cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3310660.v1
title: Proteomic Analysis of Rac1 Signalling Regulation by Guanine Nucleotide Exchange Factors

description: The small GTPase Rac1 is implicated in various cellular processes that are essential for normal cell function. Deregulation of Rac1 signalling has also been linked to a number of diseases, including cancer. The diversity of Rac1 functioning in cells is mainly attributed to its ability to bind to a multitude of downstream effectors following activation by Guanine nucleotide Exchange Factors (GEFs). Despite the identification of a large number of Rac1 binding partners, factors influencing downstream specificity are poorly defined, thus hindering the detailed understanding of both Rac1's normal and pathological functions. In a recent study we demonstrated a role for two Rac-specific GEFs, Tiam1 and P-Rex1 in mediating Rac1 anti- versus pro-migratory effects, respectively. Importantly, via conducting a quantitative proteomic screen we identified distinct changes in the Rac1 interactome following activation by either GEF indicating that these opposing effects are mediated through GEF modulation of the Rac1 interactome. Here we present the full list of identified Rac1 interactors together with functional annotation of the differentially regulated Rac1 binding partners. In light of this data we also provide additional insights into known and novel signalling cascades that might account for the GEF-mediated Rac1-driven cellular effects.
DOI: 10.6084/m9.figshare.3310600.v1
title: <b>RNA helicase SACY-1 is required for the longevity caused by various genetic perturbations in</b><i><b>Caenorhabditis elegans</b></i>

description: RNA helicases, which unwind RNAs, are essential for RNA metabolism and homeostasis. However, the roles of RNA helicases in specific physiological processes remain poorly understood. We recently reported that an RNA helicase, HEL-1, promotes long lifespan conferred by reduced insulin/insulin-like growth factor-1 (IGF-1) signaling (IIS) in <i>Caenorhabditis elegans</i>. We also showed that HEL-1 induces the expression of longevity genes by physically interacting with Forkhead box O (FOXO) transcription factor. Thus, the HEL-1 RNA helicase appears to regulate lifespan by specifically activating FOXO in IIS. In the current study, we report another longevity-promoting RNA helicase, Suppressor of ACY-4 sterility 1 (SACY-1). SACY-1 contributed to the longevity of <i>daf-2</i>/insulin/IGF-1 receptor mutants. Unlike HEL-1, SACY-1 was also required for the longevity due to mutations in the genes involved in non-IIS pathways. Thus, SACY-1 appears to function as a general longevity factor for various signaling pathways, which is different from the specific function of HEL-1.
DOI: 10.6084/m9.figshare.3309430
title: Comparative analysis of cardiovascular effects of selenium nanoparticles and sodium selenite in zebrafish embryos

description: Selenium acts as an important element in the prevention and treatment of cardiovascular diseases but their health-related effects have not been fully explored. As a novel attempt, zebrafish embryos were treated separately with SeNPs (5–25 μg/ml) and sodium selenite (5–25 μg/ml) starting at early blastula stage. Abnormalities were also observed in the morphology of the zebrafish embryos. The SeNPs-treated embryos exhibited concentration-dependent increased in mortality, pericardial edema, and cardiac arrhythmia. In contrast, sodium selenite showed no significant malformation effect in developing zebrafish embryos. The results of the present study conclude that the SeNPs were more toxic than sodium selenite. The results also suggest that lower concentrations of SeNPs and sodium selenite can be used as possible therapeutic agents for cardiovascular-related problems.
DOI: 10.6084/m9.figshare.3309442
title: Transcriptome analysis of reproductive-stage <i>Arabidopsis</i> plants exposed gamma-ray irradiation at various doses

description: <b>Purpose:</b> Gamma rays (GR) induce significant changes in the structure and expression of genes involved in the regulation of diverse biochemical and physiological processes. <i>Arabidopsis</i> plants exhibit different growth and development patterns in response to exposure to GR. The effects on gene expression of different radiation doses of GR (100 and 800 Gy) administered to <i>Arabidopsis</i> plants were examined at the reproductive stage. <b>Materials and methods:</b> We irradiated 26-day-old plants with three replications [developmental stages 5.1–6.0, according to Boyes et al. (2001)] using a GR irradiator (60 Co, <i>ca</i>. 150 TBq capacity, Atomic Energy of Canada Limited, Ontario, Canada) at the Korea Atomic Energy Research Institute. Plants were treated with 100, 200, 300, 400, 800, 1200, 1600, or 2000 Gy, and the doses were made from varying the distance to the source. <b>Results:</b> We conducted a high-throughput screening analysis and detected 883 GR-responsive genes that showed significant changes; these were involved in several putative metabolic pathways related to biotic stress. Additionally, five overrepresented <i>cis</i>-regulatory elements were identified in the 1-kb upstream regions of GR-responsive genes by using motif enrichment analysis. We also detected three GR-responsive genes associated with stamen development and confirmed their co-regulation with functionally interacting genes. <b>Conclusions:</b> This finding suggests that a network-based analysis is a viable approach to identify significant GR-responsive genes associated with the reproductive stage of <i>Arabidopsis</i>. Our results provide further insights into the complex biological systems involved in the response to different doses of GR in plants.
DOI: 10.6084/m9.figshare.3309424
title: UNH tow tank and turbine test bed CAD files

description: Full SolidWorks 2016 CAD assembly for the UNH tow tank and turbine test bed.
DOI: 10.6084/m9.figshare.3309442.v1
title: Transcriptome analysis of reproductive-stage <i>Arabidopsis</i> plants exposed gamma-ray irradiation at various doses

description: <b>Purpose:</b> Gamma rays (GR) induce significant changes in the structure and expression of genes involved in the regulation of diverse biochemical and physiological processes. <i>Arabidopsis</i> plants exhibit different growth and development patterns in response to exposure to GR. The effects on gene expression of different radiation doses of GR (100 and 800 Gy) administered to <i>Arabidopsis</i> plants were examined at the reproductive stage. <b>Materials and methods:</b> We irradiated 26-day-old plants with three replications [developmental stages 5.1–6.0, according to Boyes et al. (2001)] using a GR irradiator (60 Co, <i>ca</i>. 150 TBq capacity, Atomic Energy of Canada Limited, Ontario, Canada) at the Korea Atomic Energy Research Institute. Plants were treated with 100, 200, 300, 400, 800, 1200, 1600, or 2000 Gy, and the doses were made from varying the distance to the source. <b>Results:</b> We conducted a high-throughput screening analysis and detected 883 GR-responsive genes that showed significant changes; these were involved in several putative metabolic pathways related to biotic stress. Additionally, five overrepresented <i>cis</i>-regulatory elements were identified in the 1-kb upstream regions of GR-responsive genes by using motif enrichment analysis. We also detected three GR-responsive genes associated with stamen development and confirmed their co-regulation with functionally interacting genes. <b>Conclusions:</b> This finding suggests that a network-based analysis is a viable approach to identify significant GR-responsive genes associated with the reproductive stage of <i>Arabidopsis</i>. Our results provide further insights into the complex biological systems involved in the response to different doses of GR in plants.
DOI: 10.6084/m9.figshare.3309430.v1
title: Comparative analysis of cardiovascular effects of selenium nanoparticles and sodium selenite in zebrafish embryos

description: Selenium acts as an important element in the prevention and treatment of cardiovascular diseases but their health-related effects have not been fully explored. As a novel attempt, zebrafish embryos were treated separately with SeNPs (5–25 μg/ml) and sodium selenite (5–25 μg/ml) starting at early blastula stage. Abnormalities were also observed in the morphology of the zebrafish embryos. The SeNPs-treated embryos exhibited concentration-dependent increased in mortality, pericardial edema, and cardiac arrhythmia. In contrast, sodium selenite showed no significant malformation effect in developing zebrafish embryos. The results of the present study conclude that the SeNPs were more toxic than sodium selenite. The results also suggest that lower concentrations of SeNPs and sodium selenite can be used as possible therapeutic agents for cardiovascular-related problems.
DOI: 10.6084/m9.figshare.3309352
title: A Hybrid Hashing Security Algorithm for Data Storage on Cloud Computing.pdf

description: <b>In today's modern IT everything is possible</b><br><b>on the web by cloud computing, it allows us to create,</b><br><b>configure, use and customize the applications, services,</b><br><b>and storage online. The Cloud Computing is a kind of</b><br><b>Internet-based computing, where shared data, information</b><br><b>and resources are provided with computers and other</b><br><b>devices on-demand. The Cloud Computing offers several</b><br><b>advantages to the organizations such as scalability, low</b><br><b>cost, and flexibility. In spite of these advantages, there is a</b><br><b>major problem of cloud computing, which is the security</b><br><b>of cloud storage. There are a lot of mechanisms that is</b><br><b>used to realize the security of data in the cloud storage.</b><br><b>Cryptography is the most used mechanism. The science of</b><br><b>designing ciphers, block ciphers, stream ciphers and hash</b><br><b>functions is called cryptography. Cryptographic</b><br><b>techniques in the cloud must enable security services such</b><br><b>as authorization, availability, confidentiality, integrity, and</b><br><b>non-repudiation. To ensure these services of security, we</b><br><b>propose an effective mechanism with a significant feature</b><br><b>of the data. This paper is to show how to improve the</b><br><b>security of the Cloud storage using the implementation of</b><br><b>a hybrid encryption algorithm and hash functions. It</b><br><b>proposes the implementation of two algorithms, RivestShamir-Adleman (RSA) and Advanced Encryption</b><br><b>Standard (AES) with a secure hashing algorithm</b><br><b>(SHA256) by using Netbeans IDE 8.0.2, JDK 1.7 tool and</b><br><b>EyeOS2.5 as a cloud platform on ubuntu14.04</b><br><br>
DOI: 10.6084/m9.figshare.3273898
title: Discriminant analysis of defective and non-defective field pea (Pisium sativum L.) into broad market grades based on digital image features

description: This data relates to the manuscript entitled 'Discriminant analysis of defective and non-defective field pea (Pisium sativum L.) into broad market grades based on digital image features.'<br>Data includes the market grade classifications, defect classifications and image features, used to build the LDA models, for each field pea sample in both the calibration and validation sets. Also included are the model predictions of market grade and defect class for each sample.<br>
DOI: 10.6084/m9.figshare.3278932
title: Uncomplicated malaria features and efficacy of ASAQ in DR Congo.dta

description: Data related to the manuscript entitled:Uncomplicated clinical malaria features, the efficacy of artesunate-amodiaquine and their relation with multiplicity of infection in the Democratic Republic of Congo.<br><br>This was a cohort that allowed to describe uncomplicated malaria features and assess efficacy of artesunate-amodiaquine. Participants were followed up during 42 days. Clinical failures had to be recruited in a randomized clinical trial to assess the efficacy and safety of rescue treatments. <b><br></b>
DOI: 10.5281/zenodo.4014948
title: Drone aerial imagery of macroalgae growing in a small embayment at the western end of the Nuussuaq Peninsula in Northwest Greenland

description: Aerial images of a small embayment at the western tip of the Nuussuaq Peninsula (NW Greenland) were acquired on 10 August 2019 using a DJI Phantom 3 Standard quadcopter drone. The imagery was acquired during the Vaigat Iceberg-Microbial Oil Degradation and Archaeological Heritage Investiga- tion (VIMOA) research cruise. Overlapping images were acquired during two consecutive flights using the 'interval' setting with a period of 5 seconds in the DJI Go app. The drone was flown manually. This drone survey was carried out with two primary objectives in mind: 1) Identify and quantify the macroalgae growing on the coast; 2) Identify any archaeological and cultural heritage sites that may be present. Images were processed using Agisoft PhotoScan Pro (v1.4.4; Linux Ubuntu). Images were aligned using the script CARMA_PhotoScan_Align.py (see this script for settings). After image alignment, the bounding box was visually inspected and the sparse point cloud was thinned using thresholds for the reconstruction uncertainty, projection accuracy, and reprojection error (gradual selection). The remaining tie points in the sparse cloud were then used to build the dense cloud. The settings used for this step can be found in the script CARMA_PhotoScan_GS_DC_v2.py. Next, the dense point cloud was used to generate a digital elevation model (DEM) and, subsequently, an orthomosaic. The Agisoft PhotoScan processing report is also included.
DOI: 10.6084/m9.figshare.3261007
title: A case study of potential human health impacts from petroleum coke transfer facilities

description: Petroleum coke or “petcoke” is a solid material created during petroleum refinement and is distributed via transfer facilities that may be located in densely populated areas. The health impacts from petcoke exposure to residents living in proximity to such facilities were evaluated for a petcoke transfer facilities located in Chicago, Illinois. Site-specific, margin of safety (MOS) and margin of exposure (MOE) analyses were conducted using estimated airborne and dermal exposures. The exposure assessment was based on a combined measurement and modeling program that included multiyear on-site air monitoring, air dispersion modeling, and analyses of soil and surfaces in residential areas adjacent to two petcoke transfer facilities located in industrial areas. Airborne particulate matter less than 10 microns (PM<sub>10</sub>) were used as a marker for petcoke. Based on daily fence line monitoring, the average daily PM<sub>10</sub> concentration at the KCBX Terminals measured on-site was 32 μg/m<sup>3</sup>, with 89% of 24-hr average PM<sub>10</sub> concentrations below 50 μg/m<sup>3</sup> and 99% below 100 μg/m<sup>3</sup>. A dispersion model estimated that the emission sources at the KCBX Terminals produced peak PM<sub>10</sub> levels attributed to the petcoke facility at the most highly impacted residence of 11 μg/m<sup>3</sup> on an annual average basis and 54 μg/m<sup>3</sup> on 24-hr average basis. Chemical indicators of petcoke in soil and surface samples collected from residential neighborhoods adjacent to the facilities were equivalent to levels in corresponding samples collected at reference locations elsewhere in Chicago, a finding that is consistent with limited potential for off-site exposure indicated by the fence line monitoring and air dispersion modeling. The MOE based upon dispersion model estimates ranged from 800 to 900 for potential inhalation, the primary route of concern for particulate matter. This indicates a low likelihood of adverse health effects in the surrounding community. <i>Implications</i>: Handling of petroleum coke at bulk material transfer facilities has been identified as a concern for the public health of surrounding populations. The current assessment, based on measurements and modeling of two facilities located in a densely populated urban area, indicates that petcoke transport and accumulation in off-site locations is minimal. In addition, estimated human exposures, if any, are well below levels that could be anticipated to produce adverse health effects in the general population.
DOI: 10.5281/zenodo.4014947
title: Drone aerial imagery of macroalgae growing in a small embayment at the western end of the Nuussuaq Peninsula in Northwest Greenland

description: Aerial images of a small embayment at the western tip of the Nuussuaq Peninsula (NW Greenland) were acquired on 10 August 2019 using a DJI Phantom 3 Standard quadcopter drone. The imagery was acquired during the Vaigat Iceberg-Microbial Oil Degradation and Archaeological Heritage Investiga- tion (VIMOA) research cruise. Overlapping images were acquired during two consecutive flights using the 'interval' setting with a period of 5 seconds in the DJI Go app. The drone was flown manually. This drone survey was carried out with two primary objectives in mind: 1) Identify and quantify the macroalgae growing on the coast; 2) Identify any archaeological and cultural heritage sites that may be present. Images were processed using Agisoft PhotoScan Pro (v1.4.4; Linux Ubuntu). Images were aligned using the script CARMA_PhotoScan_Align.py (see this script for settings). After image alignment, the bounding box was visually inspected and the sparse point cloud was thinned using thresholds for the reconstruction uncertainty, projection accuracy, and reprojection error (gradual selection). The remaining tie points in the sparse cloud were then used to build the dense cloud. The settings used for this step can be found in the script CARMA_PhotoScan_GS_DC_v2.py. Next, the dense point cloud was used to generate a digital elevation model (DEM) and, subsequently, an orthomosaic. The Agisoft PhotoScan processing report is also included.
DOI: 10.6084/m9.figshare.3262210
title: Perturbation Detection Through Modeling of Gene Expression on a Latent Biological Pathway Network: A Bayesian Hierarchical Approach

description: Cellular response to a perturbation is the result of a dynamic system of biological variables linked in a complex network. A major challenge in drug and disease studies is identifying the key factors of a biological network that are essential in determining the cell’s fate. Here, our goal is the identification of perturbed pathways from high-throughput gene expression data. We develop a three-level hierarchical model, where (i) the first level captures the relationship between gene expression and biological pathways using confirmatory factor analysis, (ii) the second level models the behavior within an underlying network of pathways induced by an unknown perturbation using a conditional autoregressive model, and (iii) the third level is a spike-and-slab prior on the perturbations. We then identify perturbations through posterior-based variable selection. We illustrate our approach using gene transcription drug perturbation profiles from the DREAM7 drug sensitivity predication challenge dataset. Our proposed method identified regulatory pathways that are known to play a causative role and that were not readily resolved using gene set enrichment analysis or exploratory factor models. Simulation results are presented assessing the performance of this model relative to a network-free variant and its robustness to inaccuracies in biological databases. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.3261007.v2
title: A case study of potential human health impacts from petroleum coke transfer facilities

description: Petroleum coke or “petcoke” is a solid material created during petroleum refinement and is distributed via transfer facilities that may be located in densely populated areas. The health impacts from petcoke exposure to residents living in proximity to such facilities were evaluated for a petcoke transfer facilities located in Chicago, Illinois. Site-specific, margin of safety (MOS) and margin of exposure (MOE) analyses were conducted using estimated airborne and dermal exposures. The exposure assessment was based on a combined measurement and modeling program that included multiyear on-site air monitoring, air dispersion modeling, and analyses of soil and surfaces in residential areas adjacent to two petcoke transfer facilities located in industrial areas. Airborne particulate matter less than 10 microns (PM<sub>10</sub>) were used as a marker for petcoke. Based on daily fence line monitoring, the average daily PM<sub>10</sub> concentration at the KCBX Terminals measured on-site was 32 μg/m<sup>3</sup>, with 89% of 24-hr average PM<sub>10</sub> concentrations below 50 μg/m<sup>3</sup> and 99% below 100 μg/m<sup>3</sup>. A dispersion model estimated that the emission sources at the KCBX Terminals produced peak PM<sub>10</sub> levels attributed to the petcoke facility at the most highly impacted residence of 11 μg/m<sup>3</sup> on an annual average basis and 54 μg/m<sup>3</sup> on 24-hr average basis. Chemical indicators of petcoke in soil and surface samples collected from residential neighborhoods adjacent to the facilities were equivalent to levels in corresponding samples collected at reference locations elsewhere in Chicago, a finding that is consistent with limited potential for off-site exposure indicated by the fence line monitoring and air dispersion modeling. The MOE based upon dispersion model estimates ranged from 800 to 900 for potential inhalation, the primary route of concern for particulate matter. This indicates a low likelihood of adverse health effects in the surrounding community. <i>Implications</i>: Handling of petroleum coke at bulk material transfer facilities has been identified as a concern for the public health of surrounding populations. The current assessment, based on measurements and modeling of two facilities located in a densely populated urban area, indicates that petcoke transport and accumulation in off-site locations is minimal. In addition, estimated human exposures, if any, are well below levels that could be anticipated to produce adverse health effects in the general population.
DOI: 10.6084/m9.figshare.3262210.v1
title: Perturbation Detection Through Modeling of Gene Expression on a Latent Biological Pathway Network: A Bayesian Hierarchical Approach

description: Cellular response to a perturbation is the result of a dynamic system of biological variables linked in a complex network. A major challenge in drug and disease studies is identifying the key factors of a biological network that are essential in determining the cell’s fate. Here, our goal is the identification of perturbed pathways from high-throughput gene expression data. We develop a three-level hierarchical model, where (i) the first level captures the relationship between gene expression and biological pathways using confirmatory factor analysis, (ii) the second level models the behavior within an underlying network of pathways induced by an unknown perturbation using a conditional autoregressive model, and (iii) the third level is a spike-and-slab prior on the perturbations. We then identify perturbations through posterior-based variable selection. We illustrate our approach using gene transcription drug perturbation profiles from the DREAM7 drug sensitivity predication challenge dataset. Our proposed method identified regulatory pathways that are known to play a causative role and that were not readily resolved using gene set enrichment analysis or exploratory factor models. Simulation results are presented assessing the performance of this model relative to a network-free variant and its robustness to inaccuracies in biological databases. Supplementary materials for this article are available online.