cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20026005
title: Timeline analysis of IgA and IgG levels in Covid-19 hospitalized patients according to the clinical outcome

description: ABSTRACT Introduction: Studies suggest the association between antibody production and the severity of coronavirus disease 2019 (Covid-19). Objectives: To evaluate the concentrations of immunoglobulins class A (IgA) and class G (IgG) during the hospitalization period of Covid-19 patients according to the outcome (survival vs death). Materials and methods: Patients with severe acute respiratory syndrome of coronavirus 2 (Sars-CoV-2) infection confirmed by reverse transcriptase reaction followed by polymerase chain reaction (RT-PCR) were included in this prospective study. Samples were obtained weekly during the follow-up of individuals, considering symptom onset. Titers of anti-Sars-CoV-2 IgA and IgG were measured using a commercial immunoassay. Correlations between IgA/IgG and cycle threshold (Ct) values for N1 and N2 target genes were also assessed. Results: We studied 55 Covid-19 patients (59.7±16.2 years, 63.6% male), of which 28 (50.9%) died. We observed IgA and IgG positivity (IgA+ and IgG+) in 90.9% and 80% of patients, respectively. The highest IgA+ frequency was observed at weeks 2 and 3 and the highest IgG+ at weeks 3 and 4. It is important to note that patients who died presented lower IgA titers in the first two weeks (p &lt; 0.05); however, a significant increase in IgA levels was observed in the subsequent weeks. Lastly, we identified that significant correlations between Ct values and immunoglobulins levels, both IgA and IgG were correlated with Ct N2 in patients who died. Conclusion: Our results suggest that lower IgA titers in early Covid-19, which is associated with lower Ct values, may indicate patients at higher risk for death.
DOI: 10.6084/m9.figshare.20026008
title: Reticulocyte parameters for monitoring anemia in patients with chronic kidney disease on peritoneal dialysis

description: ABSTRACT Introduction: Anemia is a complication with impact on morbidity and mortality in chronic kidney disease (CKD) patients. Current markers for the diagnosis and monitoring of anemia in CKD are limited by the interrelation between erythropoiesis, iron stores, inflammation, and the resistance to treatment with erythropoiesis stimulant agents (ESA). Objective: The aim of this study was to analyze the role of immature reticulocyte fraction (IRF) and hemoglobin concentration in reticulocytes (RET-He) by the hematology analyser Sysmex XN-5000 in the monitoring of CKD anemia in peritoneal dialysis patients. Methods: This was a prospective, observational multicenter study which compared IRF and RET-He with parameters recommended by the guidelines. Inflammatory biomarkers were analyzed by the Luminex® Multiplexing Instruments system. Thirty-five patients (59 ± 13 years old; 51% men) were included in the analysis. Results: Hemoglobin was 12.2 ± 2 g/dl; 87% had resistance to ESA. Patients with erythropoietin resistance index (ERI) in the upper quartile presented a significantly higher of IRF and a lower percentage of iron deficiency (12%) compared to ferritin (82%) and transferrin saturation index (STI) (51%). Interleukin-6 (IL-6) levels correlated with the percentage of medium fluorescence reticulocyte (MFR) (r = 0.45, p &lt; 0.03). Hemoglobin values after 60 and 180 days were consistently higher in the group of patients with a IRF% lower than 10.5. Conclusion: IRF and RET-He may add value in the iron deficiency investigation, as well as in the identification of patients with ERI. Due to the restricted number of patients analyzed in this study, future studies should be encouraged in larger populations and with prospective follow-up, to validate our findings.
DOI: 10.6084/m9.figshare.20026008.v1
title: Reticulocyte parameters for monitoring anemia in patients with chronic kidney disease on peritoneal dialysis

description: ABSTRACT Introduction: Anemia is a complication with impact on morbidity and mortality in chronic kidney disease (CKD) patients. Current markers for the diagnosis and monitoring of anemia in CKD are limited by the interrelation between erythropoiesis, iron stores, inflammation, and the resistance to treatment with erythropoiesis stimulant agents (ESA). Objective: The aim of this study was to analyze the role of immature reticulocyte fraction (IRF) and hemoglobin concentration in reticulocytes (RET-He) by the hematology analyser Sysmex XN-5000 in the monitoring of CKD anemia in peritoneal dialysis patients. Methods: This was a prospective, observational multicenter study which compared IRF and RET-He with parameters recommended by the guidelines. Inflammatory biomarkers were analyzed by the Luminex® Multiplexing Instruments system. Thirty-five patients (59 ± 13 years old; 51% men) were included in the analysis. Results: Hemoglobin was 12.2 ± 2 g/dl; 87% had resistance to ESA. Patients with erythropoietin resistance index (ERI) in the upper quartile presented a significantly higher of IRF and a lower percentage of iron deficiency (12%) compared to ferritin (82%) and transferrin saturation index (STI) (51%). Interleukin-6 (IL-6) levels correlated with the percentage of medium fluorescence reticulocyte (MFR) (r = 0.45, p &lt; 0.03). Hemoglobin values after 60 and 180 days were consistently higher in the group of patients with a IRF% lower than 10.5. Conclusion: IRF and RET-He may add value in the iron deficiency investigation, as well as in the identification of patients with ERI. Due to the restricted number of patients analyzed in this study, future studies should be encouraged in larger populations and with prospective follow-up, to validate our findings.
DOI: 10.6084/m9.figshare.20026009
title: Diagnostic performance between histopathological and molecular methods in the detection of Helicobacter pylori

description: ABSTRACT Introduction: Helicobacter pylori (H. pylori) is a Gram negative bacterium considered to be the etiologic agent of various gastric diseases. The prevalence of bacterial infection varies according to age, geographic location, ethnicity and socioeconomic status. The chronic infection caused by microorganism can favor the development of severe pathologies such as gastric adenocarcinoma. In this sense, early diagnosis is essential for a better prognosis and therapeutic success. Several diagnostic methods performed using invasive and non-invasive techniques, with different sensitivity and specificity, have been used in the detection of H. pylori. Objective: To compare the performance of the molecular and histopathological technique used in the diagnosis of H. pylori infection. Methods: 76 gastric tissue samples were collected from dyspeptic patients who underwent molecular and histopathological diagnosis. Molecular detection was performed using the ribosomal gene (16S rRNA) using the polymerase chain reaction (PCR) technique. Results: The PCR-based molecular diagnostic method detected the bacterium in 63.1% of the samples, while the histopathological test identified the microorganism in only 38.1% of gastric biopsies. The data demonstrated that the PCR technique was about 1.6 times more sensitive than the histopathological technique. Conclusion: The PCR technique was the most efficient diagnostic method for detecting H. pylori and can be implemented in the laboratory routine as a complementary test for the early detection of H. pylori.
DOI: 10.6084/m9.figshare.20026009.v1
title: Diagnostic performance between histopathological and molecular methods in the detection of Helicobacter pylori

description: ABSTRACT Introduction: Helicobacter pylori (H. pylori) is a Gram negative bacterium considered to be the etiologic agent of various gastric diseases. The prevalence of bacterial infection varies according to age, geographic location, ethnicity and socioeconomic status. The chronic infection caused by microorganism can favor the development of severe pathologies such as gastric adenocarcinoma. In this sense, early diagnosis is essential for a better prognosis and therapeutic success. Several diagnostic methods performed using invasive and non-invasive techniques, with different sensitivity and specificity, have been used in the detection of H. pylori. Objective: To compare the performance of the molecular and histopathological technique used in the diagnosis of H. pylori infection. Methods: 76 gastric tissue samples were collected from dyspeptic patients who underwent molecular and histopathological diagnosis. Molecular detection was performed using the ribosomal gene (16S rRNA) using the polymerase chain reaction (PCR) technique. Results: The PCR-based molecular diagnostic method detected the bacterium in 63.1% of the samples, while the histopathological test identified the microorganism in only 38.1% of gastric biopsies. The data demonstrated that the PCR technique was about 1.6 times more sensitive than the histopathological technique. Conclusion: The PCR technique was the most efficient diagnostic method for detecting H. pylori and can be implemented in the laboratory routine as a complementary test for the early detection of H. pylori.
DOI: 10.6084/m9.figshare.20026011
title: Performance evaluation of a Sars-CoV-2 rapid test and two automated immunoassays

description: ABSTRACT Introduction: Due to urgency and demand of a response to the Covid-19 pandemic, numerous Sars-CoV-2 immunoassays have been rapidly developed. Objective: This study aimed at assessing the performance of rapid Sars-CoV-2 antibody test in comparison to high-throughput serological assays. Methods: A total of 86 serum samples were evaluated in the three assays: a lateral flow immunoassay - Wondfo Sars-CoV-2 Antibody Test (WRT) - and two chemiluminescence immunoassays: Elecsys Anti-Sars-CoV-2 (ECLIA), and Sars-CoV-2 IgG (CMIA-IgG). Results: The estimated diagnostic sensitivities of serological tests in the evaluation of serum samples from the epidemiological survey were: WRT 59% [95% confidence interval (CI) 43.4%-72.9%], ECLIA 66.7% (51%-79.4%), and CMIA-IgG 61.5% (47.1%-73%). Meanwhile, the estimated diagnostic specificity was for WRT 78.7% (95% CI 65.1%-88%), ECLIA 72.3% (58.2%-83.1%), and CMIA-IgG 76.6% (74%-95.5%). The sensitivity and specificity values were lower than manufacturers’ claimed. Although 16.2% (14/86) of serological results were discordant among the three Sars-CoV-2 serological assays, the degree of agreement by the kappa index was adequate: WRT/CMIA-IgG [0.757 (95% CI 0.615-0.899)], WRT/ECLIA [0.715 (0.565-0.864)], and ECLIA/CMIA-IgG [0.858 (0.748-0.968)]. Conclusion: The serological testing may be a useful diagnostic tool, which reinforces its careful evaluation, and, as well as the correct time to use it.
DOI: 10.6084/m9.figshare.20026011.v1
title: Performance evaluation of a Sars-CoV-2 rapid test and two automated immunoassays

description: ABSTRACT Introduction: Due to urgency and demand of a response to the Covid-19 pandemic, numerous Sars-CoV-2 immunoassays have been rapidly developed. Objective: This study aimed at assessing the performance of rapid Sars-CoV-2 antibody test in comparison to high-throughput serological assays. Methods: A total of 86 serum samples were evaluated in the three assays: a lateral flow immunoassay - Wondfo Sars-CoV-2 Antibody Test (WRT) - and two chemiluminescence immunoassays: Elecsys Anti-Sars-CoV-2 (ECLIA), and Sars-CoV-2 IgG (CMIA-IgG). Results: The estimated diagnostic sensitivities of serological tests in the evaluation of serum samples from the epidemiological survey were: WRT 59% [95% confidence interval (CI) 43.4%-72.9%], ECLIA 66.7% (51%-79.4%), and CMIA-IgG 61.5% (47.1%-73%). Meanwhile, the estimated diagnostic specificity was for WRT 78.7% (95% CI 65.1%-88%), ECLIA 72.3% (58.2%-83.1%), and CMIA-IgG 76.6% (74%-95.5%). The sensitivity and specificity values were lower than manufacturers’ claimed. Although 16.2% (14/86) of serological results were discordant among the three Sars-CoV-2 serological assays, the degree of agreement by the kappa index was adequate: WRT/CMIA-IgG [0.757 (95% CI 0.615-0.899)], WRT/ECLIA [0.715 (0.565-0.864)], and ECLIA/CMIA-IgG [0.858 (0.748-0.968)]. Conclusion: The serological testing may be a useful diagnostic tool, which reinforces its careful evaluation, and, as well as the correct time to use it.
DOI: 10.6084/m9.figshare.20026014
title: Soft tissue myoepithelial carcinoma: is it a low-grade cancer?

description: ABSTRACT Myoepithelial carcinoma is a rare neoplasm of very heterogeneous manifestation that represents a major challenge to the adoption of categorical prognostic criteria since, despite being classified as a low-grade cancer, it behaves very aggressively. While several studies have indicated complete surgical resection as the best treatment for myoepithelial carcinoma, adjuvant therapies have proven effective in preventing relapse. This study describes the case of a patient who developed myoepithelial carcinoma in the right thigh, affecting deep tissues, which were conducted as indicated in the current literature, however, presenting an unfavorable outcome. The available information comes from few studies; therefore, we emphasize the importance of gathering data on the subject, which are still scarce.
DOI: 10.6084/m9.figshare.20026014.v1
title: Soft tissue myoepithelial carcinoma: is it a low-grade cancer?

description: ABSTRACT Myoepithelial carcinoma is a rare neoplasm of very heterogeneous manifestation that represents a major challenge to the adoption of categorical prognostic criteria since, despite being classified as a low-grade cancer, it behaves very aggressively. While several studies have indicated complete surgical resection as the best treatment for myoepithelial carcinoma, adjuvant therapies have proven effective in preventing relapse. This study describes the case of a patient who developed myoepithelial carcinoma in the right thigh, affecting deep tissues, which were conducted as indicated in the current literature, however, presenting an unfavorable outcome. The available information comes from few studies; therefore, we emphasize the importance of gathering data on the subject, which are still scarce.
DOI: 10.6084/m9.figshare.20026015
title: Pancreatic panniculitis in systemic lupus erythematosus and Crohn’s disease: rare event

description: ABSTRACT Pancreatic panniculitis (PP) is a rare manifestation of pancreatic disease, involving subcutaneous adipose tissue. We report two cases of this entity: a 37-year-old female patient with systemic lupus erythematosus (SLE) and an elderly woman with Crohn’s disease. These are two chronic autoimmune inflammatory diseases that can be uncommonly related to acute pancreatitis and that culminates in PP. We also provide a brief review of the treatment, diagnosis and morphology of the lesions, as well as the pathophysiology of the disease. The importance of histopathological analysis of lesion biopsies is highlighted as an important diagnostic tool.
DOI: 10.6084/m9.figshare.20026015.v1
title: Pancreatic panniculitis in systemic lupus erythematosus and Crohn’s disease: rare event

description: ABSTRACT Pancreatic panniculitis (PP) is a rare manifestation of pancreatic disease, involving subcutaneous adipose tissue. We report two cases of this entity: a 37-year-old female patient with systemic lupus erythematosus (SLE) and an elderly woman with Crohn’s disease. These are two chronic autoimmune inflammatory diseases that can be uncommonly related to acute pancreatitis and that culminates in PP. We also provide a brief review of the treatment, diagnosis and morphology of the lesions, as well as the pathophysiology of the disease. The importance of histopathological analysis of lesion biopsies is highlighted as an important diagnostic tool.
DOI: 10.6084/m9.figshare.20026023
title: Extensive central ossifying fibroma of mandible: case report

description: ABSTRACT A 34-year-old female patient attended a referral center for oral diagnosis presenting hardened increased volume in the posterior mandible. Panoramic radiography revealed a mixed unilocular lesion with clear and well-defined limits. The incisional biopsy showed proliferation of mesenchymal cells amid dense fibrous connective tissue. Mineralized material in different degrees of maturation was also observed. Regarding the histopathological aspects associated with the clinical, radiographic, and intraoperative data, the diagnosis of central ossifying fibroma (COF) was performed. COF has similar characteristics to other fibro-osseous lesions, and its diagnosis is a challenge for dental surgeons.
DOI: 10.6084/m9.figshare.20026023.v1
title: Extensive central ossifying fibroma of mandible: case report

description: ABSTRACT A 34-year-old female patient attended a referral center for oral diagnosis presenting hardened increased volume in the posterior mandible. Panoramic radiography revealed a mixed unilocular lesion with clear and well-defined limits. The incisional biopsy showed proliferation of mesenchymal cells amid dense fibrous connective tissue. Mineralized material in different degrees of maturation was also observed. Regarding the histopathological aspects associated with the clinical, radiographic, and intraoperative data, the diagnosis of central ossifying fibroma (COF) was performed. COF has similar characteristics to other fibro-osseous lesions, and its diagnosis is a challenge for dental surgeons.
DOI: 10.6084/m9.figshare.16550013
title: Collection of simulated medical exams

description: The compressed folder contains a collections of simulated medical exams in mp3 format and the corresponding text files.
DOI: 10.5281/zenodo.6620567
title: Low impact of clonal hematopoiesis on the determination of RAS mutations by cell-free DNA testing in routine clincal diagnostics

description: BAM files from liquid biposy samples analyzed with Oncomine PanCancer Assay
DOI: 10.5281/zenodo.6620566
title: Low impact of clonal hematopoiesis on the determination of RAS mutations by cell-free DNA testing in routine clincal diagnostics

description: BAM files from liquid biposy samples analyzed with Oncomine PanCancer Assay
DOI: 10.6084/m9.figshare.20026024
title: Clinicopathological study of cystic and atypical uterine leiomyoma: a rare entity

description: ABSTRACT A 43-years-old Brazilian woman, Caucasian, premenopausal, was attended with a history of lower abdominal pain, distension, and bleeding. Pelvic and transvaginal ultrasound revealed an enlarged uterus with a large, well-defined, uniformly hyperechoic lesion. The patient underwent total hysterectomy and the specimen was sent for anatomopathological evaluation. The histopathological analyses revealed a leiomyoma with extensive cystic degeneration and atypical characteristics, the immunohistochemical study confirmed the benignity of the case. The finding of atypical leiomyoma with cystic degeneration is rare and should be carefully evaluated to exclude malignant diseases.
DOI: 10.6084/m9.figshare.20026024.v1
title: Clinicopathological study of cystic and atypical uterine leiomyoma: a rare entity

description: ABSTRACT A 43-years-old Brazilian woman, Caucasian, premenopausal, was attended with a history of lower abdominal pain, distension, and bleeding. Pelvic and transvaginal ultrasound revealed an enlarged uterus with a large, well-defined, uniformly hyperechoic lesion. The patient underwent total hysterectomy and the specimen was sent for anatomopathological evaluation. The histopathological analyses revealed a leiomyoma with extensive cystic degeneration and atypical characteristics, the immunohistochemical study confirmed the benignity of the case. The finding of atypical leiomyoma with cystic degeneration is rare and should be carefully evaluated to exclude malignant diseases.
DOI: 10.6084/m9.figshare.20026026
title: Sclerosing variant of well-differentiated testicular liposarcoma: a case report

description: ABSTRACT Testicular cancers are classified in germ cell and non-germ cell tumors, as well as, liposarcomas. We report the case of a patient with a large testicular liposarcoma, submitted to surgical treatment with excision of scrotal pouch and segment of the spermatic cord, and the left testicle, showing a good evolution. This report presents one of the first cases of a sclerosing variant of well-differentiated testicular liposarcoma, large in size and with no association with another cancer. Due to their location, the diagnosis is difficult and unusual. Complete tumor resection and regular medical follow-up show a good prognosis, less recurrence, and little cellular differentiation.
DOI: 10.6084/m9.figshare.20026026.v1
title: Sclerosing variant of well-differentiated testicular liposarcoma: a case report

description: ABSTRACT Testicular cancers are classified in germ cell and non-germ cell tumors, as well as, liposarcomas. We report the case of a patient with a large testicular liposarcoma, submitted to surgical treatment with excision of scrotal pouch and segment of the spermatic cord, and the left testicle, showing a good evolution. This report presents one of the first cases of a sclerosing variant of well-differentiated testicular liposarcoma, large in size and with no association with another cancer. Due to their location, the diagnosis is difficult and unusual. Complete tumor resection and regular medical follow-up show a good prognosis, less recurrence, and little cellular differentiation.
DOI: 10.5281/zenodo.6610449
title: Intrinsic vulnerabilty maps for the Telesina Valley (IT), Marchfeld (AT) and Zala County (HU)

description: The dataset contains the maps of the soil intrinsic vulnerability for three case studies, the Telesina Valley in Italy, the Marchfeld region in Austria and the Zala County in Hungary, simulated using the TFM-ext model (Bancheri et al.,2021). The maps show the intrinsic vulnerability, categorized in 6 classes, from very low to extremely high, according to the estimated mean travel times. The model considered the spatially varying pedoclimatic conditions (i.e., georeferenced hydraulic properties and climate) to evaluate the mean travel times of a generic non-reactive solute till the bottom of the soil profiles. Then, the normalized values were computed and categorized.
description: {"references": ["Bancheri, Marialaura, Antonio Coppola, and Angelo Basile. \"A new transfer function model for the estimation of non-point-source solute travel times.\" Journal of Hydrology 598 (2021): 126157."]}
DOI: 10.5281/zenodo.6610448
title: Intrinsic vulnerabilty maps for the Telesina Valley (IT), Marchfeld (AT) and Zala County (HU)

description: The dataset contains the maps of the soil intrinsic vulnerability for three case studies, the Telesina Valley in Italy, the Marchfeld region in Austria and the Zala County in Hungary, simulated using the TFM-ext model (Bancheri et al.,2021). The maps show the intrinsic vulnerability, categorized in 6 classes, from very low to extremely high, according to the estimated mean travel times. The model considered the spatially varying pedoclimatic conditions (i.e., georeferenced hydraulic properties and climate) to evaluate the mean travel times of a generic non-reactive solute till the bottom of the soil profiles. Then, the normalized values were computed and categorized.
description: {"references": ["Bancheri, Marialaura, Antonio Coppola, and Angelo Basile. \"A new transfer function model for the estimation of non-point-source solute travel times.\" Journal of Hydrology 598 (2021): 126157."]}
DOI: 10.6084/m9.figshare.20026036
title: Clear cell-rich salivary duct carcinoma involving the palate

description: ABSTRACT Salivary duct carcinoma (SDC) is a rare and aggressive neoplasm arising from salivary glands. SDC occurs most frequently in major salivary glands, with isolated cases arising from the minor salivary glands. The occurrence of clear cells in salivary gland tumors is uncommon and is rarer in SDC cases. We report the case of a 51-year-old male diagnosed with a clear cell variant of SDC in the minor salivary gland, involving the left hard palate. Immunohistochemical analysis revealed positivity for HER2/neu and GATA-3. The patient was submitted to radical surgical excision, neck dissection, and radiotherapy. Unfortunately, he died 14 months after the cancer diagnosis.