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Developing and Validating an Automatic Support System for Tumor Coding in Pathology Reports in Spanish
(American Society of Clinical Oncology (ASCO), 2025-02)
Fabián Villena
;
Pablo Báez
;
Sergio Peñafiel
;
Matías Rojas
;
Inti Paredes
Purpose Pathology reports provide valuable information for cancer registries to understand, plan, and implement strategies to mitigate the impact of cancer. However, coding essential information from unstructured reports is performed by experts in a time-consuming manual process. We developed and validated a novel two-step automatic coding system that first recognizes tumor morphology and topography mentions from free text and then suggests codes from the International Classification of Diseases for Oncology (ICD-O) in Spanish. Materials and Methods We created an annotated corpus of tumor morphology and topography mentions consisting of 1,101 documents. We combined it with the CANTEMIST corpus (Cancer Text Mining Shared Task). Specifically, we implemented a named entity recognition (NER) model using the bidirectional long short-term memory network-conditional random field architecture enhanced with a stacked embedding layer. We applied transfer learning from state-of-the-art pretrained language models to obtain high-quality contextual representations, thus improving the detection of entities. The mentions found using this model were subsequently oded using a search engine tailored to the ICD-O codes. Results Our NER models achieved an F1 score of 0.86 and 0.90 for tumor morphology and topography, respectively. The overall performance of our automatic coding system achieved an accuracy at five suggestions of 0.72 and 0.65 for tumor morphology and topography, respectively. Conclusion These results demonstrate the feasibility of implementing natural language processing tools in the routine of a cancer center to extract and code valuable information from pathology reports. Our recommender system allows reliable and transparent coding at the moment of consultation. This publication shares the annotated corpus in Spanish, annotation guidelines, and source code to reproduce our experiments.
Scopus© Citations 3 1
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Editorial: Immune response to gram-negative bacteria in the lungs
(2024)
Agnes Jara-Collao
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POLI HARLOWE, MARIA CECILIA BERTA
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William Bain
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Hernán F. Peñaloza
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Variations in management of A3 and A4 cervical spine fractures as designated by the AO Spine Subaxial Injury Classification System
(2022)
Barry Ting Sheen Kweh
;
Jin Wee Tee
;
Sander Muijs
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F. Cumhur Oner
;
Klaus John Schnake
<jats:sec> <jats:title>OBJECTIVE</jats:title> <jats:p>Optimal management of A3 and A4 cervical spine fractures, as defined by the AO Spine Subaxial Injury Classification System, remains controversial. The objectives of this study were to determine whether significant management variations exist with respect to 1) fracture location across the upper, middle, and lower subaxial cervical spine and 2) geographic region, experience, or specialty.</jats:p> </jats:sec> <jats:sec> <jats:title>METHODS</jats:title> <jats:p>A survey was internationally distributed to 272 AO Spine members across six geographic regions (North America, South America, Europe, Africa, Asia, and the Middle East). Participants’ management of A3 and A4 subaxial cervical fractures across cervical regions was assessed in four clinical scenarios. Key characteristics considered in the vignettes included degree of neurological deficit, pain severity, cervical spine stability, presence of comorbidities, and fitness for surgery. Respondents were also directly asked about their preferences for operative management and misalignment acceptance across the subaxial cervical spine.</jats:p> </jats:sec> <jats:sec> <jats:title>RESULTS</jats:title> <jats:p>In total, 155 (57.0%) participants completed the survey. Pooled analysis demonstrated that surgeons were more likely to offer operative intervention for both A3 (p < 0.001) and A4 (p < 0.001) fractures located at the cervicothoracic junction compared with fractures at the upper or middle subaxial cervical regions. There were no significant variations in management for junctional incomplete (p = 0.116) or complete (p = 0.342) burst fractures between geographic regions. Surgeons with more than 10 years of experience were more likely to operatively manage A3 (p < 0.001) and A4 (p < 0.001) fractures than their younger counterparts. Neurosurgeons were more likely to offer surgical stabilization of A3 (p < 0.001) and A4 (p < 0.001) fractures than their orthopedic colleagues. Clinicians from both specialties agreed regarding their preference for fixation of lower junctional A3 (p = 0.866) and A4 (p = 0.368) fractures. Overall, surgical fixation was recommended more often for A4 than A3 fractures in all four scenarios (p < 0.001).</jats:p> </jats:sec> <jats:sec> <jats:title>CONCLUSIONS</jats:title> <jats:p>The subaxial cervical spine should not be considered a single unified entity. Both A3 and A4 fracture subtypes were more likely to be surgically managed at the cervicothoracic junction than the upper or middle subaxial cervical regions. The authors also determined that treatment strategies for A3 and A4 subaxial cervical spine fractures varied significantly, with the latter demonstrating a greater likelihood of operative management. These findings should be reflected in future subaxial cervical spine trauma algorithms.</jats:p> </jats:sec>
17Scopus© Citations 3
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Primer Consenso Chileno de Grupo de Estudio de Tuberculosis Ocular
(2023)
Cristhian A. Urzua
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Paulina Liberman
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Nadia Escobar
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Pablo Sabat
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Mariluz Hernández
9Scopus© Citations 1
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Evidence-Based Treatment Algorithm for Freiberg Disease
(2023)
Ichiro Yoshimura
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Masato Takao
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WAGNER HITSCHFFELD, EMILIO
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Sjoerd Stufkens
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Jari Dahmen
<jats:p> Freiberg disease is a type of osteonecrosis of the metatarsal head that predominantly occurs in young females and adolescents, although it may occur at any age. The pathophysiology is multifactorial and may involve trauma, altered foot biomechanics, systemic disorders, and arterial insufficiency. The most typical location is the second metatarsal head, but Freiberg disease may also occur in other lesser toes. Nonoperative treatment is best applied in the early stage of the disease; if this is ineffective, surgical treatment is recommended. Currently available surgical procedures include debridement, osteotomy, osteochondral grafting, microfracture, interposition arthroplasty, implant arthroplasty, and metatarsal shortening arthroplasty. In this article, we propose a treatment algorithm for Freiberg disease based on the current literature and expert opinion. </jats:p>
Scopus© Citations 9 1
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Development of an algorithm to generate and evaluate cutting solutions in edging and trimming operations at sawmills
(2011)
Francisco Vergara Gonzalez
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BAESLER ABUFARDE, FELIPE
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Mario A. Ramos Maldonado
3
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Independent Reliability Analysis of a New Classification for Pyogenic Spondylodiscitis
(2020)
Gaston Camino Willhuber
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Alfredo Guiroy
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ZAMORANO PÉREZ, JUAN JOSÉ
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Nelson Astur
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Marcelo Valacco
<jats:sec><jats:title>Study Design:</jats:title><jats:p> Diagnostic study, level of evidence III. </jats:p></jats:sec><jats:sec><jats:title>Objective:</jats:title><jats:p> Pyogenic spondylodiscitis can cause deformity, neurological compromise, disability, and death. Recently, a new classification of spondylodiscitis based on magnetic resonance imaging was published. The objective of this study is to perform an independent reliability analysis of this new classification. </jats:p></jats:sec><jats:sec><jats:title>Methods:</jats:title><jats:p> We selected 35 cases from our database of different spine centers in Latin America and from the literature; 8 observers evaluated the classification and graded the scenarios according to the methodological grading of the classification developed by Pola et al. Cases were sent to the observers in a random sequence after 3 weeks to assess intraobserver reliability. The interobserver and intraobserver reliabilities were performed with Fleiss and Cohen statistics, respectively. </jats:p></jats:sec><jats:sec><jats:title>Results:</jats:title><jats:p> The overall Fleiss κ value for interobserver agreement was substantial, with 0.67 (95% CI = 0.43-0.91) in the first reading and 0.67 (95% CI = 0.45-0.89) in second reading for the main types of classification. The Cohen κ value for intraobserver agreement was also substantial, with 0.68 (95% CI = 0.45-0.92). The interobserver agreement analysis for the subtypes of this classification was overall substantial, with 0.60 (95% CI = 0.37-0.83) in the first reading and 0.61 (95% CI = 0.41-0.81) in the second reading. The overall intraobserver agreement for subtypes of the classification was also substantial, with 0.63 (95% CI = 0.34-0.93). </jats:p></jats:sec><jats:sec><jats:title>Conclusion:</jats:title><jats:p> The new classification developed by Pola et al showed substantial interobserver and intraobserver agreements. More studies are required to validate the usefulness of this classification especially in clinical practice. </jats:p></jats:sec>
Scopus© Citations 14 7
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Modelling cost-effectiveness of syphilis detection strategies in prisoners: exploratory exercise in a Chilean male prison
(2021)
CASTILLO LABORDE, CARLA CECILIA
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Pedro Gajardo
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Manuel Nájera-De Ferrari
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MATUTE WILLEMSEM, MARIA ISABEL
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Macarena Hirmas-Adauy
<jats:title>Abstract</jats:title><jats:sec> <jats:title>Background</jats:title> <jats:p>Syphilis, together with other sexually transmitted infections, remains a global public health problem that is far from controlled. People deprived of liberty are a vulnerable population. Control activities in prisons rely mostly on passive case detection, despite the existence of affordable alternatives that would allow switching to active case-finding strategies. Our objective was to develop a mathematical modelling framework for cost-effectiveness evaluation, from a health system perspective, of different approaches using rapid tests for the detection of syphilis in inmates' populations and to explore the results based on a Chilean male prison population.</jats:p> </jats:sec><jats:sec> <jats:title>Methods</jats:title> <jats:p>A compartmental model was developed to characterize the transmission dynamics of syphilis inside a prison with the ongoing strategy (passive case detection, with VRDL + FTA-ABS), considering the entrance and exit of inmates over a 40 year period. The model allows simulation of the implementation of a reverse algorithm for the current situation (rapid test + VDRL), different screening strategies (entry point, massive periodically; both with rapid test + VDRL) and treatment of detected cases. The parameters for the exploratory exercise were obtained from systematic searches of indexed and grey literature and field work (EQ-5D questionnaire application and key actors interviews). Probabilistic sensitivity analysis was conducted to account for uncertainty in relevant parameters.</jats:p> </jats:sec><jats:sec> <jats:title>Results</jats:title> <jats:p>The proposed framework allows the evaluation of different detection strategies. In this study, all the strategies were cost-effective in the baseline scenario when considering an ICER threshold of 1 Chilean GDP per capita (US$15,000). The strategies most likely to be cost-effective (over 80% probability) were: current situation with reverse algorithm, entry point screening and mass screening every two years; the latter was the most effective, achieving the lowest prevalence (0.7% and 1.7% over the period versus the 3% prevalence in the current situation).</jats:p> </jats:sec><jats:sec> <jats:title>Conclusions</jats:title> <jats:p>Mathematical modelling that considers the performance of different tests and detection strategies could be a useful tool for decision making. The exploratory results show the efficiency of adopting both the use of the rapid tests and performing active case detection to significantly reduce the burden of syphilis in Chilean prisons in the near future.</jats:p> </jats:sec>
Scopus© Citations 5 1
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A case-control study of a combination of single nucleotide polymorphisms and clinical parameters to predict clinically relevant toxicity associated with fluoropyrimidine and platinum-based chemotherapy in gastric cancer
(2021)
Miguel Cordova-Delgado
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María Loreto Bravo
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Elisa Cumsille
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Charlotte N. Hill
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Matías Muñoz-Medel
<jats:title>Abstract</jats:title><jats:sec> <jats:title>Background</jats:title> <jats:p>Fluoropyrimidine plus platinum chemotherapy remains the standard first line treatment for gastric cancer (GC). Guidelines exist for the clinical interpretation of four DPYD genotypes related to severe fluoropyrimidine toxicity within European populations. However, the frequency of these single nucleotide polymorphisms (SNPs) in the Latin American population is low (< 0.7%). No guidelines have been development for platinum. Herein, we present association between clinical factors and common SNPs in the development of grade 3–4 toxicity.</jats:p> </jats:sec><jats:sec> <jats:title>Methods</jats:title> <jats:p>Retrospectively, 224 clinical records of GC patient were screened, of which 93 patients were incorporated into the study. Eleven SNPs with minor allelic frequency above 5% in <jats:italic>GSTP1</jats:italic>, <jats:italic>ERCC2</jats:italic>, <jats:italic>ERCC1</jats:italic>, <jats:italic>TP53</jats:italic>, <jats:italic>UMPS</jats:italic>, <jats:italic>SHMT1</jats:italic>, <jats:italic>MTHFR</jats:italic>, <jats:italic>ABCC2</jats:italic> and <jats:italic>DPYD</jats:italic> were assessed. Association between patient clinical characteristics and toxicity was estimated using logistic regression models and classification algorithms.</jats:p> </jats:sec><jats:sec> <jats:title>Results</jats:title> <jats:p>Reported grade ≤ 2 and 3–4 toxicities were 64.6% (61/93) and 34.4% (32/93) respectively. Selected <jats:italic>DPYD</jats:italic> SNPs were associated with higher toxicity (rs1801265; OR = 4.20; 95% CI = 1.70–10.95, <jats:italic>p</jats:italic> = 0.002), while others displayed a trend towards lower toxicity (rs1801159; OR = 0.45; 95% CI = 0.19–1.08; <jats:italic>p</jats:italic> = 0.071). Combination of paired SNPs demonstrated significant associations in <jats:italic>DPYD</jats:italic> (rs1801265), <jats:italic>UMPS</jats:italic> (rs1801019), <jats:italic>ABCC2</jats:italic> (rs717620) and <jats:italic>SHMT1</jats:italic> (rs1979277). Using multivariate logistic regression that combined age, sex, peri-operative chemotherapy, 5-FU regimen, the binary combination of the SNPs <jats:italic>DPYD</jats:italic> (rs1801265) + <jats:italic>ABCC2</jats:italic> (rs717620), and <jats:italic>DPYD</jats:italic> (rs1801159) displayed the best predictive performance. A nomogram was constructed to assess the risk of developing overall toxicity.</jats:p> </jats:sec><jats:sec> <jats:title>Conclusion</jats:title> <jats:p>Pending further validation, this model could predict chemotherapy associated toxicity and improve GC patient quality of life.</jats:p> </jats:sec>
Scopus© Citations 11 3
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BacAv, a new free online platform for clinical back-averaging
(2020)
VIAL UNDURRAGA, FELIPE AGUSTIN
;
Sanaz Attaripour
;
Patrick McGurrin
;
Mark Hallett
Scopus© Citations 6 4

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