Search Results (35)

Background: Anatomopathological reports are largely unstructured, which limits automated data extraction, interoperability, and large-scale research. Manual extraction and standardization are costly and difficult to scale. Objective: We developed and evaluated an automated pipeline for entity extraction and multi-ontology normalization of anatomopathological reports. Methods: A corpus of 560 reports from the Military Hospital of Tunis, Tunisia, was manually annotated for three entity types: sample type, test performed, and finding. The entity extraction utilized BioBERT v1.1, while the normalization combined BioClinicalBERT multi-label classification with retrieval-augmented generation, incorporating both dense and BM25 sparse retrieval over SNOMED CT, LOINC, and ICD-11. The performance was measured using precision, recall, F1-score, and statistical tests. Results: BioBERT achieved high extraction performance (F1: 0.97 for the sample type, 0.98 for the test performed, and 0.93 for the finding; overall 0.963, 95% CI: 0.933–0.982), with low absolute errors. For terminology mapping, the combination of BioClinicalBERT and dense retrieval outperformed the standalone and BM25-based approaches (macro-F1: 0.6159 for SNOMED CT, 0.9294 for LOINC, and 0.7201 for ICD-11). Cohen’s Kappa ranged from 0.7829 to 0.9773, indicating substantial to near-perfect agreement. Conclusions: The pipeline provides robust automated extraction and multi-ontology coding of anatomopathological entities, supporting transformer-based named entity recognition with retrieval-augmented generation. However, given the limitations of this study, multi-institutional validation is needed before clinical deployment. Full article

Background and aim: The death of a woman while pregnant or within 42 days of delivery, regardless of the cause of death, or even up to one year after the end of the pregnancy, due to causes related to or aggravated by pregnancy remains a critical public health problem globally and in Colombia. While the country shows a general decreasing trend (preliminary Maternal Mortality Ratio 38.6/100,000 live births in 2023), significant regional disparities persist. Understanding precise underlying causes, especially in high-complexity referral centers, is vital. This study describes the sociodemographic and anatomopathological characteristics associated with autopsy-verified maternal mortality cases at a Level-4 hospital in southwestern Colombia (2000–2023). Methodology: A descriptive observational retrospective study analyzed 42 maternal mortality cases verified by clinical autopsy (2000–2023) at the Pathology Department of Universidad del Valle, a Level-4 referral center in Cali, Colombia. Cases met the WHO definition. Data on sociodemographic, clinical, and pathological characteristics were retrospectively extracted from clinical records and autopsy reports. Results: The analysis of 42 autopsies (2000–2023) showed that 85.7% were early maternal deaths. Indirect causes predominated (57.1%, n = 24) over direct (42.9%, n = 18). Septic shock was the main indirect cause (65.2% of indirect), often from endemic infections. Hypovolemic shock due to PPH was the main direct cause (50% of direct). A high proportion were from subsidized/uninsured schemes (65.7%) and had a migratory history (20%). Discussion and conclusions: This study highlights the value of autopsy in revealing maternal mortality etiologies, showing a predominance of indirect/infectious causes and endemic diseases often missed clinically, despite PPH remaining the main direct cause. Findings reaffirm the strong link between maternal death and social/economic inequity, access barriers, and regional/migratory vulnerabilities. Effectively reducing maternal mortality necessitates rigorous clinical management, regionalized public health strategies addressing inequities, and integrating pathological data for targeted surveillance. Full article

Objective: Sudden infant death syndrome (SIDS), sudden neonatal unexpected death (SNUD), and sudden intrauterine unexpected death (SIUD) are major unsolved, shocking forms of death that occur frequently and without warning. The body of literature on the anatomo-pathological substrates in the cardiac conduction system of SIDS-SIUD and their possible relationship with risk factors and triggers is fragmentary and scarce. The work aims is to analyze the cardiac conduction system findings collected at the national referral center for SIDS-SIUD. Methods: A total of 123 autopsied cases of SIDS (59.35% males, 40.65% females, mean age ± SD: 103.49 ± 67.17 days), 36 cases of SNUD (61.11% males, 38.89% females, mean age ± SD: 8.4 ± 9.17 days), and 127 cases of SIUD (45.67% males, 54.33% females, mean age ± SD: 36 ± 4.59 gestational weeks) were analyzed. In-depth pathological examinations of the cardiac conduction system were performed on serial sections according to the Lino Rossi Research Center’s protocol. Results: Among the studied cases, the following findings were observed: resorptive degeneration (SIDS: 88.7%, SNUD: 88.88%, SIUD: 56.69%), fetal dispersion (SIDS: 73.17%, SNUD: 91.66%, SIUD: 78.74%), Mahaim fibers (SIDS: 40.65%, SNUD: 44.44%, SIUD: 32.28%), cartilaginous meta-hyperplasia (SIDS: 56.91%, SNUD: 25%, SIUD: 33.07%), septated atrio-ventricular junction (AVJ) (SIDS: 21.14%, SNUD: 33.33%, SIUD: 38.58%), AVJ duplicity (SIDS: 6.5%, SNUD: 11.11%, SIUD: 2.36%), intramural bifurcation (SIDS: 3.25%, SNUD: 2.77%, SIUD: 4.72%). Conclusions: The prevalence of cardiac conduction findings was consistent across the SIDS, SNUD and SIUD groups. These findings provide valuable insights into the pathological characteristics of the cardiac conduction system in SIDS-SIUD that are potential morphological substrates for the development of cardiac arrhythmias. Further investigation and study of the conduction system are needed to understand the underlying mechanisms of these forms of death. Full article

The Atlantic puffin (Fratercula arctica) is a seabird species characterized by great diving capabilities and transoceanic migratory behavior. These movements contribute to the dispersion of the species during migration, and episodes of mortality associated with migration may be a normal event in the dynamic of the Atlantic puffin populations. This study aimed to describe the anatomopathological findings of an unusual mortality event of Atlantic puffins observed during the non-breeding period along the coast of the Canary Islands. The most consistent gross finding during necropsy was generalized muscle atrophy and fat depletion. The main histological findings were centered in the urinary tract, with dilation and inflammation of the primary ureter branch and medullary cones, and intraluminal trematodes identified as Renicola sloanei based on morphology and molecular analysis. Influenza virus infection was ruled out. The postmortem investigations performed in this mortality event of Atlantic puffins indicate that the animals were severely emaciated and suffered from nephropathy. The etiopathological investigation performed in relation to this mortality event of Atlantic puffins indicates starvation associated with bad weather conditions during migratory movement as the most likely cause of the unusual mortality event. Full article

The term “overkilling” in forensic medicine is not clearly defined and is used to refer to homicides involving unusually massive injuries, far exceeding those necessary to kill the victim. This is the clinical case of a dog found in February 2023 in a town near Naples, with a rope around its neck and the metacarpal region of its forelimbs. The dog was taken to the Istituto Zooprofilattico Sperimentale del Mezzogiorno (IZSM, Portici, Southern Italy), where it underwent a total body radiographic study performed using the “Philosophy HF400” X-ray device (Pan Vet, Kildare Town, Ireland). Subsequently, a full autopsy was performed, and samples of the injured organs were analyzed by accredited in-house laboratories for microbiological, histological and toxicological analyses. The autopsy revealed anatomopathological lesions compatible with strangulation, which were confirmed by histological examination. The autopsy also reported serosanguineous chest effusion, food material mixed with blackish microgranules and harmful substances in the stomach and, finally, uncoagulated blood in the atrioventricular chambers of the heart. These findings raised the suspicion of poisoning, which was confirmed by the positive outcome of toxicological tests. Full article

Background: Lupus podocytopathy (LP) is a non-immune complex-mediated glomerular lesion in systemic lupus erythematosus (SLE), characterized by the diffuse effacement of podocyte processes without immune complex deposition or with only mesangial immune complex deposition. LP is a rare cause of nephrotic syndrome in SLE patients with implications for prognosis and treatment. Case Report: We present the case of a 28-year-old woman with a medical history of type 1 diabetes mellitus (T1DM) who presented with lower limb edema, dyspnea, hypercholesterolemia, with nephrotic range proteinuria, without acute kidney injury, and laboratory findings compatible with auto-immune hemolytic anemia. They had negative infectious serology, positive antinuclear antibody (ANA), and an eye fundus examination showing diabetic retinopathy. A biopsy was performed to define the etiology of the renal involvement, which was compatible with LP. Following immuno-suppressive and antiproteinuric therapy, the patient evolved with the complete remission of the nephrotic syndrome. Conclusions: Lupus podocytopathy is an infrequent anatomopathological entity, so this case is presented as the first reported in Peru, and a literature review is made. Full article

Background: Aspergillosis is a fungal disease caused by the inhalation of fungal spores of the genus Aspergillus spp. This fungus mainly affects the lungs but can spread and infect the maxillofacial region through the bloodstream or inoculation of the fungus after extraction or endodontic treatment, especially in the upper posterior teeth. The disease has nonspecific clinical manifestations that hinder its early diagnosis. Although the Polymerase Chain Reaction (PCR) technique holds promise as a diagnostic tool for aspergillosis, anatomopathological analysis services do not routinely adopt this method. Objectives: Therefore, the present study aimed to evaluate the applicability of PCR and standardise the techniques of preparation of biological samples for the detection of the three species: Aspergillus niger, Aspergillus fumigatus and Aspergillus flavus. Methods: Six samples of formalin-fixed, paraffin-embedded tissue (FFPE) with a histopathological diagnosis suggestive of aspergillosis were investigated using PCR. As a positive control for the PCR reaction, morphologically and genetically characterized cultures were used, with their sequences deposited at NCBI under accession codes MW837777 (A. fumigatus) and MW837779 (A. niger). The A. flavus culture used is reference RC 2053. Results: Four of the six samples evaluated were positive for Aspergillus spp., of which one was co-infected with A. fumigatus and A. flavus species, while two others were positive only for A. flavus, and one sample was positive only for A. fumigatus. Conclusions: These findings suggest that PCR can be used as an auxiliary method for diagnosing aspergillosis. However, this was a pilot study, and expansion of the sample size and the evaluation of PCR in comparison with other diagnostic tests for aspergillosis are essential to determine the accuracy of the method. Full article

Background: When the body temperature falls below 35 °C, a condition known as hypothermia occurs. This renders it impossible to regulate the body temperature and produce heat. In these cases, death is due to a cessation of vital functions and is triggered by a body temperature below 25 °C. A multidisciplinary approach is typically required when hypothermia is suspected to combine circumstantial evidence, external examination, autopsy, microscopic and biochemical findings, and other data useful to assess the diagnosis of fatal hypothermia. Post-mortem diagnosis of death by hypothermia frequently presents a medico-legal dilemma. Methods and Results: The authors present a case of hypothermia in which site inspection, autopsy, and histological examination simultaneously revealed the forensic and anatomopathological characteristic findings of hypothermia with some peculiar evidence: paradoxical undressing, thanatochronological phenomena, frost erythema, polyvisceral congestion and Wischnewski spots, and subnuclear vacuolization of renal tubular epithelial cells. Full article

Brain abscesses in ruminants often arise from primary infection foci, leading to an unfavorable prognosis for affected animals. This highlights the need for comprehensive studies on brain abscesses across different ruminant species. We retrospectively investigated medical records of epidemiological, clinical, neuroimaging, anatomopathological, and bacteriological findings in six ruminants (three goats, two cows, and one sheep) diagnosed with brain abscesses. All animals studied were female. Apathy (50%), compulsive walking (33%), decreased facial sensitivity (33%), head pressing (33%), seizures (33%), semicomatous mental status (33%), strabismus (33%), unilateral blindness (33%), and circling (33%) represented the most common neurologic signs. Leukocytosis and neutrophilia were the main findings in the hematological evaluation. Cerebrospinal fluid (CSF) analysis revealed predominant hyperproteinorrachia and pleocytosis. In three cases, computed tomography or magnetic resonance imaging were used, enabling the identification of typical abscess lesions, which were subsequently confirmed during postmortem examination. Microbiological culture of the abscess samples and/or CSF revealed bacterial coinfections in most cases. Advanced imaging examinations, combined with CSF analysis, can aid in diagnosis, although confirmation typically relies on postmortem evaluation and isolation of the causative agent. This study contributes to clinicopathological aspects, neuroimages, and bacteriological diagnosis of brain abscesses in domestic ruminants. Full article

Avian influenza viruses (AIVs) are highly contagious respiratory viruses of birds, leading to significant morbidity and mortality globally and causing substantial economic losses to the poultry industry and agriculture. Since their first isolation in 2013–2014, the Asian-origin H5 highly pathogenic avian influenza viruses (HPAI) of clade 2.3.4.4b have undergone unprecedented evolution and reassortment of internal gene segments. In just a few years, it supplanted other AIV clades, and now it is widespread in the wild migratory waterfowl, spreading to Asia, Europe, Africa, and the Americas. Wild waterfowl, the natural reservoir of LPAIVs and generally more resistant to the disease, also manifested high morbidity and mortality with HPAIV clade 2.3.4.4b. This clade also caused overt clinical signs and mass mortality in a variety of avian and mammalian species never reported before, such as raptors, seabirds, sealions, foxes, and others. Most notably, the recent outbreaks in dairy cattle were associated with the emergence of a few critical mutations related to mammalian adaptation, raising concerns about the possibility of jumping species and acquisition of sustained human-to-human transmission. The main clinical signs and anatomopathological findings associated with clade 2.3.4.4b virus infection in birds and non-human mammals are hereby summarized. Full article

The amnion rupture sequence is a rare condition occurring early in pregnancy, resulting in complex fetal anomalies by disrupting normal embryonic development. The prevalence of amnion rupture sequence is reported to be 1.16 in 10,000 live births. This article explores the uncommon case of early amnion rupture leading to fetal encephalocele, suspected in the first trimester. Despite the variable and intricate nature of anomalies associated with this condition, cranio-facial and abdominal defects are frequently observed. Genetic testing was conducted, with normal results supporting our theory of amnion rupture. The patient decided to terminate the pregnancy, and the anatomopathological results confirmed the findings. This article discusses the diagnostic challenges, emphasizing the importance of timely identification through advanced imaging techniques. Full article

Abdominal wall defects encompass three primary classifications: gastroschisis, omphalocele and anomalies resembling body stalk. Potential causative factors include early amnion rupture, amniotic bands, vascular disruptions or abnormal folding of the embryo. The prevalence of these defects stands at 1 in 14,000 live births. Body stalk anomaly is characterized by a substantial abdominal defect coupled with spine and limb anomalies, along with a very short or absent umbilical cord. We present a case of a rare abdominal defect known as body stalk anomaly, the most severe form of this spectrum of diseases. The diagnosis of this anomaly was established during the first trimester of pregnancy. Subsequently, the patient opted for pregnancy termination and chose not to undergo genetic testing. The anatomo-pathological results confirmed the findings. Body stalk anomaly is not compatible with life; therefore, early identification and understanding the clinical implications of this rare anomaly for informed decision-making in prenatal care are very important. Full article

Infective valve endocarditis is caused by different pathogens and 60% of those involve the aortic valve with valve failure. Although S. aureus is recognized as the most frequently isolated causative bacterium associated with IE in high-income countries, Gram-positive cocci nevertheless play a crucial role in promoting infection in relation to their adhesive matrix molecules. The presence of pili on the surface of Gram-positive bacteria such as in different strains of Enterococcus faecalis and Streptococcus spp., grants these causative pathogens a great offensive capacity due to the formation of biofilms and resistance to antibiotics. The indications and timing of surgery in endocarditis are debated as well as the choice of the ideal valve substitute to replace the diseased valve(s) when repair is not possible. We reviewed the literature and elaborated a systematic approach to endocarditis management based on clinical, microbiological, and anatomopathological variables known to affect postoperative outcomes with the aim to stratify the patients and orient decision making. From this review emerges significant findings on the risk of infection in the allograft used in patients with endocarditis and no endocarditis etiology suggesting that the use of allografts has proved safety and effectiveness in patients with both pathologies. Full article

This study aimed to investigate the histopathological changes associated with SARS-CoV-2 infection in placentas. A case series of anatomopathological analysis was conducted on the placentas of pregnant women with SARS-CoV-2 who delivered between March and December 2020 at Santo Amaro Hospital (HSA) in Salvador, Brazil. Out of the 29 placentas examined, the median weight was 423.0 (IQR: 385.0–521.0) g. Among them, 58.3% (n = 14) had inadequate weight relative to the newborn’s weight. The histopathological findings revealed that 86.2% (n = 25) of the placentas had poorly defined lobes, and the fetal and maternal surface color was normal in 89.7% (n = 26) and 93.1% (n = 27), respectively. Additionally, 51.7% (n = 15) of the umbilical cords displayed hypercoiling. The most frequent microscopic finding was infarction, present in 35.3% (n = 6) of the cases, followed by 11.8% (n = 2) for each of chorioamnionitis, chronic villitis, focal perivillositis, and laminar necrosis. Analysis of the umbilical cords identified 23.5% (n = 4) cases of intervillous thrombosis, while amnion analysis showed 13.8% (n = 4) cases of squamous metaplasia. Extraplacental membrane examination revealed fibrin deposition in 93.1% (n = 27) of the cases, necrosis in 62.0% (n = 18), calcifications in 51.7% (n = 15), cysts in 37.9% (n = 11), neutrophilic exudate in 17.2% (n = 5), thrombosis in 13.7% (n = 4), and delayed placental maturation in 6.9% (n = 2). All analyzed placentas exhibited histopathological changes, primarily vascular and inflammatory, which indicate SARS-CoV-2 infection in term pregnancies. These alterations could be associated with impaired placental function, fetal growth restriction, preeclampsia, and prematurity. However, further prospective studies are required to validate the type, prevalence, and prognosis of each of these changes. Full article

Objectives: to analyse the clinical–pathological characteristics, treatment, and evolution of uterine smooth muscle tumours with uncertain malignant potential (STUMP) diagnosed in the Salamanca University Hospital with the implementation of the 2014 WHO criteria. Materials and methods: a retrospective descriptive study of patients diagnosed with STUMP from January 2015 to March 2023 at the Salamanca University Hospital. Demographic data, preoperative clinical data, treatment, complications, therapeutic results, anatomopathological findings and recurrence time were obtained. Results: a total of four patients were identified and included in the study. The mean age at diagnosis was 48 years (range 36–67). The surgical indications were abnormal uterine bleeding, compressive symptoms, and the growth of a pelvic mass suspected to be a degenerated myoma from the residual cervix after a subtotal hysterectomy 6 years earlier. In all cases, a laparotomic procedure was performed. A total hysterectomy, sub-total hysterectomy, and the excision of the cervix with STUMP localization were accomplished in two, one, and one patient, respectively. The mean diameter of the tumour pieces was 13 cm (range 8–17 cm), with a mean volume of 816 cc (range 234–1467 cc). The mean follow-up was 47 months, with no recurrence to date. Conclusions: STUMPs are a heterogeneous group of tumours with a difficult-to-predict clinical evolution. In most cases, their diagnosis is histological after performing surgery for suspected leiomyoma. Due to their low incidence, there are no specific guidelines for their treatment and control. However, considering their potential risk of recurrence and metastasis, it is advisable to maintain six-monthly controls for 5 years and then annual controls for 5 years more. Full article