cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23586198
title: Supplementary Material for: Circulating Cell-Free DNA as a Biomarker for Prognosis and Response to Systemic Therapy in Patients with Unresectable Hepatocellular Carcinoma

description: Introduction: Systemic therapy provides clinical benefits to a subset of patients with advanced unresectable hepatocellular carcinoma (HCC). However, few biomarkers are available for predicting prognosis and treatment response in patients with advanced HCC undergoing treatment with systemic therapies. This study aimed to examine whether circulating cell-free DNA (cfDNA) containing circulating tumor DNA can act as a therapeutic response and prognostic biomarker in patients with advanced HCC. Methods: We analyzed longitudinally collected plasma cfDNA of patients with advanced HCC who were naïve to systemic therapy, and assessed their prognostic and predictive values to determine treatment responses. Results: cfDNA concentration positively correlated with entire tumor volume on computed tomography before (P = 0.0231) and at the end (P &lt; 0.0001) of the first-line systemic therapy. The overall survival rate was higher in patients with cfDNA concentrations lower than the median cfDNA level at baseline compared to patients with higher cfDNA concentrations (hazard ratio, 0.2765; 95% confidence interval, 0.08–0.81; P = 0.0197). The ratio of cfDNA at four weeks to that at baseline was predictive of radiographic disease response. In patients with progressive disease, cfDNA concentration at four weeks increased significantly (P = 0.0245), whereas the concentration remained unchanged in patients with other disease courses (P = 0.9375). Conclusion: The baseline plasma cfDNA concentration can be used as a prognostic biomarker in patients with advanced HCC. cfDNA kinetics may also predict the tumor response to therapy and disease progression.
DOI: 10.6084/m9.figshare.23606709
title: Supplementary Material for: Enrichment of Immune-Related Genes in Aggressive Primary Breast Angiosarcoma: A Case Report

description: Primary breast angiosarcoma is an extremely rare disease with a poor prognosis. Primary angiosarcoma is distinct from secondary angiosarcoma, which usually occurs in patients who have been previously treated for breast cancer. The low incidence of primary breast angiosarcoma has hindered the elucidation of its etiology and potential therapies. Here, we report a case of a patient with primary breast angiosarcoma who experienced recurrence after surgery. The tumor was refractory to systemic treatments, and the patient died 18 months after the surgery. We used RNA sequencing for gene expression profiling of the tumor. A high tumor inflammation signature score indicated enrichment in immune-related signaling. CIBERSORTx, a tool used to characterize the cellular composition of complex tissues based on gene expression, indicated that the immune cells in the tumor were predominantly macrophages, and this was confirmed using immunohistochemical analysis. These findings indicate the possible use of checkpoint immunotherapy for the treatment of primary breast angiosarcoma.
DOI: 10.6084/m9.figshare.23790672
title: Supplementary Material for: Higher house dust mite-specific IgE levels among chronic spontaneous urticaria patients may implicate higher basophil reactivity

description: Introduction: Allergen-specific IgE (sIgE) sensitization exists in a considerable fraction of chronic spontaneous urticaria (CSU) patients. Basophils have been implicated in the pathogenesis of CSU. This paper aimed to explore the relationship between allergic sensitization and basophil reactivity in CSU and the possible underlying mechanism. Methods: Basophil-enriched leukocytes were isolated from the peripheral blood of 76 CSU patients and 9 healthy controls. Basophil CD63 and FcεRIα (the alpha subunit of the high-affinity IgE receptor) expression in the blood samples with various house dust mite (HDM)-sIgE levels were determined by flow cytometry. Basophil reactivity and SHIP-1 (a molecule related to the IgE/FcεRI signaling pathway) expression were analyzed after stimulation with an HDM allergen or other stimuli. Results: HDM-sIgEstrong positive (≥ 3.5 kU/L) CSU patients had a significantly higher mean percentage of basophil CD63 and higher baseline levels of FcεRIα expressed by basophils than HDM-sIgEnormal (&lt; 0.35 kU/L) CSU patients and healthy controls; the same went for total serum IgE. After stimulation with Dermatophagoides pteronyssinus peptidase 1 (Derp1) alone or together with Derp1-sIgE, the stimulation index of CD63 and levels of FcεRIα expressed by basophils in HDM-sIgEstrong positive CSU patients were significantly higher than those in HDM-sIgEnormal CSU patients and healthy controls. Significantly more SHIP-1 mRNA expression in HDM-sIgEstrong positive CSU patients was induced after the combined stimulation in comparison to other subjects. Conclusion: CSU patients with higher HDM-sIgE levels (≥ 3.5 kU/L) may have higher CD63 and FcεRIα expression on peripheral blood basophils. Peripheral blood basophils in these CSU patients are more responsive to HDM allergen stimulation. Higher HDM-specific IgE levels among CSU patients may implicate higher basophil reactivity.
DOI: 10.6084/m9.figshare.23812776
title: Supplementary Material for: Retrospective study of treatment patterns and natural history of patients with T1a/b N0 TNBCs—A single-institution experience.

description: Introduction: T1a/b, node-negative (node-), triple-negative breast cancers (TNBCs) are underrepresented in randomized drug-approving clinical trials. Given their low incidence, the clinicopathological features, natural history, and treatment patterns of these tumors remain insufficiently understood. Methods: We conducted a single-institution retrospective cohort study of patients with T1a/b, N0, M0 TNBCs. Deidentified patient- and tumor-related data were collected and summarized. Kruskal-Wallis, chi-square, or Fisher exact tests were used to evaluate associations of interest. Kaplan-Meier methods, log-rank tests, and Cox's proportional hazards models were applied for survival analyses. Results: Of 108 cases of node- TNBCs measuring ≤2 cm, 34 node- T1a/b tumors were included in our analysis. All cases had an intermediate to high histological grade, and most had a Ki-67 score of ≥20%. All patients received adjuvant chemotherapy, and many underwent mastectomy (47%). Docetaxel combined with cyclophosphamide was the most common adjuvant chemotherapy regimen (75%). We did not observe significant associations between improved outcomes and treatment with anthracycline-containing regimens. Among patients with node- pT1a/b tumors, the estimated 3-year recurrence-free survival and distant recurrence-free survival rates were both 96.3% (95% CI, 76.5-99.5), and the overall survival rate was estimated to be 100% (95% CI, 100-100). There were no cases of local recurrences observed. Discussion/Conclusions: In our cohort, all patients with T1a/b node- TNBCs were treated with adjuvant chemotherapy and had favorable outcomes even when treated with anthracycline-sparing regimens.
DOI: 10.6084/m9.figshare.23812815
title: Supplementary Material for: Lipid metabolism pathway genes and lung cancer: ACADSB rs12220683G&gt;C is associated with better survival outcome in patients with non-small cell lung cancer

description: Altered lipid metabolism has been reported to be associated with prognosis in multiple cancers. This study aimed to investigate the association of polymorphisms in lipid metabolism pathway genes with survival outcomes in patients with surgically resected non-small cell lung cancer (NSCLC). In total, 744 patients with surgically resected NSCLC (380 in the discovery cohort and 364 in the validation cohort) were included in this study. Among the 176 investigated polymorphisms, ACADSB rs10902859G&gt;A was associated with significantly better overall survival (OS) in the discovery, validation, and combined cohorts. ACADSB rs10902859G&gt;A was located in the repressed region and had strong linkage disequilibrium (D′ = 1.00 and r2 = 0.94), with rs12220683G&gt;C located in the H3K4me3 peak region, which indicates the presence of active promoters. ACADSB rs12220683G&gt;C was also associated with better OS in the discovery, validation, and combined cohorts (in a dominant model; adjusted hazard ratio [aHR] = 0.53, 95% confidence interval [CI] = 0.30–0.94, P = 0.03; aHR = 0.37, 95% CI = 0.15–0.89, P = 0.03; and aHR = 0.47, 95% CI = 0.29–0.75, P = 0.002, respectively). In vitro luciferase assay demonstrated that the promoter activity of ACADSB was significantly increased in the rs12220683 variant C allele compared with that in the wild G allele (P = 3 × 10−5). These results suggest that ACADSB rs12220683G&gt;C increases promoter activity and that increased ACADSB expression may result in better OS in patients with surgically resected NSCLC.
DOI: 10.6084/m9.figshare.23904345
title: Supplementary Material for: Synthetic Inversion Image Generation Using MP2RAGE T1 Mapping for Surgical Targeting in Deep Brain Stimulation and Lesioning

description: Background Advances in MRI technology have increased interest in direct targeting for deep brain stimulation (DBS). Various imaging sequences have been shown to provide increased contrast of numerous common DBS targets, such as T1-weighted, Fast Gray Matter Acquisition T1 Inversion Recovery (FGATIR), gray matter nulled, and Edge-Enhancing Gradient Echo (EDGE); however, the continual increase in the number of necessary sequences has led to an increase in imaging time, which is undesirable. Additionally, carefully timed inversion pulses can often lead to less-than-ideal contrast in some subjects, particularly in ultra-high field MRI, where B1+ field inhomogeneity can lead to substantial contrast variation. Objectives This study proposes using 3D MP2RAGE-based T1 maps to retrospectively synthesize images of any desired inversion time, including T1-weighted, FGATIR, and EDGE contrasts, to visualize specific DBS targets at both 3T and 7T. Method First, a systematic sequence optimization framework was applied to optimize MP2RAGE T1 mapping sequence parameters for the purpose of DBS planning. Next, we show that synthetic inversion time images can be generated through a mathematical transformation of the T1 maps. The sequence was then applied to patients undergoing preoperative planning for DBS at 3T and 7T to generate synthetic contrasts used in surgical planning. Results We show that synthetic image contrasts can be generated across a full range of Tis at 3T and 7T, including commonly used sequences for DBS targeting, such as T1-weighted, FGATIR, and EDGE. Acquisition through a single sequence shortens scan time compared to acquiring the sequences independently without affecting image quality or contrast. Conclusions The generation of synthetic images for DBS targeting allows faster acquisition of many key sequences, as well as the ability to optimize contrast properties post-acquisition to account for the variable B1+ effects present in ultra-high field MRI. The proposed approach has the potential to reduce imaging time and improve the accuracy of DBS targeting at 1.5T, 3T, and 7T.
DOI: 10.6084/m9.figshare.23922012
title: Supplementary Material for: Resolving the Smoking Paradox: No Evidence for Smoking-Induced Preconditioning in Large Vessel Occlusion Stroke

description: Introduction: Smoking is an established risk factor for stroke. However, several studies have reported a better outcome after stroke for patients who smoke. According to this “smoking paradox” hypothesis, smoking might promote less severe strokes, higher collateral scores and smaller infarct cores. Methods: In this retrospective study, we screened data of 2980 acute ischemic stroke patients with MCA-M1 occlusion treated with mechanical thrombectomy. Patients were categorized according to smoking status (current, former or never). We assessed univariate associations between clinical characteristics and smoking status. Subsequently, we used adjusted regression analysis to evaluate associations of smoking with stroke severity on admission (NIHSS, primary endpoint), infarct core volume and collateral status (secondary endpoints). Results: Out of 320 patients, 19.7% (n = 63) were current and 18.8% (n = 60) former smokers. Admission NIHSS, reperfusion success and mRS after 3-6 months were similar in all groups. Current smokers were younger, more often male and less likely to have atrial fibrillation compared to former and never smokers. In regression analyses, smoking status was neither associated with admission NIHSS (estimate 0.54, 95% CI -1.27 – 2.35, p = 0.557) nor with collateral status (estimate 0.79, 95% CI 0.44 – 1.44, p = 0.447) or infarct core volume (estimate -0.69, 95% CI -15.15 – 13.77, p = 0.925 for current vs. never smokers). Discussion/Conclusion: We could not confirm the smoking paradox. Our results support the fact that smoking causes stroke at a younger age, highlighting the role of smoking as a modifiable vascular risk factor.
DOI: 10.6084/m9.figshare.23931432
title: Supplementary Material for: Staghorn Calculus With Adenomatoid Tumor; A Case Report

description: Testicular adenomatoid tumor is very rare. More understating of the tumor and treatment is required for better outcomes.A 63-year-old man visited a urologist for staghorn calculus. During follow-up, he had recurrent left flank pain and intermittent hematuria. Computed tomography demonstrated left staghorn calculus then further assessment revealed left testicular swelling. Ultrasound showed epidimal mass. Percutaneous nephrolithotomy was deferred and we performed left radical orchiectomy. A pathologic examination revealed testicular adenomatoid tumor. This case highlights the importance of awareness of a very rare benign tumor in a patient with staghorn calculus.
DOI: 10.6084/m9.figshare.23996673
title: Supplementary Material for: Risk of Reintervention or Postoperative Bleeding after Laparoscopy for Benign Gynecological Disease: a Clinical Prediction Model

description: Objective: To develop a clinically applicable prediction tool to early seek for postoperative major complications after laparoscopic surgery for benign pathologies. Design: Retrospective analysis of prospectively collected data Setting: Tertiary-care University Hospital Participants: Reproductive aged women undergoing laparoscopy for benign conditions Methods: Anamnestic, intraoperative, and postoperative characteristics from January 2019 to December 2021 were retrospectively reviewed. Patients with postoperative complications (reintervention or postoperative bleeding) were matched in a 1:2 ratio with women with same surgical indications without complications. Cases and controls were matched for preoperative hemoglobin, hematocrit, weight, height, body mass index (BMI), age and blood volume. A prediction model was created by inserting multiple independent modifying factors through logistic regression. The receiver operating characteristic (ROC) curve was used to evaluate the predictive accuracy of the model, and the Hosmer–Lemeshow (H–L) test was carried out to evaluate the goodness- of-fit and a calibration curve was drawn to confirm the predictive performance. A nomogram was depicted to visualize the prediction model. Results: Thirty-nine complicated procedures were matched with 78 uncomplicated controls. According to the multivariate logistic regression analysis findings, the prediction model was developed using C reactive protein (CRP), intraoperative blood loss and 24 hours postoperative urinary volume, therefore a nomogram was generated. The area under the ROC curve (AUC) of the prediction model was 0.879, depicting good accuracy, the sensitivity was 60.00%, while specificity reached 93.59%. The H–L test (χ2 = 4.45, p= 0.931) and the calibration curve indicated a good goodness-of-fit and prediction stability. Limitations: The retrospective design, moderate sensitivity and study population limit the generalization of the findings, requiring additional research. Conclusions: This prediction model based on CRP, intraoperative blood loss and 24 hours postoperative urinary volume might be a potentially useful tool for predicting reintervention and postoperative bleeding in patients undergoing planned gynecological laparoscopy.
DOI: 10.6084/m9.figshare.24025716
title: Supplementary Material for: A Case of Lamina Lucida-Type Linear IgA Disease Complicated by Colon Polyposis and Rectal Adenocarcinoma

description: Linear IgA disease (LAD) is a rare autoimmune bullous disease characterized by IgA deposition in the basement membrane zone (BMZ). A 66-year-old male was treated for myelodysplastic syndrome at our hospital for five years, during which his condition remained stable. He visited our department because of erythema with itching, which appeared one year ago and gradually exacerbated with the development of blisters and erosions. During the first visit, multiple erythemas with erosions and crusts on their periphery were observed on the trunk and lower limbs. Histopathological examination revealed subepidermal blisters with inflammatory cell infiltration, mainly constituting of neutrophils, eosinophils, and lymphocytes. Direct and indirect immunofluorescence showed linear IgA deposits in the BMZ and IgA anti-BMZ antibodies, respectively, while immunoblotting using a concentrated culture supernatant of HaCaT cells detected IgA antibodies reactive to 120kDa LAD-1. Accordingly, the patient was diagnosed with lamina lucida-type LAD. Subsequent colonoscopy revealed multiple colorectal polyps and rectal adenocarcinoma (Tis, N0, and M0). Multigene panel test showed an ATM variant of unknown significance but did not detect any pathogenic variants associated with intestinal polyposis syndrome. The skin lesions quickly resolved with oral diaphenylsulfone 50 mg/day and resection of the colorectal polyps and adenocarcinoma. To our knowledge, this is the first reported case of LAD associated with multiple colorectal polyps and rectal adenocarcinoma. Additionally, we also analyzed reported cases of LAD associated with malignancy from the literature.
DOI: 10.6084/m9.figshare.24031845
title: Supplementary Material for: A case of pneumothorax required surgical treatment as a complication of paclitaxel with bevacizumab treatment

description: A 63-year-old woman had a history of neoadjuvant chemotherapy, mastectomy, and adjuvant endocrine therapy for five years before being diagnosed with recurrent lesions involving the right anterior chest wall, multiple lymph nodes, and pulmonary metastases. The patient was subsequently initiated on a paclitaxel and bevacizumab regimen. During this treatment, the patient complained of palpitations and malaise. Chest radiography revealed a left pneumothorax. Despite attempts at conservative treatment, the pneumothorax did not improve and a thoracoscopic approach was required. One of the metastatic tumors in the left lower lobe appeared to rupture, and this area was estimated to be the cause of air leak. The tumor was covered with a tissue seal sheet, and the patient’s condition improved with no recurrence of pneumothorax. This case highlights the importance of early conversion to surgical treatment when conservative treatment for pneumothorax is unresponsive due to the potential side effects of bevacizumab. The findings of this case report may be of interest to oncologists, pulmonologists, and other healthcare professionals involved in the care of patients with breast cancer and pulmonary metastases who are undergoing bevacizumab chemotherapy.
DOI: 10.6084/m9.figshare.24031998
title: Supplementary Material for: A case of lip psoriasis in a 14-year-old boy successfully treated with Adalimumab

description: Psoriasis is a common chronic skin disease mainly located in areas of friction. Psoriasis of the lips as an exclusive presentation is rare and often misdiagnosed. Different anti-psoriatic therapies have been proposed, but literature is limited to case studies with partial results. Biologic therapies have revolutionized the management of many dermatologic conditions, including psoriasis, and they are approved for pediatric use. We report the case of a 14-year-old boy with a two-year history of white-yellowish scaling lesions on his lips, without intraoral involvement. Lip biopsy showed a psoriasiform pattern. Treatment with Adalimumab 40 mg every other week was started and after 6 months of therapy we obtained a complete remission of the patient’s lip psoriasis.
DOI: 10.6084/m9.figshare.24056331
title: Supplementary Material for: Management of status epilepticus by different pediatric departments: neurology, intensive care and emergency medicine

description: Introduction: The aim of this study was to explore the differences in status epilepticus (SE) management among pediatric neurology, emergency medicine and intensive care specialists in Turkey. Methods: A 22-item questionnaire regarding first, second and third-line management strategies of SE including demographic characteristics and common etiologies according to speciality of participants was mailed to 370 specialists working in Turkey. Results: A total of 334 participants (response rate 90%); with 136 pediatric neurologists, 102 pediatric emergency medicine and 96 pediatric intensive care specialists completed the survey. While intensive care specialists frequently managed SE due to metabolic and autoimmune reasons; the most common etiologies encountered by emergency medicine specialists were epilepsy and infections. More than half of intensive care specialists (64.6%) reported using non-BDZ antiseizure medications in the 5th minute of the seizure. Most of neurologists (76.4%) preferred to administer intravenous (iv) levetiracetam infusion as a second line agent. About half of intensive care specialists and neurologists tried immunomodulatory therapies in super refractory SE. Intensive care and emergency medicine specialists were less likely to favor ketogenic diet and pyridoxine therapy for the treatment of super refractory SE. The rate of requesting EEG monitoring to recognize nonconvulsive SE was found to be very low except for neurologists. Conclusion: There was no consensus among neurologists, intensive care and emergency medicine specialists in the management of SE in Turkey. Familiarity with particular antiseizure medications and the etiologies they manage seem to be the most important factors influencing the attitudes.
DOI: 10.6084/m9.figshare.24064203
title: Supplementary Material for: Commentary on ‘Early (&lt; 7 days) systemic postnatal corticosteroids for prevention of bronchopulmonary dysplasia in preterm infants’

description: Medicine
DOI: 10.6084/m9.figshare.24072345
title: Supplementary Material for: An asymptomatic patient with colonic leiomyoma

description: Subepithelial lesions (SELs) originating from muscularis mucosae of the colon are very rare findings on endoscopy. Appropriate management of SELs involves making a correct diagnosis and estimating their malignant potential. In this case study a 58-year-old Saudi man presented with a small, 8-mm sigmoid polyp during screening colonoscopy. The polyp was removed by hot snare polypectomy and sent to pathology lab. Report showed an unremarkable colonic mucosa and underlying well-circumscribed submucosal lesion composed of monotonous spindle cells. Immunohistochemical (IHC) analysis ruled out CD117- / DOG1-positive GIST tumor and confirmed the lesion as leiomyomatous polyp. Colonic leiomyomas are usually benign and often asymptomatic, and discovered during CRC screening procedures. Diagnosis is made on histology / IHC since endoscopically they might be indistinguishable from other SELs. Conventional polypectomy is an appropriate treatment for small colonic leiomyoma and these benign lesions typically do not recur.