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Figure 4 from: Abbas AH, Mahmood AAR, Tahtamouni LH, Al-Mazaydeh ZA, Rammaha MS, Alsoubani F, Al-bayati RI (2021) A novel derivative of picolinic acid induces endoplasmic reticulum stress-mediated apoptosis in human non-small cell lung cancer cells: synthesis, docking study, and anticancer activity. Pharmacia 68(3): 679-692. https://doi.org/10.3897/pharmacia.68.e70654
Figure 4 Compound 5 causes caspase activation. A) qRT-PCR analysis of caspase 3, 4, 8 and 9 mRNA in compound 5-treated cells (GI50) as compared to vehicle-treated control cells [set as 1 arbitrary unit (a.u.)]. Values were normalized to β-actin. Scale bars: mean ± SEM of three independent experiments performed in triplicates. *p < 0.05, **p < 0.01 compared to vehicle-treated control cells, B) Representative Western blots showing cleavage "activation' of procaspase 3 to the active form p17, procaspase 4 to the active form p20, and procaspase 9 to the active forms p35/p37. C: vehicle-treated control cells; 0.5%: 0.5% DMSO-treated cells; 1%: 1% DMSO-treated cells; 5%: 5% DMSO-treated cells; C.5: Compound 5-treated cells. The experiment was repeated three times.
Figure 2 from: Abbas AH, Mahmood AAR, Tahtamouni LH, Al-Mazaydeh ZA, Rammaha MS, Alsoubani F, Al-bayati RI (2021) A novel derivative of picolinic acid induces endoplasmic reticulum stress-mediated apoptosis in human non-small cell lung cancer cells: synthesis, docking study, and anticancer activity. Pharmacia 68(3): 679-692. https://doi.org/10.3897/pharmacia.68.e70654
Figure 2 The MTT (3-(4,5-dimethylthiazol-2-yl)-2,5 diphenyltetrazolium bromide) assay results for compound 5 against MCF10A cells, and white blood cells (WBC) after 24, 48 and 72 h of treatment.
Figure 3 from: Abbas AH, Mahmood AAR, Tahtamouni LH, Al-Mazaydeh ZA, Rammaha MS, Alsoubani F, Al-bayati RI (2021) A novel derivative of picolinic acid induces endoplasmic reticulum stress-mediated apoptosis in human non-small cell lung cancer cells: synthesis, docking study, and anticancer activity. Pharmacia 68(3): 679-692. https://doi.org/10.3897/pharmacia.68.e70654
Figure 3 Compound 5 induces apoptosis in A549 lung cancer cells. A) Fluorescence images of A549 lung cancer cells showing fragmented nuclei after DAPI staining. Scale bar: 10 µm, B) Detection of DNA fragmentation by agarose gel electrophoresis. Cells were treated and genomic DNA was extracted and electrophoresed on 1.5% agarose gels. M: DNA molecular weight marker; C: vehicle-treated control cells; 1%: 1% DMSO-treated cells; 5%: 5% DMSO-treated cells; C.5: Compound 5-treated cells. Arrows indicate DNA fragments. Three experiments were performed with similar results.
Figure 6 from: Abbas AH, Mahmood AAR, Tahtamouni LH, Al-Mazaydeh ZA, Rammaha MS, Alsoubani F, Al-bayati RI (2021) A novel derivative of picolinic acid induces endoplasmic reticulum stress-mediated apoptosis in human non-small cell lung cancer cells: synthesis, docking study, and anticancer activity. Pharmacia 68(3): 679-692. https://doi.org/10.3897/pharmacia.68.e70654
Figure 6 3D View of the target compounds (5, 7A, 6B and 6C) docked against ATP binding site of EGFR kinase.
Figure 2 from: Quicke D, Butcher B, Smith M (2011) A new derived species group of Aleiodes parasitoid wasps (Hymenoptera, Braconidae, Rogadinae) from Asia with descriptions of three new species. Journal of Hymenoptera Research 23: 35-42. https://doi.org/10.3897/jhr.23.1663
Figure 2 - Cell^D montage images of holotype of Aleiodes spurivena sp. n. a habitus b face c mesosoma, dorsal view d metasoma.
Figure 3 from: Quicke D, Butcher B, Smith M (2011) A new derived species group of Aleiodes parasitoid wasps (Hymenoptera, Braconidae, Rogadinae) from Asia with descriptions of three new species. Journal of Hymenoptera Research 23: 35-42. https://doi.org/10.3897/jhr.23.1663
Figure 3 - Cell^D montage images of paratype Aleiodes spurivena sp. n. specimens a detail of fore wing venation b–d showing variation in metasomal colour pattern b voucher BF00928 from Vietnam c specimen from India d voucher BF00932 from Vietnam.
Figure 1 from: Quicke D, Butcher B, Smith M (2011) A new derived species group of Aleiodes parasitoid wasps (Hymenoptera, Braconidae, Rogadinae) from Asia with descriptions of three new species. Journal of Hymenoptera Research 23: 35-42. https://doi.org/10.3897/jhr.23.1663
Figure 1 - Features of fore wing venation of a Aleiodes spurivenatriplus sp. n. b Aleiodes spurivena sp. n. c Aleiodes spurivenaduplus sp. n.
Figure 8 from: Work T, St Onge B, Jacobs J (2011) Response of female beetles to LIDAR derived topographic variables in Eastern boreal mixedwood forests (Coleoptera, Carabidae). ZooKeys 147: 623-639. https://doi.org/10.3897/zookeys.147.2013
Figure 8 - Probability of collecting female Platynus decentis with changes in azimuth and slope when additional variables are held constant at their respective means. Both dashed and solid lines represent model parameters derived from full logistic model. Regression slopes for elevation appear near zero as total range of elevation is relatively small.
Figure 6 from: Work T, St Onge B, Jacobs J (2011) Response of female beetles to LIDAR derived topographic variables in Eastern boreal mixedwood forests (Coleoptera, Carabidae). ZooKeys 147: 623-639. https://doi.org/10.3897/zookeys.147.2013
Figure 6 - Probability of collecting female Pterostichus pensylvanicus with changes in azimuth and slope when additional variables are held constant at their respective means. Dashed lines represent model parameters derived from full logistic model. Solid lines represent model parameters of reduced logistic model including only curvature, FAC and intercept.
Figure 2 from: Work T, St Onge B, Jacobs J (2011) Response of female beetles to LIDAR derived topographic variables in Eastern boreal mixedwood forests (Coleoptera, Carabidae). ZooKeys 147: 623-639. https://doi.org/10.3897/zookeys.147.2013
Figure 2 - Probability of collecting female Calathus ingratus with changes in azimuth and slope when additional variables are held constant at their respective means. Dashed lines represent model parameters derived from full logistic model. Solid lines represent model parameters of reduced logistic model including only azimuth, slope and intercept.
Figure 7 from: Work T, St Onge B, Jacobs J (2011) Response of female beetles to LIDAR derived topographic variables in Eastern boreal mixedwood forests (Coleoptera, Carabidae). ZooKeys 147: 623-639. https://doi.org/10.3897/zookeys.147.2013
Figure 7 - Probability of collecting female Sphaeroderus nitidicollis with changes in azimuth and slope when additional variables are held constant at their respective means. Dashed lines represent model parameters derived from full logistic model. Solid lines represent model parameters of reduced logistic model including only curvature, FAC and intercept.
Figure 5 from: Work T, St Onge B, Jacobs J (2011) Response of female beetles to LIDAR derived topographic variables in Eastern boreal mixedwood forests (Coleoptera, Carabidae). ZooKeys 147: 623-639. https://doi.org/10.3897/zookeys.147.2013
Figure 5 - Figure 5. Probability of collecting female Synuchus impunctatus with changes in azimuth and slope when additional variables are held constant at their respective means. Dashed lines represent model parameters derived from full logistic model. Solid lines represent model parameters of reduced logistic model including only curvature, FAC and intercept.
Figure 4 from: Work T, St Onge B, Jacobs J (2011) Response of female beetles to LIDAR derived topographic variables in Eastern boreal mixedwood forests (Coleoptera, Carabidae). ZooKeys 147: 623-639. https://doi.org/10.3897/zookeys.147.2013
Figure 4 - Probability of collecting female Pterostichus coracinus with changes in azimuth, slope and elevation when additional variables are held constant at their respective means. Dashed lines represent model parameters derived from full logistic model. Solid lines represent model parameters of reduced logistic model including only azimuth, slope, elevation and intercept. Regression slopes for elevation appear near zero as total range of elevation is relatively small.
Figure 1 from: Work T, St Onge B, Jacobs J (2011) Response of female beetles to LIDAR derived topographic variables in Eastern boreal mixedwood forests (Coleoptera, Carabidae). ZooKeys 147: 623-639. https://doi.org/10.3897/zookeys.147.2013
Figure 1 - Probability of collecting female Agonum retractum with changes in azimuth and slope when additional variables are held constant at their respective means. Dashed lines represent model parameters derived from full logistic model. Solid lines represent model parameters of reduced logistic model including only azimuth, slope and intercept.
Figure 3 from: Work T, St Onge B, Jacobs J (2011) Response of female beetles to LIDAR derived topographic variables in Eastern boreal mixedwood forests (Coleoptera, Carabidae). ZooKeys 147: 623-639. https://doi.org/10.3897/zookeys.147.2013
Figure 3 - Probability of collecting female Pterostichus adstrictus with changes in azimuth, slope and elevation when additional variables are held constant at their respective means. Dashed lines represent model parameters derived from full logistic model. Solid lines represent model parameters of reduced logistic model including only azimuth, slope, elevation and intercept. Regression slopes for elevation appear near zero as total range of elevation is relatively small.
Transcriptome profiling of derived-hepatocyte progenitors from human iPSCs with nanoCAGE - part1 - genomic alignments (hg19 + hg38)
<p>This repository contains genomic alignments (BED files) of paired-end nanoCAGE sequencing data (CAGEscan data) collected from Illumina MiSeq run IDs "170630_M00528_0292_000000000-B9JY8" (aka "NC_LIMMS") and "180221_M00528_0334_000000000-B6PJM" (aka "NC_LIMMS2"). FASTQ files were processed with the MOIRAI pipeline OP-WORKFLOW-CAGEscan-short-reads-v2.1 (Hasegawa et al. BMC Bioinformatics 2014 May 16;15:144. doi: 10.1186/1471-2105-15-144.). Filtered pairs of reads were aligned on the human genome assemblies hg19 and hg38. See tables below for a detailed description of the samples contained in each nanoCAGE library, including barcodes and index sequences used for the demultiplexing of sequencing reads. Corresponding raw sequencing data files (FASTQ files) were deposited at Zenodo under the following Digital Object Identifier: 10.5281/zenodo.1014009.</p> <p> </p> <p><em><strong>"170630_M00528_0292_000000000-B9JY8" ("NC_LIMMS") :</strong></em></p> <p><strong>ID Sample_name Barcode_number Barcode_sequence Index_sequence</strong></p> <p>1 iPSC_control_rep1 4 ACAGAT NNNNNNNN</p> <p>2 iPSC_control_rep2 24 ATCGTG NNNNNNNN</p> <p>3 iPSC_control_rep3 31 CACGAT NNNNNNNN</p> <p>4 S3P1_OK_rep1 36 CACTGA NNNNNNNN</p> <p>5 S3P1_OK_rep2 46 CTGACG NNNNNNNN</p> <p>6 S3P1_OK_rep3 63 GAGTGA NNNNNNNN</p> <p>7 S4P1_OK_rep1 79 GTATAC NNNNNNNN</p> <p>8 S4P1_OK_rep2 92 TCGAGC NNNNNNNN</p> <p>9 S4P1_OK_rep3 9 ACATGA NNNNNNNN</p> <p>10 S4P2_OK_rep1 21 ATCATA NNNNNNNN</p> <p>11 S4P2_OK_rep2 33 CACGTG NNNNNNNN</p> <p>12 S4P2_OK_rep3 45 CGATGA NNNNNNNN</p> <p>13 S1P1_rep1 57 GAGATA NNNNNNNN</p> <p>14 S1P1_rep2 69 GCTCTC NNNNNNNN</p> <p>15 S1P1_rep3 81 GTATGA NNNNNNNN</p> <p>16 S3P1_FAILED_rep1 93 TCGATA NNNNNNNN</p> <p>17 S3P1_FAILED_rep2 11 AGTAGC NNNNNNNN</p> <p>18 S3P1_FAILED_rep3 23 ATCGCA NNNNNNNN</p> <p>19 S4P1_FAILED_rep1 35 CACTCT NNNNNNNN</p> <p>20 S4P1_FAILED_rep2 47 CTGAGC NNNNNNNN</p> <p>21 S4P1_FAILED_rep3 59 GAGCGT NNNNNNNN</p> <p>22 S4P2_FAILED_rep1 71 GCTGCA NNNNNNNN</p> <p>23 S4P2_FAILED_rep2 83 TATAGC NNNNNNNN</p> <p>24 S4P2_FAILED_rep3 95 TCGCGT NNNNNNNN</p> <p> </p> <p><em><strong>"180221_M00528_0334_000000000-B6PJM" ("NC_LIMMS2"):</strong></em></p> <p><strong>ID Sample_name Barcode_number Barcode_sequence Index_sequence</strong></p> <p>25 PETRI_rep1 04 ACAGAT NNNNNNNN</p> <p>26 PETRI_rep2 24 ATCGTG NNNNNNNN</p> <p>27 PETRI_rep3 31 CACGAT NNNNNNNN</p> <p>28 BIOCHIP_E_rep1 6 CACTGA NNNNNNNN</p> <p>29 BIOCHIP_M_rep1 46 CTGACG NNNNNNNN</p> <p>30 BIOCHIP_S_rep1 63 GAGTGA NNNNNNNN</p> <p>31 BIOCHIP_E_rep2 79 GTATAC NNNNNNNN</p> <p>32 BIOCHIP_M_rep2 92 TCGAGC NNNNNNNN</p> <p>33 BIOCHIP_S_rep2 09 ACATGA NNNNNNNN</p> <p>34 BIOCHIP_E_rep3 21 ATCATA NNNNNNNN</p> <p>35 BIOCHIP_M_rep3 33 CACGTG NNNNNNNN</p> <p>36 BIOCHIP_S_rep3 45 CGATGA NNNNNNNN</p> <p>37 HEPATOCYTES_rep1 57 GAGATA NNNNNNNN</p> <p>38 HEPATOCYTES_rep2 69 GCTCTC NNNNNNNN</p> <p>39 iPSC_control_rep1-2 81 GTATGA NNNNNNNN</p> <p>40 BIOCHIP_E_rep2-2 93 TCGATA NNNNNNNN</p> <p>41 BIOCHIP_M_rep1-2 11 AGTAGC NNNNNNNN</p> <p>42 BIOCHIP_S_rep2-2 23 ATCGCA NNNNNNNN</p> <p> </p>
Figure 2 from: Doshi P, Póss AM, Tóth F, Szalai M, Turóczi G (2018) Effect of neem-derived plant protection products on the isopod species Porcellionides pruinosus (Brandt, 1833). In: Hornung E, Taiti S, Szlavecz K (Eds) Isopods in a Changing World. ZooKeys 801: 415-425. https://doi.org/10.3897/zookeys.801.25510
Figure 2 Mortality rate of the isopod Porcellionidespruinosus after 120 hours to at different concentrations of neem leaf extract. The vertically jittered circles (to avoid perfect overlapping) indicate the individual isopods whereas the line indicates the trend of the mortality with respect to increasing concentrations and the grey area being the 95% confidence level.
Figure 1 from: Doshi P, Póss AM, Tóth F, Szalai M, Turóczi G (2018) Effect of neem-derived plant protection products on the isopod species Porcellionides pruinosus (Brandt, 1833). In: Hornung E, Taiti S, Szlavecz K (Eds) Isopods in a Changing World. ZooKeys 801: 415-425. https://doi.org/10.3897/zookeys.801.25510
Figure 1 Mortality rate of the isopod Porcellionidespruinosus after 120 hours at different concentrations of NeemAzal T/S (1% azadirachtin). The vertically jittered circles (to avoid perfect overlapping) indicate the individual isopods whereas the line indicates the trend of the mortality with respect to increasing concentrations and the grey area represents the 95% confidence level.
Linking population dynamics models with empirically derived models through phytoplankton primary production
<p>There are alternative methods for estimation of phytoplankton primary production (PP) that are fundamentally different in the calculation approach. The process-oriented PP model is a mechanistic, empirically derived method based on the photosynthesis–light relationships. The population dynamics-based PP calculation, which is a synthetic method, provides a production estimate based on population dynamics of phytoplankton. These alternative methods were here compared with regard to production estimates and linked to enhance the performance of the existing models of population dynamics applied to a wide variety of lakes worldwide in terms of morphometry, nutrient status, and light environments. Estimates of primary production were shown to be sensitive to changes in phytoplankton sinking and zooplankton grazing rates in both methods. Production estimates in the process-oriented PP model were also sensitive to light-associated parameters such as day length. Although the production estimated from the population dynamics-based PP calculation tended to be lower than that from the process-oriented PP model irrespective of lake morphometry, production estimates calculated from both methods with standard parameterization were comparable when production was estimated on an annual timescale. However, it was also shown that the alternative methods could produce different production estimates when estimated on shorter timescales such as cyanobacterial blooms in summer. Cyanobacteria with low mortality due to grazing and sinking losses have been considered as trophic bottlenecks, but there is increasing evidence that their mortality is, to a considerable extent, due to parasitic pathogens. In the case of cyanobacterial blooms, an addition of parasite-related loss term (19–33% of standing stock) resulted in a resolution of the difference in production estimates between the methods. These analyses theoretically support the critical role of parasitism and resolve the bottleneck problem in aquatic ecosystem metabolism.</p>
Localisation of oestrogen receptors in stem cells and in stem cell derived neurons of the mouse
<p>This dataset is linked to a publication in the Journal of Neuroendocrinology with the following DOI: 10.1111/jne.13220</p> <p>The Readme file gives details of the organisation of this dataset. All data here are raw data obtained from image analyses using the EZcoloc plugin for Fiji (Image J) and this raw data was used to construct the data graphs that are shown in the paper. In some graphs that involve ratios, integrated density values from Fiji were used.</p> <p>The softwares used are EZcoloc plugin and Image J referenced in the Readme file.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.