cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19682099
title: Additional file 1 of Insight into the CBL and CIPK gene families in pecan (Carya illinoinensis): identification, evolution and expression patterns in drought response

description: Additional file 1: Table S1. CBL and CIPK genes identified in pecan and their sequence characteristics. Table S2. Motif sequences of pecan CBLs. Table S3. Motif sequences of pecan CIPKs. Table S4. Duplication events and related Ka/Ks values of pecan CBLs and CIPKs. Table S5. The CBL and CIPK protein numbers in different plant species. Table S6. Specific primers of pecan CBL and CIPK genes for qRT-PCR analysis.
DOI: 10.6084/m9.figshare.8148383
title: Additional file 3: of Prediction of pathologic stage in non-small cell lung cancer using machine learning algorithm based on CT image feature analysis

description: Table S3. Association between Radiomic Score and TNM factors. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8148242.v1
title: Additional file 1: of Development of a transcriptomic database for 14 species of scleractinian corals

description: Table S1. Information on published transcriptome datasets from Scleractinia. Table S2. Symbiotic algae types determined by BLAST coral transcriptomes against the ITS2 and rRNA genes (i.e. 18S, 28S 23S rRNA) from GenBank database. Table S3. The accession numbers of sequences in the GenBank database used for symbiotic algae clade identification. (XLSX 179 kb)
DOI: 10.6084/m9.figshare.8148050
title: MOESM2 of Effect of cold atmospheric plasma treatment on the metabolites of human leukemia cells

description: Additional file 2: Table S2. Differential metabolites.
DOI: 10.6084/m9.figshare.14963845.v1
title: A Normality Test for High-dimensional Data based on a Nearest Neighbor Approach

description: Many statistical methodologies for high-dimensional data assume the population is normal. Although a few multivariate normality tests have been proposed, to the best of our knowledge, none of them can properly control the type I error when the dimension is larger than the number of observations. In this work, we propose a novel nonparametric test that utilizes the nearest neighbor information. The proposed method guarantees the asymptotic type I error control under the high-dimensional setting. Simulation studies verify the empirical size performance of the proposed test when the dimension grows with the sample size and at the same time exhibit a superior power performance of the new test compared with alternative methods. We also illustrate our approach through two popularly used data sets in high-dimensional classification and clustering literatures where deviation from the normality assumption may lead to invalid conclusions.
DOI: 10.6084/m9.figshare.8148056
title: MOESM3 of Effect of cold atmospheric plasma treatment on the metabolites of human leukemia cells

description: Additional file 3: Table S3. KEGG pathway.
DOI: 10.6084/m9.figshare.14963845.v2
title: A Normality Test for High-dimensional Data Based on the Nearest Neighbor Approach

description: Many statistical methodologies for high-dimensional data assume the population is normal. Although a few multivariate normality tests have been proposed, to the best of our knowledge, none of them can properly control the Type I error when the dimension is larger than the number of observations. In this work, we propose a novel nonparametric test that uses the nearest neighbor information. The proposed method guarantees the asymptotic Type I error control under the high-dimensional setting. Simulation studies verify the empirical size performance of the proposed test when the dimension grows with the sample size and at the same time exhibit a superior power performance of the new test compared with alternative methods. We also illustrate our approach through two popularly used datasets in high-dimensional classification and clustering literatures where deviation from the normality assumption may lead to invalid conclusions.
DOI: 10.6084/m9.figshare.8148062.v1
title: MOESM4 of Effect of cold atmospheric plasma treatment on the metabolites of human leukemia cells

description: Additional file 4: Table S4. Pathway analysis.
DOI: 10.6084/m9.figshare.8148488.v1
title: Additional file 1: of Time series analysis of mumps and meteorological factors in Beijing, China

description: Table S1. Monthly mumps data from January 1990 to December 2012, Beijing, China. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.22828289.v1
title: Protective Effect of Combined Metoprolol and Atractylenolide I in Rats with Acute Myocardial Infarction via Modulation of the SIRT3/β-CATENIN/PPAR-γ Signaling Pathway

description: ABSTRACT Herein, we examined the protective effect of metoprolol combined with atractylenolide I (Atr I) in acute myocardial infarction (AMI) by regulating the SIRT3 (silent information regulator 3)/β-catenin/peroxisome proliferator-activated receptor gamma (PPAR-γ) signaling pathway. Briefly, 50 rats were randomly divided into the sham operation, model, metoprolol, Atr I, and combination metoprolol with Atr I groups (combined treatment group). The AMI model was established by ligating the left anterior descending coronary artery. After treatment, infarct size, histopathological changes, and cell apoptosis were examined using 2,3,5-triphenyltetrazolium chloride staining, hematoxylin-eosin staining, and the TUNEL assay. The left ventricular ejection fraction (LVEF), left ventricular fraction shortening (LVFS), and left ventricular mass index (LVMI) were detected by echocardiography. Endothelin-1 (ET-1), nitric oxide (NO), tumor necrosis factor-alpha (TNF-α), and interleukin-6 (IL-6) levels were detected using enzyme-linked immunosorbent assays. Furthermore, we measured lactate dehydrogenase (LDH), creatine kinase (CK) isoenzyme (CK-MB), and CK levels. Western blotting was performed to determine the expression of SIRT3, β-catenin, and PPAR-γ. Herein, the combined treatment group exhibited increased levels of LVEF, LVFS, and NO, whereas LVMI, ET-1, TNF-α, IL-6, LDH, CK-MB, and CK levels were decreased. Importantly, the underlying mechanism may afford protection against AMI by increasing the expression levels of SIRT3, β-catenin, and PPAR-γ.
DOI: 10.6084/m9.figshare.25226240
title: Supplementary Material for: Negative Impact of Gemtuzumab Ozogamicin on CD33-Positive Early T-Cell Precursor Acute Lymphoblastic Leukemia: A Case Report

description: <b><i>Introduction:</i></b> Early T-cell precursor acute lymphoblastic leukemia (ETP-ALL) is a rare subtype of T-cell leukemia that phenotypically expresses mature T-cell markers and immature myeloid markers such as CD33. Gemtuzumab ozogamicin (GO) is a novel agent for the CD33 molecular targeting antibody conjugated to the cytotoxic agent calicheamicin. GO is anticipated to be effective against ETP-ALL. In vivo studies promise antileukemic effects in cell lines; however, clinical reports to support this research are lacking. We treated a patient who suffered from CD33-positive ETP-ALL using GO. <b><i>Case Presentation:</i></b> We treated an 81-year-old man who suffered from ETP-ALL. The patient’s leukemia expressed T cell and myeloid markers including cyCD3, CD5, CD7, CD33, and HLA-DR. Initially, the patient was treated using a standard chemotherapy regimen for acute lymphoblastic leukemia comprising cyclophosphamide, daunorubicin, vincristine, l-asparaginase, and prednisolone. The induction chemotherapy produced the expected complete hematological response; however, bone marrow blasts remained. Following consolidation chemotherapy, the patient maintained a full hematological response. Thereafter, we changed the consolidation regimen to nelarabine, which did not reduce bone marrow blasts effectively. After two courses of nelarabine therapy, we finally used GO at an 8 mg/m<sup>2</sup> weekly dose after confirming that CD33 expression was still positive in the patient’s residual leukemic cells. GO was ineffective in treating the patient’s leukemia, and peripheral blasts increased 30 days following treatment. The patient died 81 days after initiating GO therapy. <b><i>Conclusion:</i></b> This is the first clinical case of GO having a negative impact on ETP-ALL. Because the GO resistance mechanism for ETP-ALL has not been fully elucidated, treatment modification should be considered to achieve optimal clinical efficacy.
DOI: 10.6084/m9.figshare.25226240.v1
title: Supplementary Material for: Negative Impact of Gemtuzumab Ozogamicin on CD33-Positive Early T-Cell Precursor Acute Lymphoblastic Leukemia: A Case Report

description: <b><i>Introduction:</i></b> Early T-cell precursor acute lymphoblastic leukemia (ETP-ALL) is a rare subtype of T-cell leukemia that phenotypically expresses mature T-cell markers and immature myeloid markers such as CD33. Gemtuzumab ozogamicin (GO) is a novel agent for the CD33 molecular targeting antibody conjugated to the cytotoxic agent calicheamicin. GO is anticipated to be effective against ETP-ALL. In vivo studies promise antileukemic effects in cell lines; however, clinical reports to support this research are lacking. We treated a patient who suffered from CD33-positive ETP-ALL using GO. <b><i>Case Presentation:</i></b> We treated an 81-year-old man who suffered from ETP-ALL. The patient’s leukemia expressed T cell and myeloid markers including cyCD3, CD5, CD7, CD33, and HLA-DR. Initially, the patient was treated using a standard chemotherapy regimen for acute lymphoblastic leukemia comprising cyclophosphamide, daunorubicin, vincristine, l-asparaginase, and prednisolone. The induction chemotherapy produced the expected complete hematological response; however, bone marrow blasts remained. Following consolidation chemotherapy, the patient maintained a full hematological response. Thereafter, we changed the consolidation regimen to nelarabine, which did not reduce bone marrow blasts effectively. After two courses of nelarabine therapy, we finally used GO at an 8 mg/m<sup>2</sup> weekly dose after confirming that CD33 expression was still positive in the patient’s residual leukemic cells. GO was ineffective in treating the patient’s leukemia, and peripheral blasts increased 30 days following treatment. The patient died 81 days after initiating GO therapy. <b><i>Conclusion:</i></b> This is the first clinical case of GO having a negative impact on ETP-ALL. Because the GO resistance mechanism for ETP-ALL has not been fully elucidated, treatment modification should be considered to achieve optimal clinical efficacy.
DOI: 10.34740/kaggle/dsv/7631696
title: Mahanagar Yatayat Transport Dataset
DOI: 10.6084/m9.figshare.19159137.v1
title: Additional file 5 of A novel immune-related lncRNA pair signature for prognostic prediction and immune response evaluation in gastric cancer: a bioinformatics and biological validation study

description: Additional file 5: Table S3. The target genes of these lncRNAs in our IRLPs signature.
DOI: 10.6084/m9.figshare.19159140
title: Additional file 6 of A novel immune-related lncRNA pair signature for prognostic prediction and immune response evaluation in gastric cancer: a bioinformatics and biological validation study

description: Additional file 6: Table S4. The comparison of our IRLPs signature with other immune-related gene/lncRNA models in GC.
DOI: 10.6084/m9.figshare.8148380.v1
title: Additional file 4: of Proteomics analysis reveals heat shock proteins involved in caprine parainfluenza virus type 3 infection

description: Figure S4 and Data Sheet 5. Proteins were annotated based on the KOG (ZIP 669 kb)
DOI: 10.6084/m9.figshare.11295389
title: Incidence and mortality of renal dysfunction in cirrhotic patients with acute gastrointestinal bleeding: a systematic review and meta-analysis

description: <b>Background</b>: Gastrointestinal bleeding (GIB) is a common complication in cirrhosis. Renal dysfunction may be crucial for the outcomes of cirrhotic patients with acute GIB. This study aimed to explore the incidence and mortality of renal dysfunction in cirrhotic patients with acute GIB. <b>Methods</b>: The PubMed, EMBASE, and Cochrane Library databases were searched. We pooled the incidence and mortality of renal dysfunction in cirrhotic patients using a random-effect model. Odds ratio (OR) with 95% confidence interval (CI) were calculated. <b>Results</b>: Seventeen studies were included. The pooled incidence of renal dysfunction was 21% (95%CI = 16%-25%) in cirrhosis with acute GIB. In subgroup analyses, the pooled incidence of renal failure, acute kidney injury (AKI), and renal impairment were 21%, 25%, and 15%, respectively. The pooled mortality was 46% (95%CI = 37%-55%) in cirrhosis with acute GIB and renal dysfunction. In subgroup analyses, the pooled mortality in patients with renal failure, AKI, and renal impairment were 42%, 47%, and 49%, respectively. Renal dysfunction significantly increased the mortality of cirrhosis with acute GIB (OR = 4.92; 95%CI = 3.47–6.96; P &lt; 0.001). <b>Conclusion</b>: Renal dysfunction is a common indicator for poor outcome of cirrhosis with acute GIB. Prevention of renal dysfunction in such patients should be further explored.
DOI: 10.6084/m9.figshare.11295389.v1
title: Incidence and mortality of renal dysfunction in cirrhotic patients with acute gastrointestinal bleeding: a systematic review and meta-analysis

description: <b>Background</b>: Gastrointestinal bleeding (GIB) is a common complication in cirrhosis. Renal dysfunction may be crucial for the outcomes of cirrhotic patients with acute GIB. This study aimed to explore the incidence and mortality of renal dysfunction in cirrhotic patients with acute GIB. <b>Methods</b>: The PubMed, EMBASE, and Cochrane Library databases were searched. We pooled the incidence and mortality of renal dysfunction in cirrhotic patients using a random-effect model. Odds ratio (OR) with 95% confidence interval (CI) were calculated. <b>Results</b>: Seventeen studies were included. The pooled incidence of renal dysfunction was 21% (95%CI = 16%-25%) in cirrhosis with acute GIB. In subgroup analyses, the pooled incidence of renal failure, acute kidney injury (AKI), and renal impairment were 21%, 25%, and 15%, respectively. The pooled mortality was 46% (95%CI = 37%-55%) in cirrhosis with acute GIB and renal dysfunction. In subgroup analyses, the pooled mortality in patients with renal failure, AKI, and renal impairment were 42%, 47%, and 49%, respectively. Renal dysfunction significantly increased the mortality of cirrhosis with acute GIB (OR = 4.92; 95%CI = 3.47–6.96; P &lt; 0.001). <b>Conclusion</b>: Renal dysfunction is a common indicator for poor outcome of cirrhosis with acute GIB. Prevention of renal dysfunction in such patients should be further explored.
DOI: 10.6084/m9.figshare.8148386.v1
title: Additional file 5: of Proteomics analysis reveals heat shock proteins involved in caprine parainfluenza virus type 3 infection

description: Figure S6 and S7 Heat map and scatterplot (ZIP 1116 kb)
DOI: 10.6084/m9.figshare.23354115
title: Possible cerebroprotective effect of citronellal: molecular docking, MD simulation and <i>in vivo</i> investigations

description: This study focused on molecular docking, dynamic simulation, and <i>in vivo</i> approaches to examine the molecular interactions between citronellal (CT) and neurotoxic proteins. In silico studies of CT were performed using proteins involved in the pathophysiology of stroke, such as interleukin-6 (IL-6), interleukin-12 (IL-12), TNF-α, and nitric oxide synthase (NOS), to determine the binding affinity based on their interactions. The docking results of CT revealed that, among the targets, NOS had a better binding energy of −6.4 Kcal/mol. NOS showed good hydrophobic interactions: TYR A, 347; VAL A, 352; PRO A, 350; TYR A, 373 amino acids. Interactions with IL-6, TNF-α, and IL-12 resulted in lower binding affinities of −3.7, −3.9 and −3.1 Kcal/mol. Based on molecular dynamics simulations of 100 ns, the binding affinity of CT (-66.782 ± 7.309 kJ/mol) was well complemented, and NOS stability at the docked site was confirmed. In <i>in vivo</i> studies, cerebral stroke was induced by occlusion of the bilateral common carotid arteries for 30 min and reperfusion for 4 h. CT treatment protected the brain by decreasing cerebral infarction size, increasing GSH(<i>p</i> &lt; 0.001***), decreasing MPO (<i>p</i> &lt; 0.001***), MDA (<i>p</i> &lt; 0.001***), NO production (<i>p</i> &lt; 0.01**), and AChE (<i>p</i> &lt; 0.001***) compared to stroke rats. Histopathological examination revealed that CT treatment reduced the severity of cerebral damage. The investigation concluded that CT strongly binds to NOS, as observed in molecular docking and dynamic simulation studies, which are involved in nitric oxide production, leading to cerebral damage, and CT treatment reduces NO production and oxidative stress parameters, and increases antioxidants <i>via</i> inhibition of NOS function. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.23354115.v3
title: Possible cerebroprotective effect of citronellal: molecular docking, MD simulation and <i>in vivo</i> investigations

description: This study focused on molecular docking, dynamic simulation, and <i>in vivo</i> approaches to examine the molecular interactions between citronellal (CT) and neurotoxic proteins. In silico studies of CT were performed using proteins involved in the pathophysiology of stroke, such as interleukin-6 (IL-6), interleukin-12 (IL-12), TNF-α, and nitric oxide synthase (NOS), to determine the binding affinity based on their interactions. The docking results of CT revealed that, among the targets, NOS had a better binding energy of −6.4 Kcal/mol. NOS showed good hydrophobic interactions: TYR A, 347; VAL A, 352; PRO A, 350; TYR A, 373 amino acids. Interactions with IL-6, TNF-α, and IL-12 resulted in lower binding affinities of −3.7, −3.9 and −3.1 Kcal/mol. Based on molecular dynamics simulations of 100 ns, the binding affinity of CT (-66.782 ± 7.309 kJ/mol) was well complemented, and NOS stability at the docked site was confirmed. In <i>in vivo</i> studies, cerebral stroke was induced by occlusion of the bilateral common carotid arteries for 30 min and reperfusion for 4 h. CT treatment protected the brain by decreasing cerebral infarction size, increasing GSH(<i>p</i> &lt; 0.001***), decreasing MPO (<i>p</i> &lt; 0.001***), MDA (<i>p</i> &lt; 0.001***), NO production (<i>p</i> &lt; 0.01**), and AChE (<i>p</i> &lt; 0.001***) compared to stroke rats. Histopathological examination revealed that CT treatment reduced the severity of cerebral damage. The investigation concluded that CT strongly binds to NOS, as observed in molecular docking and dynamic simulation studies, which are involved in nitric oxide production, leading to cerebral damage, and CT treatment reduces NO production and oxidative stress parameters, and increases antioxidants <i>via</i> inhibition of NOS function. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.8148401.v1
title: Additional file 7: of Proteomics analysis reveals heat shock proteins involved in caprine parainfluenza virus type 3 infection

description: Data Sheet 9. The 93 DEPs were annotated into six KEGG pathway categories (XLS 32 kb)
DOI: 10.6084/m9.figshare.25226255
title: Supplementary Material for: Appropriateness of Mini-Invasive Approaches for Nausea and Vomiting Refractory to Medical Therapy in Palliative Care Setting: A Case Report

description: <b><i>Introduction:</i></b> Nausea and vomiting are frequent multifactorial symptoms in oncological patients. These manifestations, mainly affecting the advanced disease stages, may lead to existential, psychological, and physical suffering, with a negative impact on the quality of life (QoL) of the individual and his family. The medical approach makes use of a wide range of drugs, with different antiemetic potency and various mechanisms of action, taking into account the etiology and the patient’s response to the different therapeutic strategies. In recent years, in addition to pharmacological treatments, some endoscopic procedures have been integrated into clinical practice as promising palliative approaches. <b><i>Case Presentation:</i></b> Herein, we describe and discuss a case of a 64-year-old female affected by advanced stage pancreatic adenocarcinoma, in which different techniques – both medical and endoscopic – have been used to approach a refractory symptomatology with a negative impact on the patient’s QoL. In the context of a multidisciplinary approach in primary palliative care, a tailored intervention encompassing invasive methods for palliative purposes, may be considered adequate and appropriate when the prognostic expectation and the physical functionality indices allow it. <b><i>Conclusion:</i></b> Minimally invasive palliative interventions should be offered to patients with advanced cancer when symptoms become refractory to standard medical therapies, as part of the holistic approach in modern treatments. Therefore, the integration of an early palliative approach into the patient’s therapeutic path becomes essential for the management of all the individual’s needs.
DOI: 10.6084/m9.figshare.25226207
title: Homegarden and participant characteristics

description: The dataset used for summary statistics and structural equation model in Durrant et al., 2024. The file contains the dataset and an accompanying READ_ME sheet describing each variable. <br>
DOI: 10.6084/m9.figshare.25226216
title: Homegarden tree inventory

description: A dataset containing the tree inventory for each home garden measured in Durrant et al., 2024.
DOI: 10.5281/zenodo.10666655
title: Reverse InSoLiTo Database

description: Database storing the articles where the bioinformatic tools are cited. The bioinformatic tools are infered from the articles thanks to the information provided in OpenEBench.
DOI: 10.5281/zenodo.10666656
title: Reverse InSoLiTo Database

description: Database storing the articles where the bioinformatic tools are cited. The bioinformatic tools are infered from the articles thanks to the information provided in OpenEBench.
DOI: 10.6084/m9.figshare.8148242
title: Additional file 1: of Development of a transcriptomic database for 14 species of scleractinian corals

description: Table S1. Information on published transcriptome datasets from Scleractinia. Table S2. Symbiotic algae types determined by BLAST coral transcriptomes against the ITS2 and rRNA genes (i.e. 18S, 28S 23S rRNA) from GenBank database. Table S3. The accession numbers of sequences in the GenBank database used for symbiotic algae clade identification. (XLSX 179 kb)
DOI: 10.6084/m9.figshare.22826946
title: Additional file 2 of ARHGAP39 is a prognostic biomarker involved in immune infiltration in breast cancer

description: Additional file 2: Supplementary Table S1. The GO functionalenrichments of ARHGAP39 and its interacting proteins. Supplementary Table S2. Biological Processes. Supplementary Table S3. Cellular Components. Supplementary Table S4. Molecular Functions. Supplementary Table S5. KEGG Pathways. Supplementary Table S6. GSEA Analysis.
DOI: 10.6084/m9.figshare.8148380
title: Additional file 4: of Proteomics analysis reveals heat shock proteins involved in caprine parainfluenza virus type 3 infection

description: Figure S4 and Data Sheet 5. Proteins were annotated based on the KOG (ZIP 669 kb)