Automated extraction of information from free text of Spanish oncology pathology reports.

Background: Pathology reports are stored as unstructured, ungrammatical, fragmented, and abbreviated free text with linguistic variability among pathologists. For this reason, tumor information extraction requires a significant human effort. Recording data in an efficient and high-quality format is essential in implementing and establishing a hospital-based-cancer registry. Objective: This study aimed to describe implementing a natural language processing algorithm for oncology pathology reports. Methods: An algorithm was developed to process oncology pathology reports in Spanish to extract 20 medical descriptors. The approach is based on the successive coincidence of regular expressions. Results: The validation was performed with 140 pathological reports. The topography identification was performed manually by humans and the algorithm in all reports. The human identified morphology in 138 reports and by the algorithm in 137. The average fuzzy matching score was 68.3 for Topography and 89.5 for Morphology. Conclusions: A preliminary algorithm validation against human extraction was performed over a small set of reports with satisfactory results. This shows that a regular-expression approach can accurately and precisely extract multiple specimen attributes from free-text Spanish pathology reports. Additionally, we developed a website to facilitate collaborative validation at a larger scale which may be helpful for future research on the subject.

Introducción: Los reportes de patología están almacenados como texto libre sin estructura, gramática, fragmentados o abreviados, con variabilidad lingüística entre patólogos. Por esta razón, la extracción de información de tumores requiere un esfuerzo humano significativo. Almacenar información en un formato eficiente y de alta calidad es esencial para implementar y establecer un registro hospitalario de cáncer. Objetivo: Este estudio busca describir la implementación de un algoritmo de Procesamiento de Lenguaje Natural para reportes de patología oncológica. Métodos: Desarrollamos un algoritmo para procesar reportes de patología oncológica en Español, con el objetivo de extraer 20 descriptores médicos. El abordaje se basa en la coincidencia sucesiva de expresiones regulares. Resultados: La validación se hizo con 140 reportes de patología. La identificación topográfica se realizó por humanos y por el algoritmo en todos los reportes. La morfología fue identificada por humanos en 138 reportes y por el algoritmo en 137. El valor de coincidencias parciales (fuzzy matches) promedio fue de 68.3 para Topografía y 89.5 para Morfología. Conclusiones: Se hizo una validación preliminar del algoritmo contra extracción humana sobre un pequeño grupo de reportes, con resultados satisfactorios. Esto muestra que múltiples atributos del espécimen pueden ser extraídos de manera precisa de texto libre de reportes de patología en Español, usando un abordaje de expresiones regulares. Adicionalmente, desarrollamos una página web para facilitar la validación colaborativa a gran escala, lo que puede ser beneficioso para futuras investigaciones en el tema.

Challenges in the care of Ewing's sarcoma in a Jehovah's Witness patient / Desafíos en el manejo del sarcoma de Ewing en una paciente testigo de Jehová

Ewing's sarcoma is a bone and soft tissue neoplasm, whose management is related to hematological toxicity. This aspect represents a medical and ethical challenge in Jehovah's Witnesses patients, who, due to their religious beliefs, reject the blood component transfusion, with the risk of discontinuing chemotherapy or using suboptimal doses. We present the case of a 34-year-old Colombian woman, Jehovah's Witness, diagnosed with Ewing's sarcoma with clinical stage IIB (T1N0M0) in the left maxillary and mandibular regions, treated with chemotherapy, who presented a hemoglobin nadir of up to 4.5 g/dL, and surgical indication as part of the treatment. In these patients, the transfusion decision has ethical implications that require therapeutic alternatives and a multidisciplinary approach.

El sarcoma de Ewing es una neoplasia de hueso y tejidos blandos, cuyo manejo se relaciona con toxicidad hematológica. Este aspecto representa un desafío médico y ético en los pacientes testigos de Jehová quienes, por sus creencias religiosas, rechazan la aplicación de hemoderivados, con riesgo de que se descontinúe la quimioterapia o de que se utilicen dosis subóptimas. Se presenta el caso de una mujer colombiana de 34 años, testigo de Jehová, con diagnóstico de sarcoma de Ewing con estadificación clínica IIB (T1N0M0) en las regiones maxilar y mandibular izquierdas, tratada con  quimioterapia, quien presentó un valor mínimo de hemoglobina de hasta 4,5 g/dl y tuvo indicación quirúrgica como parte del tratamiento. En estos pacientes, la decisión de practicar una transfusión comprende implicaciones éticas que requieren alternativas terapéuticas y un abordaje multidisciplinario.

Survival in Elderly Patients Diagnosed With Acute Myeloid Leukemia: A Hospital-Based Study.

Background: Acute myeloid leukemia (AML) is a hematological neoplasm that is more frequent in elderly patients. The objective of this study was to evaluate elderly patients' survival with de novo AML and acute myeloid leukemia myelodysplasia-related (AML-MR), treated with intensive and less-intensive chemotherapy and supportive care. Methods: A retrospective cohort study was conducted in Fundacion Valle del Lili (Cali, Colombia), between 2013 and 2019. We included patients ≥ 60 years old diagnosed with AML. The statistical analysis considered the leukemia type (de novo vs. myelodysplasia-related) and treatment (intensive chemotherapy regimen, less-intensive chemotherapy regimen, and without chemotherapy). Survival analysis was performed using Kaplan-Meier method and Cox regression models. Results: A total of 53 patients were included (31 de novo and 22 AML-MR). Intensive chemotherapy regimens were more frequent in patients with de novo leukemia (54.8%), and 77.3% of patients with AML-MR received less-intensive regimens. Survival was higher in the chemotherapy group (P = 0.006), but with no difference between chemotherapy modalities. Additionally, patients without chemotherapy were 10 times more likely to die than those who received any regimen, independent of age, sex, Eastern Cooperative Oncology performance status, and Charlson comorbidity index (adjusted hazard ratio (HR) = 11.6, 95% confidence interval (CI) 3.47 - 38.8). Conclusions: Elderly patients with AML had longer survival time when receiving chemotherapy, regardless of the type of regimen.

Gastric adenocarcinoma burden, trends and survival in Cali, Colombia: A retrospective cohort study.

Background: Gastric adenocarcinoma (GA) has changed in recent decades. Cancer estimates are often calculated from population-based cancer registries, which lack valuable information to guide decision-making (clinical outcomes). We describe the trends in clinical practice for GA using a hospital-based cancer registry over a timespan of 15 years. Methods: A retrospective cohort study was conducted. Data were gathered from adults diagnosed and treated for GA at Fundación Valle del Lili (FVL), between 2000 and 2014, from the hospital's own cancer registry and crossed with Cali's Cancer Registry. Additional data were obtained directly from clinical records, pathology reports and the clinical laboratory. Patients younger than 18 years and those for whom limited information was available in the medical history were excluded. A survival analysis was conducted using Kaplan-Meier method. Results: A total of 500 patients met eligibility criteria. Median age was 64 years (IQR: 54-74 years), 39.8% were female, 22.2% were at an early stage, 32.2% had a locally advanced disease, and 29% a metastatic disease, 69% had intestinal subtype, 48.6% had a positive H. pylori test, 85.2% had a distal lesion, 62% underwent gastrectomy, 60.6% lymphadenectomy, and 40.6% received chemotherapy. Survival at 5 years for all cases was 39.9% (CI 95% 35.3-44.5). Survival decreased over time in all groups and was lower in age-groups <39 and 60-79 with either locally advanced or metastatic disease. Prognostic factors that were significant in the Cox proportional-hazards model were late stages of the tumor (locally advanced: HR=2.52; metastatic: HR=4.17), diffuse subtype (HR=1.40), gastrectomy (subtotal: HR=0.42; total: 0.44) and palliative chemotherapy (HR=0.61). Conclusions: The treatment of GA has changed in recent decades. GA survival was associated with clinical staging, diffuse subtype, gastrectomy and palliative chemotherapy. These findings must be interpreted in the context of a hospital-based study.

Automated extraction of information from free text of Spanish oncology pathology reports

Background: Pathology reports are stored as unstructured, ungrammatical, fragmented, and abbreviated free text with linguistic variability among pathologists. For this reason, tumor information extraction requires a significant human effort. Recording data in an efficient and high-quality format is essential in implementing and establishing a hospital-based-cancer registry Objective: This study aimed to describe implementing a natural language processing algorithm for oncology pathology reports. Methods: An algorithm was developed to process oncology pathology reports in Spanish to extract 20 medical descriptors. The approach is based on the successive coincidence of regular expressions. Results: The validation was performed with 140 pathological reports. The topography identification was performed manually by humans and the algorithm in all reports. The human identified morphology in 138 reports and by the algorithm in 137. The average fuzzy matching score was 68.3 for Topography and 89.5 for Morphology. Conclusions: A preliminary algorithm validation against human extraction was performed over a small set of reports with satisfactory results. This shows that a regular-expression approach can accurately and precisely extract multiple specimen attributes from free-text Spanish pathology reports. Additionally, we developed a website to facilitate collaborative validation at a larger scale which may be helpful for future research on the subject.

Introducción: Los reportes de patología están almacenados como texto libre sin estructura, gramática, fragmentados o abreviados, con variabilidad lingüística entre patólogos. Por esta razón, la extracción de información de tumores requiere un esfuerzo humano significativo. Almacenar información en un formato eficiente y de alta calidad es esencial para implementar y establecer un registro hospitalario de cáncer. Objetivo: Este estudio busca describir la implementación de un algoritmo de Procesamiento de Lenguaje Natural para reportes de patología oncológica. Métodos: Desarrollamos un algoritmo para procesar reportes de patología oncológica en Español, con el objetivo de extraer 20 descriptores médicos. El abordaje se basa en la coincidencia sucesiva de expresiones regulares. Resultados: La validación se hizo con 140 reportes de patología. La identificación topográfica se realizó por humanos y por el algoritmo en todos los reportes. La morfología fue identificada por humanos en 138 reportes y por el algoritmo en 137. El valor de coincidencias parciales (fuzzy matches) promedio fue de 68.3 para Topografía y 89.5 para Morfología. Conclusiones: Se hizo una validación preliminar del algoritmo contra extracción humana sobre un pequeño grupo de reportes, con resultados satisfactorios. Esto muestra que múltiples atributos del espécimen pueden ser extraídos de manera precisa de texto libre de reportes de patología en Español, usando un abordaje de expresiones regulares. Adicionalmente, desarrollamos una página web para facilitar la validación colaborativa a gran escala, lo que puede ser beneficioso para futuras investigaciones en el tema.

Desafíos en el manejo del sarcoma de Ewing en una paciente testigo de Jehová / Challenges in the care of Ewing's sarcoma in a Jehovah's Witness patient

El sarcoma de Ewing es una neoplasia de hueso y tejidos blandos, cuyo manejo se relaciona con toxicidad hematológica. Este aspecto representa un desafío médico y ético en los pacientes testigos de Jehová quienes, por sus creencias religiosas, rechazan la aplicación de hemoderivados, con riesgo de que se descontinúe la quimioterapia o de que se utilicen dosis subóptimas. Se presenta el caso de una mujer colombiana de 34 años, testigo de Jehová, con diagnóstico de sarcoma de Ewing con estadificación clínica IIB (T1N0M0) en las regiones maxilar y mandibular izquierdas, tratada con quimioterapia, quien presentó un valor mínimo de hemoglobina de hasta 4,5 g/dl y tuvo indicación quirúrgica como parte del tratamiento. En estos pacientes, la decisión de practicar una transfusión comprende implicaciones éticas que requieren alternativas terapéuticas y un abordaje multidisciplinario.

Ewing's sarcoma is a bone and soft tissue neoplasm, whose management is related to hematological toxicity. This aspect represents a medical and ethical challenge in Jehovah's Witnesses patients, who, due to their religious beliefs, reject the blood component transfusion, with the risk of discontinuing chemotherapy or using suboptimal doses. We present the case of a 34-year-old Colombian woman, Jehovah's Witness, diagnosed with Ewing's sarcoma with clinical stage IIB (T1N0M0) in the left maxillary and mandibular regions, treated with chemotherapy, who presented a hemoglobin nadir of up to 4.5 g/dL, and surgical indication as part of the treatment. In these patients, the transfusion decision has ethical implications that require therapeutic alternatives and a multidisciplinary approach.

Indigenous communities in Colombia: A cultural and holistic view of cancer management.

Cancer is one of the most burdening global health challenges. Indigenous communities are at high risk for worse healthcare outcomes because of inequalities in the incidence, prevalence, and mortality of oncological diseases, that arise from socioeconomic, racial, cultural, religious beliefs, and ethnic factors. Their perception about themselves is closely related to what affects their territory, making them possess a profound rooted feeling with their surroundings, and intense spiritual believes. Consequently, the disease process is linked to physical and emotional imbalances and alterations in their territory. Researchers from the United States, Canada, New Zealand, and Australia have worked diligently to learn about barriers to cancer management among these populations. Unfortunately, robust cancer data is lacking for most of the world's Indigenous, leading to obstacles in information systems and consequently, inequities in healthcare with the perpetuation of the problem. Therefore, a better understanding of cancer as a global health problem is required. Our study aims to propose a holistic and culturally adapted framework to improve cancer health services and outcomes among Indigenous peoples in Colombia.

Methods and implementation of a Hospital-Based Cancer Registry in a major city in a low-to middle-income country: the case of Cali, Colombia.

PURPOSE: To describe our experience upon developing and implementing a hospital-based cancer registry (HBCR) in a quaternary-level of care private non-profit academic medical center in Cali, Colombia. METHODS: HBCRs capture, in a given institution, every single patient with a confirmed malignancy. In this study, all cases evaluated between 2014 and 2018 were included in the HBCR. In compliance with the International Agency for Research on Cancer recommendations, cases were classified as analytic or non-analytic. Data derived from an exhaustive selection of patients was stored in a computing platform owned by the institution, meeting the 2016 Facility Oncology Registry Data Standards recommendations. Quality control was performed by evaluating comparability, timeliness, validity, and completeness. RESULTS: A total of 24,405 new cases were registered between 2014 and 2018, from which 4253 (17.4%) died. Among all cases, based on the anatomic location, most common malignancies were breast (n = 1554), thyroid (n = 1346), hematolymphoid (n = 1251), prostatic (n = 805), and colorectal (n = 624). The behavior of the new cases was consistent with an incremental trend. CONCLUSION: Upon implementing the HBCR, major challenges were identified (i.e., a precise definition of cases, the development of processes for capturing new cases, a standardized data collection strategy, and carrying-out an appropriate patient follow-up). Based on our experience, the success of an HBCR largely relies on the interest from the institution, the engagement of stakeholders and financial support, that is, it depends on the adequate access over time to funding, technological, and staffing resources.

Coffee Consumption and Its Inverse Relationship with Gastric Cancer: An Ecological Study.

Coffee is the second most popular drink worldwide, and it has various components with antioxidant and antitumor properties. Due to its chemical composition, it could act as an antitumor substance in the gastrointestinal tract. The objective of this study was to explore the relationship between coffee consumption and the incidence/mortality of stomach cancer in the highest-consuming countries. An ecological study using Spearman's correlation coefficient was performed. The WorldAtlas's dataset of coffee consumption and the incidence/mortality rates database of the International Agency for Research were used as sources of information. A total of 25 countries were entered to the study. There was an inverse linear correlation between coffee consumption in kg per person per year and estimated age-adjusted incidence (r = 0.5984, p = 0.0016) and mortality (r = 0.5877, p = 0.0020) of stomach cancer. Coffee may potentially have beneficial effects on the incidence and mortality of stomach cancer, as supported by the data from each country analyzed.

[Risk factors associated with the development of perinatal asphyxia in neonates at the Hospital Universitario del Valle, Cali, Colombia, 2010-2011].

INTRODUCTION: Perinatal asphyxia is one of the main causes of perinatal mortality and morbidity worldwide and it generates high costs for health systems; however, it has modifiable risk factors. OBJECTIVE: To identify the risk factors associated with the development of perinatal asphyxia in newborns at Hospital Universitario del Valle, Cali, Colombia. MATERIALS AND METHODS: Incident cases and concurrent controls were examined. Cases were defined as newborns with moderate to severe perinatal asphyxia who were older than or equal to 36 weeks of gestational age, needed advanced resuscitation and presented one of the following: early neurological disorders, multi-organ commitment or a sentinel event. The controls were newborns without asphyxia who were born one week apart from the case at the most and had a comparable gestational age. Patients with major congenital malformations and syndromes were excluded. RESULTS: Fifty-six cases and 168 controls were examined. Premature placental abruption (OR=41.09; 95%CI: 4.61-366.56), labor with a prolonged expulsive phase (OR=31.76; 95%CI: 8.33-121.19), lack of oxytocin use (OR=2.57; 95% CI: 1.08 - 6.13) and mothers without a partner (OR=2.56; 95% CI: 1.21-5.41) were risk factors for the development of perinatal asphyxia in the study population. Social difficulties were found in a greater proportion among the mothers of cases. CONCLUSIONS: Proper control and monitoring of labor, development of a thorough partograph, and active searches are recommended to ensure that all pregnant women have adequate prenatal care with the provision of social support to reduce the frequency and negative impact of perinatal asphyxia.

Risk factors associated with the development of perinatal asphyxia in neonates at the Hospital Universitario del Valle, Cali, Colombia, 2010-2011 / Factores de riesgo asociados con el desarrollo de asfixia perinatal en neonatos en el Hospital Universitario del Valle, Cali, Colombia, 2010-2011

Abstract Introduction: Perinatal asphyxia is one of the main causes of perinatal mortality and morbidity worldwide and it generates high costs for health systems; however, it has modifiable risk factors. Objective: To identify the risk factors associated with the development of perinatal asphyxia in newborns at Hospital Universitario del Valle, Cali, Colombia. Materials and methods: Incident cases and concurrent controls were examined. Cases were defined as newborns with moderate to severe perinatal asphyxia who were older than or equal to 36 weeks of gestational age, needed advanced resuscitation and presented one of the following: early neurological disorders, multi-organ commitment or a sentinel event. The controls were newborns without asphyxia who were born one week apart from the case at the most and had a comparable gestational age. Patients with major congenital malformations and syndromes were excluded. Results: Fifty-six cases and 168 controls were examined. Premature placental abruption (OR=41.09; 95%CI: 4.61-366.56), labor with a prolonged expulsive phase (OR=31.76; 95%CI: 8.33-121.19), lack of oxytocin use (OR=2.57; 95% CI: 1.08 - 6.13) and mothers without a partner (OR=2.56; 95% CI: 1.21-5.41) were risk factors for the development of perinatal asphyxia in the study population. Social difficulties were found in a greater proportion among the mothers of cases. Conclusions: Proper control and monitoring of labor, development of a thorough partograph, and active searches are recommended to ensure that all pregnant women have adequate prenatal care with the provision of social support to reduce the frequency and negative impact of perinatal asphyxia.

Resumen Introducción: La asfixia perinatal constituye una de las principales causas de morbilidad y mortalidad perinatal en el mundo, tiene factores de riesgo modificables y genera altos costos para los sistemas de salud. Objetivo: Determinar los factores de riesgo asociados al desarrollo de asfixia perinatal en recién nacidos en el Hospital Universitario del Valle, Cali, Colombia. Materiales y métodos: Se llevó a cabo un estudio de casos incidentes y controles concurrentes. Los casos se definieron como neonatos con asfixia perinatal moderada a grave, de edad de gestación mayor o igual a 36 semanas, que requirieron reanimación avanzada y presentaron, al menos, una de las siguientes condiciones: alteraciones neurológicas tempranas, falla orgánica múltiple o aparición de un evento centinela. Los controles se definieron como neonatos sin diagnóstico de asfixia, nacidos hasta con una semana de diferencia con respecto al caso y de edad de gestación comparable. Se excluyeron los pacientes con malformaciones congénitas mayores y síndromes. Resultados: Se estudiaron 56 casos y 168 controles. El desprendimiento prematuro de la placenta (odds ratio, OR=41,09; IC95% 4,61-366,56), un trabajo de parto con fase expulsiva prolongada (OR=31,76; IC95% 8,33-121,19), no usar oxitocina (OR=2,57; IC95% 1,08-6,13) y ser madre soltera (OR=2,56; IC95% 1,21-5,41) fueron factores de riesgo para el desarrollo de asfixia perinatal en la población bajo estudio. En las madres de los casos se encontraron dificultades sociales en mayor proporción. Conclusiones: Se recomienda un control adecuado y una vigilancia apropiada del trabajo de parto, hacer un estricto partograma, y una búsqueda activa, de manera que cada mujer embarazada tenga un adecuado control prenatal y reciba apoyo social.

Piebaldismo-Moebius y exposición prenatal a misoprostol: reporte de un caso / Piebaldism-Moebius and prenatal exposure to misoprostol: a case report / Piebaldismo-Moebius e exposição pré-natal a misoprostol: reporte de um caso

El piebaldismo es una enfermedad congénita rara de curso estático, con prevalencia de 1/100.000; se caracteriza por despigmentación en parches de la piel y presencia de un mechón blanco frontal. Por lo demás los pacientes son sanos. Se hereda con un patrón autosómico dominante. Es causado por mutaciones en el gen c-kit, un protoncogén que participa en la migración, proliferación, diferenciación y supervivencia de los melanoblastos. Por otro lado, el síndrome de Moebius es una parálisis congénita del VII par craneal, que puede estar asociada a compromiso de otros pares craneales, o incluso de otros sistemas. En Estados Unidos se ha calculado su frecuencia en 0,002 % - 0,0002 % del total de nacimientos. Presentamos el caso de una recién nacida con piebaldismo y síndrome de Moebius asociado a exposición prenatal a misoprostol. Se hace una búsqueda bibliográfica sobre las anomalías de la paciente y la asociación entre la exposición prenatal a misoprostol y anomalías congénitas. El piebaldismo es un trastorno raro de etiología genética. El síndrome de Moebius, en cambio, es de causa heterogénea y no bien definida, y se ha asociado a exposición prenatal a misoprostol. La paciente reportada presenta simultáneamente ambas entidades, una netamente genética y la otra posiblemente teratogénica.

Piebaldism is a rare congenital disease with prevalence of 1/100.000, characterized by patchy depigmentation of the skin and the presence of a white forelock. Its course is static and otherwise patients are healthy. It is inherited in an autosomal dominant pattern and is caused by mutations in the gene c-kit, a proto-oncogene involved in the migration, proliferation, differentiation and survival of melanoblasts. On the other hand, Moebius syndrome is a congenital palsy of the VII cranial nerve, which may be associated with involvement of other cranial nerves, or even of other systems. In the United States its frequency has been calculated from 0.002% to 0.0002% of total births. We report the case of a newborn girl with piebaldism and Moebius syndrome associated with prenatal exposure to misoprostol. A search was made about these anomalies and the association between prenatal exposure to misoprostol and congenital anomalies. Piebaldism is a rare genetic disorder. On the other hand, the cause of Moebius syndrome is heterogeneous and not well defined, and it has been associated with prenatal exposure to misoprostol. Our patient had simultaneously two diseases: one purely genetic and the other potentially teratogenic.

O piebaldismo é uma doença congênita esquisita de curso estático, com prevalência de 1/100.000; caracteriza- se por despigmentação em parches da pele e presença de uma mecha branca frontal. Pelo demais os pacientes são sãos. Herda-se com um padrão autossômico dominante. É causado por mutações no gene c-kit, um proto-oncogene que participa na migração, proliferação, diferenciação e sobrevivência dos melanoblastos. Por outro lado, a síndrome de Moebius é uma paralisia congênita do VII par craniano, que pode estar associada a compromisso de outros pares cranianos, ou inclusive de outros sistemas. Nos Estados Unidos se calculou sua frequência em 0,002 % - 0,0002 % do total de nascimentos. Apresentamos o caso de uma recém-nascida com piebaldismo e síndrome de Moebius associado a exposição pré-natal a misoprostol. Faz-se uma busca bibliográfica sobre as anomalias da paciente e a associação entre a exposição pré-natal a misoprostol e anomalias congênitas. O piebaldismo é um transtorno raro de etiologia genética. A síndrome de Moebius, em mudança, é de causa heterogênea e não bem definida, e se associou a exposição pré-natal a misoprostol. A paciente reportada apresenta simultaneamente ambas entidades, uma netamente genética e a outra possivelmente teratogênica.