cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7814099
title: Intra-articular injection of triamcinolone acetonide releasing biomaterial microspheres inhibits pain and inflammation in an acute arthritis model

description: Inflammation of the synovium and joint capsule is a main driver of pain in an osteoarthritic (OA) joint. Triamcinolone acetonide (TAA) is a classical corticosteroid that reduces synovitis and alleviates pain, albeit transiently. Biomaterial-based local TAA release may prolong the suppression of pain without the need for multiple injections. Polylactic-co-glycolic acid (PLGA) formulations of TAA prolong OA pain relief to a limited extent. A novel polyesteramide (PEA) microsphere platform allows for extended release in the OA joint for over 3 months. To evaluate their effect on pain and inflammation, TAA-loaded microspheres were intra-articularly delivered to the knee joint in a rat model of acute arthritis induced by intra-articular injection of streptococcal cell wall peptidoglycan-polysaccharide (PGPS) and subsequent flare-ups by intravenous PGPS injections. PEA-loaded microspheres were benchmarked with TAA-loaded PLGA microspheres and bolus TAA injection. TAA treatments were injected intra-articularly before the first induced flare-up. TAA-loaded PEA and PLGA microspheres reduced joint swelling and signs of pain-like behavior over the entire study period, as assessed by weight bearing and referred mechanical hypersensitivity, whereas bolus suspension was effective for a shorter time period. TAA-loaded PEA microspheres reduced lameness to a greater extent than TAA-loaded PLGA microspheres. In conclusion, a single intra-articular injection of TAA-loaded PEA microspheres reduced joint swelling and induced longer pain relief compared to bolus injection. Hence relief of inflammation and pain by PEA-based delivery of TAA may prove to be effective and durable.
DOI: 10.6084/m9.figshare.9165029.v1
title: Ganoderic acid loaded nano-lipidic carriers improvise treatment of hepatocellular carcinoma

description: This work evaluates nano-lipid carrier of ganoderic acid (GA) and molecular docking on various cancer signaling pathways, an attempt to improve the hepatic condition associated with hepatic carcinoma (HCC) induced by diethyl-nitrosamine (DEN) in Wistar rats. Molecular docking mechanism of GA was performed through binding simulation analysis for various cancer signaling pathway, viz., Bcl-2, Pl3K, NF-κB, Akt/PKB, and Stat-3. Double emulsion solvent displacement method was implied for preparation of GA-loaded nano-lipid carrier. GA-NLCs were evaluated for drug loading capacity, entrapment efficiency, particle size, gastric stability, <i>in vitro</i> drug release, cytotoxicity, cellular uptake, and <i>in vivo</i> studies including macroscopical, hepatic injury markers, non-hepatic, biochemical, antioxidant parameters, and histopathological evaluation. HCC was induced by intraperitoneal injection of DEN (200 mg/kg). Both <i>in vivo</i> and molecular docking results were compatible in establishing the alteration in hepatic nodules, hepatic, non-hepatic, and antioxidant parameters, in a significant manner (<i>p</i> &lt; .001) by GA and GA-NLC along with signal alteration of Bcl-2, Pl3K, NF-κB Akt/PKB, and Stat-3 pathway. Histopathological observation confirmed and supported the above result by GA and GA-NLC. On the basis of our results, we can advocate that, GA interferes with various cancer signaling proteins involved in pathogenesis of cancer and was able to cease the progression of disease. Additionally, GA-NLCs proved its chemoprotective effect against the DEN-induced HCC by modulation of hepatic and non-hepatic parameters through various mechanisms.
DOI: 10.6084/m9.figshare.9165029
title: Ganoderic acid loaded nano-lipidic carriers improvise treatment of hepatocellular carcinoma

description: This work evaluates nano-lipid carrier of ganoderic acid (GA) and molecular docking on various cancer signaling pathways, an attempt to improve the hepatic condition associated with hepatic carcinoma (HCC) induced by diethyl-nitrosamine (DEN) in Wistar rats. Molecular docking mechanism of GA was performed through binding simulation analysis for various cancer signaling pathway, viz., Bcl-2, Pl3K, NF-κB, Akt/PKB, and Stat-3. Double emulsion solvent displacement method was implied for preparation of GA-loaded nano-lipid carrier. GA-NLCs were evaluated for drug loading capacity, entrapment efficiency, particle size, gastric stability, <i>in vitro</i> drug release, cytotoxicity, cellular uptake, and <i>in vivo</i> studies including macroscopical, hepatic injury markers, non-hepatic, biochemical, antioxidant parameters, and histopathological evaluation. HCC was induced by intraperitoneal injection of DEN (200 mg/kg). Both <i>in vivo</i> and molecular docking results were compatible in establishing the alteration in hepatic nodules, hepatic, non-hepatic, and antioxidant parameters, in a significant manner (<i>p</i> &lt; .001) by GA and GA-NLC along with signal alteration of Bcl-2, Pl3K, NF-κB Akt/PKB, and Stat-3 pathway. Histopathological observation confirmed and supported the above result by GA and GA-NLC. On the basis of our results, we can advocate that, GA interferes with various cancer signaling proteins involved in pathogenesis of cancer and was able to cease the progression of disease. Additionally, GA-NLCs proved its chemoprotective effect against the DEN-induced HCC by modulation of hepatic and non-hepatic parameters through various mechanisms.
DOI: 10.6084/m9.figshare.7763051
title: Magnetic aerosol drug targeting in lung cancer therapy using permanent magnet

description: Primary bronchial cancer accounts for almost 20% of all cancer death worldwide. One of the emerging techniques with tremendous power for lung cancer therapy is magnetic aerosol drug targeting (MADT). The use of a permanent magnet for effective drug delivery in a desired location throughout the lung requires extensive optimization, but it has not been addressed yet. In the present study, the possibility of using a permanent magnet for trapping the particles on a lung tumor is evaluated numerically in the Weibel's model from G0 to G3. The effect of different parameters is considered on the efficiency of particle deposition in a tumor located on a distant position of the lung bronchi and bronchioles. Also, the effective position of the magnetic source, tumor size, and location are the objectives for particle deposition. The results show that a limited particle deposition occurs on the lung branches in passive targeting. However, the incorporation of a permanent magnet next to the tumor enhanced the particle deposition fraction on G2 to up to 49% for the particles of 7 µm diameter. Optimizing the magnet size could also improve the particle deposition fraction by 68%. It was also shown that the utilization of MADT is essential for effective drug delivery to the tumors located on the lower wall of airway branches given the dominance of the air velocity and resultant drag force in this region. The results demonstrated the high competence and necessity of MADT as a noninvasive drug delivery method for lung cancer therapy.
DOI: 10.6084/m9.figshare.7763051.v1
title: Magnetic aerosol drug targeting in lung cancer therapy using permanent magnet

description: Primary bronchial cancer accounts for almost 20% of all cancer death worldwide. One of the emerging techniques with tremendous power for lung cancer therapy is magnetic aerosol drug targeting (MADT). The use of a permanent magnet for effective drug delivery in a desired location throughout the lung requires extensive optimization, but it has not been addressed yet. In the present study, the possibility of using a permanent magnet for trapping the particles on a lung tumor is evaluated numerically in the Weibel's model from G0 to G3. The effect of different parameters is considered on the efficiency of particle deposition in a tumor located on a distant position of the lung bronchi and bronchioles. Also, the effective position of the magnetic source, tumor size, and location are the objectives for particle deposition. The results show that a limited particle deposition occurs on the lung branches in passive targeting. However, the incorporation of a permanent magnet next to the tumor enhanced the particle deposition fraction on G2 to up to 49% for the particles of 7 µm diameter. Optimizing the magnet size could also improve the particle deposition fraction by 68%. It was also shown that the utilization of MADT is essential for effective drug delivery to the tumors located on the lower wall of airway branches given the dominance of the air velocity and resultant drag force in this region. The results demonstrated the high competence and necessity of MADT as a noninvasive drug delivery method for lung cancer therapy.
DOI: 10.5281/zenodo.6956755
title: Biotechnology data analysis training with Jupyter Notebooks

description: Biotechnology has experienced innovations in analytics and data processing. As the volume of data and its complexity grows, new computational procedures for extracting information are developed. However, the rate of change outpaces the adaptation of biotechnology curricula, necessitating new teaching methodologies to equip biotechnologists with data analysis abilities. To simulate experimental data, we created a virtual organism simulator (<em>silvio</em>) by combining diverse cellular and sub-cellular microbial models. With the <em>silvio </em>Python package, we constructed a computer-based instructional workflow to teach growth curve data analysis, promoter sequence design, and expression rate measurement. The instructional workflow is a Jupyter Notebook with background explanations and Python-based experiment simulations combined. The data analysis is either conducted within the Notebook in Python or externally with Excel. This instructional workflow was separately implemented in two distance courses for Master's students in biology and biotechnology with assessment of the pedagogic efficiency. The concept of using virtual organism simulations that generate coherent results across different experiments can be used to construct consistent and motivating case studies for biotechnological data literacy. Here, the supplementary material is provided. 2207_BLS-RecExpSim.mbz Moodle backup file for import as new moodle function. BLS_RecExpSim_PerformanceEvaluation Rubric.docx Expected learning outcomes with associated performance levels. BLS_SurveryQuestions.docx Survey questions to evaluate the educational approach. RecExpSim.html Html-Export of the Jupyter Notebook to teach biotechnology data analysis. This only serves as visual impression of the course because the dynamic Python-evaluations are not functioning. RecExpSim_Lecture.pdf Static pdf of preparatory lecture to cover the theoretical aspects in the simulations and to get student on comparable level. RecExpSim_Lecture.pptx Adjustable pptx of preparatory lecture to cover the theoretical aspects in the simulations and to get student on comparable level.
DOI: 10.5281/zenodo.6956754
title: Biotechnology data analysis training with Jupyter Notebooks

description: Biotechnology has experienced innovations in analytics and data processing. As the volume of data and its complexity grows, new computational procedures for extracting information are developed. However, the rate of change outpaces the adaptation of biotechnology curricula, necessitating new teaching methodologies to equip biotechnologists with data analysis abilities. To simulate experimental data, we created a virtual organism simulator (<em>silvio</em>) by combining diverse cellular and sub-cellular microbial models. With the <em>silvio </em>Python package, we constructed a computer-based instructional workflow to teach growth curve data analysis, promoter sequence design, and expression rate measurement. The instructional workflow is a Jupyter Notebook with background explanations and Python-based experiment simulations combined. The data analysis is either conducted within the Notebook in Python or externally with Excel. This instructional workflow was separately implemented in two distance courses for Master's students in biology and biotechnology with assessment of the pedagogic efficiency. The concept of using virtual organism simulations that generate coherent results across different experiments can be used to construct consistent and motivating case studies for biotechnological data literacy. Here, the supplementary material is provided. 2207_BLS-RecExpSim.mbz Moodle backup file for import as new moodle function. BLS_RecExpSim_PerformanceEvaluation Rubric.docx Expected learning outcomes with associated performance levels. BLS_SurveryQuestions.docx Survey questions to evaluate the educational approach. RecExpSim.html Html-Export of the Jupyter Notebook to teach biotechnology data analysis. This only serves as visual impression of the course because the dynamic Python-evaluations are not functioning. RecExpSim_Lecture.pdf Static pdf of preparatory lecture to cover the theoretical aspects in the simulations and to get student on comparable level. RecExpSim_Lecture.pptx Adjustable pptx of preparatory lecture to cover the theoretical aspects in the simulations and to get student on comparable level.
DOI: 10.6084/m9.figshare.17182985.v6
title: A bankfull geometry dataset for major exorheic rivers on the Qinghai-Tibet Plateau

description: Based on the Sentinel-2 and Landsat 5/7/8 multispectral instrument imageries combined with in-situ measured hydrological data, bankfull river geometry of six major exorheic river basins of the Qinghai-Tibet Plateau (the upper Yellow River, upper Jinsha River, Yalong River, Lantsang River, Nu River and Yalung Zangbo River) are presented. River surface of six mainstreams and major tributaries are included. For each river basin, two types of rivers are included: connected and disconnected rivers. Format of the dataset is .shp exported from the ArcGIS 10.5. Three products are included in the dataset: one original product (bankfull river surface dataset) and two derived products (bankfull river width dataset and bankfull river surface area dataset with a 1 km river length interval). These three products are in three folders. The first folder, “1-Bankfull River Surface”, contains river surface vectors for six river basins in the .shp file. The second folder, “2-Bankfull River Width”, contains bankfull river widths and corresponding coordinates with a 1 km-step river length for six mainstreams and some connected tributaries in .xlsx format. The river width vectors in the .shp files are also provided in the second folder. The third folder, “3-Bankfull River Surface Area”, contains bankfull river surface areas and corresponding coordinates with a 1 km-step river length for six mainstreams and some connected tributaries in .xlsx format. Two Supplementary Information are included: Supplementary 2, used for river surface extraction based on GEE platform; Supplementary 3, used for river width extraction based on Matlab.
DOI: 10.34740/kaggle/dsv/4023453
title: Micro-Organism Image Classification
DOI: 10.6084/m9.figshare.20424375
title: Supplementary Material for: Control of Diabetes Mellitus and Long-Term Prognosis in Stroke Patients: The Shiga Stroke and Heart Attack Registry

description: <b><i>Background:</i></b> The relationship between diabetes control status and long-term prognosis after stroke incidence remains unclear. This study aimed to investigate the effect of diabetes status at admission on long-term survival in patients with first-ever stroke. <b><i>Methods:</i></b> A retrospective cohort study was conducted based on the Shiga Stroke and Heart Attack Registry in Japan. Patients were classified according to their diabetes status and glycated hemoglobin (HbA1c) value at hospital admission into the following: (1) free of diabetes (no history of diabetes and HbA1c &lt;6.5%); (2) good control (history of diabetes and HbA1c &lt;7%; free of history and 6.5% ≤HbA1c &lt;7%); and (3) poor control (with or without a history of diabetes and HbA1c ≥7%). Multivariable Cox regression models were used to evaluate the association between diabetes status and long-term survival from stroke onset. Additionally, we also evaluated the association between diabetes status and conditional survival, beginning 29 days after stroke onset. <b><i>Results:</i></b> A total of 6,331 first-ever stroke patients were eligible for this study. Among study patients, the mean (±SD) age was 72.85 ± 13.19 years, and the mean (±SD) follow-up year was 2.76 ± 1.66 years; additionally, 42.09% of patients were women. Among patients with all strokes, considering the free-of-diabetes group as the reference group, the adjusted hazard ratio (95% confidence interval) for mortality was 1.26 (1.10, 1.44) in the good control group and 1.22 (1.05, 1.41) in the poor control group. Among patients with ischemic stroke, the adjusted hazard ratio was 1.24 (1.06, 1.46) in good control group and 1.27 (1.08, 1.50) in poor control group. After excluding patients who died within 28 days, the adjusted hazard ratio for conditional mortality in the poor control group was 1.31 (1.12, 1.54) among all stroke patients and 1.29 (1.08, 1.54) among ischemic stroke patients. No significant associations were observed between diabetic status and long-term mortality in intracerebral hemorrhage patients. <b><i>Conclusions:</i></b> The findings suggest that first-ever stroke patients with diabetes exhibited a higher risk of all-cause mortality than those without diabetes, particularly in the overall stroke and ischemic stroke populations. Additionally, in stroke populations after 28 days of onset, high risk of long-term mortality was stated in stroke patients with poor HbA1c control.
DOI: 10.5285/e28496a4-0c72-0e7a-e053-6c86abc0d7c7
title: Calanus helgolandicus weekly egg production time series between 1992-2021, using females from the Western English Channel site L4.

description: Ongoing zooplankton research at the Plymouth Marine Laboratory has established a time series of Calanus egg production using females from L4, a coastal station off Plymouth, UK. The time series was started in 1992. Weekly samples are collected, upon return to the laboratory  female Calanus sp are picked from the live sample. Five replicates each containing five females are incubated in filtered seawater for 24 hours at ambient L4 temperature. The eggs produced are collected and counted. Data are presented as average egg production rate (EPR) per female per day.
DOI: 10.6084/m9.figshare.20424369.v1
title: Mytilus coruscus.zip

description: The main body of this database is the transcriptome sequencing on the gonad organs in male and female <em>Mytilus coruscus</em>.
DOI: 10.6084/m9.figshare.18327465
title: Carnitine is a pharmacological allosteric chaperone of the human lysosomal <i>α</i>-glucosidase

description: Pompe disease is an inherited metabolic disorder due to the deficiency of the lysosomal acid <i>α</i>-glucosidase (GAA). The only approved treatment is enzyme replacement therapy with the recombinant enzyme (rhGAA). Further approaches like pharmacological chaperone therapy, based on the stabilising effect induced by small molecules on the target enzyme, could be a promising strategy. However, most known chaperones could be limited by their potential inhibitory effects on patient’s enzymes. Here we report on the discovery of novel chaperones for rhGAA, L- and D-carnitine, and the related compound acetyl-D-carnitine. These drugs stabilise the enzyme at pH and temperature without inhibiting the activity and acted synergistically with active-site directed pharmacological chaperones. Remarkably, they enhanced by 4-fold the acid <i>α</i>-glucosidase activity in fibroblasts from three Pompe patients with added rhGAA. This synergistic effect of L-carnitine and rhGAA has the potential to be translated into improved therapeutic efficacy of ERT in Pompe disease.
DOI: 10.6084/m9.figshare.18327465.v1
title: Carnitine is a pharmacological allosteric chaperone of the human lysosomal <i>α</i>-glucosidase

description: Pompe disease is an inherited metabolic disorder due to the deficiency of the lysosomal acid <i>α</i>-glucosidase (GAA). The only approved treatment is enzyme replacement therapy with the recombinant enzyme (rhGAA). Further approaches like pharmacological chaperone therapy, based on the stabilising effect induced by small molecules on the target enzyme, could be a promising strategy. However, most known chaperones could be limited by their potential inhibitory effects on patient’s enzymes. Here we report on the discovery of novel chaperones for rhGAA, L- and D-carnitine, and the related compound acetyl-D-carnitine. These drugs stabilise the enzyme at pH and temperature without inhibiting the activity and acted synergistically with active-site directed pharmacological chaperones. Remarkably, they enhanced by 4-fold the acid <i>α</i>-glucosidase activity in fibroblasts from three Pompe patients with added rhGAA. This synergistic effect of L-carnitine and rhGAA has the potential to be translated into improved therapeutic efficacy of ERT in Pompe disease.
DOI: 10.6084/m9.figshare.14329726
title: Modulation of SETDB1 activity by APQ ameliorates heterochromatin condensation, motor function, and neuropathology in a Huntington’s disease mouse model

description: The present study describes evaluation of epigenetic regulation by a small molecule as the therapeutic potential for treatment of Huntington’s disease (HD). We identified 5-allyloxy-2-(pyrrolidin-1-yl)quinoline (APQ) as a novel SETDB1/ESET inhibitor using a combined <i>in silico</i> and <i>in vitro</i> cell based screening system. APQ reduced SETDB1 activity and H3K9me3 levels in a HD cell line model. In particular, not only APQ reduced H3K9me3 levels in the striatum but it also improved motor function and neuropathological symptoms such as neuronal size and activity in HD transgenic (YAC128) mice with minimal toxicity. Using H3K9me3-ChIP and genome-wide sequencing, we also confirmed that APQ modulates H3K9me3-landscaped epigenomes in YAC128 mice. These data provide that APQ, a novel small molecule SETDB1 inhibitor, coordinates H3K9me-dependent heterochromatin remodelling and can be an epigenetic drug for treating HD, leading with hope in clinical trials of HD.
DOI: 10.6084/m9.figshare.14329726.v1
title: Modulation of SETDB1 activity by APQ ameliorates heterochromatin condensation, motor function, and neuropathology in a Huntington’s disease mouse model

description: The present study describes evaluation of epigenetic regulation by a small molecule as the therapeutic potential for treatment of Huntington’s disease (HD). We identified 5-allyloxy-2-(pyrrolidin-1-yl)quinoline (APQ) as a novel SETDB1/ESET inhibitor using a combined <i>in silico</i> and <i>in vitro</i> cell based screening system. APQ reduced SETDB1 activity and H3K9me3 levels in a HD cell line model. In particular, not only APQ reduced H3K9me3 levels in the striatum but it also improved motor function and neuropathological symptoms such as neuronal size and activity in HD transgenic (YAC128) mice with minimal toxicity. Using H3K9me3-ChIP and genome-wide sequencing, we also confirmed that APQ modulates H3K9me3-landscaped epigenomes in YAC128 mice. These data provide that APQ, a novel small molecule SETDB1 inhibitor, coordinates H3K9me-dependent heterochromatin remodelling and can be an epigenetic drug for treating HD, leading with hope in clinical trials of HD.