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The dataset generation failed because of a cast error
Error code: DatasetGenerationCastError
Exception: DatasetGenerationCastError
Message: An error occurred while generating the dataset
All the data files must have the same columns, but at some point there are 2 new columns ({'Document_ID', 'ID'}) and 1 missing columns ({'Paragraph_ID'}).
This happened while the csv dataset builder was generating data using
hf://datasets/sanuyah/CondRelBench/data/splits/extraction/domain_exp3_1_extraction_splits/reddit/reddit_exp3_1_extraction_train.csv (at revision 1bdbdb38bbc40166c68450383441dacba33a32f4), ['hf://datasets/sanuyah/CondRelBench@1bdbdb38bbc40166c68450383441dacba33a32f4/data/splits/extraction/domain_exp3_1_extraction_splits/pubmed/pubmed_exp3_1_extraction_train.csv', 'hf://datasets/sanuyah/CondRelBench@1bdbdb38bbc40166c68450383441dacba33a32f4/data/splits/extraction/domain_exp3_1_extraction_splits/reddit/reddit_exp3_1_extraction_train.csv', 'hf://datasets/sanuyah/CondRelBench@1bdbdb38bbc40166c68450383441dacba33a32f4/data/splits/extraction/domain_exp3_1_extraction_splits/synthetic/synthetic_exp3_1_extraction_train.csv', 'hf://datasets/sanuyah/CondRelBench@1bdbdb38bbc40166c68450383441dacba33a32f4/data/splits/probes/pubmed/pubmed_exp3_2_probe_train.csv', 'hf://datasets/sanuyah/CondRelBench@1bdbdb38bbc40166c68450383441dacba33a32f4/data/splits/probes/reddit/reddit_exp3_2_probe_train.csv', 'hf://datasets/sanuyah/CondRelBench@1bdbdb38bbc40166c68450383441dacba33a32f4/data/splits/probes/synthetic/exp3_2_probe_train.csv']
Please either edit the data files to have matching columns, or separate them into different configurations (see docs at https://hf.co/docs/hub/datasets-manual-configuration#multiple-configurations)
Traceback: Traceback (most recent call last):
File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1848, in _prepare_split_single
writer.write_table(table)
~~~~~~~~~~~~~~~~~~^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/arrow_writer.py", line 765, in write_table
self._write_table(pa_table, writer_batch_size=writer_batch_size)
~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/arrow_writer.py", line 773, in _write_table
pa_table = table_cast(pa_table, self._schema)
File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 2378, in table_cast
return cast_table_to_schema(table, schema)
File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 2306, in cast_table_to_schema
raise CastError(
...<3 lines>...
)
datasets.table.CastError: Couldn't cast
ID: string
Document_ID: string
Paragraph: string
Gold Annotation: string
-- schema metadata --
pandas: '{"index_columns": [{"kind": "range", "name": null, "start": 0, "' + 753
to
{'Paragraph_ID': Value('string'), 'Paragraph': Value('string'), 'Gold Annotation': Value('string')}
because column names don't match
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1369, in compute_config_parquet_and_info_response
parquet_operations, partial, estimated_dataset_info = stream_convert_to_parquet(
~~~~~~~~~~~~~~~~~~~~~~~~~^
builder, max_dataset_size_bytes=max_dataset_size_bytes
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 948, in stream_convert_to_parquet
builder._prepare_split(split_generator=splits_generators[split], file_format="parquet")
~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1694, in _prepare_split
for job_id, done, content in self._prepare_split_single(
~~~~~~~~~~~~~~~~~~~~~~~~~~^
gen_kwargs=gen_kwargs, job_id=job_id, **_prepare_split_args
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
):
^
File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1850, in _prepare_split_single
raise DatasetGenerationCastError.from_cast_error(
...<4 lines>...
)
datasets.exceptions.DatasetGenerationCastError: An error occurred while generating the dataset
All the data files must have the same columns, but at some point there are 2 new columns ({'Document_ID', 'ID'}) and 1 missing columns ({'Paragraph_ID'}).
This happened while the csv dataset builder was generating data using
hf://datasets/sanuyah/CondRelBench/data/splits/extraction/domain_exp3_1_extraction_splits/reddit/reddit_exp3_1_extraction_train.csv (at revision 1bdbdb38bbc40166c68450383441dacba33a32f4), ['hf://datasets/sanuyah/CondRelBench@1bdbdb38bbc40166c68450383441dacba33a32f4/data/splits/extraction/domain_exp3_1_extraction_splits/pubmed/pubmed_exp3_1_extraction_train.csv', 'hf://datasets/sanuyah/CondRelBench@1bdbdb38bbc40166c68450383441dacba33a32f4/data/splits/extraction/domain_exp3_1_extraction_splits/reddit/reddit_exp3_1_extraction_train.csv', 'hf://datasets/sanuyah/CondRelBench@1bdbdb38bbc40166c68450383441dacba33a32f4/data/splits/extraction/domain_exp3_1_extraction_splits/synthetic/synthetic_exp3_1_extraction_train.csv', 'hf://datasets/sanuyah/CondRelBench@1bdbdb38bbc40166c68450383441dacba33a32f4/data/splits/probes/pubmed/pubmed_exp3_2_probe_train.csv', 'hf://datasets/sanuyah/CondRelBench@1bdbdb38bbc40166c68450383441dacba33a32f4/data/splits/probes/reddit/reddit_exp3_2_probe_train.csv', 'hf://datasets/sanuyah/CondRelBench@1bdbdb38bbc40166c68450383441dacba33a32f4/data/splits/probes/synthetic/exp3_2_probe_train.csv']
Please either edit the data files to have matching columns, or separate them into different configurations (see docs at https://hf.co/docs/hub/datasets-manual-configuration#multiple-configurations)Need help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.
Paragraph_ID string | Paragraph string | Gold Annotation string |
|---|---|---|
P196P3 | By NCCN subclassification, 33 (27.3%) and 87 (71.9%) of men were classified as having favorable and unfavorable IR-PCa, respectively (1 case unclassifiable). GC scores were high in 3 favorable IR-PCa and low in 60 unfavorable IR-PCa. Higher GC scores, but not NCCN risk subgroups, were associated with biochemical relaps... | [{'e1': ' GC ', 'e2': ' biochemical failure ', 'relation': 'predicted', 'condition': 'at 5 years'}] |
P163P9 | Second generation androgen receptor pathway inhibitors can induce resistance through different mechanisms. One of these mechanisms is the expression of androgen receptor splice variants. More specifically, the ARV7 variant was found to be a marker for second-generation antiandrogen resistance in mCRPC. There is a lack ... | [{'e1': 'Second generation androgen receptor pathway inhibitors ', 'e2': 'resistance ', 'relation': 'can induce ', 'condition': 'through different mechanisms'}, {'e1': 'the ARV7 variant ', 'e2': 'second-generation antiandrogen resistance ', 'relation': 'was found to be a marker for ', 'condition': 'in mCRPC'}] |
P12PR6 | As the proteomic footprint of microRNAs in PC had not previously been defined comprehensively, we performed RPPA analysis in LNCaP cells transfected with SiM-miRNA mimetics. Importantly, only 12%, at most, of the SiM-miRNA effects measured via RPPA could be explained by direct miRNA binding onto the corresponding mRNAs... | [{'e1': 'common pathways ', 'e2': 'the SiM miRNAs ', 'relation': 'concordantly regulated by ', 'condition': 'in metPC'}] |
P12PR8 | Next we examined the relationship between SiM-miRNAs and AR transcriptional activity in PC tissue. We determined that for 11 of the 12 SiM-miRNAs, the miRNA levels were positively correlated with the presence of a gene signature generated by silencing AR (that is, inversely correlated with AR transcriptional activity).... | [{'e1': 'the miRNA levels ', 'e2': 'the presence of a gene signature generated ', 'relation': 'were positively correlated with ', 'condition': 'by silencing AR '}, {'e1': 'the role of SiM-miRNAs ', 'e2': 'the AR axis ', 'relation': 'in the regulation of ', 'condition': 'in PC'}, {'e1': 'silencing of miR135a-5p ', 'e2':... |
P37P9 | In conclusion, we have shown that the combination of multiple miRNAs into molecular classifiers may improve the diagnostic and prognostic biomarker potential of miRNAs for PC. In order to translate our new diagnostic and prognostic miRNA classifiers into potential future clinical use, they must be further validated in ... | [{'e1': 'combination of multiple miRNAs into molecular classifiers ', 'e2': 'diagnostic and prognostic biomarker potential ', 'relation': 'may improve the ', 'condition': 'of miRNAs for PC'}] |
P113P4 | We found that the identified miRNAs through meta-analysis are candidate predictive markers for recurrent PCa after radical prostatectomy. | [{'e1': 'miRNAs through meta-analysis ', 'e2': 'recurrent PCa ', 'relation': 'are candidate predictive markers for ', 'condition': 'after radical prostatectomy.'}] |
P106P5 | While early toxicities might compromise treatment completion, they can usually be managed with adequate care. In contrast, late toxicities can significantly affect quality of life in survivors and may require extensive treatments to alleviate symptoms. However, acute radiation reactions are not necessarily an indicator... | [{'e1': ' late toxicities ', 'e2': 'quality of life ', 'relation': 'can significantly affect ', 'condition': 'in survivors'}] |
P81P1 | Radioresistance remains a significant obstacle in the treatment of Prostate Cancer (PCa). To simulate the clinical scenario of irradiation resistance (IRR), we created DU145-IRR PCa cell lines by treatment with 2 Gy daily IR for 59 fractions. DU145-IRR cells acquired an aggressive phenotype as evidenced by increased cl... | [{'e1': 'transcriptome profiling ', 'e2': 'dysregulated genes ', 'relation': 'to discover ', 'condition': 'in DU145-IRR cells'}, {'e1': 'UCA1 abundance ', 'e2': ' in DU145-IRR cells ', 'relation': 'was significantly higher', 'condition': 'compared to control cells'}, {'e1': 'UCA1 over-expression ', 'e2': 'decreased 5-y... |
P68P3 | CDO1 was hypermethylated in PCa compared to normal adjacent tissues and benign prostatic hyperplasia and was associated with reduced gene expression. Using two different methodologies for methylation quantification, high CDO1 methylation as continuous variable was associated with BCR in univariate analysis in both coho... | [{'e1': 'CDO1 ', 'e2': 'with reduced gene expression', 'relation': 'was associated ', 'condition': 'in PCa'}, {'e1': 'high CDO1 methylation as continuous variable ', 'e2': ' BCR ', 'relation': 'was associated with', 'condition': 'in univariate analysis in both cohorts'}] |
P33P4 | To address the issue of being unable to accurately predict PCa prognosis, novel biomarkers have been shown to determine whether PCa is aggressive and to predict poor prognosis. In addition, new approaches that utilize new genomic technologies can assess genetic alterations and epigenetic events. Among them, RNA testing... | [{'e1': 'Several RNA tests ', 'e2': 'clinical use ', 'relation': 'have been approved for ', 'condition': 'in prostate cancer '}, {'e1': 'Several RNA tests ', 'e2': 'clinical and pathological risks', 'relation': 'have been found to add value to ', 'condition': ' for prostate cancer progression'}] |
P12PR3 | miRNAs bind preferentially to specific sequences in the 3′-untranslated region (3′UTR) of mRNAs and regulate protein output through translational repression and/or mRNA destabilization. Most protein-coding genes and virtually every biological process are subject to miRNA-mediated regulation. Several studies have ex... | [{'e1': 'miRNAs ', 'e2': ' specific sequences', 'relation': 'bind preferentially to', 'condition': ' in the 3′-untranslated region (3′UTR) of mRNAs'}, {'e1': 'miRNAs ', 'e2': 'protein output', 'relation': ' regulate ', 'condition': ' through translational repression '}, {'e1': 'miRNAs ', 'e2': 'protein output', 're... |
P73P2 | Precision oncology entails therapeutic decision-making on the basis of an individual patient’s molecular tumor profile. To that end, it is imperative to develop strategies to rapidly identify clinically relevant patient subgroups. While next-generation sequencing technologies have greatly advanced molecular classific... | [{'e1': 'histological variants ', 'e2': 'genomic alterations ', 'relation': 'can correlate with ', 'condition': 'in other malignancies'}] |
P168P1 | Single nucleotide polymorphisms (SNPs) within the regulatory elements of a gene can alter gene expression, making these SNPs of prime importance for candidate gene association studies. We aimed to determine whether such regulatory variants are associated with clinical outcomes in three cohorts of patients with prostate... | [{'e1': ' rs1646724 ', 'e2': ' increased risk of recurrence', 'relation': 'was consistently associated with', 'condition': ' in localized disease '}, {'e1': ' rs1646724 ', 'e2': 'mortality', 'relation': 'was consistently associated with', 'condition': ' in patients with advanced prostate cancer '}, {'e1': ' rs1646724 '... |
P73P8 | Determining which patients have hypermutated prostate tumors may have important implications for future precision oncology trials, as mutational burden has been shown to correlate with response to immune checkpoint blockade in several tumor types (e.g. anti-CTLA4, anti-PD1, anti-PDL1). Although objective responses to i... | [{'e1': 'mutational burden ', 'e2': 'response to immune checkpoint blockade ', 'relation': 'has been shown to correlate with ', 'condition': 'in several tumor types'}] |
P99P15 | In men with adverse pathology or early disease progression after prostatectomy, the Decipher 22 gene genomic classifier predicts risk of prostate cancer death. When combined with the Cancer of the Prostate Risk Assessment Postsurgical Score it further stratifies risk, which may be useful for decisions about postprostat... | [{'e1': 'the Decipher 22 gene genomic classifier ', 'e2': ' risk of prostate cancer death', 'relation': 'predicts', 'condition': 'In men with adverse pathology '}, {'e1': 'the Decipher 22 gene genomic classifier ', 'e2': ' risk of prostate cancer death', 'relation': 'predicts', 'condition': 'in men with early disease p... |
P84P1 | Hypermethylation of the paired-like homeodomain transcription factor 2 (PITX2) gene is a strong predictor of the risk of biochemical recurrence in patients with prostate cancer (PCa) after radical prostatectomy. We investigate whether PITX2 methylation is feasible for individualized risk assessment in prostate core bio... | [{'e1': 'Hypermethylation of the paired-like homeodomain transcription factor 2 (PITX2) gene ', 'e2': 'the risk of biochemical recurrence ', 'relation': 'is a strong predictor of ', 'condition': 'in patients with prostate cancer (PCa) after radical prostatectomy'}, {'e1': 'Hypermethylation of the paired-like homeodomai... |
P122P7 | Decisions regarding ART and SRT after RP are complex for patients and clinicians, since choices can be influenced by an individual's recurrence risk, medical comorbidities and personal preferences and values. A recent Markov decision analysis model considering length and quality of life for ART versus SRT showed that t... | [{'e1': 'the Decipher genomic classifier (GC) test ', 'e2': 'individual estimates of the risk of metastasis ', 'relation': 'provides ', 'condition': 'after RP'}, {'e1': ' the information provided by the GC test ', 'e2': 'influence the recommendations of clinicians for ART', 'relation': 'has been shown to ', 'condition'... |
P86P3 | There was good concordance between central pathology review and local pathologists for seminal vesicle invasion [pT3b: 91%; k = 0.95 (95% CI 0.89, 1.00)], for extraprostatic extension [pT3a/b: 94%; k = 0.82 (95% CI 0.75, 0.89)], and for positive surgical margin status [87%; k = 0.7 (95% CI 0.62, 0.79)]. Agreement was l... | [{'e1': '49 patients (18%) ', 'e2': 'rapid biochemical progression ', 'relation': 'experienced ', 'condition': 'after salvage RT'}, {'e1': 'largest diameter of carcinoma', 'e2': 'rapid progression', 'relation': 'remained associated with', 'condition': 'after salvage RT'}, {'e1': 'resection margin status', 'e2': 'rapid ... |
P25P1 | This study examined whether differential DNA methylation is associated with clinical features of more aggressive disease at diagnosis and prostate cancer recurrence in African American men, who are more likely to die from prostate cancer than other populations. Tumor tissues from 76 African Americans diagnosed with pro... | [{'e1': 'differential DNA methylation ', 'e2': 'clinical features of more aggressive disease at diagnosis and prostate cancer recurrence ', 'relation': 'is associated with ', 'condition': 'in African American men, who are more likely to die from prostate cancer than other populations'}] |
P177P6 | Regarding IFN-γ, prostate cancer cells have been shown to be poorly sensitive to its cytotoxic effects. Furthermore, it has been suggested that IFN-γ might induce immune-suppressive effects in prostate cancer. | [{'e1': 'IFN-γ ', 'e2': 'immune-suppressive effects ', 'relation': 'might induce ', 'condition': 'in prostate cancer.'}] |
P48P4 | Despite these advances, application of these insights into clinical decision making, particularly for patients with metastatic disease, remains in its infancy and therapeutic strategies are largely driven by the presence, and extent of routine clinical and pathological factors. Over the next decade, insights from genom... | [{'e1': 'insights from genomics', 'e2': 'prominent role ', 'relation': ' are likely to have a much more ', 'condition': 'in drug development'}, {'e1': 'insights from genomics', 'e2': 'prominent role ', 'relation': ' are likely to have a much more ', 'condition': 'in prognostication'}, {'e1': 'insights from genomics', '... |
P139P3 | Our results showed that expression level of CPNE1 is higher in prostate cancer than in normal prostate tissues. In the GSE35988 dataset, CPNE1 expression was found to be upregulated in castration-resistant prostate cancer compared with non-castration-resistant prostate cancer. Furthermore, we found that CPNE1 high expr... | [{'e1': ' CPNE1 high expression ', 'e2': 'tumor stage', 'relation': 'was significantly related to ', 'condition': 'in prostate cancer patients'}, {'e1': ' CPNE1 high expression ', 'e2': 'Gleason score ', 'relation': 'was significantly related to ', 'condition': 'in prostate cancer patients'}, {'e1': ' CPNE1 high expres... |
P96P13 | We investigated the relationship between disease-free survival and every possible candidate gene set based on the core gene set, defined as the power set of the core gene set. The Kaplan–Meier log-rank statistic was used for unbiased exploration of these gene subsets in correlation with disease-free survival, produci... | [{'e1': 'the Kaplan–Meier p-values ', 'e2': 'statistically significant ', 'relation': 'were found to be ', 'condition': 'for only two gene sets, at a probability of 2/2047 = 0.1%'}] |
P192P1 | Pentatricopeptide repeat domain protein 3 (PTCD3) is a mitochondrial RNA-binding protein that serves a role in mitochondrial translation. PTCD3 was originally reported as an oncogene that is involved in breast cancer and lymphoma. However, the expression and function of PTCD3 in prostate cancer (PCa) are unknown. There... | [{'e1': 'PTCD3 mRNA expression ', 'e2': 'tissue malignancy', 'relation': 'was positively correlated with ', 'condition': 'in The Cancer Genome Atlas dataset'}, {'e1': 'PTCD3 mRNA expression ', 'e2': ' high Gleason score ', 'relation': 'was positively correlated with ', 'condition': 'in The Cancer Genome Atlas dataset'}... |
P112P8 | The growing importance of miR-100-5p in carcinogenesis has been realized by several groups, which have investigated the multifaceted role of this microRNA in numerous cancers. More specifically, miR-100 has been shown to regulate apoptosis and cell cycle arrest through regulating myotubularin related protein 3 in breas... | [{'e1': 'miR-100 ', 'e2': 'apoptosis ', 'relation': 'has been shown to regulate ', 'condition': 'through regulating myotubularin related protein 3 in breast cancer cells'}, {'e1': 'miR-100 ', 'e2': 'cell cycle arrest ', 'relation': 'has been shown to regulate ', 'condition': 'through regulating myotubularin related pro... |
P185P1 | We report here numerous novel genes and multiple new signatures which robustly predict prostate cancer recurrence. We extracted 696 differentially expressed genes relative to a reported prostate cancer signature from the TCGA dataset and built a 15-gene signature using Elastic-net with 10-fold cross-validation through ... | [{'e1': ' The signature ', 'e2': 'biochemical recurrence ', 'relation': 'predicts ', 'condition': 'following surgery with 56.4% sensitivity, 72.6% specificity, and 63.24 median months disease free'}, {'e1': ' These genes ', 'e2': ' biochemical recurrence', 'relation': 'individually associate with', 'condition': ' using... |
P90P9 | The identification of loss of heterozygosity on specific genetic loci and other genetic changes has been helpful for understanding carcinogenesis, and has led to the description of new biomarkers and tools for prostate cancer. Recently the Oncotype Prostate DX was indicated as a test for counseling male patients with r... | [{'e1': 'Genomic Prostate Score ', 'e2': ' the probability of harboring adverse pathologies ', 'relation': 'correlates with', 'condition': 'at surgery.'}] |
P100P13 | Consistent with the molecular subgroup representing metastatic biology, the assay was better at predicting metastatic recurrence rather than biochemical recurrence. The latter does not necessarily predict metastatic development; only one-third of patients with biochemical recurrence develop measurable metastatic diseas... | [{'e1': 'only one-third of patients with biochemical recurrence ', 'e2': 'measurable metastatic disease ', 'relation': 'develop ', 'condition': '8 years after resection'}] |
P11PR13 | After examining the incidence of Gleason score upgrading in a low-risk patient population, Kulkarni et al concluded that ''caution should be exercised in recommending nonradical therapy to individuals with a high probability of undetected high-grade disease.'' Similar conclusions were drawn by Isariyawongse et al, who ... | [{'e1': 'caution ', 'e2': 'active surveillance ', 'relation': 'should be exercised when recommending ', 'condition': 'in older men'}, {'e1': 'Several novel genomic markers ', 'e2': 'disease recurrence and progression ', 'relation': 'have been developed to predict the risk of ', 'condition': 'in patients who have underg... |
P192P5 | In conclusion, our data strongly suggested that PTCD3 overexpression may play an important role in the characteristics and aggressive behaviour of PCa, especially in groups with advanced pathological or clinical stage and high Gleason score. Additionally, PTCD3 upregulation is associated with poor prognosis in patients... | [{'e1': 'PTCD3 upregulation ', 'e2': 'poor prognosis ', 'relation': 'is associated with ', 'condition': 'in patients with PCa'}] |
P81P4 | Urothelial carcinoma associated 1 (UCA1) is a recently identified lncRNA with aberrant expression in various types of cancer. UCA1 expression regulates cancer cell proliferation, migration, and invasion. Recent studies have shown that UCA1 is a functional oncogenic lncRNA upregulated in several malignancies. UCA1 abund... | [{'e1': 'UCA1 abundance ', 'e2': 'clinico-pathological parameters', 'relation': 'is correlated with ', 'condition': 'particularly in bladder cancer'}] |
P84P4 | The paired-like homeodomain transcription factor 2 (PITX2) gene, located on chromosome 4q25, encodes three isoforms (PITX2A, PITX2B, PITX2C) of bicoid transcription factors involved in embryonic development. Interestingly, PITX2 has also been identified as an upstream regulator of the insulin-like growth factor 1 recep... | [{'e1': 'PITX2 ', 'e2': 'the insulin-like growth factor 1 receptor and androgen receptor ', 'relation': 'has also been identified as an upstream regulator of ', 'condition': 'in prostate cancer, indicating an important role in prostate carcinogenesis'}, {'e1': 'PITX2 hypermethylation ', 'e2': ' biochemical recurrence '... |
P113P22 | Previous studies have reported that the diminished activity of TCF3 plays a role in lymphoid malignancies, and up-regulation of it is involved in the development and progression of colorectal cancer. TCF3 is regulated by androgens and acts as a tumor promoter in PCa. Overexpression, mutations, translocation and rearran... | [{'e1': 'TCF3 ', 'e2': 'tumor promoter ', 'relation': 'acts as a ', 'condition': 'in PCa'}] |
P153P3 | Although the mechanism underlying prostate cancer is not yet completely understood, multiple genes to help predict prostate cancer risk have been proposed by considerable researches. Brian R. Hu et al reported that AXIN2 expression could not only predict prostate cancer recurrence, but also promoted tumor growth and me... | [{'e1': 'AXIN2 expression ', 'e2': ' tumor growth ', 'relation': 'promoted', 'condition': 'in vivo and vitro'}, {'e1': 'AXIN2 expression ', 'e2': 'metastasis ', 'relation': 'promoted', 'condition': 'in vivo and vitro'}] |
P11PR7 | The risk of biochemical recurrence associated with adverse patho- logic findings at prostatectomy is reduced by approximately 50% in men with clinically low-risk prostate cancer. | [{'e1': ' risk of biochemical recurrence ', 'e2': 'adverse pathologic findings', 'relation': 'associated with ', 'condition': ' at prostatectomy'}, {'e1': 'The risk of biochemical recurrence', 'e2': 'approximately 50% ', 'relation': ' is reduced by ', 'condition': 'in men with clinically low-risk prostate cancer.'}] |
P11PR11 | As clinicians have grown aware of the hazards associated with overdiagnosis and overtreatment of PCa, active surveillance (AS) has emerged as a viable option for the conservative management of low-risk organ-confined disease. The D'Amico classification is the most commonly used criterion for the definition of clinical ... | [{'e1': ' low-risk patients ', 'e2': 'low-volume disease ', 'relation': 'who are found to have ', 'condition': 'on biopsy'}, {'e1': 'Preliminary data from several prospective AS series ', 'e2': 'promising results, with very low rates of disease-specific mortality ', 'relation': 'have shown ', 'condition': ' in the firs... |
P131P5 | In conclusion, our study indicates that reduced expression of MT1E is an independent predictor of poor prognosis in PCa. Measurement of MT1E level, along with other indicators of the disease progression, may serve for better prognostic stratification of PCa at the time of diagnosis or surgery. | [{'e1': 'reduced expression of MT1E ', 'e2': 'poor prognosis ', 'relation': 'is an independent predictor of ', 'condition': 'in PCa'}, {'e1': ' Measurement of MT1E level, along with other indicators of the disease progression ', 'e2': 'better prognostic stratification of PCa ', 'relation': 'may serve for ', 'condition'... |
P116P2 | It is now well established that androgens play a central role in the development and progression of prostate cancer. Indeed, even at the metastatic level, androgens and more precisely the androgen receptor are well known to stimulate proliferation. However, androgen deprivation therapy does not cure prostate cancer, as... | [{'e1': ' the androgen receptor', 'e2': 'proliferation', 'relation': 'is known to stimulate ', 'condition': ' at the metastatic level'}] |
P182P9 | In summary, we have created and validated a tumor-tissue based DNA methylation score to predict metastatic progression and prostate cancer death in men diagnosed with clinically localized prostate cancer. Compared to Gleason sum alone, the score incorporating five CpGs and Gleason sum provided better prognostic stratif... | [{'e1': 'a tumor-tissue based DNA methylation score created ', 'e2': 'metastatic progression ', 'relation': 'to predict ', 'condition': 'in men diagnosed with clinically localized prostate cancer'}, {'e1': 'a tumor-tissue based DNA methylation score created ', 'e2': 'prostate cancer death ', 'relation': 'to predict ', ... |
P78P1 | Deletion of 18q recurrently occurs in prostate cancer. To evaluate its clinical relevance, dual labeling fluorescence in-situ hybridization using probes for 18q21 and centromere 18 was performed on a prostate cancer tissue microarray. An 18q deletion was found in 517 of 6,881 successfully analyzed cancers. 18q deletion... | [{'e1': '18q deletion ', 'e2': 'independent prognostic parameter', 'relation': 'identified as an ', 'condition': ' in prostate cancer'}] |
P33P2 | Prostate cancer (PCa) has become the second leading cause of cancer-related death among men, with an estimated 914,000 new cases and 258,000 deaths worldwide every year. This makes PCa a major public health problem worldwide. | [{'e1': 'Prostate cancer (PCa) ', 'e2': 'cancer-related death', 'relation': 'has become the second leading cause of ', 'condition': ' among men'}] |
P175P3 | PSCA staining was absent in normal epithelial and stromal cells of the prostate. Membranous and cytoplasmic PSCA staining was seen in 53.7% of 9642 interpretable tumors. Staining was weak in 22.4%, moderate in 24.5% and strong in 6.8% of tumors. PSCA expression was associated with favorable pathological and clinical tu... | [{'e1': 'PSCA expression ', 'e2': 'prognosis ', 'relation': 'was an independent predictor of ', 'condition': 'in multivariate analysis '}] |
P124P7 | Apoptosis, also known as programmed cell death, has been shown to be related to changes in cell morphology, including cell shrinkage, chromatin condensation, and nuclear fragmentation. Both extrinsic and intrinsic apoptosis pathways were extensively studied in past years. The intrinsic apoptosis pathway is activated by... | [{'e1': ' Endogenous TRAIL secreted by natural killer cells ', 'e2': 'cancer cells ', 'relation': 'can effectively kill ', 'condition': 'in the liver after implantation of breast and renal cancer cells'}, {'e1': 'various molecules ', 'e2': 'TRAIL-induced apoptosis ', 'relation': 'have been found to regulate ', 'conditi... |
P145P6 | Altered abundance of acetyl marks on lysine residues on histone 4 and histone 3 are common in several cancers and have prognostic information. Furthermore, it is possible to differentiate between benign and malignant prostatic tissue based on certain epigenetic characteristics. For example, Seligson et al. have shown s... | [{'e1': 'stratifying primary prostatectomy tissue samples by overall acetylated H3 and H4 immunostaining ', 'e2': ' tumor recurrence', 'relation': 'predicted', 'condition': ' in patients with low-grade prostate cancers'}, {'e1': 'acetylation of H3 and trimethylation of H4 ', 'e2': 'the likelihood of recurrence', 'relat... |
P12PR1 | MicroRNAs are important epigenetic regulators of protein expression by triggering degradation of target mRNAs and/or inhibiting their translation. Dysregulation of microRNA expression has been reported in several cancers, including prostate cancer (PC). We comprehensively characterized the proteomic footprint of a pane... | [{'e1': 'MicroRNAs ', 'e2': 'protein expression ', 'relation': 'are important epigenetic regulators of ', 'condition': 'by triggering degradation of target mRNAs '}, {'e1': 'MicroRNAs ', 'e2': 'protein expression ', 'relation': 'are important epigenetic regulators of ', 'condition': 'by inhibiting their translation'}, ... |
P104P2 | The results from clinical breast cancer samples indicated that PLA2G7 is overexpressed in a subset of breast cancer samples compared to its expression in benign breast tissue samples and that high PLA2G7 expression associated with hormone receptor negativity as well as with poor prognosis in a subset of breast cancer s... | [{'e1': 'high PLA2G7 expression ', 'e2': 'hormone receptor negativity', 'relation': 'associated with ', 'condition': 'in a subset of breast cancer samples'}, {'e1': 'high PLA2G7 expression ', 'e2': 'poor prognosis ', 'relation': 'associated with ', 'condition': 'in a subset of breast cancer samples'}, {'e1': 'high PLA2... |
P188P2 | Endometrial cancer is the fourth leading cancer in women from developed countries. In Europe, the number of new cases was about 100,000 in 2012, with an incidence of 13.6 per 100,000 women. This tumour originates in the inner layer of the uterus when epithelial cells lining the myometrium start to proliferate abnormall... | [{'e1': 'This tumour ', 'e2': 'the inner layer of the uterus ', 'relation': 'originates in ', 'condition': 'when epithelial cells lining the myometrium start to proliferate abnormally'}] |
P11PR8 | Widespread use of prostate-specific antigen (PSA) as a primary screening tool for prostate cancer (PCa) has led to the increased detection of clinically insignificant tumors. It is estimated that up to 60% of men diagnosed by PSA screening have low-risk PCa. Such interventions carry a non-negligible risk of urinary and... | [{'e1': '60% of men diagnosed', 'e2': 'low-risk PCa', 'relation': ' have ', 'condition': 'by PSA screening '}] |
P67P1 | The prostanoid thromboxane (TX)A2 plays a central role in haemostasis and is increasingly implicated in cancer progression. TXA2 signals through two T Prostanoid receptor (TP) isoforms termed TPα and TPβ, with both encoded by the TBXA2R gene. Despite exhibiting several functional and regulatory differences, the role ... | [{'e1': 'The prostanoid thromboxane (TX)A2 ', 'e2': 'a central role ', 'relation': 'plays ', 'condition': 'in haemostasis '}] |
P62P3 | PTEN (phosphatase and tensin homolog deleted on chromosome 10; also known as MMAC1 and TEP1) is one of the most frequently altered tumor suppressor genes in cancer, and in particular, prostate cancer. It catalyzes the conversion of the membrane lipid second messenger PIP3 to PIP2 and is therefore a key mediator of the ... | [{'e1': 'miRNAs ', 'e2': 'carcinogenesis', 'relation': 'may influence ', 'condition': 'through PTEN regulation.'}] |
P139P5 | Prostate cancer is one of the most common cancer types in aging men. There were approximate 220 800 new cases and 27 540 deaths in the United States in 2015. The incidence rate of prostate cancer has also been increasing in Asian populations. Different treatments, including surgical resection, radiological therapy, and... | [{'e1': 'prostate cancer ', 'e2': 'an androgen-refractory state ', 'relation': 'eventually progresses to ', 'condition': 'in most patients'}] |
P115P1 | The RTK/ERK signaling pathway has been implicated in prostate cancer progression. However, the genetic relevance of this pathway to aggressive prostate cancer at the SNP level remains undefined. Here we performed a SNP and gene-based association analysis of the RTK/ERK pathway with aggressive prostate cancer in a cohor... | [{'e1': 'the lower expression levels of CCND2 ', 'e2': 'independent predictor of biochemical relapse and overall survival ', 'relation': 'served as an ', 'condition': 'in a large cohort of prostate cancer patients'}] |
P103P5 | In this study, we focus on analysing the expression pattern of PLA2G7 in breast cancer and investigate the functional role of PLA2G7 in cultured breast cancer cells using genome-wide gene expression analysis, immunohistochemistry and functional assays. The results indicate a role for PLA2G7 in the regulation of metasta... | [{'e1': ' high PLA2G7 protein expression in lymph node metastases ', 'e2': 'unfavourable prognosis ', 'relation': 'associates with ', 'condition': 'in breast cancer.'}] |
P32P5 | Initial prostate cancer staging is an important diagnostic procedure for patient stratification. During the last years, non-invasive multi-parametric magnetic resonance imaging has been introduced and clinically well established for T-staging in prostate cancer patients. Multi-parametric magnetic resonance imaging (MP-... | [{'e1': ' non-invasive multi-parametric magnetic resonance imaging ', 'e2': 'T-staging ', 'relation': 'has been introduced and clinically well established for ', 'condition': 'in prostate cancer patients'}] |
P194P3 | Baseline mean age, PSA, and GPS score for the cohort were 61.1 years, 8 ng/dL, and 32.8. PTEN loss was noted in 38% of patients by fluorescence in situ hybridization and 25% by immunohistochemistry. The concordance between fluorescence in situ hybridization and immunohistochemistry for PTEN loss was 66%. In univariable... | [{'e1': 'PTEN loss ', 'e2': '38% of patients ', 'relation': 'was noted in ', 'condition': 'by fluorescence in situ hybridization '}, {'e1': 'PTEN loss ', 'e2': '25% of patients ', 'relation': 'was noted in ', 'condition': 'by immunohistochemistry'}, {'e1': ' loss of PTEN by fluorescence in situ hybridization or immunoh... |
P172P4 | Patients with high androgen deprivation therapy Response Signature benefited from adjuvant androgen deprivation therapy. In combination with prognostic risk factors, use of androgen deprivation therapy Response Signature may thus allow for identification of androgen deprivation therapy-responsive tumors that may benefi... | [{'e1': 'a gene signature that when present in primary prostate tumors ', 'e2': 'patients who may respond to early androgen deprivation therapy ', 'relation': 'may be useful to predict ', 'condition': 'after surgery.'}] |
P93P8 | The large number of cancers included in our study enabled us to investigate possible associations of ADAM15 expression with previously established molecular key features of prostate cancer. Our data demonstrate a strong link of ADAM15 expression to ERG activation. In about 50% of tumors, fusion of the androgen receptor... | [{'e1': ' fusion of the androgen receptor-regulated TMPRSS2 gene with ERG ', 'e2': 'AR-stimulated overexpression of ERG', 'relation': 'leads to ', 'condition': ' In about 50% of tumors'}] |
P159P7 | In conclusion, there are now two systemic therapies, DocP and AAP, which have shown a survival benefit from RCTs when added to treatment of patients starting long-term ADT for the first time. The evidence from our directly randomised data comparing these two therapies showed no evidence of a difference in overall or pr... | [{'e1': ' DocP and AAP ', 'e2': 'RCTs ', 'relation': 'have shown a survival benefit from ', 'condition': 'when added to treatment of patients starting long-term ADT for the first time'}] |
P124P13 | It was reported that c-Flip/Caspase-8 signalling plays a vital role in regulating the extrinsic apoptosis pathway. Our results indicate that TRAF2 overexpression inhibits Caspase-8 activation in TRAIL-treated DU-145 cells, and TRAF2 overexpression upregulates c-Flip expression in TRAIL-treated DU-145 cells. Furthermore... | [{'e1': ' TRAF2 overexpression ', 'e2': 'Caspase-8 activation ', 'relation': 'inhibits ', 'condition': 'in TRAIL-treated DU-145 cells'}, {'e1': 'TRAF2 overexpression', 'e2': 'c-Flip expression ', 'relation': ' upregulates ', 'condition': 'in TRAIL-treated DU-145 cells'}, {'e1': 'TRAF2 ', 'e2': ' TRAIL-induced apoptosis... |
P59P5 | Collectively, we have provided a novel association between Btk and GBM malignancy first by bioinformatics approach followed by in vitro and in vivo validation. Notably, clinical tissue arrays revealed that Btk expression was associated with the later stage of the disease. The role of Btk in GSC generation and ability t... | [{'e1': 'the usage of ibrutinib with temozolomide ', 'e2': 'GBM ', 'relation': 'for the treatment of ', 'condition': 'in mouse xenograft models'}, {'e1': 'This combination ', 'e2': 'GBM patients ', 'relation': 'may provide improved therapeutic efficacy for ', 'condition': 'in clinical settings.'}] |
P96P3 | As a case study, we applied this pipeline to systematically analyze the role of ALDH1A2 in prostate cancer. We have previously found this gene to have multiple roles in disease and homeostasis, and here we investigate the role of the associated ALDH1A2 gene/protein networks in prostate cancer, using our methodology in ... | [{'e1': ' CYP26A1 and RDH10 ', 'e2': 'ALDH1A2 ', 'relation': 'are strongly associated with ', 'condition': 'in the retinoic acid pathways'}, {'e1': 'Our pipeline ', 'e2': 'human expertise ', 'relation': 'complements ', 'condition': 'in the search for prognostic biomarkers in large-scale datasets.'}] |
P86P7 | It has been described that around one fifth of patients experience rapid biochemical progression after RT and these patients may harbor micrometastatic or radioresistant disease and may require a more tailored treatment approach. Thus it it appears to be important to search for clinical and histopathological predictors... | [{'e1': 'around one fifth of patients ', 'e2': 'rapid biochemical progression ', 'relation': 'experience ', 'condition': 'after RT'}] |
P113P26 | LIM and SH3 protein 1, a promoter of cell proliferation and migration, play a significant role in cancer development and progression. LASP-1 is involved in numerous biological and pathological processes. It plays an important role in the regulation of dynamic actin-based and cytoskeletal activities. LASP-1 is highly ex... | [{'e1': 'LASP-1 ', 'e2': 'formation of prostate cancer ', 'relation': 'contributes to the ', 'condition': 'through a NF-KB pathway.'}, {'e1': 'LASP-1 ', 'e2': 'progression of prostate cancer ', 'relation': 'contributes to the ', 'condition': 'through a NF-KB pathway.'}] |
P73P9 | Consistent with our prior observations, we found that somatic loss-of-function mutations in MSH2 and MSH6 were the primary cause of microsatellite instability in patients with prostate cancer. This is in contrast to colorectal cancer where hypermutation has been found to be associated with epigenetic silencing of MLH1,... | [{'e1': 'somatic loss-of-function mutations in MSH2 and MSH6', 'e2': 'microsatellite instability ', 'relation': ' were the primary cause of ', 'condition': 'in patients with prostate cancer'}, {'e1': 'hypermutation ', 'e2': 'epigenetic silencing of MLH1', 'relation': 'has been found to be associated with ', 'condition'... |
P177P7 | In this study, we have comparatively analyzed the expression of genes encoding IFN-γ, TNF-α, and their receptors in prostate cancer and in benign prostatic hyperplasia tissues. Moreover, we have investigated the ability of these cytokines to induce in prostate cancer cells the production of factors promoting tumor pr... | [{'e1': ' cytokines ', 'e2': 'the production of factors promoting tumor progression ', 'relation': 'induce ', 'condition': 'in prostate cancer cells'}, {'e1': 'production of factors ', 'e2': 'tumor progression ', 'relation': 'promoting ', 'condition': 'through the inhibition of adaptive immune responses '}, {'e1': 'pro... |
P83P4 | Several studies have provided evidence for paracrine HH signaling in human and mouse PCa, a cellular relationship resembling the epithelial-to-stromal HH signaling in developing and adult mouse prostates. Autocrine HH signaling in PCa epithelial cells has also been reported, particularly in advanced and metastatic PCa ... | [{'e1': 'HH ', 'e2': ' in mouse models.', 'relation': 'signaling in vivo ', 'condition': 'during PCa progression'}, {'e1': 'HH ', 'e2': 'during PCa progression', 'relation': 'signaling in vivo ', 'condition': ' in mouse models.'}] |
P99P14 | In a large multicenter sample of men with adverse pathologic features with the longest follow-up to date, the Decipher genomic classifier demonstrated a potentially clinically important improvement in prediction of prostate cancer-specific mortality at 10 years in all men, as well as in subgroups considered high risk b... | [{'e1': 'the Decipher genomic classifier ', 'e2': 'potentially clinically important improvement ', 'relation': 'demonstrated a ', 'condition': 'in prediction of prostate cancer-specific mortality at 10 years in all men'}, {'e1': 'the Decipher genomic classifier ', 'e2': 'potentially clinically important improvement ', ... |
P139P8 | In this report, our findings showed that CPNE1 expression is significantly increased in prostate cancer. CPNE1 expression is related to tumor stage and Gleason score. A novel finding is that CPNE1 expression is significantly related to TRAF2 expression. CPNE1 overexpression can upregulate TRAF2 expression in prostate c... | [{'e1': ' CPNE1 overexpression ', 'e2': 'TRAF2 expression ', 'relation': 'can upregulate ', 'condition': 'in prostate cancer DU-145 cells'}, {'e1': 'CPNE1 ', 'e2': 'TRAF2 expression ', 'relation': 'is positively related to ', 'condition': 'in prostate cancer.'}] |
P128P2 | Prostate cancer (PC) is the most common male- specific malignancy in the developed world. The disease progresses with a heterogeneous path. A large proportion of the low- grade [Gleason score 6/WHO grade (group) I] tumors are indolent. Approximately 30% of patients after radical prostatectomy (RP) will experience a ris... | [{'e1': ' 30% of patients ', 'e2': 'a rise in serum prostate- specific antigen (PSA)', 'relation': 'will experience ', 'condition': 'after radical prostatectomy (RP) '}] |
P36P4 | We performed a meta-analysis of the expression of an androgen-regulated gene set across datasets using Oncomine. Differential expression of selected genes in the prostate TCGA database was probed using the edgeR Bioconductor package. Changes in tumour PSA density with stage and grade were assessed by Student’s t-test... | [{'e1': ' Differential expression of selected genes', 'e2': 'the edgeR Bioconductor package', 'relation': ' was probed using ', 'condition': ' in the prostate TCGA database'}] |
P72P6 | As potential biomarkers, epigenetic modifications such as hyper- or hypomethylation of tumor-related genes have lately emerged as one of the key alterations in cancer development. Aberrant patterns of methylation have aroused interest in the molecular subclassification of urologic tumors and might potentially serve as ... | [{'e1': 'epigenetic modifications ', 'e2': 'one of the key alterations', 'relation': 'have lately emerged as ', 'condition': ' in cancer development.'}, {'e1': 'Aberrant patterns of methylation ', 'e2': 'prognostic and predictive biomarkers ', 'relation': 'might potentially serve as ', 'condition': 'in PCa'}] |
P22P11 | Despite these limitations, our findings are particularly intriguing and provide a unique, more individualized approach to managing men receiving SRT post-RP. Indeed, the GC biomarker provides accurate and comprehensive insight regarding tumor aggressiveness in these individuals. Specifically, this biomarker accurately ... | [{'e1': 'the GC biomarker ', 'e2': 'tumor aggressiveness ', 'relation': 'provides accurate and comprehensive insight regarding ', 'condition': 'in these individuals'}] |
P61P2 | Prostate cancer is the most common male malignancy worldwide and a leading cause of cancer related mortality amongst men with an estimated 26,120 deaths predicted for 2016 within the US. Prostate tumors are often indolent and can be effectively managed by active surveillance and watchful waiting. However, a significant... | [{'e1': ' approximately 40% of men with localized prostate cancer', 'e2': 'relapse ', 'relation': ' suffering from ', 'condition': 'after initial therapy '}] |
P24P2 | Prostate cancer (PCa) is the most common cancer in men in the US. The natural history and clinical course of PCa is very heterogeneous: some are indolent with little effect on overall lifespan, whereas others can progress to lethal metastatic disease. The test commonly used to screen for PCa is the prostate specific an... | [{'e1': 'Prostate cancer (PCa) ', 'e2': ' cancer in men ', 'relation': 'is the most common', 'condition': 'in the US'}] |
P124P8 | The tumor necrosis factor receptor-associated factor 2, also known as a signalling adaptor, belongs to the TRAF superfamily, which consists of TRAF1 to 7 in mammals. One of these functions is to serve as an adaptor protein in the assembly of receptor-associated signalling complexes and to link upstream receptors to dow... | [{'e1': ' TRAF2 ', 'e2': ' invasion and metastasis of breast cancer', 'relation': 'might be a potential prognostic factor and biomarker for predicting', 'condition': 'in malignant pleural effusion cells '}, {'e1': 'TRAF2 ', 'e2': 'growth of prostate cancer cells ', 'relation': 'may affect ', 'condition': 'via regulatin... |
P79P8 | The variable prognostic impact of 8p deletions in cancers with different Gleason grades is of particular interest. That 8p deletions were prognostically most relevant in the subgroup of 3 + 4 carcinomas in univariate as well as in multivariate analysis, when combined with Gleason score, is encouraging because Gleason 3... | [{'e1': 'prognostic Gleason grade information ', 'e2': 'using the percentage of Gleason 4 patterns as a continuous variable', 'relation': 'can be expanded by ', 'condition': 'in Gleason 3 + 4 and 4 + 3 cancers'}, {'e1': ' prostate cancer prognosis ', 'e2': 'increasing percentage of Gleason 4 pattern', 'relation': 'cont... |
P31P5 | PCa is the most common cancer among men but could be the least life-threatening if it receives proper treatment. However, the current prevailing clinical screening or testing approach suffers from limitations because of the inability to manage patients particularly with respect to prevent over- or insufficient treatmen... | [{'e1': 'DNA methylation ', 'e2': ' prostate tumorigenesis', 'relation': 'might play critical roles in contributing to', 'condition': 'in Distal and Genic regions'}, {'e1': 'DNA methylation ', 'e2': 'gene regulation ', 'relation': ' acts positively or negatively with TSS to alter ', 'condition': 'in tumors.'}] |
P62P5 | In this study we report that: (i) miR-4534 is overexpressed in prostate cancer tissues and cell lines compared to matched normal samples and cell lines; (ii) miR-4534 has potential to distinguish malignant from normal tissues; (iii) miR-4534 functions as an oncomiR as its attenuation results in cell cycle arrest, apopt... | [{'e1': 'intra-tumoral delivery of anti-miR-4534 (anti4534) ', 'e2': 'in-vivo tumor growth ', 'relation': 'inhibits ', 'condition': 'in nude mice xenografts.'}] |
P87P3 | Wnt ligands bind to Frizzled (Fzd) receptors to activate the WP, which then induces signal transduction cascades. The WP is generally divided into a β-catenin-dependent canonical WP (CWP), and a β-catenin-independent non-canonical WP (NCWP). The importance of the CWP in carcinogenesis was first discovered in colorect... | [{'e1': 'mutations of the APC gene ', 'e2': 'stabilization of β-catenin', 'relation': 'resulted in ', 'condition': ' in colorectal cancer'}, {'e1': 'mutations of the APC gene ', 'e2': 'nuclear translocation of β-catenin', 'relation': 'resulted in ', 'condition': ' in colorectal cancer'}, {'e1': 'β-catenin translocat... |
P75P2 | Prostate cancer (PC) is the most prevalent male-specific cancer in the developed world. PC progresses from high grade prostatic intra-epithelial neoplasia, to local carcinoma, to metastatic disease with bone as the preferential site. Localized tumors can be effectively managed through a variety of approaches, including... | [{'e1': 'Prostate cancer (PC) ', 'e2': 'male-specific cancer ', 'relation': 'is the most prevalent ', 'condition': 'in the developed world'}] |
P153P1 | The present study aimed to identify potential genes associated with prostate cancer recurrence following radical prostatectomy in order to improve the prediction of the prognosis of patients with prostate cancer. The GSE25136 microarray dataset, including 39 recurrent and 40 non-recurrent prostate cancer samples, was d... | [{'e1': 'potential genes ', 'e2': 'prostate cancer recurrence ', 'relation': 'is associated with ', 'condition': 'following radical prostatectomy'}] |
P40P7 | Although these results are intriguing, most studies to date have assessed methylation profiles with DNA isolated from blood. We are not aware of any studies that have quantified the relation between smoking and methylome-wide DNA alterations in primary prostate tumor tissue. In addition, although a role for methylation... | [{'e1': ' smoking ', 'e2': 'a significant increase ', 'relation': 'is associated with ', 'condition': 'in prostate cancer progression and mortality'}] |
P70P7 | Circulating tumor cells and single-cell high-content analysis may overcome critical limitations of tumor biopsies in dissecting temporal and spatial intratumor heterogeneity in the individual patient. Yet, circulating tumor cells as a population are also heterogeneous, molecularly and in their ability to form metastase... | [{'e1': 'Circulating tumor cells and single-cell high-content analysis ', 'e2': 'critical limitations of tumor biopsies ', 'relation': 'may overcome ', 'condition': 'in dissecting temporal and spatial intratumor heterogeneity in the individual patient'}, {'e1': ' high-definition single-cell analysis assay ', 'e2': 'pai... |
P12PR11 | Therefore, epigenetic silencing appears to be a widespread phenomenon that suppresses the expression of SiM-miRNAs in metPC, which, in turn, results in diverse impact across cellular functions, including increased AR activity, mitosis, AKT/mTOR signaling, epithelial-to-mesenchymal transition and metastatic potential, w... | [{'e1': 'epigenetic silencing appears to be a widespread phenomenon ', 'e2': ' expression of SiM-miRNAs ', 'relation': 'that suppresses the', 'condition': 'in metPC'}, {'e1': 'epigenetic therapies', 'e2': 'existing hormonal agents in order to inhibit the AR axis ', 'relation': ' could complement ', 'condition': 'in CRP... |
P186P3 | The immune response affects cancer development by acting as an extrinsic tumor suppressor that restrains tumor expansion or destroys tumors. However, tumor cells can escape immune surveillance. T-lymphocyte associated antigen-4 and programmed death-1 are the two immunoregulatory proteins expressed on T cell membranes. ... | [{'e1': 'The immune response ', 'e2': 'cancer development ', 'relation': 'affects ', 'condition': 'by acting as an extrinsic tumor suppressor that restrains tumor expansion or destroys tumors. However, tumor cells can escape immune surveillance'}, {'e1': 'Radiotherapy ', 'e2': 'some potentially anti-therapeutic effects... |
P44P6 | While GS 6 prostate cancer demonstrates an indolent disease course in many patients, 55–90% of patients still undergo radical prostatectomy. A widely used alternative to surgery is active surveillance. Up to 33% of patients on active surveillance, however, will eventually undergo therapeutic intervention after a medi... | [{'e1': ' GS 6 prostate cancer ', 'e2': 'an indolent disease course', 'relation': 'demonstrates ', 'condition': ' in many patients'}] |
P82P2 | Considering susceptibility, the polymorphic allele in the SNP rs2660753 on chromosome 3 was significantly more prevalent in controls. For familial clustering, the polymorphic homozygote genotype of the SNP rs7931342 was five times more frequent in patients with familial PC compared to sporadic PC. Regarding the SNP 144... | [{'e1': 'the polymorphic allele ', 'e2': 'SNP rs2660753 on chromosome 3 was significantly more prevalent', 'relation': 'in the ', 'condition': ' in controls'}, {'e1': 'the polymorphic homozygote genotype ', 'e2': 'SNP rs7931342 was five times more frequent ', 'relation': 'of the ', 'condition': 'in patients with famili... |
P35P4 | Our results collectively showed a progression-driving role of SPAG5 in PCa which can be regulated by miR-539, suggesting that miR-539/SPAG5 can serve as a potential therapeutic target for PCa. | [{'e1': ' miR-539/SPAG5 ', 'e2': 'potential therapeutic target', 'relation': 'can serve as a ', 'condition': ' for PCa.'}] |
P161P5 | However, the significance of SLCO2B1 gene expression on the recurrence after RP in PCa has not been investigated. We hypothesized that the expression level of SLCO genes will affect the progression of PCa and lead micro-metastasis by promoting the influx of androgen. In the present study, we investigated the impact of ... | [{'e1': ' the expression level of SLCO genes ', 'e2': 'the progression of PCa and lead micro-metastasis ', 'relation': 'will affect ', 'condition': 'by promoting the influx of androgen'}] |
P102P2 | In many biomedical studies, it is of great interest to conduct feature selection of high-dimensional data such as genomic biomarkers in relation to disease risk and prognosis while also incorporating biological information on pathway memberships and interactions among biomarkers, which has been shown in previous work t... | [{'e1': 'biological information on pathway memberships', 'e2': 'performance ', 'relation': 'has been shown to improve ', 'condition': 'in feature selection'}, {'e1': 'interactions among biomarkers', 'e2': 'performance ', 'relation': 'has been shown to improve ', 'condition': ' in risk prediction'}] |
P17P10 | Tremendous enthusiasm has developed for the use of circulating tumor cells for real-time monitoring of dynamic events in both primary and metastatic cancer settings without the need for invasive tissue biopsy. A great deal has been learned through the analysis of circulating tumor content regarding the prevalence and c... | [{'e1': 'Tremendous enthusiasm ', 'e2': 'circulating tumor cells for real-time monitoring of dynamic events ', 'relation': 'has developed for the use of ', 'condition': 'in both primary and metastatic cancer settings without the need for invasive tissue biopsy'}, {'e1': ' the analysis of circulating tumor content ', 'e... |
P76P5 | Recently, the blockade of the programmed death 1 (PD-1)/programmed death ligand 1 (PD-L1) signaling pathway, either with antibodies against the receptor PD-1 or its ligand PD-L1, has shown promising results in several advanced cancers, e.g. malignant melanoma, non-small cell lung cancer, bladder cancer, head and neck c... | [{'e1': 'the blockade of the programmed death 1 (PD-1)/programmed death ligand 1 (PD-L1) signaling pathway ', 'e2': 'promising results ', 'relation': 'has shown ', 'condition': 'in several advanced cancers'}] |
P101P7 | The prognostic impact of FAM13C expression was independent of established prognostic features, both in preoperative and in postoperative scenarios. This highlights the potential applicability of FAM13C measurement either alone or in combination with other factors for a better assessment of prostate cancer aggressivenes... | [{'e1': 'The prognostic impact of FAM13C expression ', 'e2': 'established prognostic features', 'relation': 'was independent of ', 'condition': ' in preoperative scenarios'}, {'e1': 'The prognostic impact of FAM13C expression ', 'e2': 'established prognostic features', 'relation': 'was independent of ', 'condition': 'i... |
P167P7 | Overall, this life history of prostate cancer implies that early identification of tumors with multiple subclones and aggressive genomic and epigenomic features will improve cure rates through personalized therapy. These patients with highly aggressive tumors may benefit from adjuvant systemic treatment to prevent fail... | [{'e1': 'early identification of tumors with multiple subclones and aggressive genomic and epigenomic features ', 'e2': ' cure rates', 'relation': 'will improve', 'condition': ' through personalized therapy'}] |
P103P7 | The results from three independent clinical breast cancer sample sets showed that PLA2G7 is highly expressed in hormone receptor negative breast cancers. Analysis of transcriptomic data indicated a significant association between high PLA2G7 mRNA expression and poor prognosis in primary breast cancer samples. However, ... | [{'e1': ' high PLA2G7 mRNA expression ', 'e2': 'poor prognosis ', 'relation': 'significantly associated with', 'condition': 'in primary breast cancer samples'}, {'e1': 'high PLA2G7 protein expression ', 'e2': 'poor prognosis', 'relation': 'was significantly associated with ', 'condition': 'in the lymph node metastases ... |
P124P14 | The present study firstly shows that TRAF2 may be a valuable prognostic biomarker for predicting recurrence-free survival of prostate cancer patients, which might be associated with the effects of TRAF2 on regulating TRAIL-induced apoptosis in prostate cancer. In addition, we found that TRAF2 regulates TRAIL-induced ap... | [{'e1': 'TRAF2 ', 'e2': ' recurrence-free survival ', 'relation': 'may be a valuable prognostic biomarker for predicting', 'condition': 'of prostate cancer patients'}, {'e1': 'TRAF2 ', 'e2': 'TRAIL-induced apoptosis ', 'relation': 'regulates ', 'condition': 'via c-Flip/Caspase-8 signalling in prostate cancer cells.'}] |
P108P19 | Study limitations. Based on our classification of tumour foci in tissue blocks as diploid, tetraploid or aneuploid, we found that only 14% of the total median tumour volume in the radical resections was classified as non-diploid. Classifying a tissue block as non-diploid in this way is only based on the presence of ane... | [{'e1': 'only 14% of the total median tumour volume ', 'e2': 'non-diploid', 'relation': 'was classified as ', 'condition': 'in the radical resections'}] |
P87P10 | We further investigated alterations in the CWP between low Gleason and high Gleason samples. There were no significant gene expression alterations detected for β-catenin, the Wnt ligands, the receptor-complex and the destruction complex. Of the CWP inhibitors, both SFRP2 and SFRP4 were upregulated in high Gleason comp... | [{'e1': 'SFRP2 and SFRP4 ', 'e2': 'in high Gleason cancer samples', 'relation': 'were upregulated', 'condition': 'compared to low Gleason cancer samples'}] |
P153P4 | To explore more meaningful molecular biomarker for predicting the prostate cancer prognosis, technologies with high-throughput screen was implied to identify the genes. Microarray data GSE25136 with 39 recurrent and 40 non-recurrent prostate cancer was published and analyzed by Stephenson et al via leave-one-out-cross-... | [{'e1': 'erythrocyte membrane protein band 4.9 ', 'e2': 'underexpressed gene ', 'relation': 'was the most highly ', 'condition': 'in recurrent tumors compared with primary prostate cancer'}] |
P139P6 | CPNE1 is a member of the calcium-dependent lipid-binding protein family. Currently, 9 family members have been reported in studies. It is reported that Copine1, encoded by CPNE1, is a soluble membrane-binding protein, which includes 2 tandem C2 domains at the N-terminus and an A domain at the C-terminus. Copine1 can bi... | [{'e1': 'Copine1 ', 'e2': 'different intracellular proteins ', 'relation': 'can bind with ', 'condition': 'via its A domain at the C-terminus'}, {'e1': 'Copine1', 'e2': 'calcium-dependent phospholipid binding activity ', 'relation': ' can exhibit ', 'condition': 'via its C2 domain'}, {'e1': 'CPNE1 ', 'e2': 'neuronal di... |
End of preview.
CondRelBench
CondRelBench is a mixed-domain benchmark for condition-scoped relation understanding. It contains extraction data and handcrafted P1–P5 probe families from Synthetic, PubMed, and Reddit domains.
Dataset record: https://doi.org/10.6084/m9.figshare.32948507
Code and evaluation repository: sydneyanuyah/ConditionalCausality
Dataset contents
| Path | Contents |
|---|---|
data/extraction/ |
Gold condition-scoped extraction data |
data/probes/ |
Canonical P1–P5 probe tables and gold labels |
data/splits/extraction/ |
Extraction train, validation, and test splits |
data/splits/probes/ |
Probe train, validation, and test splits |
The canonical probe files contain 52,112 rows grouped into 10,449 tuple families.
Probe structure
Each condition-scoped tuple has five intended probe claims:
| Probe | Transformation | Gold label |
|---|---|---|
| P1 | Contradict the relation | Not Supported |
| P2 | Replace the condition | Not Enough Evidence |
| P3 | Remove the condition | Not Enough Evidence |
| P4 | Preserve the original condition-scoped relation | Supported |
| P5 | Contradict the condition | Not Supported |
Tuple_ID identifies the probe family, and ProbeID identifies an individual
claim. Labels describe whether the complete claim is licensed by the supplied
paragraph.
Included documentation
data_dictionary.mdsplit_protocol.mdprobe_construction.mdannotation_and_boundary_rules.mdCITATION.mdLICENSE_DATA.md
Citation
Please cite CondRelBench: A Mixed-Domain Benchmark for Condition-Scoped Relation
Understanding and the dataset DOI. See CITATION.md for the current citation
record.
License
The dataset is distributed under Creative Commons Attribution 4.0 International
(CC BY 4.0). See LICENSE_DATA.md.
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