cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9699140
title: tRic: a user-friendly data portal to explore the expression landscape of tRNAs in human cancers

description: Transfer RNAs (tRNAs) play critical roles in human cancer. Currently, no database provides the expression landscape and clinical relevance of tRNAs across a variety of human cancers. Utilizing miRNA-seq data from The Cancer Genome Atlas, we quantified the relative expression of tRNA genes and merged them into the codon level and amino level across 31 cancer types. The expression of tRNAs is associated with clinical features of patient smoking history and overall survival, and disease stage, subtype, and grade. We further analysed codon frequency and amino acid frequency for each protein coding gene and linked alterations of tRNA expression with protein translational efficiency. We include these data resources in a user-friendly data portal, tRic (tRNA in cancer, https://hanlab.uth.edu/tRic/ or http://bioinfo.life.hust.edu.cn/tRic/), which can be of significant interest to the research community.
DOI: 10.6084/m9.figshare.12844864.v1
title: Synthesis, crystal structure, Hirshfeld surface analysis, DNA binding, DNA cleavage activity and molecular docking of a new Schiff base nickel(II) complex

description: A mononuclear nickel(II) complex, [Ni(<i>o</i>-van-tris)<sub>2</sub>]·2H<sub>2</sub>O (<i>o</i>-van-tris = Schiff base derived from <i>o</i>-vanillin and tris(hydroxymethyl)aminomethane), has been synthesized and structurally characterized. The single crystal structure shows a distorted octahedron geometry coordinated with Ni(II) atom, and 2 D plane structure has formed by O–H···O hydrogen bond interactions. An analysis to ascertain intermolecular interactions of the complex was performed based on the Hirshfeld surfaces and their associated two-dimensional fingerprint plots. The binding properties of the nickel(II) complex with CT-DNA have been investigated by spectroscopic methods and molecular docking. Absorption and fluorescence spectral studies reveal that the complex interacts with DNA through hydrogen bond and hydrophobic interactions with the DNA base pairs. Molecular docking studies show that the complex effectively docks in the major groove of DNA. The DNA cleavage experiment was performed by gel electrophoretic assay, indicating that DNA cleavage activity of the complex is concentration dependent and much sensitive to ionic strength. The efficient cleavage mediated via hydrolytically cleaving pathway. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.9699140.v1
title: tRic: A user-friendly data portal to explore the expression landscape of tRNAs in human cancers

description: Transfer RNAs (tRNAs) play critical roles in human cancer. Currently, no database provides the expression landscape and clinical relevance of tRNAs across a variety of human cancers. Utilizing miRNA-seq data from The Cancer Genome Atlas, we quantified the relative expression of tRNA genes and merged them into the codon level and amino level across 31 cancer types. The expression of tRNAs is associated with clinical features of patient smoking history and overall survival, and disease stage, subtype, and grade. We further analyzed codon frequency and amino acid frequency for each protein coding gene and linked alterations of tRNA expression with protein translational efficiency. We include these data resources in a user-friendly data portal, tRic (tRNA in cancer, https://hanlab.uth.edu/tRic/or http://bioinfo.life.hust.edu.cn/tRic/), which can be of significant interest to the research community.
DOI: 10.6084/m9.figshare.9699140.v2
title: tRic: a user-friendly data portal to explore the expression landscape of tRNAs in human cancers

description: Transfer RNAs (tRNAs) play critical roles in human cancer. Currently, no database provides the expression landscape and clinical relevance of tRNAs across a variety of human cancers. Utilizing miRNA-seq data from The Cancer Genome Atlas, we quantified the relative expression of tRNA genes and merged them into the codon level and amino level across 31 cancer types. The expression of tRNAs is associated with clinical features of patient smoking history and overall survival, and disease stage, subtype, and grade. We further analysed codon frequency and amino acid frequency for each protein coding gene and linked alterations of tRNA expression with protein translational efficiency. We include these data resources in a user-friendly data portal, tRic (tRNA in cancer, https://hanlab.uth.edu/tRic/ or http://bioinfo.life.hust.edu.cn/tRic/), which can be of significant interest to the research community.
DOI: 10.6084/m9.figshare.12844915
title: <i>In-silico</i> identification of fingerprint of pyrazolyl sulfonamide responsible for inhibition of <i>N</i>-myristoyltransferase using Monte Carlo method with index of ideality of correlation

description: Human African trypanosomiasis (HAT) or sleeping sickness like infections remain a serious health concern around the globe due to unavailability of safe and potential drugs for their treatment. Moreover, developing safe, potential and highly specific target based treatments is still a challenge for present drug discovery programs. A series of pyrazole based sulfonamides are identified as an inhibitor of <i>Trypanosoma brucei N</i>-myristoyltransferase (TbNMT). In the present manuscript, we have developed robust and reliable QSAR models by using the balance of correlation method in CORAL software. The chemical structures are represented by simplified molecular input line entry system (SMILES). The significance of the index of ideality correlation (IIC) with applicability domain (AD) is also studied at depth. The models developed by considering the index of ideality of correlation (IIC) were found to statistically more significant and robust. One QSAR model with best Rcalibration2 = 0.8638 for split 2 was considered as the leading model. A greater value of cRp<sup>2</sup> <i>i.e.</i> 0.5 for all models in Y-randomization test showed the robustness of developed models. The outliers and promoters of increase and decrease of endpoint were also extracted independently from the leading models. The mechanistic interpretation of developed models explains the role of different structural attributes in predicting the pIC<sub>50</sub> of pyrazole sulfonamides extracted from the crystal structure of Leishmania major N-myristoyltransferase (NMT) along with co-crystallized myristoyl-CoA and ligands NMT106, NMT157, NMT187 and NMT236 (PDB ID: 4A2Z, 4A30, 4A32, 2WSA). Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.12844915.v1
title: <i>In-silico</i> identification of fingerprint of pyrazolyl sulfonamide responsible for inhibition of <i>N</i>-myristoyltransferase using Monte Carlo method with index of ideality of correlation

description: Human African trypanosomiasis (HAT) or sleeping sickness like infections remain a serious health concern around the globe due to unavailability of safe and potential drugs for their treatment. Moreover, developing safe, potential and highly specific target based treatments is still a challenge for present drug discovery programs. A series of pyrazole based sulfonamides are identified as an inhibitor of <i>Trypanosoma brucei N</i>-myristoyltransferase (TbNMT). In the present manuscript, we have developed robust and reliable QSAR models by using the balance of correlation method in CORAL software. The chemical structures are represented by simplified molecular input line entry system (SMILES). The significance of the index of ideality correlation (IIC) with applicability domain (AD) is also studied at depth. The models developed by considering the index of ideality of correlation (IIC) were found to statistically more significant and robust. One QSAR model with best Rcalibration2 = 0.8638 for split 2 was considered as the leading model. A greater value of cRp<sup>2</sup> <i>i.e.</i> 0.5 for all models in Y-randomization test showed the robustness of developed models. The outliers and promoters of increase and decrease of endpoint were also extracted independently from the leading models. The mechanistic interpretation of developed models explains the role of different structural attributes in predicting the pIC<sub>50</sub> of pyrazole sulfonamides extracted from the crystal structure of Leishmania major N-myristoyltransferase (NMT) along with co-crystallized myristoyl-CoA and ligands NMT106, NMT157, NMT187 and NMT236 (PDB ID: 4A2Z, 4A30, 4A32, 2WSA). Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.12844981
title: Construction of high-density bin map and QTL mapping of horticultural traits from an interspecific cross between <i>Capsicum annuum</i> and Chinese wild <i>Capsicum frutescens</i>

description: Chinese wild pepper (<i>Capsicum frutescens</i> L.) acts as a source of genetic variability for cultivated pepper breeding. High-resolution quantitative train locus (QTL) mapping is essential for identifying genetic regions related to important phenotype variation. In this study, a set of 120 F<sub>2</sub> populations derived from a cross between cultivar <i>Capsicum annuum</i> ‘007EA’ and the wild relative <i>Capsicum frutescens</i> ‘P1512’ (Chinese wild pepper) were generated, and genotyping was performed with genotyping-by-sequencing. Next, an interspecific high-density genetic map containing 3708 bins was constructed using a sliding window approach. The genetic distance of the total map was 5601.79 cM, and the average interval between bins was 1.51 cM. Based on the genetic map, a QTL analysis of the pepper horticultural traits was performed. A total of 25 significant QTLs controlling nine horticultural traits were detected on 12 linkage groups (LGs), and contributed values of phenotypic variance explained (PVE) ranging from 1.90% to 59.03%, with LOD scores ranging from 4.2 to 24.6. In addition, the QTLs for the main stem length, flowering date and numbers of leaves were observed at the same position. Next, we mapped a set of significant QTLs for yield-related traits and other horticultural traits in pepper, based on a high-density genetic linkage map, using GBS. These genetic map and markers are valuable genomic resources for marker-assisted selection (MAS) of excellent agronomic traits and will provide a basis for further fine mapping and comparative genomics research involving pepper.
DOI: 10.6084/m9.figshare.12844981.v1
title: Construction of high-density bin map and QTL mapping of horticultural traits from an interspecific cross between <i>Capsicum annuum</i> and Chinese wild <i>Capsicum frutescens</i>

description: Chinese wild pepper (<i>Capsicum frutescens</i> L.) acts as a source of genetic variability for cultivated pepper breeding. High-resolution quantitative train locus (QTL) mapping is essential for identifying genetic regions related to important phenotype variation. In this study, a set of 120 F<sub>2</sub> populations derived from a cross between cultivar <i>Capsicum annuum</i> ‘007EA’ and the wild relative <i>Capsicum frutescens</i> ‘P1512’ (Chinese wild pepper) were generated, and genotyping was performed with genotyping-by-sequencing. Next, an interspecific high-density genetic map containing 3708 bins was constructed using a sliding window approach. The genetic distance of the total map was 5601.79 cM, and the average interval between bins was 1.51 cM. Based on the genetic map, a QTL analysis of the pepper horticultural traits was performed. A total of 25 significant QTLs controlling nine horticultural traits were detected on 12 linkage groups (LGs), and contributed values of phenotypic variance explained (PVE) ranging from 1.90% to 59.03%, with LOD scores ranging from 4.2 to 24.6. In addition, the QTLs for the main stem length, flowering date and numbers of leaves were observed at the same position. Next, we mapped a set of significant QTLs for yield-related traits and other horticultural traits in pepper, based on a high-density genetic linkage map, using GBS. These genetic map and markers are valuable genomic resources for marker-assisted selection (MAS) of excellent agronomic traits and will provide a basis for further fine mapping and comparative genomics research involving pepper.
DOI: 10.6084/m9.figshare.17039302
title: MiR-204 suppresses the progression of acute myeloid leukemia through HGF/c-Met pathway

description: Acute myeloid leukemia (AML) was confirmed to be associated with hematopoietic insufficiency, as well as abnormal proliferation, diﬀerentiation or survival of myeloid progenitors. Multiple studies reported that microRNA-204 (miR-204) and Hepatocyte growth factor (HGF) played important roles in types of cancers. However, the potential molecular regulatory mechanism between miR-204 and HGF in AML remains to be further defined. Real-time PCR (RT-PCR) was adopted to detect the expression of miR-204 and HG. Relative protein levels were detected by western blot assay. The viability, cell cycle, apoptosis, migration, and invasion were analyzed by MTT, flow cytometry, and transwell assays. Moreover, the target relationship between miR-204 and HGF was predicted by MiRcode website and confirmed by luciferase reporter, RNA pull-down, and western blot assays. Our data suggested that miR-204 was downregulated in AML serum samples and cells. MiR-204 overexpression repressed cell proliferation, migration, invasion, and induced cell apoptosis in AML cells. HGF was upregulated in AML samples and cells, and HGF knockdown inhibited the malignancy of AML cells. In addition, HGF was directly targeted by miR-204. HGF overexpression reversed the effects of miR-204 mimic on AML cell proliferation, apoptosis, migration, and invasion. Besides, miR-204 regulated the c-Met signaling by targeting HGF, thereby regulating the downstream protein levels related to cell proliferation, apoptosis, migration, and invasion in AML cells. In conclusion, miR-204 could regulate AML progression through regulating the HGF/c-Met pathway.
DOI: 10.6084/m9.figshare.17039302.v1
title: MiR-204 suppresses the progression of acute myeloid leukemia through HGF/c-Met pathway

description: Acute myeloid leukemia (AML) was confirmed to be associated with hematopoietic insufficiency, as well as abnormal proliferation, diﬀerentiation or survival of myeloid progenitors. Multiple studies reported that microRNA-204 (miR-204) and Hepatocyte growth factor (HGF) played important roles in types of cancers. However, the potential molecular regulatory mechanism between miR-204 and HGF in AML remains to be further defined. Real-time PCR (RT-PCR) was adopted to detect the expression of miR-204 and HG. Relative protein levels were detected by western blot assay. The viability, cell cycle, apoptosis, migration, and invasion were analyzed by MTT, flow cytometry, and transwell assays. Moreover, the target relationship between miR-204 and HGF was predicted by MiRcode website and confirmed by luciferase reporter, RNA pull-down, and western blot assays. Our data suggested that miR-204 was downregulated in AML serum samples and cells. MiR-204 overexpression repressed cell proliferation, migration, invasion, and induced cell apoptosis in AML cells. HGF was upregulated in AML samples and cells, and HGF knockdown inhibited the malignancy of AML cells. In addition, HGF was directly targeted by miR-204. HGF overexpression reversed the effects of miR-204 mimic on AML cell proliferation, apoptosis, migration, and invasion. Besides, miR-204 regulated the c-Met signaling by targeting HGF, thereby regulating the downstream protein levels related to cell proliferation, apoptosis, migration, and invasion in AML cells. In conclusion, miR-204 could regulate AML progression through regulating the HGF/c-Met pathway.
DOI: 10.6084/m9.figshare.12845126
title: Facile fabrication of versatile superhydrophobic coating for efficient oil/water separation

description: Nowadays, finding an efficient way to treatment oil spill and oily wastewater emission has attracted much attention all over the world. In this work, we fabricated a superhydrophobic coating (humic acid grafted by octadecylamine) with a simple method, and sprayed this coating on different structures which apply for self-cleaning, collect oil, and filter oil/water mixtures. In addition, silane-modified polymer sealant was used to strengthen the adhesive attraction between coating and structures. The coated mesh exhibited excellent superhydrophobicity (water contact angle of 153.14°) and superolephilicity (oil contact angle near 0°). Moreover, the coated mesh displayed outstanding performance in oil/water separation with huge oil flux about 16633.9 L h<sup>−1</sup> m<sup>−2</sup>, high separating efficiency more than 95%, and good reusability (more than 10 cycles). Furthermore, the pore size of the coated mesh could regulate by changing the cycle of coated process, and the micro pore size of mesh could realize water-in-oil emulsions separation. To sum up, these merits of the superhydrophobic humic acid grafted by octadecylamine coating displayed great potential for effective oil/water separation.
DOI: 10.6084/m9.figshare.9699401
title: Radiation dose and pathological response in oesophageal cancer patients treated with neoadjuvant chemoradiotherapy followed by surgery: a multi-institutional analysis

description: <b>Purpose:</b> To explore whether a higher neoadjuvant radiation dose increases the probability of a pathological complete response (pCR) or pathological major response (pMR) response in oesophageal cancer patients. <b>Material and methods:</b> Between 2000 and 2017, 1048 patients from four institutions were stratified according to prescribed neoadjuvant radiation doses of 36.0 Gy (13.3%), 40.0 Gy (7.4%), 41.4 Gy (20.1%), 45.0 Gy (25.5%) or 50.4 Gy (33.7%) in 1.8–2.0 Gy fractions. Endpoints were pCR (tumour regression grade (TRG) 1) and pMR (TRG 1 + 2). Multivariable binary (TRG 1 + 2 vs. TRG &gt; 2) and ordinal (TRG 1 vs. TRG 2 vs. TRG &gt; 2) logistic regression analyses were performed, with subgroup analyses according to histology (squamous cell carcinoma (SCC) vs. adenocarcinoma (AC)). Variables entered in the regression model along with neoadjuvant radiation dose were clinical tumour stage (cT), histology, chemotherapy regimen, induction chemotherapy and time from neoadjuvant chemoradiation to surgery. <b>Results:</b> A pCR was observed in 312 patients (29.8%); in 22.7% patients with AC and in 49.6% patients with SCC. No radiation dose–response relation was observed for pCR (OR = 1.01, 95% CI: 0.98–1.05 for AC and OR = 1.03, 95% CI: 0.96–1.10 for SCC). A pMR was observed in 597 patients (57.0%); in 53.4% patients with AC and in 67.2% patients with SCC. A higher radiation dose increased the probability of achieving pMR (OR = 1.04, 95% CI: 1.02–1.05). Factors reducing this probability were advanced cT stage (reference = cT1–2; cT3: OR = 0.54, 95% CI: 0.37–0.80; cT4: OR = 0.45, 95% CI: 0.24–0.84), AC histology (reference = SCC; OR = 0.62, 95% CI: 0.44–0.88), the use of non-platinum based chemotherapy in SCC patients (OR = 0.30, 95% CI: 0.10–0.91) and platinum based chemotherapy without induction chemotherapy in patients with AC (OR = 0.56, 95% CI: 0.42–0.76). The radiation dose–response relation was confirmed in a subgroup analysis of histologic subtypes (OR = 1.02, 95% CI: 1.01–1.04 for AC and OR = 1.05, 95% CI: 1.02–1.08 for SCC). <b>Conclusions:</b> Neoadjuvant radiation dose impacts pathological response in terms of pMR in oesophageal cancer patients. No radiation dose–response effect was observed for pCR. Further prospective trials are needed to investigate the dose–response relation in terms of pCR
DOI: 10.6084/m9.figshare.12845126.v1
title: Facile fabrication of versatile superhydrophobic coating for efficient oil/water separation

description: Nowadays, finding an efficient way to treatment oil spill and oily wastewater emission has attracted much attention all over the world. In this work, we fabricated a superhydrophobic coating (humic acid grafted by octadecylamine) with a simple method, and sprayed this coating on different structures which apply for self-cleaning, collect oil, and filter oil/water mixtures. In addition, silane-modified polymer sealant was used to strengthen the adhesive attraction between coating and structures. The coated mesh exhibited excellent superhydrophobicity (water contact angle of 153.14°) and superolephilicity (oil contact angle near 0°). Moreover, the coated mesh displayed outstanding performance in oil/water separation with huge oil flux about 16633.9 L h<sup>−1</sup> m<sup>−2</sup>, high separating efficiency more than 95%, and good reusability (more than 10 cycles). Furthermore, the pore size of the coated mesh could regulate by changing the cycle of coated process, and the micro pore size of mesh could realize water-in-oil emulsions separation. To sum up, these merits of the superhydrophobic humic acid grafted by octadecylamine coating displayed great potential for effective oil/water separation.
DOI: 10.6084/m9.figshare.9699401.v1
title: Radiation dose and pathological response in oesophageal cancer patients treated with neoadjuvant chemoradiotherapy followed by surgery: a multi-institutional analysis

description: <b>Purpose:</b> To explore whether a higher neoadjuvant radiation dose increases the probability of a pathological complete response (pCR) or pathological major response (pMR) response in oesophageal cancer patients. <b>Material and methods:</b> Between 2000 and 2017, 1048 patients from four institutions were stratified according to prescribed neoadjuvant radiation doses of 36.0 Gy (13.3%), 40.0 Gy (7.4%), 41.4 Gy (20.1%), 45.0 Gy (25.5%) or 50.4 Gy (33.7%) in 1.8–2.0 Gy fractions. Endpoints were pCR (tumour regression grade (TRG) 1) and pMR (TRG 1 + 2). Multivariable binary (TRG 1 + 2 vs. TRG &gt; 2) and ordinal (TRG 1 vs. TRG 2 vs. TRG &gt; 2) logistic regression analyses were performed, with subgroup analyses according to histology (squamous cell carcinoma (SCC) vs. adenocarcinoma (AC)). Variables entered in the regression model along with neoadjuvant radiation dose were clinical tumour stage (cT), histology, chemotherapy regimen, induction chemotherapy and time from neoadjuvant chemoradiation to surgery. <b>Results:</b> A pCR was observed in 312 patients (29.8%); in 22.7% patients with AC and in 49.6% patients with SCC. No radiation dose–response relation was observed for pCR (OR = 1.01, 95% CI: 0.98–1.05 for AC and OR = 1.03, 95% CI: 0.96–1.10 for SCC). A pMR was observed in 597 patients (57.0%); in 53.4% patients with AC and in 67.2% patients with SCC. A higher radiation dose increased the probability of achieving pMR (OR = 1.04, 95% CI: 1.02–1.05). Factors reducing this probability were advanced cT stage (reference = cT1–2; cT3: OR = 0.54, 95% CI: 0.37–0.80; cT4: OR = 0.45, 95% CI: 0.24–0.84), AC histology (reference = SCC; OR = 0.62, 95% CI: 0.44–0.88), the use of non-platinum based chemotherapy in SCC patients (OR = 0.30, 95% CI: 0.10–0.91) and platinum based chemotherapy without induction chemotherapy in patients with AC (OR = 0.56, 95% CI: 0.42–0.76). The radiation dose–response relation was confirmed in a subgroup analysis of histologic subtypes (OR = 1.02, 95% CI: 1.01–1.04 for AC and OR = 1.05, 95% CI: 1.02–1.08 for SCC). <b>Conclusions:</b> Neoadjuvant radiation dose impacts pathological response in terms of pMR in oesophageal cancer patients. No radiation dose–response effect was observed for pCR. Further prospective trials are needed to investigate the dose–response relation in terms of pCR