Datasets:

qanastek
/

HoC

document_id stringlengths 9 11	text stringlengths 6 739	label list
22239943_0	Hypoxic events frequently occur in the aquatic environment in association with micro pollutants , including heavy metals .	[ 7 ]
22239943_1	Only a few studies are however available on the uptake and biological responses of heavy metals under hypoxic conditions .	[ 7 ]
22239943_2	To elucidate the phenomenon , mirror carp Cyprinus carpio L .	[ 7 ]
22239943_3	( 16.13-16.22 g ) were exposed chronically to dietary copper ( Cu ; 250 and 500 mg kg dry wt.(-1) ) for 30 d under normoxic ( 8.25 mg O(2) L(-1) ) and hypoxic ( mg O(2) L(-1) ) conditions and adopting an integrated approach , sub-lethal biomarker responses were determined at different levels of biological organisation .	[ 7 ]
22239943_4	Level of oxidative DNA damage ( as determined by modified Comet assay ) showed strong significant difference following exposure to dietary Cu level under normoxic ( 1.6-fold ) as well as under hypoxic condition at both Cu levels ( 2.1 and 2.5-folds respectively ) .	[ 7 ]
22239943_5	Significant difference was also observed for haematological parameters ( i.e. increased red and white blood cells , haematocrit value and haemoglobin concentration ) .	[ 7 ]
22239943_6	Quantitative histology revealed alterations in tissues ( i.e. liver and gills ) for hypoxic and all dietary Cu treatment groups under both normoxic and hypoxic conditions suggesting a compensatory response to these organs ( p<0.05 ) .	[ 7 ]
22239943_7	The order of Cu accumulation in tissues ( as determined by ICP-OES ) was liver>intestine>kidney>gill .	[ 7 ]
22239943_8	Interestingly , SGR under both normoxic and hypoxic conditions reduced with elevating Cu levels ( p=0.019 ) .	[ 7 ]
22239943_9	Overall , the results provide evidence for enhanced toxicological responses in fish following exposure to Cu either alone or in combination with hypoxic condition and lends support to the evolving viewpoint that many water quality guidelines should be revisited in terms of new ecotoxicological criteria .	[ 7 ]
20839428_0	A 51-year-old previously healthy man , an ex-smoker , was admitted to the authors ' medical department with a 3-month history of dry cough ; intermittent fever ; painless , ulcerated cutaneous lesions over the trunk and limbs ( Figure 1 ) ; and progressive weight loss .	[ 7 ]
20839428_1	He was of Greek descent .	[ 7 ]
20839428_2	His medical history was remarkable for nasal polyps , which were surgically removed 15 years earlier .	[ 7 ]
20839428_3	Initially , he had been treated with antibiotics , without improvement .	[ 7 ]
20839428_4	Several days before admission , chest radiography revealed pulmonary infiltrates in the left lower lobe .	[ 7 ]
20839428_5	On admission , physical examination revealed a well-orientated man in mild distress , with inspiratory rhonchi at the lower part of the left lung and scattered erythematous nodules of variable size , some of which were ulcerated .	[ 7 ]
20839428_6	Laboratory values were notable for leukopenia , 3.3 x 10(9)/L ; total protein , 5.9 g/dL ; globulin , 2.2 g/dL ; serum glutamic oxaloacetic transaminase , 86 IU/L ; serum glutamic pyruvic transaminase , 71 IU/L ; and lactate dehydrogenase , 519 U/L .	[ 7 ]
20839428_7	Computed tomograph ( CT ) of the chest showed multiple alveolar opacities bilaterally ( Figure 2 ) .	[ 7 ]
20839428_8	Fiberoptic bronchoscopy did not reveal any important pathologic findings .	[ 7 ]
20839428_9	Results of bronchial biopsy , cytology of bronchoalveolar lavage , washing , brushing , and sputum following bronchoscopy were negative .	[ 7 ]
20839428_10	CT of the brai and sinonasal area revealed an abnormal low-density mass in the left nasal area .	[ 7 ]
20839428_11	CT findings of the abdomen were negative , as were results of a bone marrow biopsy .	[ 7 ]
20839428_12	There was no evidence of immunosuppression .	[ 10 ]
20839428_13	The differential diagnosis , considering the evidence described , included granulomatous or infectious diseases , angiocentric lymphoproliferative lesions , and lymphomas .	[ 7 ]
20839428_14	Biopsy of a skin lesion showed lymphoproliferative infiltration of the dermis with a follicular and angiocentric growth pattern and regional epidermal necrosis .	[ 4 ]
20839428_15	Immunohistochemical stains showed that the tumor cell were positive for CD56 and CD3 ( cytoplasmic positivity ) and expressed the cytotoxic proteins T-cell intracellular antigen and granzyme B ( Figure 3 ) They lacked TdT , CD34 , CD7 , CD8 , TCL-1 , and CD123 .	[ 7 ]
20839428_16	Findings from an in situ hybridization study for Epstein-Barr virus were negative .	[ 7 ]
20839428_17	Give this result , molecular analysis ofT-cell receptor ( TCR ) gene rearrangements was performed using polymerase chain reaction-based TCR-gamma gene , wit negative results .	[ 7 ]
20839428_18	The morphology and the immunophenotype were consistent with natural killer/T-cell lymphoma , nasal-type .	[ 7 ]
20839428_19	Nasal involvement must be first excluded to proceed to the diagnosis of nasal-type natural killer-cell lymphoma .	[ 7 ]
20839428_20	Indeed , histologic examination of the nasal mass revealed its polypoid nature .	[ 7 ]
20839428_21	Thus , the authors were led to the diagnosis of extranodal extranasal natural killer/T-cell lymphoma , nasal-type , CD56-positive , Ep stein-Barr virus-negative , TCR-negative .	[ 7 ]
20839428_22	The patient received combination chemotherapy and completed 4 cycles of cyclophosphamide , doxorubicin vincristine , and prednisone every 14 days for 2 months .	[ 7 ]
20839428_23	Skin lesions improved , and there was no fever soon after the initiation of therapy .	[ 7 ]
20839428_24	Reevaluatio after the fourth cycle , however , disclosed pulmonary infiltrations as well as leukemic infiltration of the central nervous system .	[ 7 ]
20839428_25	The patient had receive systemic salvage chemotherapy and intrathecal infusions of methotrexate .	[ 7 ]
20839428_26	Although the lung lesions had diminished at that time , the patient develope paraplegia , his clinical course rapidly deteriorated , and he eventually died .	[ 7 ]
22797777_0	MicroRNAs ( miRs ) are small non-coding RNAs that recently emerged as potent regulators of gene expression .	[ 7 ]
22797777_1	The members of the miR-17-92 cluster have been shown to control endothelial cell functions and neovascularization ; however , the regulation and function of the cluster in endothelial cell lineage commitment has not been explored .	[ 7 ]
22797777_2	This project aimed to test the role of the miR-17-92 cluster during endothelial differentiation .	[ 7 ]
22797777_3	We demonstrate that miR-17 , miR-18 , miR-19 and miR-20 are increased upon the induction of endothelial cell differentiation of murine embryonic stem cells or induced pluripotent stem cells .	[ 7 ]
22797777_4	In contrast , miR-92a and the primary miR-17-92 transcript were downregulated .	[ 7 ]
22797777_5	The inhibition of each individual miR of the cluster by cholesterol-modified antagomirs did not affect endothelial marker gene expression .	[ 7 ]
22797777_6	Moreover , the combination of all antagomirs had no effect .	[ 7 ]
22797777_7	These findings illustrate that although the miR-17-92 cluster regulates vascular integrity and angiogenesis , none of the members has a significant impact on the endothelial differentiation of pluripotent stem cells .	[ 8 ]
22593574_0	The solution structure of the complex of enzyme IIA of the N,N'-diacetylchitobiose ( Chb ) transporter with the histidine phosphocarrier protein HPr has been solved by NMR .	[ 7 ]
22593574_1	The IIA(Chb)-HPr complex completes the structure elucidation of representative cytoplasmic complexes for all four sugar branches of the bacterial phosphoryl transfer system ( PTS ) .	[ 7 ]
22593574_2	The active site His-89 of IIA(Chb) was mutated to Glu to mimic the phosphorylated state .	[ 7 ]
22593574_3	IIA(Chb)(H89E) and HPr form a weak complex with a K(D) of mM .	[ 7 ]
22593574_4	The interacting binding surfaces , concave for IIA(Chb) and convex for HPr , complement each other in terms of shape , residue type , and charge distribution , with predominantly hydrophobic residues , interspersed by some uncharged polar residues , located centrally , and polar and charged residues at the periphery .	[ 7 ]
22593574_5	The active site histidine of HPr , His-15 , is buried within the active site cleft of IIA(Chb) formed at the interface of two adjacent subunits of the IIA(Chb) trimer , thereby coming into close proximity with the active site residue , H89E , of IIA(Chb) .	[ 7 ]
22593574_6	A His89-P-His-15 pentacoordinate phosphoryl transition state can readily be modeled without necessitating any significant conformational changes , thereby facilitating rapid phosphoryl transfer .	[ 7 ]
22593574_7	Comparison of the IIA(Chb)-HPr complex with the IIA(Chb)-IIB(Chb) complex , as well as with other cytoplasmic complexes of the PTS , highlights a unifying mechanism for recognition of structurally diverse partners .	[ 7 ]
22593574_8	This involves generating similar binding surfaces from entirely different underlying structural elements , large interaction surfaces coupled with extensive redundancy , and side chain conformational plasticity to optimize diverse sets of intermolecular interactions .	[ 7 ]
1433375_0	Immunosuppression of humoral and cellular responses following chronic oral exposure to 1 , 5 , 10 , and 20 ppm N-nitrosodimethylamine ( NDMA ) was examined in CD-1 mice .	[ 7 ]
1433375_1	Monitoring of cumulative mortality and the incidence of peritoneal ascites in animals showed an NDMA dose-related mortality and hepatotoxicity .	[ 7 ]
1433375_2	No visible changes in immunological parameters were noted at the 1 ppm NDMA dose .	[ 7 ]
1433375_3	Immunosuppression of immunoglobulin M ( IgM ) antibody response by NDMA to sheep red blood cells ( SRBC ) was time-related , dose-related , and could be reversed within 30 d by removal of the chemical from the drinking water .	[ 10 ]
1433375_4	Cellular immune response , monitored by allogeneic stimulation of cells in mixed lymphocyte reaction ( MLR ) , was markedly suppressed by 10 and 20 ppm NDMA .	[ 10 ]
1433375_5	Thus , chronic exposure to NDMA , except for the low-hepatotoxic doses of nitrosamine , resulted in a marked and persistent immunosuppression of cellular and humoral responses in CD-1 mice .	[ 10 ]
1433375_6	In conclusion , chronic exposure to the hepatotoxic ( ascite-inducing ) doses of NDMA suppressed humoral and cellular immunity .	[ 10 ]
1433375_7	The persistent immunosuppression could be reversed after the removal of NDMA from the drinking water .	[ 10 ]
1433375_8	Although no direct NDMA-related cancer was reported in humans , our data point to a potential epigenetic carcinogenicity of nitrosamines due to chronic immunosuppression .	[ 10 ]
11896073_0	AIMS Tumour cell growth results from a disturbance in the balance between the rate of proliferation and cell death .	[ 7 ]
11896073_1	In this study , proteins involved in the regulation of cell cycle arrest and apoptosis were studied as possible factors responsible for uncontrolled cell growth in colorectal cancer .	[ 7 ]
11896073_2	METHODS The expression of proteins involved in these processes was investigated in 48 metastases from patients with colorectal cancer and compared with eight normal colon mucosa samples and 14 primary tumours .	[ 7 ]
11896073_3	Both primary tumours and metastases were obtained from eight patients .	[ 7 ]
11896073_4	The expression of thymidylate synthase ( TS ) , p53 , retinoblastoma protein ( Rb ) , Fas receptor , Fas ligand , bcl-2 , mcl-1 , bax , and bcl-x was measured using immunohistochemistry .	[ 7 ]
11896073_5	Proliferation was determined by Ki67 staining , whereas apoptosis was assessed by M30 immunostaining , which recognises cleaved cytokeratin 18 .	[ 7 ]
11896073_6	RESULTS In the limited number of cases in which paired comparisons were possible , the expression of TS and Ki67 was significantly higher in metastases than in the matched primary tumour samples ( p = 0.014 and 0.016 , respectively ) , whereas Rb expression was lower in metastases than in primary tumours ( p = 0.024 ) .	[ 9, 5 ]
11896073_7	Fas receptor expression was high in normal mucosa but absent in primary tumours and metastases , whereas the opposite was seen for p53 .	[ 4, 5 ]
11896073_8	The expression of bax , mcl-1 , and bcl-x in normal mucosa was more apical than that seen in malignant cells , where a more diffuse expression pattern was seen ( p < 0.04 ) .	[ 7 ]
11896073_9	Apoptosis was more abundant in primary tumours than in metastases .	[ 4, 5 ]
11896073_10	CONCLUSIONS These results demonstrate that proliferation and apoptosis are disturbed during colorectal cancer progression , and this is accompanied by loss of Rb and Fas expression , the accumulation of p53 and TS , and changes in the expression patterns of bax , mcl-1 , and bcl-xl .	[ 4, 9 ]
21116101_0	The radioprotective effects of dimethyl sulfoxide ( DMSO ) have been known for many years , and the suppression of hydroxyl ( OH ) radicals induced by ionizing radiation has been thought to be the main cause of this effect .	[ 7 ]
21116101_1	However , the DMSO concentration used was very high , and might be toxic , in earlier studies .	[ 7 ]
21116101_2	In the present study , we administered a lower , non-toxic concentration ( 0.5% , i.e. , 64 mM ) of DMSO before irradiation and examined its radioprotective effects .	[ 7 ]
21116101_3	Colony formation assay and micronucleus assay showed significant radioprotective effects in CHO , but not in xrs5 , which is defective in the repair function of DNA double-strand breaks .	[ 6 ]
21116101_4	The levels of phosphorylated H2AX and the formation of 53BP1 foci 15 minutes after irradiation , which might reflect initial DNA double-strand breaks , in DMSO-treated CHO cells were similar to those in non-treated cells , suggesting that the radioprotective effects were not attributable to the suppression of general indirect action in the lower concentration of DMSO .	[ 6 ]
21116101_5	On the other hand , 2 hours after irradiation , the average number of 53BP1 foci , which might reflect residual DNA double-strand breaks , was significantly decreased in DMSO-treated CHO cells compared to non-treated cells .	[ 6 ]
21116101_6	The results indicated that low concentration of DMSO exerts radioprotective effects through the facilitation of DNA double-strand break repair rather than through the suppression of indirect action .	[ 6 ]
23250485_0	Androgens regulate both the physiological development of the prostate and the pathology of prostatic diseases .	[ 7 ]
23250485_1	However , the mechanisms by which androgens exert their regulatory activities on these processes are poorly understood .	[ 7 ]
23250485_2	In this study , we have determined that androgens regulate overall cell metabolism and cell growth , in part , by increasing autophagy in prostate cancer cells .	[ 4 ]
23250485_3	Importantly , inhibition of autophagy using either pharmacological or molecular inhibitors significantly abrogated androgen-induced prostate cancer cell growth .	[ 7 ]
23250485_4	Mechanistically , androgen-mediated autophagy appears to promote cell growth by augmenting intracellular lipid accumulation , an effect previously demonstrated to be necessary for prostate cancer cell growth .	[ 7 ]
23250485_5	Further , autophagy and subsequent cell growth is potentiated , in part , by androgen-mediated increases in reactive oxygen species .	[ 4, 1 ]
23250485_6	These findings demonstrate a role for increased fat metabolism and autophagy in prostatic neoplasias and highlight the potential of targeting underexplored metabolic pathways for the development of novel therapeutics .	[ 4 ]
12489119_0	Cis-diamminedichloroplatinum ( II ) ( cisplatin ) is a well characterized antitumor drug used for the treatment of a variety of human cancers .	[ 7 ]
12489119_1	The cytotoxicity of cisplatin is mainly mediated through the formation of DNA adducts , which are also believed to be responsible for the secondary malignancies produced by the drug .	[ 7 ]
12489119_2	The aim of this study was to determine the in vivo mutagenic activity of cisplatin in the lacZ plasmid-based transgenic mouse model .	[ 7 ]
12489119_3	The mutant frequency ( MF ) and the spectrum of mutations induced by cisplatin in the mouse liver were analyzed and compared to controls .	[ 7 ]
12489119_4	The mean MF in the lacZ gene was increased 2-fold in mice treated with a single 6 mg/kg body weight dose of cisplatin and sacrificed after 17 and 28 days ( P = 0.001 and P < 0.0001 ) .	[ 6 ]
12489119_5	Restriction analysis and sequencing of mutant DNA showed that cisplatin was able to induce both large deletions and point mutations .	[ 6 ]
12489119_6	A specific profile of base substitution and frameshift mutations was identified in treated mice , consisting primarily of G:C-->A:T transitions at GpG and ApG sites , the preferential DNA binding sites of cisplatin , and single basepair deletions/insertions .	[ 6 ]
12489119_7	The present results provide the first evidence that cisplatin has mutagenic activity in vivo and induces a characteristic pattern of mutations in the mouse liver .	[ 6 ]
12489119_8	This mutagenicity may be responsible for its tumorigenic activity .	[ 6 ]
23132960_0	A prominent feature of inflammatory diseases is endothelial dysfunction .	[ 7 ]
23132960_1	Factors associated with endothelial dysfunction include proinflammatory cytokines , adhesion molecules , and matrix degrading enzymes .	[ 7 ]
23132960_2	At the transcriptional level , they are regulated by the histone deacetylase sirtuin ( SIRT ) 1 via its actions on the proinflammatory transcription factor nuclear factor-κB ( NF-κB ) .	[ 7 ]

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HoC : Hallmarks of Cancer Corpus

Dataset Summary

The Hallmarks of Cancer Corpus for text classification

The Hallmarks of Cancer (HOC) Corpus consists of 1852 PubMed publication abstracts manually annotated by experts according to a taxonomy. The taxonomy consists of 37 classes in a hierarchy. Zero or more class labels are assigned to each sentence in the corpus. The labels are found under the "labels" directory, while the tokenized text can be found under "text" directory. The filenames are the corresponding PubMed IDs (PMID).

In addition to the HOC corpus, we also have the Cancer Hallmarks Analytics Tool which classifes all of PubMed according to the HoC taxonomy.

Supported Tasks and Leaderboards

The dataset can be used to train a model for multi-class-classification.

Languages

The corpora consists of PubMed article only in english:

English - United States (en-US)

Load the dataset with HuggingFace

from datasets import load_dataset
dataset = load_dataset("qanastek/HoC")
validation = dataset["validation"]
print("First element of the validation set : ", validation[0])

Dataset Structure

Data Instances

{
  "document_id": "12634122_5",
  "text": "Genes that were overexpressed in OM3 included oncogenes , cell cycle regulators , and those involved in signal transduction , whereas genes for DNA repair enzymes and inhibitors of transformation and metastasis were suppressed .",
  "label": [9, 5, 0, 6]
}

Data Fields

document_id: Unique identifier of the document.

text: Raw text of the PubMed abstracts.

label: One of the 10 currently known hallmarks of cancer.

Hallmark	Search term
1. Sustaining proliferative signaling (PS)	Proliferation Receptor Cancer
	'Growth factor' Cancer
	'Cell cycle' Cancer
2. Evading growth suppressors (GS)	'Cell cycle' Cancer
	'Contact inhibition'
3. Resisting cell death (CD)	Apoptosis Cancer
	Necrosis Cancer
	Autophagy Cancer
4. Enabling replicative immortality (RI)	Senescence Cancer
	Immortalization Cancer
5. Inducing angiogenesis (A)	Angiogenesis Cancer
	'Angiogenic factor'
6. Activating invasion & metastasis (IM)	Metastasis Invasion Cancer
7. Genome instability & mutation (GI)	Mutation Cancer
	'DNA repair' Cancer
	Adducts Cancer
	'Strand breaks' Cancer
	'DNA damage' Cancer
8. Tumor-promoting inflammation (TPI)	Inflammation Cancer
	'Oxidative stress' Cancer
	Inflammation 'Immune response' Cancer
9. Deregulating cellular energetics (CE)	Glycolysis Cancer; 'Warburg effect' Cancer
10. Avoiding immune destruction (ID)	'Immune system' Cancer
	Immunosuppression Cancer

Data Splits

Distribution of data for the 10 hallmarks:

Hallmark	No. abstracts	No. sentences
1. PS	462	993
2. GS	242	468
3. CD	430	883
4. RI	115	295
5. A	143	357
6. IM	291	667
7. GI	333	771
8. TPI	194	437
9. CE	105	213
10. ID	108	226

Dataset Creation

Source Data

Who are the source language producers?

The corpus has been produced and uploaded by Baker Simon and Silins Ilona and Guo Yufan and Ali Imran and Hogberg Johan and Stenius Ulla and Korhonen Anna.

Personal and Sensitive Information

The corpora is free of personal or sensitive information.

Additional Information

Dataset Curators

HoC: Baker Simon and Silins Ilona and Guo Yufan and Ali Imran and Hogberg Johan and Stenius Ulla and Korhonen Anna

Hugging Face: Labrak Yanis (Not affiliated with the original corpus)

Licensing Information

GNU General Public License v3.0

Permissions
- Commercial use
- Modification
- Distribution
- Patent use
- Private use
Limitations
- Liability
- Warranty
Conditions
- License and copyright notice
- State changes
- Disclose source
- Same license

Citation Information

We would very much appreciate it if you cite our publications:

Automatic semantic classification of scientific literature according to the hallmarks of cancer

@article{baker2015automatic,
  title={Automatic semantic classification of scientific literature according to the hallmarks of cancer},
  author={Baker, Simon and Silins, Ilona and Guo, Yufan and Ali, Imran and H{\"o}gberg, Johan and Stenius, Ulla and Korhonen, Anna},
  journal={Bioinformatics},
  volume={32},
  number={3},
  pages={432--440},
  year={2015},
  publisher={Oxford University Press}
}

Cancer Hallmarks Analytics Tool (CHAT): a text mining approach to organize and evaluate scientific literature on cancer

@article{baker2017cancer,
  title={Cancer Hallmarks Analytics Tool (CHAT): a text mining approach to organize and evaluate scientific literature on cancer},
  author={Baker, Simon and Ali, Imran and Silins, Ilona and Pyysalo, Sampo and Guo, Yufan and H{\"o}gberg, Johan and Stenius, Ulla and Korhonen, Anna},
  journal={Bioinformatics},
  volume={33},
  number={24},
  pages={3973--3981},
  year={2017},
  publisher={Oxford University Press}
}

Cancer hallmark text classification using convolutional neural networks

@article{baker2017cancer,
  title={Cancer hallmark text classification using convolutional neural networks},
  author={Baker, Simon and Korhonen, Anna-Leena and Pyysalo, Sampo},
  year={2016}
}

Initializing neural networks for hierarchical multi-label text classification

@article{baker2017initializing,
  title={Initializing neural networks for hierarchical multi-label text classification},
  author={Baker, Simon and Korhonen, Anna},
  journal={BioNLP 2017},
  pages={307--315},
  year={2017}
}

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