net and a finite transition system, are they equivalent?; given a labelled Petri net, is it equivalent to some (unspecified) finite transition system? We show that both problems are decidable for strong bisimulation and undecidable for weak bisimulation. 1 Introduction The decidability of equivalence notions for infinite-state systems has been extensively studied in the last years. Among other results, it has been shown that trace equivalence is undecidable for Basic Process Algebra (BPA) and Basic Parallel Processes (BPP), while bisimulation equivalence is decidable in both cases [1, 2, 4]

Outcomes of initially nonoperative management of diverticulits with abscess formation in inmunosuppressed patients. DIPLICAB study COLLABORATIVE group

Aim: Management of diverticulitis with abscess formation in immunosuppressed patients (IMS) remains unclear. The main objective of the study was to assess short- and long-term outcomes between IMS and immunocompetent patients (IC). The secondary aim was to identify risk factors for emergency surgery. Methods: A nationwide retrospective cohort study was performed at 29 Spanish referral centres between 2015–2019 including consecutive patients with first episode of diverticulitis classified as modified Hinchey Ib or II. IMS included immunosuppressive therapy, biologic therapy, malignant neoplasm with active chemotherapy and chronic steroid therapy. A multivariate analysis was performed to identify independent risk factors to emergency surgery in IMS. Results: A total of 1395 patients were included; 118 IMS and 1277 IC. There were no significant differences in emergency surgery between IMS and IC (19.5% and 13.5%, p = 0.075) but IMS was associated with higher mortality (15.1% vs. 0.6%, p < 0.001). Similar recurrent episodes were found between IMS and IC (28% vs. 28.2%, p = 0.963). Following multivariate analysis, immunosuppressive treatment, p = 0.002; OR: 3.35 (1.57–7.15), free gas bubbles, p < 0.001; OR: 2.91 (2.01–4.21), Hinchey II, p = 0.002; OR: 1.88 (1.26–2.83), use of morphine, p < 0.001; OR: 3.08 (1.98–4.80), abscess size ≥5 cm, p = 0.001; OR: 1.97 (1.33–2.93) and leucocytosis at third day, p < 0.001; OR: 1.001 (1.001–1.002) were independently associated with emergency surgery in IMS. Conclusion: Nonoperative management in IMS has been shown to be safe with similar treatment failure than IC. IMS presented higher mortality in emergency surgery and similar rate of recurrent diverticulitis than IC. Identifying risk factors to emergency surgery may anticipate emergency surgery.Depto. de CirugíaFac. de MedicinaTRUEpu

Can physiological stimulation prior to ileostomy closure reduce postoperative ileus: a prospective multicenter pilot study

Background The aim of this study was to assess the impact of ileostomy closure following preoperative physiological stimulation (PPS) on postoperative ileus (POI) in patients with loop ileostomy after low anterior resection for rectal cancer. Methods Patients who underwent ileostomy closure between January 2017 and February 2020 in two tertiary referral centers were prospectively included. PPS stimulation was compared to standard treatment. Stimulation was carried out daily during the 15 days prior to ileostomy closure by the patient's self-instillation of 200 ml of fecal contents from the ileostomy bag via the efferent loop, using a rectal catheter. Standard treatment (ST) consisted of observation. Outcomes measures were POI, morbidity, stimulation feasibility, and predictors to ileus. Results A total of 58 patients were included [42 males and 16 females, median age 67 (43–85) years]. PPS was used in 24 patients, who completed the entire stimulation process, and ST in 34 patients. No differences in preoperative factors were found between the two groups. POI was significantly lower in the PPS group (4.2%) vs the ST group (32.4%); p < 0.01, OR: 0.05 (CI 95% 0.01–0.65). The PPS group had a shorter time to restoration of bowel function (1 day vs 3 days) p = 0.02 and a shorter time to tolerance of liquids (1 day vs 2 days), p = 0.04. Age (p = 0.01), open approach at index surgery, p = 0.03, adjuvant capecitabine (p = 0.01). and previous abdominal surgeries (p = 0.02) were associated with POI in the multivariate analysis. C-reactive-protein values on the 3rd (p = 0.02) and 5th (p < 0.01) postoperative day were also associated with POI. Conclusions PPS for patients who underwent ileostomy closure after low anterior resection for rectal cancer is feasible and might reduce POI.Depto. de CirugíaFac. de MedicinaTRUEpu

Diverticulitis with abscess formation: Outcomes of non-operative management and nomogram for predicting emergency surgery: The Diplicab Study Collaborative Group.

Background To assess short- and long-term outcomes from non-surgical management of diverticulitis with abscess formation and to develop a nomogram to predict emergency surgery. Methods This nationwide retrospective cohort study was performed in 29 Spanish referral centers, including patients with a first episode of a diverticular abscess (modified Hinchey Ib-II) from 2015 to 2019. Emergency surgery, complications, and recurrent episodes were analyzed. Regression analysis was used to assess risk factors, and a nomogram for emergency surgery was designed. Results Overall, 1,395 patients were included (1,078 Hinchey Ib and 317 Hinchey II). Most (1,184, 84.9%) patients were treated with antibiotics without percutaneous drainage, and 194 (13.90%) patients required emergency surgery during admission. Percutaneous drainage (208 patients) was associated with a lower risk of emergency surgery in patients with abscesses of ≥5 cm (19.9% vs 29.3%, P = .035; odds ratio 0.59 [0.37-0.96]). The multivariate analysis showed that immunosuppression treatment, C-reactive protein (odds ratio: 1.003; 1.001-1.005), free pneumoperitoneum (odds ratio: 3.01; 2.04-4.44), Hinchey II (odds ratio: 2.15; 1.42-3.26), abscess size 3 to 4.9 cm (odds ratio: 1.87; 1.06-3.29), abscess size ≥5 cm (odds ratio: 3.62; 2.08-6.32), and use of morphine (odds ratio: 3.68; 2.29-5.92) were associated with emergency surgery. A nomogram was developed with an area under the receiver operating characteristic curve of 0.81 (95% confidence interval: 0.77-0.85). Conclusion Percutaneous drainage must be considered in abscesses ≥5 cm to reduce emergency surgery rates; however, there are insufficient data to recommend it in smaller abscesses. The use of the nomogram could help the surgeon develop a targeted approach

Hackathon en docencia: aprendizaje automático aplicado a Ciencias de la Vida

La programación ha sido tradicionalmente una competencia perteneciente a las ingenierías, que recientemente está adquiriendo una importancia significativa en áreas como Ciencias de la Vida, donde resulta fundamental para la resolución de problemas basados en análisis de datos. Entre el alumnado de dichas áreas, se observa una necesidad de mejorar las habilidades relacionadas con la programación aplicadas al análisis de datos. Similarmente, estudiantes de ingeniería con capacidad técnica demostrada pueden carecer de la base temática, igualmente fundamental para la resolución de problemas. Mediante la herramienta del hackathon, y el trabajo en equipo, se ha combinado a especialistas (profesorado y alumnado) de ambas disciplinas a los cuales se enfrentó a una serie de problemas en los campos de la biología, genética, ciencias forestales y ambientales. Para la resolución de estos problemas se utilizaron dinámicas de competición entre los grupos. De cada equipo se valoró la metodología empleada para la obtención de los datos, su análisis, interpretación de resultados, y exposición de las diversas tareas aplicadas para su resolución. El proyecto ha conseguido que el alumnado resuelva los problemas planteados, difícilmente abordables con equipos de una sola titulación, generando un aprendizaje común y una experiencia multidisciplinar para su formación

Prognostic value of stem cell quantification in stage II colon cancer.

Cancer stem cells (CSCs) are a subset of tumor cells with capacity to self-renew and generate the diverse cells that make up the tumor. The aim of this study is to evaluate the prognostic value of CSCs in a highly homogeneous population of stage II colon cancer.One hundred stage II colon cancer patients treated by the same surgical team between 1977 and 2005 were retrospectively analyzed. None of the patients received adjuvant chemotherapy. Inmunohistochemistry expression of CD133, NANOG and CK20 was scored, using four levels: 50% positivity. Kaplan-Meier analysis and log rank test were used to compare survival.The average patient age was 68 years (patients were between 45-92 years of age) and median follow up was 5.8 years. There was recurrent disease in 17 (17%); CD133 expression (defined by >10% positivity) was shown in 60% of the tumors, in 95% for NANOG and 78% for CK20. No correlation was found among expression levels of CD133, NANOG or CK20 and relapse-free survival (RFS) or overall survival (OS). However, a statistical significant correlation was found between established pathological prognostic factors and RFS and OS.Stem Cell quantification defined by CD133 and NANOG expression has no correlation with RFS or OS in this cohort of Stage II colon cancer