cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25392/leicester.data.8796335
title: Response dataset from Rey et al, Nat Comm, 2018

description: File 'Reyetal_NatComm_dataset.mat' is a Matlab file with the response dataset associated to the paper: <br>Rey et al, "Encoding of long-term associations through neural unitization in the human medial temporal lobe", Nat Commun. 2018 Oct 22;9(1):4372. doi: 10.1038/s41467-018-06870-2.<br>There are 3 variables common to all the responses:<br>time_pre_stim = 1; number of seconds from stimulus onset that were epoched on each trial. Same value for LFP and spikestime_pos_stim = 2; number of seconds after stimulus onset that were epoched on each trial. Same value for LFP and spikestime_LFP_extra = 0.5; number of additional seconds on each LFP trial at the beginning and end of the epoched LFP. This is to avoid border effects when the LFP is further filtered<br>The structure 'resp' has all the responses, with the following fields:<br>1) sessionID. The session number in which the response was found. From 1 to 21.2) stimulus_name. The name of the jpg file that was presented as a stimulus3) recording_site. Area where the electrode was implanted. RAH = right anterior hippocampus, LAH = left anterior hippocampus, RAM = right amygdala, LAM = left amygdala, RPH = right posterior hippocampus, LPH = left posterior hippocampus. 4) channel_number. Channel number in the recording setup.5) cluster_number. Cluster number following spike sorting. Each cluster is associated to a different putative single neuron.6) LFP_sr. Sampling rate for the LFP signal7) original_sr. Original sampling rate used in the acquisition system8) LFP. Matrix where each row is associated to a trial and columns are samples. The samples on each trial are structured as: [ceil((time_LFP_extra+time_pre_stim)*LFP_sr),ceil((time_pos_stim+time_LFP_extra)*LFP_sr)]. 9) spike_stimes. Cell array where each row contains a vector with the spike times associated to the occurrence of each spike, measured in msec for stimulus onset.
DOI: 10.5281/zenodo.10694740
title: Function to correct cosmic rays and Raman images

description: A function to clean cosmic rays in Raman images and datasets used during the development. 

Raman images obtained from pre formulation samples and lyophilized nanostructured lipid carriers.
DOI: 10.5281/zenodo.10694741
title: Function to correct cosmic rays and Raman images

description: A function to clean cosmic rays in Raman images and datasets used during the development. 

Raman images obtained from pre formulation samples and lyophilized nanostructured lipid carriers.
DOI: 10.25392/leicester.data.8796335.v1
title: Response dataset from Rey et al, Nat Comm, 2018

description: File 'Reyetal_NatComm_dataset.mat' is a Matlab file with the response dataset associated to the paper: <br>Rey et al, "Encoding of long-term associations through neural unitization in the human medial temporal lobe", Nat Commun. 2018 Oct 22;9(1):4372. doi: 10.1038/s41467-018-06870-2.<br>There are 3 variables common to all the responses:<br>time_pre_stim = 1; number of seconds from stimulus onset that were epoched on each trial. Same value for LFP and spikestime_pos_stim = 2; number of seconds after stimulus onset that were epoched on each trial. Same value for LFP and spikestime_LFP_extra = 0.5; number of additional seconds on each LFP trial at the beginning and end of the epoched LFP. This is to avoid border effects when the LFP is further filtered<br>The structure 'resp' has all the responses, with the following fields:<br>1) sessionID. The session number in which the response was found. From 1 to 21.2) stimulus_name. The name of the jpg file that was presented as a stimulus3) recording_site. Area where the electrode was implanted. RAH = right anterior hippocampus, LAH = left anterior hippocampus, RAM = right amygdala, LAM = left amygdala, RPH = right posterior hippocampus, LPH = left posterior hippocampus. 4) channel_number. Channel number in the recording setup.5) cluster_number. Cluster number following spike sorting. Each cluster is associated to a different putative single neuron.6) LFP_sr. Sampling rate for the LFP signal7) original_sr. Original sampling rate used in the acquisition system8) LFP. Matrix where each row is associated to a trial and columns are samples. The samples on each trial are structured as: [ceil((time_LFP_extra+time_pre_stim)*LFP_sr),ceil((time_pos_stim+time_LFP_extra)*LFP_sr)]. 9) spike_stimes. Cell array where each row contains a vector with the spike times associated to the occurrence of each spike, measured in msec for stimulus onset.
DOI: 10.6084/m9.figshare.21379060.v1
title: Thymosin β4, a potential marker of malignancy and prognosis in hepatocellular carcinoma

description: The lack of effective early diagnostic markers is an obstacle in clinical diagnosis and treatment of hepatocellular carcinoma (HCC). Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is an increasing popular approach for identification of clinically relevant parameters including biomarkers. 540 subjects, including 274 HCC, 119 liver cirrhosis, 89 hepatitis, and 58 healthy volunteers were enrolled. MALDI-TOF MS was used to select potential novel biomarkers from serum of HCC patients. Its clinical application was evaluated by experiments and clinical data analysis. We identified Thymosin β4 (Tβ4) in serum by MALDI-TOF MS. The expression of Tβ4 was detected up-regulating in HCC cells and tissues which enhanced motility of HCC cells. More important, the level of serum Tβ4 was significantly elevated in HCC patients. The AUROC showed the optimum diagnostic cut-off was 1063.6 ng/mL, ROC and 95% CI of Tβ4 (0.908; 0.880–0.935) were larger than that of serum AFP (0.712; 0.662–0.762; <i>p</i> &lt; 0.001). The sensitivity (91.3% vs 83.1%) and specificity (81.2% vs 20.3%) of serum Tβ4 were higher than alpha-fetoprotein (AFP). In AFP-negative HCC, the sensitivity could reach to 80.5%. ROC analysis showed serum Tβ4 had a better performance compared with AFP in distinguishing early-stage and small HCC. Tβ4 is correlated with TNM stage (<i>p</i> = 0.016) and vascular invasion (<i>p</i> = 0.005). Survival analysis indicated the survival time of Tβ4 positive patients was shorter (<i>p</i> <b>&lt;</b> 0.001). Cox analysis suggested Tβ4 could be an independent factor for HCC prognosis. Tβ4 may serve as a novel biomarker for HCC diagnosis and prognosis.
DOI: 10.6084/m9.figshare.8796140
title: Epigenome-wide association study of DNA methylation and microRNA expression highlights novel pathways for human complex traits

description: DNA methylation (DNAm) and microRNAs (miRNAs) have been implicated in a wide-range of human diseases. While often studied in isolation, DNAm and miRNAs are not independent. We analyzed associations of expression of 283 miRNAs with DNAm at &gt;400K CpG sites in whole blood obtained from 3565 individuals and identified 227 CpGs at which differential methylation was associated with the expression of 40 nearby miRNAs (<i>cis</i>-miR-eQTMs) at FDR&lt;0.01, including 91 independent CpG sites at <i>r<sup>2</sup></i> &lt; 0.2. <i>cis-</i>miR-eQTMs were enriched for CpGs in promoter and polycomb-repressed state regions, and 60% were inversely associated with miRNA expression. Bidirectional Mendelian randomization (MR) analysis further identified 58 <i>cis</i>-miR-eQTMCpG-miRNA pairs where DNAm changes appeared to drive miRNA expression changes and opposite directional effects were unlikely. Integration of genetic variants in joint analyses revealed an average partial between <i>cis-</i>miR-eQTM CpGs and miRNAs of 2% after conditioning on site-specific genetic variation, suggesting that DNAm is an important epigenetic regulator of miRNA expression. Finally, two-step MR analysis was performed to identify putatively causal CpGs driving miRNA expression in relation to human complex traits. We found that an imprinted region on 14q32 that was previously identified in relation to age at menarche is enriched with <i>cis-</i>miR-eQTMs. Nine CpGs and three miRNAs at this locus tested causal for age at menarche, reflecting novel epigenetic-driven molecular pathways underlying this complex trait. Our study sheds light on the joint genetic and epigenetic regulation of miRNA expression and provides insights into the relations of miRNAs to their targets and to complex phenotypes.
DOI: 10.6084/m9.figshare.15087376.v1
title: Additional file 3 of Cancer-associated fibroblast infiltration in gastric cancer: the discrepancy in subtypes pathways and immunosuppression

description: Additional file 3: GSEA results in GSE62254 cohort.
DOI: 10.6084/m9.figshare.25273183
title: Tabla 2. Diseños de investigación e instrumentos para medir efectos

description: El objetivo de este artículo fue sistematizar los diseños, tipos de resultados y características de las intervenciones a la violencia digital que existen a nivel internacional en contextos escolares, con la finalidad de realizar una comparación meta analítica que permita recuperar las mejores prácticas, por lo que en esta Tabla se describen las características de los diseños de investigación e instrumentos para medir efectos de 25 estudios que evaluaron programas de intervención a la ciberviolencia.
DOI: 10.6084/m9.figshare.25273183.v1
title: Tabla 2. Diseños de investigación e instrumentos para medir efectos

description: El objetivo de este artículo fue sistematizar los diseños, tipos de resultados y características de las intervenciones a la violencia digital que existen a nivel internacional en contextos escolares, con la finalidad de realizar una comparación meta analítica que permita recuperar las mejores prácticas, por lo que en esta Tabla se describen las características de los diseños de investigación e instrumentos para medir efectos de 25 estudios que evaluaron programas de intervención a la ciberviolencia.
DOI: 10.6084/m9.figshare.15087882
title: A high-speed railway network dataset from train operation records and weather data

description: High-speed train operation data are reliable and rich resources in data-driven research. However, the data released by railway companies are poorly organized and not comprehensive enough to be applied directly and effectively. A high-speed railway network dataset suitable for research is still lacking. To support the research in large-scale complex network, complex dynamic system and intelligent transportation, we develop a high-speed railway network dataset, containing the train operation data in different directions from October 8, 2019 to January 27, 2020, the train delay data of the railway stations, the junction stations data, and the mileage data of adjacent stations. In the dataset, weather, temperature, wind power and major holidays are considered as factors affecting train operation. Potential research values of the dataset include but are not limited to complex dynamic system pattern mining, community detection and discovery, and train delay analysis. Besides, the dataset can be used to solve various railway operation and management problems, such as passenger service network improvement, train real-time dispatching and intelligent driving assistance.
DOI: 10.6084/m9.figshare.9320966
title: δ<sup>13</sup>C and fatty acid composition of mesopelagic fishes in the South China Sea and their influence factors

description: Study of the ecology of mesopelagic fishes is central for assessing the active biological pump in the ocean, especially in the mesopelagic layers. The use of δ<sup>13</sup>C and fatty acid analysis can help to analysis the ecology of mesopelagic fishes. Here, we analysed the fatty acid composition of mesopelagic fishes from the continental northern slope of the South China Sea (NSSCS) and compared with nearshore SCS fishes and mesopelagic fishes collected from the Southern Ocean. The mesopelagic fishes had unusually high lipids, which resulted in Δδ<sup>13</sup>C values exceeding 1‰, more than the enrichment factor in the food web. The mesopelagic fishes had higher C18:1n-9/C18:1n-7 and C20:1n-9/ C18:1n-7 ratios compared with other fishes in the SCS, which confirmed that plankton were their main dietary source. The mesopelagic fishes from SCS and Southern Ocean had different ratios of C20:5n-3/C22:6n-3 (EPA/DHA), suggesting geographical locations and diet sources had obvious influence on their fatty acid composition. The SCS mesopelagic fishes had higher C20:4n-6/C22:6n-3 (ARA/DHA) and C20:4n-6/C20:5n-3 (ARA/EPA) ratios than mesopelagic fishes in the Southern Ocean, indicating the influence of physical factors on fatty acid composition. Thus, future studies of the fatty acids in mesopelagic fishes should consider both dietary sources and physical environments.
DOI: 10.6084/m9.figshare.9320966.v1
title: δ<sup>13</sup>C and fatty acid composition of mesopelagic fishes in the South China Sea and their influence factors

description: Study of the ecology of mesopelagic fishes is central for assessing the active biological pump in the ocean, especially in the mesopelagic layers. The use of δ<sup>13</sup>C and fatty acid analysis can help to analysis the ecology of mesopelagic fishes. Here, we analysed the fatty acid composition of mesopelagic fishes from the continental northern slope of the South China Sea (NSSCS) and compared with nearshore SCS fishes and mesopelagic fishes collected from the Southern Ocean. The mesopelagic fishes had unusually high lipids, which resulted in Δδ<sup>13</sup>C values exceeding 1‰, more than the enrichment factor in the food web. The mesopelagic fishes had higher C18:1n-9/C18:1n-7 and C20:1n-9/ C18:1n-7 ratios compared with other fishes in the SCS, which confirmed that plankton were their main dietary source. The mesopelagic fishes from SCS and Southern Ocean had different ratios of C20:5n-3/C22:6n-3 (EPA/DHA), suggesting geographical locations and diet sources had obvious influence on their fatty acid composition. The SCS mesopelagic fishes had higher C20:4n-6/C22:6n-3 (ARA/DHA) and C20:4n-6/C20:5n-3 (ARA/EPA) ratios than mesopelagic fishes in the Southern Ocean, indicating the influence of physical factors on fatty acid composition. Thus, future studies of the fatty acids in mesopelagic fishes should consider both dietary sources and physical environments.
DOI: 10.6084/m9.figshare.21379060
title: Thymosin β4, a potential marker of malignancy and prognosis in hepatocellular carcinoma

description: The lack of effective early diagnostic markers is an obstacle in clinical diagnosis and treatment of hepatocellular carcinoma (HCC). Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is an increasing popular approach for identification of clinically relevant parameters including biomarkers. 540 subjects, including 274 HCC, 119 liver cirrhosis, 89 hepatitis, and 58 healthy volunteers were enrolled. MALDI-TOF MS was used to select potential novel biomarkers from serum of HCC patients. Its clinical application was evaluated by experiments and clinical data analysis. We identified Thymosin β4 (Tβ4) in serum by MALDI-TOF MS. The expression of Tβ4 was detected up-regulating in HCC cells and tissues which enhanced motility of HCC cells. More important, the level of serum Tβ4 was significantly elevated in HCC patients. The AUROC showed the optimum diagnostic cut-off was 1063.6 ng/mL, ROC and 95% CI of Tβ4 (0.908; 0.880–0.935) were larger than that of serum AFP (0.712; 0.662–0.762; <i>p</i> &lt; 0.001). The sensitivity (91.3% vs 83.1%) and specificity (81.2% vs 20.3%) of serum Tβ4 were higher than alpha-fetoprotein (AFP). In AFP-negative HCC, the sensitivity could reach to 80.5%. ROC analysis showed serum Tβ4 had a better performance compared with AFP in distinguishing early-stage and small HCC. Tβ4 is correlated with TNM stage (<i>p</i> = 0.016) and vascular invasion (<i>p</i> = 0.005). Survival analysis indicated the survival time of Tβ4 positive patients was shorter (<i>p</i> <b>&lt;</b> 0.001). Cox analysis suggested Tβ4 could be an independent factor for HCC prognosis. Tβ4 may serve as a novel biomarker for HCC diagnosis and prognosis.
DOI: 10.6084/m9.figshare.8796140.v1
title: Epigenome-wide association study of DNA methylation and microRNA expression highlights novel pathways for human complex traits

description: DNA methylation (DNAm) and microRNAs (miRNAs) have been implicated in a wide-range of human diseases. While often studied in isolation, DNAm and miRNAs are not independent. We analyzed associations of expression of 283 miRNAs with DNAm at &gt;400K CpG sites in whole blood obtained from 3565 individuals and identified 227 CpGs at which differential methylation was associated with the expression of 40 nearby miRNAs (<i>cis</i>-miR-eQTMs) at FDR&lt;0.01, including 91 independent CpG sites at <i>r<sup>2</sup></i> &lt; 0.2. <i>cis-</i>miR-eQTMs were enriched for CpGs in promoter and polycomb-repressed state regions, and 60% were inversely associated with miRNA expression. Bidirectional Mendelian randomization (MR) analysis further identified 58 <i>cis</i>-miR-eQTMCpG-miRNA pairs where DNAm changes appeared to drive miRNA expression changes and opposite directional effects were unlikely. Integration of genetic variants in joint analyses revealed an average partial between <i>cis-</i>miR-eQTM CpGs and miRNAs of 2% after conditioning on site-specific genetic variation, suggesting that DNAm is an important epigenetic regulator of miRNA expression. Finally, two-step MR analysis was performed to identify putatively causal CpGs driving miRNA expression in relation to human complex traits. We found that an imprinted region on 14q32 that was previously identified in relation to age at menarche is enriched with <i>cis-</i>miR-eQTMs. Nine CpGs and three miRNAs at this locus tested causal for age at menarche, reflecting novel epigenetic-driven molecular pathways underlying this complex trait. Our study sheds light on the joint genetic and epigenetic regulation of miRNA expression and provides insights into the relations of miRNAs to their targets and to complex phenotypes.
DOI: 10.6084/m9.figshare.20330560
title: Development of ammonium nitrate free nutrient media for aluminium toxicity tolerance screening of rice genotypes from North-Eastern India

description: North-Eastern India is blessed with a vast diversity of rice genotypes with varying yielding abilities. However, the predominant strong soil acidity induced nutrient stresses from the toxicity of aluminum (Al<sup>3+</sup>) ions often causes sub-optimal rice productivity. The lack of suitable nutrient media for the screening of aluminum (Al) toxicity tolerance of rice genotypes is one of the limiting factors in Al tolerant varieties' development. Modified Magnavaca's solution has been the most recommended nutrient solution for this purpose where ammonium nitrate is the primary nitrogen source. However, strict regulations related to the handling and storage of ammonium nitrate in India limit the preparation of Modified Magnavaca’s solution for laboratory use. Here, a modified ammonium nitrate-free formulation based upon the Magnavaca's solution has been proposed. The modified formulation was found to have 160.9 µM of active Al<sup>3+</sup> concentration when 550 µM of aluminum chloride hexahydrate (AlCl<sub>3</sub>.6H<sub>2</sub>O) was added at pH 4.1 to the solution. Through a plant growth screening experiment using ten diverse rice genotypes a significant difference in the response of various genotypes to differential Al toxicity levels on root growth performance indicators was observed. Based on the response, we could able to categorize the genotypes into tolerant and sensitive in relative terms. Thus, the present experiment provided an important nutrient formulation suitable for screening rice genotypes under Al toxicity conditions. Moreover, the selected tolerant and sensitive genotypes can further pave the way for studying the molecular mechanism of Al toxicity response in rice and their use in the breeding program.
DOI: 10.6084/m9.figshare.20330560.v1
title: Development of ammonium nitrate free nutrient media for aluminium toxicity tolerance screening of rice genotypes from North-Eastern India

description: North-Eastern India is blessed with a vast diversity of rice genotypes with varying yielding abilities. However, the predominant strong soil acidity induced nutrient stresses from the toxicity of aluminum (Al<sup>3+</sup>) ions often causes sub-optimal rice productivity. The lack of suitable nutrient media for the screening of aluminum (Al) toxicity tolerance of rice genotypes is one of the limiting factors in Al tolerant varieties' development. Modified Magnavaca's solution has been the most recommended nutrient solution for this purpose where ammonium nitrate is the primary nitrogen source. However, strict regulations related to the handling and storage of ammonium nitrate in India limit the preparation of Modified Magnavaca’s solution for laboratory use. Here, a modified ammonium nitrate-free formulation based upon the Magnavaca's solution has been proposed. The modified formulation was found to have 160.9 µM of active Al<sup>3+</sup> concentration when 550 µM of aluminum chloride hexahydrate (AlCl<sub>3</sub>.6H<sub>2</sub>O) was added at pH 4.1 to the solution. Through a plant growth screening experiment using ten diverse rice genotypes a significant difference in the response of various genotypes to differential Al toxicity levels on root growth performance indicators was observed. Based on the response, we could able to categorize the genotypes into tolerant and sensitive in relative terms. Thus, the present experiment provided an important nutrient formulation suitable for screening rice genotypes under Al toxicity conditions. Moreover, the selected tolerant and sensitive genotypes can further pave the way for studying the molecular mechanism of Al toxicity response in rice and their use in the breeding program.
DOI: 10.6084/m9.figshare.4601950.v1
title: Phylogenetic analysis among 27 Chinese populations and genetic polymorphisms of 20 autosomal STR loci in a Chinese Uyghur ethnic minority group

description: Allele frequency data and forensic statistical parameters were determined for 20 autosomal short tandem repeat (STR) loci of the PowerPlex 21 System in 214 unrelated healthy individuals of a Uyghur ethnic minority group living in Xinjiang province, northwest China. A total of 232 alleles were observed with the corresponding allele frequencies ranging from 0.0023 to 0.5304. All loci were consistent with Hardy–Weinberg equilibrium (HWE) after the Bonferroni correction (<i>p</i> &gt; 0.0025). The combined probability of exclusion, power of discrimination, probability of matching value were 0.999999999, 0.9999999999999999999999995, and 4.78246 × 10<sup>−25</sup>, respectively. Our results revealed that the 20 STRs were highly polymorphic and informative, and could be suitable for forensic application, especially parentage test and personal identification. The further population comparison between the Uyghur and other 26 reference populations revealed that the loci of D13S317, TH01 and D6S1043 showed high ethnical specificity. Phylogenetic analysis based on 19 shared loci demonstrated that the Uyghur had a close genetic relationship with the Kazakh, but a distinct genetic distance with other Chinese populations from different ethnicity and regions.