cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24962493
title: State-of-the-art in managing reliability in mega railway projects. A systematic literature review

description: Mega Railway Projects (MRPs) are expensive and account for an increasing percentage of many a nation’s annual infrastructure expenditure. These MRPs frequently exceed their budget and schedule. The challenge of achieving reliability or availability targets stands out as a contributing factor to these overruns. A robust and targeted Reliability, Availability, and Maintainability (RAM) process, which covers systems and subsystems that comprise the railway, that is imbedded in the project from the outset and that is managed throughout the life cycle of the project, is crucial for success. However, a RAM process for MRPs is not readily available. While BS EN 50126-1<sup>1</sup> sets out the required RAM related tasks there is no guidance on how these tasks are to be undertaken or managed. This omission is likely to increase the challenge faced by RAM or Systems engineers as they put forth their case for ring-fenced funds and labour at the outset of an MRP. It is therefore important that RAM on an MRP is reviewed so that next steps in developing robust RAM process plan guidelines can be determined. The authors of this paper discuss why RAM is undertaken and the conceptualisation of RAM along with its fundamental features. Its application on railways focusing on RAM techniques and BS EN 50126-1 is outlined. A Systematic Literature Review (SLR) is undertaken to show the state-of-the-art by using a meta and content analysis within the context of railway systems, RAM techniques, RAM standards and Reliability levels. Furthermore, a set of Derived RAM requirements (DRR) based on BS EN 50126-1 are derived to determine the critical areas of RAM and are thus recommended for further development by researchers or RAM practitioners.
DOI: 10.6084/m9.figshare.24962493.v1
title: State-of-the-art in managing reliability in mega railway projects. A systematic literature review

description: Mega Railway Projects (MRPs) are expensive and account for an increasing percentage of many a nation’s annual infrastructure expenditure. These MRPs frequently exceed their budget and schedule. The challenge of achieving reliability or availability targets stands out as a contributing factor to these overruns. A robust and targeted Reliability, Availability, and Maintainability (RAM) process, which covers systems and subsystems that comprise the railway, that is imbedded in the project from the outset and that is managed throughout the life cycle of the project, is crucial for success. However, a RAM process for MRPs is not readily available. While BS EN 50126-1<sup>1</sup> sets out the required RAM related tasks there is no guidance on how these tasks are to be undertaken or managed. This omission is likely to increase the challenge faced by RAM or Systems engineers as they put forth their case for ring-fenced funds and labour at the outset of an MRP. It is therefore important that RAM on an MRP is reviewed so that next steps in developing robust RAM process plan guidelines can be determined. The authors of this paper discuss why RAM is undertaken and the conceptualisation of RAM along with its fundamental features. Its application on railways focusing on RAM techniques and BS EN 50126-1 is outlined. A Systematic Literature Review (SLR) is undertaken to show the state-of-the-art by using a meta and content analysis within the context of railway systems, RAM techniques, RAM standards and Reliability levels. Furthermore, a set of Derived RAM requirements (DRR) based on BS EN 50126-1 are derived to determine the critical areas of RAM and are thus recommended for further development by researchers or RAM practitioners.
DOI: 10.6084/m9.figshare.14692003.v1
title: Additional file 2 of Genetic alteration of Chinese patients with rectal mucosal melanoma

description: Additional file 2: Table S2. CNVs and SVs variants in 36 RMM.
DOI: 10.6084/m9.figshare.14692006
title: Additional file 3 of Genetic alteration of Chinese patients with rectal mucosal melanoma

description: Additional file 3: Table S3. Univariate analysis to identify OS-related clinicopathological features.
DOI: 10.6084/m9.figshare.13642139.v1
title: Additional file 1 of Environmental and genetic regulation of plant height in soybean

description: Additional file 1: Table S1. Putative QTLs detected for plant height traits by MapQTL 6.0 and QTL IciMaping 4.1 using 168 F9 soybean RILs under different environments.
DOI: 10.17179/excli2023-6621/supplementary_data
title: Immunoaffinity proteomics for kidney injury biomarkers in male beagle dogs

description: Drug-induced kidney injury (DIKI) is a cause of drug development failure. Dogs represent a common non-rodent animal model in pre-clinical safety studies; however, biomarker assays for detecting nephrotoxicity in dogs are limited. To identify novel proteins and gain insight into the molecular mechanisms involved in DIKI, we developed an assay to evaluate proteomic changes associated with DIKI in male beagle dogs that received nephrotoxic doses of tobramycin for 10 consecutive days. Label-free quantitative discovery proteomics analysis on representative kidney cortex tissues collected on Day 11 showed that the tobramycin-induced kidney injury led to a significant differential regulation of 94 proteins mostly associated with mechanisms of nephrotoxicity such as oxidative stress and proteasome degradation. For verification of the proteomic results, we developed a multiplex peptide-centric immunoaffinity liquid chromatography tandem mass spectrometry assay (IA LC-MS/MS) to evaluate the association of eight DIKI protein biomarker candidates using kidney cortices collected on Day 11 and urine samples collected on Days -4, 1, 3, 7 and 10. The results showed that most biomarkers evaluated were detected in the kidney cortices and their expression profile in tissue aligned with the label-free data. Cystatin C was the most consistent marker regardless of the magnitude of the renal injury while fatty acid-binding protein-4 (FABP4) and kidney injury molecule-1 (KIM-1) were the most affected biomarkers in response to moderate proximal tubular injury in absence of changes in serum-based concentrations of blood urea nitrogen or creatinine. In the urine, clusterin is considered the most consistent biomarker regardless of the magnitude and time of the renal injury. To our knowledge, this is the most comprehensive multiplex assay for the quantitative analysis of mechanism-based proximal tubular injury biomarkers in dogs.
description: EXCLI Journal; 23:Doc180; ISSN 1611-2156
DOI: 10.6084/m9.figshare.13340883.v1
title: The circ_0004463/miR-380-3p/FOXO1 axis modulates mitochondrial respiration and bladder cancer cell apoptosis

description: Bladder cancer is one of the most commonly diagnosed and fatal malignancies of the urinary tract. Noncoding RNAs have been reported to be new biomarkers and effective treatment targets for bladder cancer. In the present study, we identified a novel bladder cancer-related circRNA-miRNA-mRNA network, the circ_0004463/miR-380-3p/FOXO1 axis. circ_0004463 is significantly downregulated, whereas miR-380-3p is upregulated in bladder carcinoma tissue samples and cells. circ_0004463 acts as a tumor suppressor by inhibiting bladder cancer cell proliferation. Genes that negatively correlated with miR-380-3p and genes that miR-380-3p might target are enriched in mitochondrial respiration chain-related pathways. miR-380-3p promotes the proliferation of bladder cancer cells and mitochondrial respiration by acting as an oncogenic miRNA. circ_0004463 competes with FOXO1 for miR-380-3p binding to counteract miR-380-3p-mediated repression of FOXO1. Circ_0004463 overexpression inhibits cancer cell proliferation and mitochondrial respiration in bladder cancer cell lines, while miR-380-3p overexpression dramatically reverses the roles of circ_0004463 overexpression. In conclusion, the circ_0004463/miR-380-3p/FOXO1 axis could regulate mitochondrial respiration and bladder cancer cell apoptosis via FOXO1 signaling.
DOI: 10.6084/m9.figshare.19411094
title: MicroRNA-486-5p functions as a diagnostic marker for carotid artery stenosis and prevents endothelial dysfunction through inhibiting inflammation and oxidative stress

description: Carotid artery stenosis (CAS) can cause ischemic stroke, and clinical intervention for CAS is critical clinically. The purpose of this study was to explore the expression changes of microRNA-486-5p in the serum of patients with CAS and its possible mechanism. Ninety-one cases with asymptomatic CAS were recruited, and serum levels of miR-486-5p were measured using RT-qPCR. The diagnostic ability was evaluated by drawing the receiver operating characteristic (ROC) curve. Human aortic endothelial cells (HAECs) were treated with oxidized low-density lipoprotein (oxLDL) to establish cell model, and cell proliferation and apoptosis were tested. The markers of cell inflammation and oxidative stress were detected via ELISA. The target gene was analyzed using bioinformatics analysis combined with luciferase reporting assay. CAS cases exhibited significantly low serum miR-486-5p levels in comparison with the control group and can identify asymptomatic CAS. Serum miR-486-5p manifested a negative correlation with the degree of carotid stenosis. Underexpression of miR-486-5p was also detected in ox-LDL treated HAECs. OxLDL treatment contributes to inflammatory response and oxidative stress of HAECs; however, these adverse impacts caused by ox-LDL were reversed by miR-486-5p upregulation. NFAT5 was confirmed to be the target gene of miR-486-5p in HAECs. MiR-486-5p serves as a promising biomarker for the early identification of CAS. Overexpression of miR-486-5p can prevent endothelial dysfunction, and the mechanism might be related to anti-inflammation and anti-oxidation via targeting NFAT5.
DOI: 10.6084/m9.figshare.19411094.v1
title: MicroRNA-486-5p functions as a diagnostic marker for carotid artery stenosis and prevents endothelial dysfunction through inhibiting inflammation and oxidative stress

description: Carotid artery stenosis (CAS) can cause ischemic stroke, and clinical intervention for CAS is critical clinically. The purpose of this study was to explore the expression changes of microRNA-486-5p in the serum of patients with CAS and its possible mechanism. Ninety-one cases with asymptomatic CAS were recruited, and serum levels of miR-486-5p were measured using RT-qPCR. The diagnostic ability was evaluated by drawing the receiver operating characteristic (ROC) curve. Human aortic endothelial cells (HAECs) were treated with oxidized low-density lipoprotein (oxLDL) to establish cell model, and cell proliferation and apoptosis were tested. The markers of cell inflammation and oxidative stress were detected via ELISA. The target gene was analyzed using bioinformatics analysis combined with luciferase reporting assay. CAS cases exhibited significantly low serum miR-486-5p levels in comparison with the control group and can identify asymptomatic CAS. Serum miR-486-5p manifested a negative correlation with the degree of carotid stenosis. Underexpression of miR-486-5p was also detected in ox-LDL treated HAECs. OxLDL treatment contributes to inflammatory response and oxidative stress of HAECs; however, these adverse impacts caused by ox-LDL were reversed by miR-486-5p upregulation. NFAT5 was confirmed to be the target gene of miR-486-5p in HAECs. MiR-486-5p serves as a promising biomarker for the early identification of CAS. Overexpression of miR-486-5p can prevent endothelial dysfunction, and the mechanism might be related to anti-inflammation and anti-oxidation via targeting NFAT5.
DOI: 10.6084/m9.figshare.14168008
title: Additional file 10 of RNA sequencing reveals the expression profiles of circRNA and identifies a four-circRNA signature acts as a prognostic marker in esophageal squamous cell carcinoma

description: Additional file 10: Table S6: Differentially regulated circRNA analysis between ESCC versus normal.
DOI: 10.6084/m9.figshare.13642300.v1
title: Additional file 3 of Global transcriptome changes of elongating internode of sugarcane in response to mepiquat chloride

description: Additional file 3. Annotation results of isoforms from full-length transcriptome of sugarcane.
DOI: 10.6084/m9.figshare.14168014
title: Additional file 2 of RNA sequencing reveals the expression profiles of circRNA and identifies a four-circRNA signature acts as a prognostic marker in esophageal squamous cell carcinoma

description: Additional file 2: Table S2. The detail of circRNAs and GAPDH primers in this study.
DOI: 10.6084/m9.figshare.13642297.v1
title: Additional file 2 of Global transcriptome changes of elongating internode of sugarcane in response to mepiquat chloride

description: Additional file 2. Summary of full-length transcriptome of sugarcane.
DOI: 10.6084/m9.figshare.7352258
title: A mathematical analysis of improved EigenAnt algorithm

description: As a variant of Ant Colony Optimization, the EigenAnt algorithm finds the shortest path between a source node and a destination node based on negative feedback in the form of selective pheromone removal that occurs only on the path which is actually chosen for each trip. EigenAnt algorithm also could change quickly to reflect to the dynamic variety of initial pheromone concentrations and path length etc. However, in general, the solution of EigenAnt algorithm is not always convergent. In this paper, we propose an improved EigenAnt (iEigenAnt) algorithm in terms of both negative and positive feedback; that is, selective pheromone updates are decided by smart ants or stupid ones, which depends whether the amount of the pheromone at the selected path increases or not. The system modelled by our algorithm has a unique equilibrium as the shortest path. Besides, using mathematical analysis, we demonstrate that the equilibrium is global asymptotically stable, i.e., stable and convergent. Finally, we also implement the iEigenAnt algorithm under four different cases and apply it on travelling salesman problem problem, the simulation result shows that our iEigenAnt algorithm is faster convergent and more effective compared to the original EigenAnt algorithm, and some combinatorial optimisation problems can be effectively solved based on our iEigenAnt algorithm.
DOI: 10.6084/m9.figshare.14168029
title: Additional file 7 of RNA sequencing reveals the expression profiles of circRNA and identifies a four-circRNA signature acts as a prognostic marker in esophageal squamous cell carcinoma

description: Additional file 7: Table S4. The 511 signatures comprising different circRNAs in the training dataset (n = 73).
DOI: 10.6084/m9.figshare.13642300
title: Additional file 3 of Global transcriptome changes of elongating internode of sugarcane in response to mepiquat chloride

description: Additional file 3. Annotation results of isoforms from full-length transcriptome of sugarcane.
DOI: 10.6084/m9.figshare.13340883
title: The circ_0004463/miR-380-3p/FOXO1 axis modulates mitochondrial respiration and bladder cancer cell apoptosis

description: Bladder cancer is one of the most commonly diagnosed and fatal malignancies of the urinary tract. Noncoding RNAs have been reported to be new biomarkers and effective treatment targets for bladder cancer. In the present study, we identified a novel bladder cancer-related circRNA-miRNA-mRNA network, the circ_0004463/miR-380-3p/FOXO1 axis. circ_0004463 is significantly downregulated, whereas miR-380-3p is upregulated in bladder carcinoma tissue samples and cells. circ_0004463 acts as a tumor suppressor by inhibiting bladder cancer cell proliferation. Genes that negatively correlated with miR-380-3p and genes that miR-380-3p might target are enriched in mitochondrial respiration chain-related pathways. miR-380-3p promotes the proliferation of bladder cancer cells and mitochondrial respiration by acting as an oncogenic miRNA. circ_0004463 competes with FOXO1 for miR-380-3p binding to counteract miR-380-3p-mediated repression of FOXO1. Circ_0004463 overexpression inhibits cancer cell proliferation and mitochondrial respiration in bladder cancer cell lines, while miR-380-3p overexpression dramatically reverses the roles of circ_0004463 overexpression. In conclusion, the circ_0004463/miR-380-3p/FOXO1 axis could regulate mitochondrial respiration and bladder cancer cell apoptosis via FOXO1 signaling.
DOI: 10.6084/m9.figshare.13642306.v1
title: Additional file 5 of Global transcriptome changes of elongating internode of sugarcane in response to mepiquat chloride

description: Additional file 5. KEGG enrichment analysis of DEGs.
DOI: 10.6084/m9.figshare.19411103.v1
title: Long non-coding RNA MEG3 promotes tumor necrosis factor-alpha induced oxidative stress and apoptosis in interstitial cells of cajal via targeting the microRNA-21 /I-kappa-B-kinase beta axis

description: Interstitial Cells of Cajal (ICC) plays a critical role in the peristaltic contractions of the gastrointestinal and urinary tract. The dysfunction and loss of ICC contributes to hypokinetic disease, such as gallstoneand ureteropelvic junction obstruction . In the present study, we identified the underlying driving molecular signals of oxidative stress and apoptosis in ICC. ICC was isolated from small intestine of Balb/c mice, and stimulated with tumor necrosis factor-alpha (TNF-α). MTT and flow cytometry were performed to assess cell viability, apoptosis, and the level of reactive oxygen species in ICC, respectively. The level of malondialdehyde, superoxide dismutase, and glutathione peroxidase in cells were measured to assess oxidative stress. The expression of inflammatory factors (interleukin, IL-1 and IL-6) and apoptosis-related proteins were detected by western blot. We observed that TNF-αinduced inflammation, oxidative stress and cell apoptosis in ICC. By using quantitative real-time PCR , we verified that the expression of long non-coding RNAMEG3 was elevated by TNF-α in ICC. Silencing MEG3 reversed inflammation, oxidative stress, and cell apoptosisin TNF-α-treated ICC. Subsequently, we confirmed that MEG3 sponged cytoprotective miR-21 to upregulate the expression of I-kappa-B-kinase beta (IKKB) and activate the nuclear factor kappa-B (NF-κB) pathway. Both miR-21 overexpression and IKKB knockdown reduced TNF-α-induced above symptoms in ICC. Taken together, we can conclude that MEG3 mediates inflammation, oxidative stress and apoptosis in TNF-α-treated ICC via the miR-21/IKKB-NF-κB axis. The study improves our understanding of the molecular mechanism of ICC reduction related diseases.
DOI: 10.6084/m9.figshare.13642288.v1
title: Additional file 1 of Synergistic optimisation of expression, folding, and secretion improves E. coli AppA phytase production in Pichia pastoris

description: Additional file 1: Table S1. Additional tables.
DOI: 10.6084/m9.figshare.14168023.v1
title: Additional file 5 of RNA sequencing reveals the expression profiles of circRNA and identifies a four-circRNA signature acts as a prognostic marker in esophageal squamous cell carcinoma

description: Additional file 5: Table S3: circRNAs of Univariate Cox regression analysis (P &lt; 0.05) in the training set (n = 73).
DOI: 10.26025/1912/67567
title: Mobile Bay 2021 synthetic aperture radar images

description: This dataset includes satellite synthetic aperture radar images (SAR) that were obtained for the region around the mouth of Mobile Bay during the period April-June 2021. Images were collected to identify the location of oceanographic fronts associated with the outflow plume of Mobile Bay. SAR images show density fronts as regions of increased radar cross-section, i.e. image brightness.
DOI: 10.35097/1576
title: Multi-Component PtFeCoNi Core-Shell Nanoparticles on MWCNTs as Promising Bifunctional Catalyst for Oxygen Reduction and Oxygen Evolution Reactions

description: The development of commercially viable fuel cells and metal air batteries requires effective and cheap bifunctional catalysts for the oxygen reduction reaction (ORR) and the oxygen evolution reaction (OER). Multi-component Pt-Fe-Co-Ni nanoparticles on multi-walled carbon nanotubes (MWCNTs) were synthesized by wet chemistry route via NaBH4 reduction of metal salts, followed by sintering at different temperatures. The catalyst demonstrates an excellent ORR activity and a promising OER activity in 0.1 m KOH, with a bi-functional overpotential, ΔE of 0.83 V, which is comparable to the values of Pt/C or RuO2. Furthermore, it shows outstanding long-term stability in ORR and OER, namely diffusion limited current density at a potential of 0.3 V decreased just by 5.5% after 10000 cycles in ORR. The results of the PFCN@NT300 indicate a significant effect of the substitution of Pt by the transition metal (TM) and the formation of nanoparticles on the catalytic performance, especially in the OER.
description: TEM data in Velox and Digital Micrograph format, XPS data in CASA format, TGA as text file, XRD as text file with angle and intensity.
DOI: 10.6084/m9.figshare.25134380
title: Probing the Link between Vision and Language in Material Perception

description: Materials are the building blocks of our surroundings. Material perception enables us to create a vivid mental representation of our environment, allowing us to appreciate the qualities and aesthetics of things around us, and decide how to interact with them. We can visually discriminate and recognize materials and infer their properties, and previous studies have identified diagnostic image features related to visual perception. Meanwhile, language reveals our subjective understanding of visual input and allows us to communicate relevant information about the material. To what extent words encapsulate the visual material perception remains elusive. Here, we used deep generative networks to create an expandable image space that allows us to systematically create and sample stimuli of familiar and unfamiliar materials. We compared the representations of materials from two cognitive tasks: visual material similarity judgments and verbal descriptions. We observed a moderate correlation between vision and language within individuals, but language alone can not fully capture the nuances of material appearance. We further examined the latent code of the generative model and found that image-based representation only exhibited a weak correlation with human vision. Joining image- and semantic-level representations substantially improved the prediction of human perception. Our results imply that material perception involves a semantic understanding of scenes to resolve the ambiguity of visual information and beyond merely relying on image features. This work illustrates the need to consider the vision-language relationship in building a comprehensive model for material perception and other tasks in high-level vision. <b>The raw data from the behavioral tasks can be found here: </b><br>Multiple_arrangement folder: the RDMs from the Multiple Arrangement task.Verbal_description folder: the verbal description provided by the participants.
DOI: 10.6084/m9.figshare.14168212.v1
title: Additional file 3 of Hypermethylation of heparanase 2 promotes colorectal cancer proliferation and is associated with poor prognosis

description: Additional file 3: Table S2. Correlation between HPSE2 expression and CpG island methylation of CRC in TCGA database.
DOI: 10.6084/m9.figshare.13642309
title: Additional file 6 of Global transcriptome changes of elongating internode of sugarcane in response to mepiquat chloride

description: Additional file 6. Correlations between modules and the groups. (CSV 4 kb)
DOI: 10.6084/m9.figshare.13642351
title: Additional file 2 of Host reproductive cycle influences the pouch microbiota of wild southern hairy-nosed wombats (Lasiorhinus latifrons)

description: Additional file 2.