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South Sulawesi vector data

This file contains shapefiles that were used to built the bear cuscus habitat model in the southern landscape of South Sulawesi using MaxEnt in the WGS 84/UTM zone 50S coordinate system, i.e.: <ol> <li>The model area</li> <li>Rivers in South Sulawesi</li> <li>Settlements in South Sulawesi</li> <li>Roads in South Sulawesi, Bantimurung Bulusaraung National Park, and Hasanuddin University Educational Forest (consist of patrol roads (footpaths), local roads (rural roads), and arterial roads (highways)).</li> </ol>

Genome stability of murine cytomegalovirus vectors with large deletions and insertions

We investigated the basic characteristics of a new murine cytomegalovirus (MCMV) vector platform. Using BAC technology, we engineered replication-competent recombinant MCMVs with deletions of up to 26% of the wild type genome. To this end, we targeted five gene blocks (m01-m17, m106-m109, m129-m141, m144-m158, and m159-m170). BACs featuring deletions from 26-18% of the wild type genome exhibited delayed virus reconstitution, while smaller deletions (up to 16%) demonstrated reconstitution kinetics similar to the wild type. Utilizing an innovative methodology, we introduced large genomic DNA segments, up to 35 kbp, along with reporter genes into a newly designed vector with a potential cloning capacity of 46 kbp (Q4). Next, two independent stuffer DNAs were inserted into the Q4 BAC resulting in Q4-LAD and Q4-LRBAs BACs. LAD is an AT-rich DNA sequence based on inactivated human adenovirus genome (34 kbp) and a non-coding portion of human LRBA (LPS responsive beige-like anchor protein) gene a non-coding portion of human LRBA gene which is GC-rich (36 kbp). The Q4-LRBAs BAC was further modified by inserting two different transgene expression cassettes encoding for either Gaussian luciferase (GLuc) resulting in Q4-LRBAs-GLuc. First, we rescued replicating vectors after transfection of MEFs with the above described BACs. Each vector preparation was passaged up to 10 passage on MEFs. Then MEF cells (70% confluence) were infected with Q4, Q4-LAD, and Q4-LRBAs-GLuc at MOI 0.5. derived from passage 1, 5 and 10. As control we used lysates of wild type BAC derived MCMV infected MEFs after passages 1, 5, 10, 15, and 20. After 48 hpi, virus particles were harvested, purified, and DNA was extracted using the NucleoSpin Tissue kit (Macherey-Nagel, Germany). Illumina NGS was performed on 100 ng DNA template for each sample (paired end sequencing, 2×150 bp, 5 Mio reads/sample). This dataset contains the raw sequencing data (individually named .zip files) and a table (an .xlsx file packed into MCMV Vector Stability_VACCINES_2024.zip) with the detailed specifications of the dataset. The reference sequences, which we used for the analysis in our Vaccines paper (Riedl et al. Vaccines, 2024), are provided in a zipped folder in .gb format.

Transcriptional profiling of ARPE-19 cells infected with high capacity MCMV vector.

To gain a detailed knowledge about the virus cycle of murine cytomegalovirus (MCMV) and its high capacity vector in cross-species settings, we analyzed the early and late viral and host transcriptome upon infection of human cells. ARPE-19, A549, and 911 cells (5.0×105 cells/well) were infected in a 24-well format 4 h post-seeding with MCMV-wt or Q4-LRBAs-GLuc, a high capacity replication competent vector based on MCMV, at an MOI of 3. As control, we used infection of mouse embryonic fibroblast, which is the natural host of the wild type MCMV, treated similarly. Harvesting occurred at 8 hpi and 31 hpi through centrifugation at 1.000 g for 5 min. Cell pellets were washed with PBS, re-suspended in 350 µL of RLT buffer, and processed using the RNeasy Mini kit as per the manufacturer’s instructions in independent triplicates. At least 1.500 ng of RNA in a 30 µL volume was isolated and sent for Illumina next-generation sequencing, resulting in paired-end sequencing with a read length of 2×100 bp and a depth of 20 million reads. This submission contains the reads, we obtained analyzing the infections of ARPE-19 cells. The data sheet for the samples and the reference genomes (.gb), which we used in the analysis published in Riedl et al. Vaccines 2024 can be found in the REFERENCES_ARPE-19.zip folder. Please, find the control reads for uninfected cells in a separate upload entitled: Mock infected controls for transcriptional profiling of infections with high capacity MCMV vector (DOI 10.5281/zenodo.1250410).

Transcriptional profiling of 911 cells infected with high capacity MCMV vector.

To gain a detailed knowledge about the virus cycle of murine cytomegalovirus (MCMV) and its high capacity vector in cross-species settings, we analyzed the early and late viral and host transcriptome upon infection of human cells. ARPE-19, A549, and 911 cells (5.0×105 cells/well) were infected in a 24-well format 4 h post-seeding with MCMV-wt or Q4-LRBAs-GLuc, a high capacity replication competent vector based on MCMV, at an MOI of 3. As control, we used infection of mouse embryonic fibroblast, which is the natural host of the wild type MCMV, treated similarly. Harvesting occurred at 8 hpi and 31 hpi through centrifugation at 1.000 g for 5 min. Cell pellets were washed with PBS, re-suspended in 350 µL of RLT buffer, and processed using the RNeasy Mini kit as per the manufacturer’s instructions in independent triplicates. At least 1.500 ng of RNA in a 30 µL volume was isolated and sent for Illumina next-generation sequencing, resulting in paired-end sequencing with a read length of 2×100 bp and a depth of 20 million reads. This submission contains the reads, we obtained analyzing the infections of 911 cells. The data sheet for the samples and the reference genomes (.gb), which we used in the analysis published in Riedl et al. Vaccines 2024 can be found in the REFERENCES_911.zip folder. Please, find the control reads for uninfected cells in a separate upload entitled: Mock infected controls for transcriptional profiling of infections with high capacity MCMV vector (DOI 10.5281/zenodo.1250410).

opencc-by-4.0Feb 2018View details →

Mutagenesis of RRL-NSD3-Short-3xFLAG Lentiviral Vector

SGC Open Notebook Project to Characterize the HMTase NSD3 Exp013 Objective: The NSD3’s PWWP1 domain is present in both long and short isoforms. It has been shown to bind H3K36me2 (Sankaran et al.(2016) - PMID:26912663) and be required for the maintenance of AML (Chen et al.(2015 - PMID: 26912663). However, it is still unclear how this domain contributes to NSD3’s function at enhancers. To study this aspect of NSD3’s biology, I will mutate W284 to alanine in the RRLNSD3-3xFLAG-IRES-Puro plasmids I described earlier (exp010) by site-directed mutagenesis. This is the second tryptophan within the PWWP1 motif and is critical for substrate recognition (Qin, S & Min, J(2014) - PMID:25277115). This construct will be useful for understanding how NSD3 recognition of methylated histones influences its putative activity in cancer.

opencc-by-4.0Jan 2018View details →

Meshes, volume fractions, and normal vectors for paraboloid fit verification

These datasets are used to verify the results of the paper "A Paraboloid Fitting Technique for Calculating Curvature from Piecewise-Linear Interface Reconstructions on 3D Unstructured Meshes" by Z. Jibben, N. N. Carlson, and M. M. Francois.

opencc-by-4.0Mar 2018View details →

Mutagenesis to Replace IRES with T2A in NSD3-Short-3xFLAG Lentiviral Expression Vector

SGC Open Notebook Project to Characterize the HMTase NSD3 Exp016 Objective: Bicistronic elements are common features in lentiviral expression systems that allow expression of two protein products from a single promoter. The two most common bicistronic elements are the internal ribosome entry site (IRES), which allows cap-independent translation of a second open reading frame within an mRNA, and the 2A system, which introduces a self-cleaving peptide between two desired protein products. There are several advantages to the the 2A system over an IRES, which include matched expression levels of your two protein products of interest as well as having a smaller footprint (~1/10 size in kb), which may improve viral titre. Therefore, I will use site-directed mutagenesis to alter the NSD3short lentiviral expression plasmid to replace the IRES sequence with a T2A sequence.

opennotspecifiedApr 2018View details →

FIGURE 2 in The Asian tiger mosquito, Aedes (Stegomyia) albopictus (Skuse), a vector of dengue, chikungunya and zika viruses, reaches Portugal (Diptera: Culicidae)

FIGURE 2. Portuguese Aedes albopictus females seeking human blood. Note characteristic scutal white stripe, distinct silvery-white scales on the maxillary palpi and tarsi, as well as narrow scales over the wing root and silvery-white basolateral abdominal tergal markings.

opennotspecifiedApr 2018View details →

FIGURE 1 in The Asian tiger mosquito, Aedes (Stegomyia) albopictus (Skuse), a vector of dengue, chikungunya and zika viruses, reaches Portugal (Diptera: Culicidae)

FIGURE 1. Distribution of Aedes albopictus in the Iberian Península. In green, distribution in Spain according to Collantes et al. (2016). In red, highlighted by arrow, new occurrence in Portugal.

opennotspecifiedApr 2018View details →

FIGURE 3 in The Asian tiger mosquito, Aedes (Stegomyia) albopictus (Skuse), a vector of dengue, chikungunya and zika viruses, reaches Portugal (Diptera: Culicidae)

FIGURE 3. Biting activity of Ae. albopictus assessed by human-bait catches. Specimens arriving to bite were captured every 15 minutes to avoid recapture. The x axis is a timeline of 15-minute intervals; the y axis is an average of the three days of sampling.

opencc-by-sa-4.0Oct 2018View details →

Road network with roadscape vectors in Awaji Island, Japan

Summary This dataset contains road network with roadscape vectors in Awaji Island, Japan. The road network data is derived from OpenStreetMap, and it consists of 102,506 road nodes and 212,050 road links in the area of Awaji Island. Roadscape vectors are given to each road link. Road network data A road network is a directed graph G = (V, E), where  V is a road node set and E &sube; V × V is a road link set. A road node vi ∈ V represents an intersection or an end point. A road link ek = (vi, vj) ∈ E represents a directed link from the starting node vi to the ending node vj. Road nodes data <code>m_road_nodes_latlng.csv</code> Road nodes are contained in the file m_road_nodes_latlng.csv. The number of road nodes is 102,506. Each line corresponds to one node.  These lines have the following format as tab delimited:  <code>node_id, lat, lng</code> Here, node_id denotes a road node ID for identifying a road node. lat and lng denote latitude and longitude, respectively. Road links data <code>m_road_links_nodes.csv</code> Road links are contained in the file m_road_links_nodes.csv. The number of road links is 212,050. Each line corresponds to  one link. These lines have the following format as tab delimited:  <code>link_id, start_node_id, end_node_id</code> Here, link_id denotes a road link ID for identifying a road link. start_node_id and end_node_id denote starting node ID and ending node ID, which refer to node_id in the file m_road_nodes_latlng.csv (i.e. the same node ID refers to the same road node across these files), respectively. Roadscape vectors A roadscape vector is defined as a four-dimensional probability vector composed of four kinds of roadscape elements, rural, mountainous, waterside, and urban elements. Each element of the vector denotes the probability of including the roadscape element. Therefore, the sum of values over all elements is 1. Road link vectors data <code>m_road_links_vector.csv</code> Roadscape vectors of road links are contained in the file m_road_links_vector.csv. Each line corresponds to one link with its roadscape vector. These lines have the following format as tab delimited:  <code>link_id, rural, mountain, water, urban</code> Here, link_id denotes a road link ID, which refer to link_id in the file m_road_lonks_nodes.csv (i.e. the same link ID referes to the same road link across these files). The rural, mountain, water, and urban denote rural, mountainous, waterside, urban elements in its roadscape vector, respectively. Citation To make use of the dataset, please cite the following paper: <ol> <li>Koji Kawamata and Kenta Oku. Roadscape-based Route Recommender System using Coarse-to-fine Route Search, In Proceeding of the ACM RecSys Workshop on Recommenders in Tourism (RecTour 2018), pp.23--27, 2018.</li> <li>Koji Kawamata and Kenta Oku. Roadscape-based route recommender system using coarse-to-fine route search. Journal of Information Processing, 27, pp.392–403. https://doi.org/10.2197/ipsjjip.27.392</li> </ol>

opencc-by-4.0Oct 2018View details →

Compound data sets for support vector machine and regression modeling

Provided are compound data sets used for support vector machine and support vector regression modeling and associated information.

opencc-by-4.0Mar 2019View details →

Cloud motion vectors used in "Formation of the Y feature at the Venusian cloud top by planetary-scale waves and the mean circulation: analysis of Venus Express VMC images"

This is dataset  of cloud motion vectors deduced used in "Formation of the Y feature at the Venusian cloud top by planetary-scale waves and the mean circulation:  analysis of Venus Express VMC images".

opencc-by-4.0Jun 2019View details →

mTagBFP2-expressing vectors for electroporation of marine protists

Plasmid maps and genbank sequence files for the plasmids used for electroporation of model organism Nannochloropsis oceanica and environmental samples following the protocol <a href="https://www.protocols.io/view/fabrication-of-dna-constructs-by-gibson-assembly-a-7r8hm9w">Matute et al.</a> EMS initiative from Gordon and Betty Moore foundation.

Datasets used in the papers: STree: A Single Multi-class Oblique Decision Tree Based on Support Vector Machines & ODTE - An ensemble of multi-class SVM-based oblique decision trees

These are the 49 datasets used in the benchmark. 45 of them are from the UCI machine learning repository, while the other 4 correspond to a problem about fecundity estimation for fisheries

Fig. 1 in Distribution, adult phenology and life history traits of potential insect vectors of Xylella fastidiosa in Belgium

Fig. 1. Distribution map for Philaenus spumarius in Belgium. Data: RBINS; Observations.be (2010-2016); our own samplings (2016-2017).

Fig. 11 in Distribution, adult phenology and life history traits of potential insect vectors of Xylella fastidiosa in Belgium

Fig. 11. Distribution map for Aphrophora salicina in Belgium. Data: RBINS; Observations.be (2010-2016); our own samplings (2016-2017).

Fig. 8 in Distribution, adult phenology and life history traits of potential insect vectors of Xylella fastidiosa in Belgium

Fig. 8. Phenology of adult Cercopis vulnerata in Belgium. Data: RBINS; Observations.be (2005-2017); our own samplings (2016-2017).

Fig. 4 in Distribution, adult phenology and life history traits of potential insect vectors of Xylella fastidiosa in Belgium

Fig. 4. Distribution map for Cicadella viridis in Belgium. Data: RBINS; Observations.be (2010-2016); our own samplings (2016-2017).

Fig. 7 in Distribution, adult phenology and life history traits of potential insect vectors of Xylella fastidiosa in Belgium

Fig. 7. Distribution map for Cercopis vulnerata in Belgium: Data: RBINS; Observations.be (2010-2016); our own samplings (2016-2017).