cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22812368
title: Radiomics and dosiomics-based prediction of radiotherapy-induced xerostomia in head and neck cancer patients

description: Dose-response modeling for radiotherapy-induced xerostomia in head and neck cancer (HN) patients is a promising frontier for personalized therapy. Feature extraction from diagnostic and therapeutic images (radiomics and dosiomics features) can be used for data-driven response modeling. The aim of this study is to develop xerostomia predictive models based on radiomics-dosiomics features. Data from the cancer imaging archive (TCIA) for 31 HN cancer patients were employed. For all patients, parotid CT radiomics features were extracted, utilizing Lasso regression for feature selection and multivariate modeling. The models were developed by selected features from pretreatment (CT<sub>1</sub>), mid-treatment (CT<sub>2</sub>), post-treatment (CT<sub>3</sub>), and delta features (ΔCT<sub>2-1</sub>, ΔCT<sub>3-1</sub>, ΔCT<sub>3-2</sub>). We also considered dosiomics features extracted from the parotid dose distribution images (Dose model). Thus, combination models of radio-dosiomics (CT + dose & ΔCT + dose) were developed. Moreover, clinical, and dose-volume histogram (DVH) models were built. Nested 10-fold cross-validation was used to assess the predictive classification of patients into those with and without xerostomia, and the area under the receiver operative characteristic curve (AUC) was used to compare the predictive power of the models. The sensitivity and accuracy of models also were obtained. In total, 59 parotids were assessed, and 13 models were developed. Our results showed three models with AUC of 0.89 as most predictive, namely ΔCT<sub>2-1</sub> + Dose (Sensitivity 0.99, Accuracy 0.94 & Specificity 0.86), CT<sub>3</sub> model (Sensitivity 0.96, Accuracy 0.94 & Specificity 0.86) and DVH (Sensitivity 0.93, Accuracy 0.89 & Specificity 0.84). These models were followed by Clinical (AUC 0.89, Sensitivity 0.81, Accuracy 0.97 & Specificity 0.89) and CT<sub>2</sub> & Dose (AUC 0.86, Sensitivity 0.97, Accuracy 0.87 & Specificity 0.82). The Dose model (developed by dosiomics features only) had AUC, Sensitivity, Specificity, and Accuracy of 0.72, 0.98, 0.33, and 0.79 respectively. Quantitative features extracted from diagnostic imaging during and after radiotherapy alone or in combination with dosiomics markers obtained from dose distribution images can be used for radiotherapy response modeling, opening up prospects for personalization of therapies toward improved therapeutic outcomes.
DOI: 10.6084/m9.figshare.22812368.v2
title: Radiomics and dosiomics-based prediction of radiotherapy-induced xerostomia in head and neck cancer patients

description: Dose-response modeling for radiotherapy-induced xerostomia in head and neck cancer (HN) patients is a promising frontier for personalized therapy. Feature extraction from diagnostic and therapeutic images (radiomics and dosiomics features) can be used for data-driven response modeling. The aim of this study is to develop xerostomia predictive models based on radiomics-dosiomics features. Data from the cancer imaging archive (TCIA) for 31 HN cancer patients were employed. For all patients, parotid CT radiomics features were extracted, utilizing Lasso regression for feature selection and multivariate modeling. The models were developed by selected features from pretreatment (CT<sub>1</sub>), mid-treatment (CT<sub>2</sub>), post-treatment (CT<sub>3</sub>), and delta features (ΔCT<sub>2-1</sub>, ΔCT<sub>3-1</sub>, ΔCT<sub>3-2</sub>). We also considered dosiomics features extracted from the parotid dose distribution images (Dose model). Thus, combination models of radio-dosiomics (CT + dose & ΔCT + dose) were developed. Moreover, clinical, and dose-volume histogram (DVH) models were built. Nested 10-fold cross-validation was used to assess the predictive classification of patients into those with and without xerostomia, and the area under the receiver operative characteristic curve (AUC) was used to compare the predictive power of the models. The sensitivity and accuracy of models also were obtained. In total, 59 parotids were assessed, and 13 models were developed. Our results showed three models with AUC of 0.89 as most predictive, namely ΔCT<sub>2-1</sub> + Dose (Sensitivity 0.99, Accuracy 0.94 & Specificity 0.86), CT<sub>3</sub> model (Sensitivity 0.96, Accuracy 0.94 & Specificity 0.86) and DVH (Sensitivity 0.93, Accuracy 0.89 & Specificity 0.84). These models were followed by Clinical (AUC 0.89, Sensitivity 0.81, Accuracy 0.97 & Specificity 0.89) and CT<sub>2</sub> & Dose (AUC 0.86, Sensitivity 0.97, Accuracy 0.87 & Specificity 0.82). The Dose model (developed by dosiomics features only) had AUC, Sensitivity, Specificity, and Accuracy of 0.72, 0.98, 0.33, and 0.79 respectively. Quantitative features extracted from diagnostic imaging during and after radiotherapy alone or in combination with dosiomics markers obtained from dose distribution images can be used for radiotherapy response modeling, opening up prospects for personalization of therapies toward improved therapeutic outcomes.
DOI: 10.6084/m9.figshare.23056366
title: Microarray analysis of hub genes, non-coding RNAs and pathways in lung after whole body irradiation in a mouse model

description: Previous research has highlighted the impact of radiation damage, with cancer patients developing acute disorders including radiation induced pneumonitis or chronic disorders including pulmonary fibrosis months after radiation therapy ends. We sought to discover biomarkers that predict these injuries and develop treatments that mitigate this damage and improve quality of life. Six- to eight-week-old female C57BL/6 mice received 1, 2, 4, 8, 12 Gy or sham whole body irradiation. Animals were euthanized 48 h post exposure and lungs removed, snap frozen and underwent RNA isolation. Microarray analysis was performed to determine dysregulation of messenger RNA (mRNA), microRNA (miRNA), and long non-coding RNA (lncRNA) after radiation injury. We observed sustained dysregulation of specific RNA markers including: mRNAs, lncRNAs, and miRNAs across all doses. We also identified significantly upregulated genes that can indicate high dose exposure, including <i>Cpt1c, Pdk4, Gdf15</i>, and <i>Eda2r</i>, which are markers of senescence and fibrosis. Only three miRNAs were significantly dysregulated across all radiation doses: miRNA-142-3p and miRNA-142-5p were downregulated and miRNA-34a-5p was upregulated. IPA analysis predicted inhibition of several molecular pathways with increasing doses of radiation, including: T cell development, Quantity of leukocytes, Quantity of lymphocytes, and Cell viability. These RNA biomarkers might be highly relevant in the development of treatments and in predicting normal tissue injury in patients undergoing radiation treatment. We are conducting further experiments in our laboratory, which includes a human lung-on-a-chip model, to develop a decision tree model using RNA biomarkers.
DOI: 10.6084/m9.figshare.22771009.v2
title: Chemotherapy and cryopreservation affects DNA repair foci in lymphocytes of breast cancer patients

description: Although breast cancer (BC) patients benefit from radiotherapy (RT), some radiosensitive (RS) patients suffer from side effects caused by ionizing radiation in healthy tissues. It is thought that RS is underlaid by a deficiency in the repair of DNA double-strand breaks (DSB). DNA repair proteins such as p53-binding protein 1 (53BP1) and phosphorylated histone H2AX (γH2AX), form DNA repair foci at the DSB locations and thus serve as DSB biomarkers. Peripheral blood lymphocytes (PBL) are commonly believed to be an appropriate cell system for RS assessment using DNA repair foci. The amount of DSB may also be influenced by chemotherapy (CHT), which is often chosen as the first treatment modality before RT. As it is not always possible to analyze blood samples immediately after collection, there is a need for cryopreservation of PBL in liquid nitrogen. However, cryopreservation may potentially affect the number of DNA repair foci. In this work, we studied the effect of cryopreservation and CHT on the amount of DNA repair foci in PBL of BC patients undergoing radiotherapy. The effect of cryopreservation was studied by immunofluorescence analysis of 53BP1 and γH2AX proteins at different time intervals after in vitro irradiation. The effect of chemotherapy was analyzed by fluorescent labelling of 53BP1 and γH2AX proteins in PBL collected before, during, and after RT. Higher number of primary 53BP1/γH2AX foci was observed in frozen cells indicating that cryopreservation affects the formation of DNA repair foci in PBL of BC patients. In CHT-treated patients, a higher number of foci were found before RT, but no differences were observed during and after the RT. Cryopreservation is the method of choice for analyzing DNA repair residual foci, but only similarly treated and preserved cells should be used for comparison of primary foci. CHT induces DNA repair foci in PBL of BC patients, but this effect disappears during radiotherapy.
DOI: 10.6084/m9.figshare.23056366.v2
title: Microarray analysis of hub genes, non-coding RNAs and pathways in lung after whole body irradiation in a mouse model

description: Previous research has highlighted the impact of radiation damage, with cancer patients developing acute disorders including radiation induced pneumonitis or chronic disorders including pulmonary fibrosis months after radiation therapy ends. We sought to discover biomarkers that predict these injuries and develop treatments that mitigate this damage and improve quality of life. Six- to eight-week-old female C57BL/6 mice received 1, 2, 4, 8, 12 Gy or sham whole body irradiation. Animals were euthanized 48 h post exposure and lungs removed, snap frozen and underwent RNA isolation. Microarray analysis was performed to determine dysregulation of messenger RNA (mRNA), microRNA (miRNA), and long non-coding RNA (lncRNA) after radiation injury. We observed sustained dysregulation of specific RNA markers including: mRNAs, lncRNAs, and miRNAs across all doses. We also identified significantly upregulated genes that can indicate high dose exposure, including <i>Cpt1c, Pdk4, Gdf15</i>, and <i>Eda2r</i>, which are markers of senescence and fibrosis. Only three miRNAs were significantly dysregulated across all radiation doses: miRNA-142-3p and miRNA-142-5p were downregulated and miRNA-34a-5p was upregulated. IPA analysis predicted inhibition of several molecular pathways with increasing doses of radiation, including: T cell development, Quantity of leukocytes, Quantity of lymphocytes, and Cell viability. These RNA biomarkers might be highly relevant in the development of treatments and in predicting normal tissue injury in patients undergoing radiation treatment. We are conducting further experiments in our laboratory, which includes a human lung-on-a-chip model, to develop a decision tree model using RNA biomarkers.
DOI: 10.6084/m9.figshare.23056366.v1
title: Microarray analysis of hub genes, non-coding RNAs and pathways in lung after whole body irradiation in a mouse model

description: <b><i>Purpose:</i></b> Previous research has highlighted the impact of radiation damage, with cancer patients developing acute disorders including radiation induced pneumonitis or chronic disorders including pulmonary fibrosis months after radiation therapy ends. We sought to discover biomarkers that predict these injuries and develop treatments that mitigate this damage and improve quality of life. <b><i>Materials and Methods:</i></b> Six- to eight-week-old female C57BL/6 received 1, 2, 4, 8 12 Gy or sham whole body irradiation. Animals were euthanized 48 hours post exposure and lungs removed, snap frozen and underwent RNA isolation. Microarray analysis was performed to determine dysregulation of messenger RNA (mRNA), microRNA (miRNA), and long non-coding RNA (lncRNA) after radiation injury. <b><i>Results:</i></b> We observed sustained dysregulation of specific RNA markers including: mRNAs, lncRNAs, and miRNAs across all doses. We found gene dysregulation which can be used to develop a decision tree model to identify no-exposure vs radiation exposure which includes <i>Hba</i> and <i>Hbb</i> mRNA that were dysregulated even at 1 Gy. We also identified significantly upregulated genes that can indicate high dose exposure, including <i>Cpt1c, Pdk4, Gdf15</i>, and <i>Eda2r</i>, which are markers of senescence and fibrosis. Only three miRNAs were significantly dysregulated across all radiation doses: miRNA-142-3p and miRNA-142-5p were downregulated and miRNA-34a-5p was upregulated. IPA analysis predicted inhibition of several molecular pathways with increasing doses of radiation, including: T cell development, Quantity of leukocytes, Quantity of lymphocytes, and Cell viability. <b><i>Conclusions:</i></b> These RNA biomarkers might be highly relevant in the development of treatments and in predicting normal tissue injury in patients undergoing radiation treatment. We are conducting further experiments in our laboratory, which includes a human lung-on-a-chip model, to develop a decision tree model using RNA biomarkers.
DOI: 10.34740/kaggle/dsv/6796165
title: Balochi Language to English Translation Dataset
DOI: 10.18739/a2cc0tv7w
title: Litter quality and quantity effects on biogeochemical processes in a subarctic wetland. Yukon Delta National Wildlife Refuge, Alaska, 2021

description: Global change drivers that modify the quality and quantity of litter inputs to soil affect greenhouse gas fluxes, and thereby constitute a feedback to climate change. Carbon cycling in the Yukon-Kuskokwim (Y-K) River Delta, a subarctic wetland system, is influenced by landscape variations in litter quality and quantity generated by herbivores (migratory birds) that create ‘grazing lawns’ of short stature, nitrogen-rich vegetation. To identify the mechanisms by which these changes in litter inputs affect soil carbon balance, we independently manipulated qualities and quantities of litter representative of levels found in the Y-K Delta in a fully factorial microcosm experiment. We measured carbon dioxide (CO2) fluxes from these microcosms weekly. To help us identify how litter inputs influenced greenhouse gas fluxes, we sequenced soil fungal and bacterial communities, and measured soil microbial biomass carbon, dissolved carbon, inorganic nitrogen, and enzyme activity. We found that positive correlations between litter input quantity and CO2 flux were dependent upon litter type, due to differences in litter stoichiometry and changes to the structure of decomposer communities, especially the soil fungi. These community shifts were particularly pronounced when litter was added in the form of herbivore feces, and in litter input treatments that induced nitrogen limitation (i.e., senesced litter). The sensitivity of carbon cycling to litter quality and quantity in this system demonstrates that herbivores can strongly impact greenhouse gas fluxes through their influence on plant growth and tissue chemistry.
DOI: 10.5281/zenodo.10041817
title: OS MEDICAMENTOS FITOTERÁPICOS QUE CONTRIBUEM PARA O EMAGRECIMENTO PRODUZIDAS PELAS FARMÁCIAS DE MANIPULAÇÃO

description: A fitoterapia é conhecida como a forma mais antiga de tratamento de doenças, vem do grego therapeia = tratamento e phyton = vegetal. Na atualidade é bastante utilizada para diversos tipos de terapia como: anti-inflamatórios, antidepressivos, diuréticos, analgésicos, entre outros. O estudo será direcionado para o uso isolado dessas plantas medicinais voltadas para a obesidade, utilizando fitoterápicos diuréticos que auxiliam na redução do peso. Esses medicamentos diuréticos podem ser feitos apenas com a presença do princípio ativo ou associados a outros ativos com a mesma finalidade pelas farmácias de manipulação, sendo orientados corretamente pelos farmacêuticos. O objetivo da pesquisa que será realizada é mostrar a utilização incorreta e correta do uso exacerbado destes medicamentos pela população, investigando os benefícios e malefícios, os princípios ativos mais utilizados para o emagrecimento no Brasil.
DOI: 10.5281/zenodo.10041818
title: OS MEDICAMENTOS FITOTERÁPICOS QUE CONTRIBUEM PARA O EMAGRECIMENTO PRODUZIDAS PELAS FARMÁCIAS DE MANIPULAÇÃO

description: A fitoterapia é conhecida como a forma mais antiga de tratamento de doenças, vem do grego therapeia = tratamento e phyton = vegetal. Na atualidade é bastante utilizada para diversos tipos de terapia como: anti-inflamatórios, antidepressivos, diuréticos, analgésicos, entre outros. O estudo será direcionado para o uso isolado dessas plantas medicinais voltadas para a obesidade, utilizando fitoterápicos diuréticos que auxiliam na redução do peso. Esses medicamentos diuréticos podem ser feitos apenas com a presença do princípio ativo ou associados a outros ativos com a mesma finalidade pelas farmácias de manipulação, sendo orientados corretamente pelos farmacêuticos. O objetivo da pesquisa que será realizada é mostrar a utilização incorreta e correta do uso exacerbado destes medicamentos pela população, investigando os benefícios e malefícios, os princípios ativos mais utilizados para o emagrecimento no Brasil.
DOI: 10.18112/openneuro.ds004789.v2.0.0
title: Delayed Free Recall of Word Lists
DOI: 10.6084/m9.figshare.20416010
title: Efficacy and Satisfaction of Cyclosporine 0.1% in Patients with Vernal Keratoconjunctivitis

description: Vernal keratoconjunctivitis (VKC) is a severe form of ocular allergy that compromises the quality of life of affected patients. Topical cyclosporine 0.1% cationic emulsion (CsA-CE) has been recently authorized for the treatment of severe VKC. We treated 29 VKC patients with on-label CsA-CE and recorded signs and symptoms, subjective patient’s treatment satisfaction and the additional use of topical corticosteroids in case of exacerbations. CsA-CE was effective in reducing signs and symptoms in daily clinical practice. The overall subjective improvement of symptoms, efficacy of the treatment, tolerability to the drug and compliance reached a high level of subjective satisfaction score.55% of treated patients required the additional use of a 3-day course of topical dexamethasone with 1.13 ± 0.81 mean courses/month. In conclusions, VKC patients reported an overall high satisfaction with used the on-label topical CsA-CE with a limited use of additional topical corticosteroid treatment.
DOI: 10.6084/m9.figshare.20416010.v1
title: Efficacy and Satisfaction of Cyclosporine 0.1% in Patients with Vernal Keratoconjunctivitis

description: Vernal keratoconjunctivitis (VKC) is a severe form of ocular allergy that compromises the quality of life of affected patients. Topical cyclosporine 0.1% cationic emulsion (CsA-CE) has been recently authorized for the treatment of severe VKC. We treated 29 VKC patients with on-label CsA-CE and recorded signs and symptoms, subjective patient’s treatment satisfaction and the additional use of topical corticosteroids in case of exacerbations. CsA-CE was effective in reducing signs and symptoms in daily clinical practice. The overall subjective improvement of symptoms, efficacy of the treatment, tolerability to the drug and compliance reached a high level of subjective satisfaction score.55% of treated patients required the additional use of a 3-day course of topical dexamethasone with 1.13 ± 0.81 mean courses/month. In conclusions, VKC patients reported an overall high satisfaction with used the on-label topical CsA-CE with a limited use of additional topical corticosteroid treatment.
DOI: 10.6084/m9.figshare.21044228
title: Ischemic Retinopathy with Vitreous Hemorrhage Resembling Diabetic Retinopathy in a Patient with Mixed Cryoglobulinemia

description: To report a case of mixed cryoglobulinemia manifesting retinopathy with bilateral vitreous hemorrhage (VH) resembling diabetic retinopathy. A 60-year-old Japanese man with renal dysfunction of unknown origin was hospitalized for investigation of underlying disease. Laboratory examinations were positive for cryoglobulins composed of IgG and IgM in serum, and hepatitis C virus (HCV) infection. He was diagnosed with HCV-related mixed cryoglobulinemia. During hospitalization, he developed sudden loss of vision and was referred to the department of ophthalmology. Ophthalmic examination revealed VH in both eyes, and vitrectomy was performed on the right eye. Fundus examination after vitrectomy revealed sheathing vessels, mottled hemorrhages in the entire retina, and avascular areas with neovascularization. Disrupted outer retinal layers in the macula were confirmed. Vitreous fluid level of VEGF-A in the right eye was 166.6 pg/mL. Retinal ischemia resembling diabetic retinopathy may cause VH in patients with mixed cryoglobulinemia.
DOI: 10.6084/m9.figshare.21044228.v1
title: Ischemic Retinopathy with Vitreous Hemorrhage Resembling Diabetic Retinopathy in a Patient with Mixed Cryoglobulinemia

description: To report a case of mixed cryoglobulinemia manifesting retinopathy with bilateral vitreous hemorrhage (VH) resembling diabetic retinopathy. A 60-year-old Japanese man with renal dysfunction of unknown origin was hospitalized for investigation of underlying disease. Laboratory examinations were positive for cryoglobulins composed of IgG and IgM in serum, and hepatitis C virus (HCV) infection. He was diagnosed with HCV-related mixed cryoglobulinemia. During hospitalization, he developed sudden loss of vision and was referred to the department of ophthalmology. Ophthalmic examination revealed VH in both eyes, and vitrectomy was performed on the right eye. Fundus examination after vitrectomy revealed sheathing vessels, mottled hemorrhages in the entire retina, and avascular areas with neovascularization. Disrupted outer retinal layers in the macula were confirmed. Vitreous fluid level of VEGF-A in the right eye was 166.6 pg/mL. Retinal ischemia resembling diabetic retinopathy may cause VH in patients with mixed cryoglobulinemia.
DOI: 10.6084/m9.figshare.21273129
title: Expression of Long Non-Coding RNAs in Activated Human Retinal Vascular Endothelial Cells

description: Retinal endothelial cell activation is a central event in non-infectious posterior uveitis. There is recent interest in long non-coding (lnc)RNA-targeted therapeutics for retinal diseases. We aimed to identify human retinal endothelial cell lncRNAs that might be involved in activation. Eleven candidate lncRNAs were identified: GAS5, KCNQ1OT1, LINC00294, MALAT1, MEG3, MIR155HG, NEAT1, NORAD, OIP5-AS1, SENCR, TUG1. Expression was assessed by RT-PCR in human retinal endothelial cells, at baseline and following activation with interleukin (IL)-1β and tumor necrosis factor (TNF)-α. IL-1β significantly upregulated MEG3 and SENCR at 4 and 24 hours; LINC00294, NORAD, OIP5-AS1 and TUG1 at 24 hours; and MIR155HG at 4, 24 and 48 hours; but downregulated GAS5 at 24 and 48 hours. TNF-α significantly upregulated KCNQ1OT1, LINC00294, MEG3, NORAD and SENCR at 4 hours; SENCR and TUG1 at 24 hours; and MIR155HG at all time points. Future studies involving manipulation of MIR155HG may be warranted to explore potential therapeutic applications for non-infectious posterior uveitis.