SciLake 🇪🇺🔬
Collection
Models and datasets developed within the SciLake project to support large-scale scientific knowledge graphs, metadata enrichment,... • 14 items • Updated
doi stringlengths 13 36 | title stringlengths 37 233 | abstract stringlengths 0 9.8k | fulltext_sections listlengths 1 127 | fulltext_additional listlengths 0 19 |
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10.5114/aoms.2015.53289 | Systematic review/Meta-analysis The role of gender in patients with diffuse large B cell lymphoma treated with rituximab-containing regimens: a meta-analysis | Diffuse large B cell lymphoma (DLBCL) is the most common subtype of non-Hodgkin lymphoma (NHL). Although gender has not been included in prognostic systems, male gender has been found as a bad prognostic indicator in Hodgkin lymphoma, follicular lymphoma and chronic lymphocytic leukemia. The relationship between gender and prognosis is not clear in patients with DLBCL treated with rituximab-containing regimens. The aim of this meta-analysis is to determine the prognostic/predictive role of gender in patients with DLBCL treated with rituximab-containing regimens.We systematically searched for studies investigating the relationships between gender and prognosis in DLBCL treated with rituximab-containing regimens. After careful review, survival data were extracted from eligible studies. A meta-analysis was performed to generate combined hazard ratios for overall survival, disease-free survival (DFS) and event-free survival (EFS).A total of 5635 patients from 20 studies were included in the analysis. Our results showed that male gender was associated with poor prognosis in terms of overall survival (OS) (hazard ratio (HR) = 1.155; 95% confidence interval (CI): 1.037-1.286; p < 0.009). The pooled hazard ratio for DFS and EFS showed that male gender was not statistically significant (HR = 1.219; 95% CI: 0.782-1.899; p = 0.382, HR = 0.809; 95% CI: 0.577-1.133; p = 0.217).The present meta-analysis indicated male gender to be associated with a poor prognosis in patients with DLBCL treated with rituximab-containing regimens. | [
{
"section_content": "age, performance score, stage, proliferation fraction and gene expression profiles [3, 4]. Today, the International Prognostic Index (IPI) and age-adjusted International Prognostic Index (aaIPI) are the most important scores used in daily practice to determine the prognosis and treatment s... | [
{
"section_content": "",
"section_name": "Conflict of interest",
"section_num": null
},
{
"section_content": "The authors declare no conflict of interest.",
"section_name": "Conflict of interest",
"section_num": null
},
{
"section_content": "",
"section_name": "R e f e r e n ... |
10.31557/apjcp.2022.23.9.3229 | Interleukin-10-1082A>G (rs1800896) Single Nucleotide Polymorphism is Not a Risk Factor of Chronic Lymphocytic Leukemia in Sudanese Population | Objectif : La présente étude a été menée pour examiner l'association entre le polymorphismeIL-10-1082A >G (rs 1800896) et le risque de leucémie lymphoïde chronique et pour évaluer la corrélation entre ce polymorphisme et les caractères clinicopathologiques. Méthodes : Une étude cas-témoins a été menée dans l'État de Khartoum, au Soudan, entre avril 2017 et avril 2018, auprès de 110 patients atteints de LLC et de 80 volontaires sains en tant que groupe témoin. Un examen physique, une numération formule sanguine complète et un immunophénotype ont été effectués chez tous les patients pour confirmer le diagnostic. La stadification clinique telle que Rai et Binet a été étudiée. CD38 et ZAP70 ont été réalisés par cytométrie de flux. Des échantillons de sang ont été prélevés chez tous les participants ; l'ADN a été extrait à l'aide du kit d'extraction d'ADN sanguin ANALYTIKJENA et analysé le polymorphisme IL-10-1082A >G à l'aide de la réaction en chaîne de la polymérase spécifique de l'allèle. L'analyse statistique a été réalisée à l'aide d'un progiciel statistique pour la version 23.0 du logiciel des sciences sociales. Résultats : La fréquence des génotypes AA, AG et GG était de 32,7 %, 55,5 % et 11,8 % pour le groupe de patients et de 31,25 %, 51,25 % et 17,5 % dans le groupe témoin, respectivement. Le génotype de l'IL-10 (-1082A>G) n'était pas associé à la sensibilité de la LLC dans notre population. L'étude a montré que l'allèle G du gène IL-10 (-1082A >G) est associé au sexe masculin. Cependant, aucune association significative n'a été trouvée entre le génotype -1082A >G et les caractères clinicopathologiques. Conclusion : Nos résultats ne supportent pas l'implication du polymorphisme du gène promoteur IL-10 − 1082A >G dans la susceptibilité accrue à la LLC. L'allèle IL-10-1082G (IL-10-1082AG ou IL-10-1082GG) a été trouvé plus fréquemment chez les hommes. De plus, aucune association n'a été observée entre le polymorphisme IL-10-1082A >G et les systèmes de stades cliniques ainsi que les marqueurs de mauvais pronostic établis. Enfin, au sein du groupe de patients atteints de LLC, il n'y avait pas de différence entre l'âge au diagnostic et les paramètres hématologiques en fonction des distributions génotypiques. | [
{
"section_content": "Chronic lymphocytic leukemia is characterized by the progressive accumulation of monoclonal, small, mature-appearing CD5 + B-cells in the peripheral blood, bone marrow, and secondary lymphoid tissue (Caligaris-Cappio and Hamblin, 1999). Genetic variation of some immunomodulatory cytokine m... | [
{
"section_content": "",
"section_name": "Acknowledgments",
"section_num": null
},
{
"section_content": "We would like to thank the staff of the Hematology Department at Al Neelain University for facilities and supporting and we are grateful to the staff of Flow Cytometry Laboratory for Leukemia... |
10.3892/ijo.2012.1528 | Epimutation and cancer: A new carcinogenic mechanism of Lynch syndrome | Epimutation is defined as abnormal transcriptional repression of active genes and/or abnormal activation of usually repressed genes caused by errors in epigenetic gene repression. Epimutation arises in somatic cells and the germline, and constitutional epimutation may also occur. Epimutation is the first step of tumorigenesis and can be a direct cause of carcinogenesis. Cancers associated with epimutation include Lynch syndrome (hereditary non-polyposis colorectal cancer, HNPCC), chronic lymphocytic leukemia, breast cancer and ovarian cancer. Epimutation has been shown for many tumor suppressor genes, including RB, VHL, hMLH1, APC and BRCA1, in sporadic cancers. Methylation has recently been shown in DNA from normal tissues and peripheral blood in cases of sporadic colorectal cancer and many studies show constitutive epimutation in cancers. Epimutation of DNA mismatch repair (MMR) genes (BRCA1, hMLH1 and hMSH2) involved in development familial cancers has also been found. These results have led to a focus on epimutation as a novel oncogenic mechanism. | [
{
"section_content": "",
"section_name": "Recommendation",
"section_num": null
},
{
"section_content": "",
"section_name": "Reasons for Recommendation",
"section_num": null
}
] | [
{
"section_content": "",
"section_name": "Additional Comments",
"section_num": null
},
{
"section_content": "Submission of this form allows Spandidos Publications to contact your institution regarding this recommendation. If you do not want Spandidos Publications to contact your institution, thi... |
10.7554/elife.98747.3 | The Jag2/Notch1 signaling axis promotes sebaceous gland differentiation and controls progenitor proliferation | <jats:p>The sebaceous gland (SG) is a vital appendage of the epidermis, and its normal homeostasis and function is crucial for effective maintenance of the skin barrier. Notch signaling is a well-known regulator of epidermal differentiation, and has also been shown to be involved in postnatal maintenance of SGs. However, the precise role of Notch signaling in regulating SG differentiation in the adult homeostatic skin remains unclear. While there is evidence to suggest that Notch1 is the primary Notch receptor involved in regulating the differentiation process, the ligand remains unknown. Using monoclonal therapeutic antibodies designed to specifically inhibit of each of the Notch ligands or receptors, we have identified the Jag2/Notch1 signaling axis as the primary regulator of sebocyte differentiation in homeostatic skin. Mature sebocytes are lost upon specific inhibition of the Jag2 ligand or Notch1 receptor, resulting in the accumulation of proliferative stem/progenitor cells in the SG. Strikingly, this phenotype is reversible, as these stem/progenitor cells re-enter differentiation when the inhibition of Notch activity is lifted. Thus, Notch activity promotes correct sebocyte differentiation, and is required to restrict progenitor proliferation.</jats:p> | [
{
"section_content": "The skin is a vital organ that acts as a protective barrier against the external environment, and safeguards against fluid loss. An important component of this barrier function is the presence of a complex mixture of oils, known as sebum, which is produced by the SGs. SGs are part of the e... | [
{
"section_content": "",
"section_name": "Acknowledgements",
"section_num": null
},
{
"section_content": "We are grateful to C Cottonham, S Hankeova, and G Hernandez for their helpful discussions. We thank the Genentech Research Pathology, Necropsy, and Histology laboratories for their experimen... |
10.1186/s13000-017-0634-3 | Detection of 22 common leukemic fusion genes using a single-step multiplex qRT-PCR-based assay | Fusion genes generated from chromosomal translocation play an important role in hematological malignancies. Detection of fusion genes currently employ use of either conventional RT-PCR methods or fluorescent in situ hybridization (FISH), where both methods involve tedious methodologies and require prior characterization of chromosomal translocation events as determined by cytogenetic analysis. In this study, we describe a real-time quantitative reverse transcription PCR (qRT-PCR)-based multi-fusion gene screening method with the capacity to detect 22 fusion genes commonly found in leukemia. This method does not require pre-characterization of gene translocation events, thereby facilitating immediate diagnosis and therapeutic management.We performed fluorescent qRT-PCR (F-qRT-PCR) using a commercially-available multi-fusion gene detection kit on a patient cohort of 345 individuals comprising 108 cases diagnosed with acute myeloid leukemia (AML) for initial evaluation; remaining patients within the cohort were assayed for confirmatory diagnosis. Results obtained by F-qRT-PCR were compared alongside patient analysis by cytogenetic characterization.Gene translocations detected by F-qRT-PCR in AML cases were diagnosed in 69.4% of the patient cohort, which was comparatively similar to 68.5% as diagnosed by cytogenetic analysis, thereby demonstrating 99.1% concordance. Overall gene fusion was detected in 53.7% of the overall patient population by F-qRT-PCR, 52.9% by cytogenetic prediction in leukemia, and 9.1% in non-leukemia patients by both methods. The overall concordance rate was calculated to be 99.0%. Fusion genes were detected by F-qRT-PCR in 97.3% of patients with CML, followed by 69.4% with AML, 33.3% with acute lymphoblastic leukemia (ALL), 9.1% with myelodysplastic syndromes (MDS), and 0% with chronic lymphocytic leukemia (CLL).We describe the use of a F-qRT-PCR-based multi-fusion gene screening method as an efficient one-step diagnostic procedure as an effective alternative to lengthy conventional diagnostic procedures requiring both cytogenetic analysis followed by targeted quantitative reverse transcription (qRT-PCR) methods, thus allowing timely patient management. | [
{
"section_content": "Fusion genes are genetic chromosomal aberrations formed by the juxtaposition of two disparate gene loci through chromosomal translocation, interstitial deletion, or inversion and is most frequently detected through cytogenetic abnormalities. Although hundreds of fusion genes have been asso... | [
{
"section_content": "",
"section_name": "Acknowledgements",
"section_num": null
},
{
"section_content": "Not applicable.",
"section_name": "Acknowledgements",
"section_num": null
},
{
"section_content": "",
"section_name": "Funding",
"section_num": null
},
{
"sec... |
10.1038/s41467-024-46547-7 | Accelerated DNA replication fork speed due to loss of R-loops in myelodysplastic syndromes with SF3B1 mutation | <jats:title>Abstract</jats:title><jats:p>Myelodysplastic syndromes (MDS) with mutated <jats:italic>SF3B1</jats:italic> gene present features including a favourable outcome distinct from MDS with mutations in other splicing factor genes <jats:italic>SRSF2</jats:italic> or <jats:italic>U2AF1</jats:italic>. Molecular bases of these divergences are poorly understood. Here we find that <jats:italic>SF3B1</jats:italic>-mutated MDS show reduced R-loop formation predominating in gene bodies associated with intron retention reduction, not found in <jats:italic>U2AF1</jats:italic>- or <jats:italic>SRSF2</jats:italic>-mutated MDS. Compared to erythroblasts from <jats:italic>SRSF2-</jats:italic> or <jats:italic>U2AF1</jats:italic>-mutated patients, <jats:italic>SF3B1</jats:italic>-mutated erythroblasts exhibit augmented DNA synthesis, accelerated replication forks, and single-stranded DNA exposure upon differentiation. Importantly, histone deacetylase inhibition using vorinostat restores R-loop formation, slows down DNA replication forks and improves <jats:italic>SF3B1</jats:italic>-mutated erythroblast differentiation. In conclusion, loss of R-loops with associated DNA replication stress represents a hallmark of <jats:italic>SF3B1</jats:italic>-mutated MDS ineffective erythropoiesis, which could be used as a therapeutic target.</jats:p> | [
{
"section_content": "term treatment [6] [7] [8]. Deciphering the mechanisms of anemia is needed to generate treatments. \n\nSF3B1 mutation causes multiple alterations in mRNA processing. The use of alternative 3′ or 5′ splice site produces transcripts containing short intronic sequences that are degraded by th... | [
{
"section_content": "",
"section_name": "Acknowledgements",
"section_num": null
},
{
"section_content": "The authors dedicate this work to the memory of their colleague Dr Angelos Constantinou whose discoveries inspired this work. The authors acknowledge Pr Seishi Ogawa ( Kyoto University, Japa... |
10.1186/2045-824x-3-17 | Therapeutic promise and challenges of targeting DLL4/NOTCH1 | DLL4-mediated NOTCH1 signaling represents an essential pathway for vascular development and has emerged as an attractive target for angiogenesis-based cancer therapies. However, newly reported toxicity findings raise safety concerns of chronic pathway blockade. Lessons learned from the development of γ-secretase inhibitors (GSIs) might offer insights into how to safely harness this important signaling pathway. | [
{
"section_content": "In metazoans, the evolutionarily conserved NOTCH pathway functions as an essential mechanism to regulate numerous cell fate/lineage decisions during embryogenesis, postnatal development, and in the maintenance of adult tissue homeostasis. NOTCH receptors are normally constrained in a dorma... | [
{
"section_content": "",
"section_name": "Acknowledgements",
"section_num": null
},
{
"section_content": "The author would like to thank Weilan Ye, Jessica Couch and Kevin Leong for valuable suggestions and critical reading of the manuscript.",
"section_name": "Acknowledgements",
"sectio... |
10.18632/oncotarget.13712 | "Humoral immune responses toward tumor-derived antigens in previously untreated patients with chroni(...TRUNCATED) | "In chronic lymphocytic leukemia (CLL) the occurrence and the impact of antibody responses toward tu(...TRUNCATED) | [{"section_content":"Immune dysfunctions are a key feature of chronic lymphocytic leukemia (CLL) and(...TRUNCATED) | [{"section_content":"","section_name":"CONFLICTS OF INTEREST","section_num":null},{"section_content"(...TRUNCATED) |
10.1371/journal.pone.0004434 | "Tumorigenic Potential of Olfactory Bulb-Derived Human Adult Neural Stem Cells Associates with Activ(...TRUNCATED) | "Multipotent neural stem cells (NSCs) have been isolated from neurogenic regions of the adult brain.(...TRUNCATED) | [{"section_content":"Due to their ability to self-renew and to differentiate towards the neuronal ph(...TRUNCATED) | [{"section_content":"","section_name":"Acknowledgments","section_num":null},{"section_content":"We t(...TRUNCATED) |
10.1038/s41467-018-04283-9 | NOTCH-mediated non-cell autonomous regulation of chromatin structure during senescence | "<jats:title>Abstract</jats:title><jats:p>Senescent cells interact with the surrounding microenviron(...TRUNCATED) | [{"section_content":"ellular senescence is an autonomous tumour-suppressor mechanism that can be tri(...TRUNCATED) | [{"section_content":"","section_name":"Acknowledgements","section_num":null},{"section_content":"We (...TRUNCATED) |
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in Data Studio
SciLake Fulltext Corpus
The SciLake Fulltext Corpus is a collection of scientific papers parsed and segmented by section, primarily designed for research in the development and evaluation of NLP models. This dataset contains 1,000 full-text papers from various scientific domains, including Neuroscience, Cancer, Transport, and Energy, along with an additional 5,000 random papers from general scientific domains. All papers have been curated with licenses that allow for legal usage, specifically CC-BY and Public Domain.
The dataset provides detailed metadata and full-text sections, offering a robust resource for domain-specific and general scientific research, dataset annotation, model training, and evaluation.
Corpus Overview
- 1,000 Full-Text Papers Segmented by Section:
- Domain-specific sections: Neuroscience 🧠, Cancer 🦀, Transport 🛻, Energy 🪫.
- Each paper is segmented into sections such as Introduction, Methods, Results, etc.
- 5,000 Random Papers from General Scientific Domains:
- Mix of stratified sampled by MAG level 0 to ensure diversity across multiple domains and disciplines, and random sample.
Example of Dataset Structure:
{
'doi': DOI,
'title': TITLE,
'description': ABSTRACT,
'fulltext_sections': [
{
'section_name': SECTION_NAME_1,
'section_num': SECTION_NUM_1,
'section_content': SECTION_CONTENT_1,
},
...
],
'fulltext_additional': [
{
'section_name': SECTION_NAME_1,
'section_num': SECTION_NUM_1,
'section_content': SECTION_CONTENT_1,
},
...
]
How to use
from datasets import load_dataset
dataset_ds = load_dataset("SIRIS-Lab/scilake-fulltext-corpus")
Licensing Information
The SciLake Fulltext Corpus is released under the following licenses:
CC-BY (Creative Commons Attribution), licenses have been obtained from the publisher’s landing page, PDFs, metadata in OpenAire, and Unpaywall, filtering fro those with license CC-BY or Public Domain.
Dataset Acquisition
The papers included in this dataset were sourced through the OpenAIRE index, with random selection to ensure diverse content. The license information was verified by cross-referencing the publisher’s landing pages, metadata from OpenAire, and the Unpaywall database. Papers were retained if they had a CC-BY license or were in the Public Domain.
Funding
This work was partially funded by a projects under EU’s HORIZON Research and Innovation Programme:
- SciLake (grant agreement No 101058573).
Contact
For more information, or if you have questions, please contact us at sirislab[at]sirisacademic.com.
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