Real datasets for RISQ

This folder contains 8 files. They can be used to validate RNA-seq quantification tools and to make comparisons. The files "chr6.fa", "mm9chr6.gtf", "Read11.fa" and "Read22.fa" can be used for isoform quantification by different RNA-seq quantification tools. The files "chr1.fa", "chr2.fa","hg38_chr1.gtf","hg38_chr2.gtf", "file2.csv", "file3.csv" together with together with MAQC RNA-seq data (GEO Sample id: GSE83402) can be used to validate any new RNA-seq quantification tool with respect to qPCR data. "chr1.fa" is human chromosome 1 sequence (Source: UCSC database). "chr2.fa" is human chromosome 1 sequence (Source: UCSC database). "chr6.fa" is mouse chromosome 6 sequence (Source: UCSC database). "mm9chr6.gtf" is mouse chromosome 6 reference annotation with mm9 version (Source: UCSC database). "hg38_chr1.gtf" is human chromosome 1 reference annotation with hg38 version (Source: ENSEMBL database). "hg38_chr2.gtf" is human chromosome 2 reference annotation with hg38 version (Source: ENSEMBL database). "Read11.fa" and "Read22.fa" are paired end reads generated from an RNA-seq experiment (Source Publication: https://genome.cshlp.org/content/early/2013/04/28/gr.146654.112.abstract). "file2.csv" contains delta Ct values from qPCR experiment on same sample (Can also be downloaded from: https://www.nature.com/articles/s41598-017-01617-3). "file3.csv" contains informations on which gene corresponds to which of the transcripts (Can also be downloaded from: https://www.nature.com/articles/s41598-017-01617-3)

Family-based genome-wide association of inflammation biomarkers and fenofibrate treatment response in the GOLDN study

Abstract In this paper we analyzed whole-genome genetic information provided by GAW20 from the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) study for family data. Lipid levels such as triglycerides (TGs) and high-density lipoprotein (HDL) are measured at different time points before and after administration of an anti-inflammatory drug fenofibrate. Apart from that, the data contain some covariates and whole-genome genotype information. We propose 2 novel approaches based on Henderson’s iterative mixed model to identify associated loci corresponding to (a) inflammatory biomarkers like TGs and HDLs together over time, and (b) the response to fenofibrate treatment. We developed a mixed-model approach using both TG and HDL phenotypes at all 4 time points for a genetic association study whereas we used TGs only to study genetic association with response to the drug. We expect that use of complete family data in a longitudinal framework under a single model involving the appropriate correlation structures would be able to exploit the maximum possible information contained in the sample. Our analysis of whole-genome single nucleotide polymorphisms (SNPs) and genomic regions corresponding to drug treatment finds no significant locus after multiple correction. Arguably, the moderately small sample size of the data set, as compared to the sample size usually used in genome-wide association studies (GWAS), could be a reason for such a result. Nevertheless, we report the top 20 SNPs associated with the phenotypes, and the top 20 SNPs and genomic regions associated with a response to fenofibrate treatment. Application of our methods to larger GWAS and further functional validation of the reported top SNPs and genomic regions might provide important biological insight into the genetic constitution of the trait

Dried fish more prone to microplastics contamination over fresh fish – Higher potential of trophic transfer to human body

Globally, microplastics (MPs) contamination in aquatic organisms is emerging as an alarming phenomenon. In the present study, we investigated MPs in three commercially important fishes (Bombay duck Harpadon nehereus, ribbon fish Trichiurus lepturus and hairfin anchovy Setipinna phasa) in fresh and dried conditions collected from two sites (Chattogram and Kuakata) of the Bay of Bengal. It was evident that fresh T. lepturus ingested highest amount of MPs through the gills (6.41 mps/g) from Chattogram followed by in the gastrointestinal tract, GIT (6.20 mps/g) and in the muscle (1.20 mps/g) from Kuakata. Among the fresh fishes, H. nehereus from Kuakata accumulated highest amount of MPs (0.21 mps/g), while S. phasa from Kuakata contained the least amount of MPs (0.06 mps/g). On the other hand, among the dried fishes, T. lepturus from Kuakata contained highest amount of MPs (46.00 mps/g), while S. phasa from Kuakata retained lowest amount of MPs (2.17 mps/g). Strangely, all the dried fishes showed significantly higher amount of MPs compared to fresh fishes from both the locations. Fiber was the most dominant type of shape of MPs which accounted 66 %, followed by fragment (27.38 %), microbeads (3.59 %), film (1.48 %), foam (1.31 %) and pellet (0.25 %). Size-wise, the major portion (39.66 %) of MPs was present to be in size range less than 0.5 mm followed by 37.67 % in the size range of 0.5–1.0 mm group and rest 22.67 % within 1.0–5.0 mm. Red (41.55 %) colored MPs was the most prominent, followed by brown (22.11 %), blue (16.32 %), pink (11.69 %), purple (5.10 %), and green (2.25 %). Among polymer types, low-density polyethylene (LDPE) was the most common (38 %), followed by polystyrene (PS-22 %), polyvinyl chloride (PVC-16 %), polyamide (PA-13 %) and ethylene-vinyl acetate (EVA-9 %). The present study confirms high occurrence of MPs in the dried fishes over the fresh fishes from the Bay of Bengal, with high potential of trophic transfer to the human body

Self-immobilized Pd nanowires as an excellent platform for a continuous flow reactor: efficiency, stability and regeneration

Despite extensive use of Pd nanocrystals as catalysts, the realization of a Pd-based continuous flow reactor remains a challenge. Difficulties arise due to ill-defined anchoring of the nanocrystals on a substrate and reactivity of the substrate under different reaction conditions. We demonstrate the first metal (Pd) nanowire-based catalytic flow reactor that can be used across different filtration platforms, wherein, reactants flow through a porous network of nanowires (10–1000 nm pore sizes) and the product can be collected as filtrate. Controlling the growth parameters and obtaining high aspect ratio of the nanowires (diameter = ∼13 nm and length > 8000 nm) is necessary for successful fabrication of this flow reactor. The reactor performance is similar to a conventional reactor, but without requiring energy-expensive mechanical stirring. Synchrotron-based EXAFS studies were used to examine the catalyst microstructure and Operando FT-IR spectroscopic studies were used to devise a regenerative strategy. We show that after prolonged use, the catalyst performance can be regenerated up to 99% by a simple wash-off process without disturbing the catalyst bed. Thus, collection, regeneration and redispersion processes of the catalyst in conventional industrial reactors can be avoided. Another important advantage is avoiding specific catalyst-anchoring substrates, which are not only expensive, but also non-universal in nature

High expression of mesothelin in plasma and tissue is associated with poor prognosis and promotes invasion and metastasis in gastric cancer

Mesothelin (MSLN), a tumor-associated antigen, is upregulated in various malignancies, including gastric cancer (GC). In addition, MSLN is found in the blood-stream of affected individuals, where it is referred to as soluble MSLN-related protein (SMRP). This study aims to investigate the role of MSLN in GC and evaluate its potential as a plasma biomarker for diagnosis and prognosis. Toward that end, GC tissues were obtained, upon signed consent, from affected individuals undergoing surgery or endoscopy (n = 82). Quantitative RT-PCR and immunohistochemistry were performed to determine MSLN expression. Simultaneously, The Cancer Genome Atlas (TCGA) database was mined to evaluate global status of MSLN gene expression in gastric cancer. Next, in vitro cell-culture studies were conducted to evaluate MSLN-driven proliferation properties. Using ELISA, sera from 55 GC-affected individuals were tested for MSLN level. Additionally, plasma mesothelin levels were compared in 6 cases before and after surgery. Upregulated MSLN expression was found in GC tissues, compared to adjacent normal tissues (p < 0.001). Cell culture studies with a MSLN-overexpressing stable GC line showed increased cell proliferation and invasion with ectopic MSLN. Additionally, gene-set-enrichment-analysis (GSEA) revealed an association of MSLN with the genes involved in the epithelial-mesenchymal transition and G2/M checkpoint. GC-affected cases showed higher serum MSLN levels, compared to healthy controls, with rapid decrease post-surgery. We found that MSLN upregulation correlates with poor clinical outcome and promotes growth advantage to GC cells in vitro. With further experimental evidences, we propose that MSLN could potentially be used as a plasma biomarker for diagnosis of GC

Improving valuable metal ions capturing from spent Li-ion batteries with novel materials and approaches

Rapid growth in the market for batteries is imperative to meet global demand. The lack of economically feasible and environmentally benign recycling process for waste batteries may cause environmental crisis. Taking effective measures could reduce the waste-management challenge and maximize the economic benefits. In this work, environmentally benign citric acid with the presence of reluctant was used to recover cobalt, manganese, nickel and lithium from waste Lithium Nickel Manganese Cobalt oxide (NCM) batteries. Recovery of Co, Mn, Ni, and Li was optimized by varying the citric acid and H2O2 concentrations, the reaction temperature and duration. The recovery of Co, Mn, Ni, and Li were 87%, 90.5%, 93.5% and 96% respectively under the optimum leaching condition of 1.2 mol/L citric acid, 10 vol% H2O2at 95 for 120 min. Interfacial reaction controlled leaching reaction at low temperature was evident from the results of leaching kinetics with apparent activation energy of 3.75, 10.405.34 and 8.72 kJ mol1 for Co, Mn, Ni and Li, respectively. Importantly, the diffusion controlled leaching reaction was evident from the kinetic and activation energy measurement of leaching. The impact of different chemicals on the environment measured from the Biwer and Heinzle Method (BHM) revealed that the citric acid-assisted leaching process to recover valuable metals from NCM batteries was appeared lower environment impact compare to the other process reported in the literature. The high leaching efficiency and lower impact to the environment provides a novel approach for metal recovery of waste NCM batteries