Find research datasets worth reusing

opencc-by-4.0Mar 2022View details →

Copper Rings Insertion Attempts Dataset

The dataset consists of color images of different outcomes of the copper ring insertion task as well as the corresponding Cartesian pose of the robot end-effector and force torque data measured in the robot wrist. Data is organized into folders, representing one of four possible insertion slots from 1 to 4. In each of the folder, data is further split into 13 cases: - error in insertion target position ranging from -3 to 3 mm in x direction, - error in insertion target position ranging from -3 to 3 mm in y direction, - no positional error. Multiple attempts were made for each case. Each entry has unique date-time tag and comprises five files: RGB image (.jpg) and .csv files with robot reference and measured target pose in Cartesian space (positions and quaternions) and raw force-torque sensor data and force-torque data transformed to the tool frame. Total number of entries is 300. The experiments were performed with Franka Emika Panda collaborative robot. For acquisition of image data an Intel Realsense D435 RGB-D camera has been utilized. Force-torque measurements were done using ATI Nano25 sensor.

opencc-by-4.0Mar 2022View details →

Copper Rings Insertion Validation Dataset

The dataset consists of color images of the fixture with inserted copper sliding rings, which is used to evaluate and validate the process of assembly of an object with low tolerances supported by multi modal exception strategy learning and ergodic control. This dataset is used to classify the insertion process into three states: OK, NotOK or NoPart. The dataset consists of two main classes: Valid Insertion, Invalid Insertion in each of the four insertion slots.

opencc-by-4.0May 2019View details →

Genome-wide de novo L1 Retrotransposition Connects Endonuclease Activity with Replication: insertion data and derivative models

This data repository provides access to the LINE-1 (L1) insertion site data from Flasch, et al., 2019: <a href="https://www.sciencedirect.com/science/article/pii/S0092867419302338?via%3Dihub">https://www.sciencedirect.com/science/article/pii/S0092867419302338?via%3Dihub</a> Please see file L1_actual_and_random_insertions_help.docx for more detailed information. Files weighted_model_142_102917_corrected.txt and weighted_model_142_102917_uncorrected.txt carry a list of all possible 7-mer insertion sites, one per row, with site weights calculated based on observed L1 insertion sites. The files are either corrected or uncorrected for the frequency of those sites as found in the human genome, respectively. A header line defines the columns. The weight files described above were used to construct the simulated hg19 insertions sets described below. Archive all_insertion_sets.tar contains a series of insertion files, each with the complete data set used to analyze insertions from the named cell line. Column 5 is the iteration number, where: <ul> <li>iteration == 0 identifies the actual, observed insertions</li> <li>each iteration > 0 identifies one round of simulation, up to 10K total simulations</li> <li>each iteration has the same number of insertions</li> </ul> Column 4 is the insertion number within each actual or simulated insertion set. Please see the companion Zenodo data set: 10.5281/zenodo.12538130 for more information about creating insertion site models from your own insertion data.

opencc-by-sa-4.0Oct 2024View details →

Dataset for the paper "Entity Insertion in Multilingual Linked Corpora: The Case of Wikipedia"

Dataset for the EMNLP'24 Main conference paper titled "Entity Insertion in Multilingual Linked Corpora: The Case of Wikipedia".

opencc-by-4.0Oct 2024View details →

INDICATORS TO EVALUATE THE LABOUR INSERTION OF PEOPLE WITH DISABILITIES IN CONVENTIONAL COMPANIES IN SPAIN: QUANTITIATIVE DATA SET OF DELPHI STUDY (PHASE 2 AND PHASE 3)

The level of labor integration of people with disability (PwD) is notably lower than that of people without disabilities. In order to evaluate the success of the labor market integration of people with disabilities, it is necessary to establish a series of indicators that go beyond hiring rates. Hence, the objective of this study is to develop a list of indicators with their specified individual weight that will serve to evaluate the success of the labor market insertion of PwD in conventional companies. Methodology: The Delphi method was used. PHASE 1 In Phase 1, an open-ended questionnaire was distributed to 48 human resources and disability experts.  PHASE 2 Based on the theoretical dimensions obtained, a list of 52 indicators was drawn up and the experts were asked to evaluate the importance of each item using a scale of 0 to 10 points. In addition, in this second questionnaire, they were encouraged to propose improvements in the final wording of the items, as well as in the relevance and denomination of the dimensions into which they had been grouped. No suggestions were received to modify the wording or to incorporate additional items. PHASE 3 Once the scores of all the participants had been collected, a third questionnaire was sent out with the aim of achieving a statistical consensus within the group of experts. In this questionnaire, each panel member was informed of their degree of agreement or disagreement in relation to the group as a whole, without revealing the identity of the other participants. In other words, each participant was provided with information on the average rating of the group and their own initial rating (from Phase 2) of each of the 52 indicators, offering them the option to modify their response if they considered it appropriate. If they chose to change their assessment, they were asked to justify their reasons. To assess the possible convergence of opinion, the change in the responses received in the third phase with respect to the second phase was analyzed. We examined whether there had been variations in the scores given by the experts in the second phase once the group's mean ratings had been received. For this purpose, the “proportion of experts” statistic was used to verify that the average value of the responses in this third phase was within a range from [-0.5 to +0.5], compared to the average value of the scores in the second phase. In the case of non-convergence of opinion, this methodology allows for as many rounds as necessary until convergence is achieved. THIS DATA SET COLLECT THE ANSWERS OF THE EXPERTS OF PHASE 2 AND PHASE 3.

opencc-by-4.0Jul 2021View details →

Generation of transcriptional novelty by transposable element insertions in Arabidopsis, Genome Sequencing and eccDNA Data

Raw Illumina sequencing data from the Manuscript entitled "Generation of transcriptional novelty by transposable element insertions in Arabidopsis" A. Illumina genome sequencing reads of Arabidopsis control and hcLines that contain novel transposable element insertions. To identify the genomic position of the new ONSEN insertions, the extracted DNA of the 11 selected lines (nine lines with new insertions and two control lines) was sent to BGI, Hong-Kong for Illumina paired-end 150 bp sequencing, aiming for a minimum of 20X sequencing coverage. Quality control of the raw reads was done using FastQC (Andrews S. (2010). FastQC: a quality control tool for high throughput sequence data. Available online at: <a href="http://www.bioinformatics.babraham.ac.uk/projects/fastqc">http://www.bioinformatics.babraham.ac.uk/projects/fastqc</a>) and trimming/clipping was done using Trimmomatic with parameters ILLUMINACLIP: TruSeq3:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 and MINLEN:36. Quality of the reads was deemed excellent and no further actions were taken. Samples identifications: genome_hcLineX with "_1" indicating the forward and "_2" the reverse reads. B. Illumina eccDNA sequencing of Arabidopsis control and hcLines following stress treatments Extrachromosomal circular DNA was prepared and sequenced as follows: twenty plants from each petri dish were pooled separately and DNA was extracted using the CTAB method (<a href="https://dx.doi.org/10.17504/protocols.io.quidwue">dx.doi.org/10.17504/protocols.io.quidwue</a>). Following the mobilome-seq method described in (Lanciano et al., 2017), for all samples, we digested linear DNA from 2 µg of total DNA for 17 hours at 37oC using 10 U of PlasmidSafe (LubioScience cat# E3101K), followed by enzyme denaturation (30 mins at 70oC). Digested DNA was precipitated with isopropanol supplemented with 1 µg of GlycoBlue coprecipitant (Fisher Scientific cat# 10391565). Circular DNA was then amplified through rolling circle amplification (RCA) with the Illustra TempliPhi kit (GE Healthcare cat# 25-6400-10), following the manufacturer recommendation and leaving the reaction for 16h at 30oC. DNA was once again precipitated with isopropanol and sent for Illumina paired end 150 bp sequencing at BGI, Hong Kong.  Samples identification:  eccDNA_A.thaliana_ctrl: control reads eccDNA_A.thaliana_HS: heat stressed plants reads eccDNA_A.thaliana_AZ_HS: reads of alpha-amanitin, zebularine and heat-stressed plants "R1" indicates forward and "R2" reverse reads.

opencc-by-4.0Dec 2022View details →

Datasets for "Targeted insertion and reporter transgene activity at a gene safe harbor of the human blood fluke, Schistosoma mansoni"

To identify sites that could serve as potential genomic safe harbours (GSHs) for transgene integration, we conducted a genome-wide bioinformatic search based on established, widely accepted criteria, along with newly introduced criteria (below), that would satisfy benign and stable gene expression.  At the outset, we identified euchromatic regions in all developmental stages of S. mansoni to avoid silencing genes to be integrated upon CRISPR/Cas manipulation. With these criteria, we enriched for regions that were, (i) close to peaks of H3K4me3, a histone modification that is associated with euchromatin and transcription start sites, (ii) regions that did not include H3K27me3, a histone modification that is associated with heterochromatin, (iii) regions of open euchromatin accessible to Tn5 integration, in an Assay of Transposase Accessible Chromatin sequencing (ATAC-seq) providing a positive display of integration events, and (iv) given that HIV-1 integrates preferentially into euchromatin in human cell lines, we used sites of HIV proviral integration known from S. mansoni to likewise support predictions of euchromatic regions. Examination of the draft genome of S. mansoni in Worm Base Parasite, version 7 (WormBase Parasite) identified 6,884 regions with enrichment of H3K4me3 in the absence of H3K27me3 in available developmental stages (H3K4me3 not K3K27me3). In mature, adult schistosomes, we found consistently 10,533 ATAC positive regions. There were 4,027 ATAC regions that overlapped with H3K4me3 but not K3K27me3, and 2,915 genes overlapped with (ATAC and H3K4me3 not H3K27me3). Forty-two unambiguous HIV integration sites were identified, and eight genes were ≤ 11 kb upstream or downstream from these integration sites. Repeats were masked with RepeatMasker V4.1.0 using a specific repeat library produced with RepeatModeler2 V2.0.1 and stored as a GFF file. To identify intergenic GSH, we located 10,149 intergenic regions.  There were 9,985 regions beyond 2 kb upstream and 8,837 regions outside long non-coding-RNA (lncRNA), which were intersected to 95,587 unique intergenic regions outside 2 kb and lncRNA of ≥100 bp.  Two hundred regions were identified intersecting with merged ATAC H3K4me3 signal. Four of these were situated ≤ 11 kb distance from HIV integration sites.  Made at George Washington University, Justus Liebig University Giessen, Khon Kaen University, Naresuan University, Aberystwyth University, Schistosomiasis Resource Center, IHPE.

opencc-by-4.0Jan 2020View details →

DFT optimised structure used for the paper "Cation Insertion to Break the Activity/Stability Relationship for Highly Active Oxygen Evolution Reaction Catalyst"

DFT optimised structures used to calculate the OER activities in "Cation Insertion to Break the Activity/Stability Relationship for Highly Active Oxygen Evolution Reaction Catalyst". The structures are bundled in two databases, LiIrO3.db which contains all structures for alpha-LiIrO3 and KLiIrO3-disordered.db which contains all the structures for the disordered Li0.75K0.25(H2O)0.50IrO3 structure. The structures can be retrieved using the Atomic Simulation Environment (ASE, https://wiki.fysik.dtu.dk/ase/index.html). The keywords 'ads' and 'surface' can be used to search the structure, e.g. surface='Z-step' and ads='*OOH' will give the structure with OOH adsorbed on the Z-step surface (see paper for details on the different surfaces).

opencc-by-4.0May 2010View details →

Figure 13. Inserting a in DELTA for Beginners. An introduction into the taxonomy software package DELTA

Figure 13. Inserting a taxon that was marked as a variant (Treat as variant) in the Taxon editor, indicated by (+) preceding the taxon name.

opengpl-3.0-or-laterOct 2024View details →

T-DNAreader: fast and precise identification of T-DNA insertion sites using RNA-seq data

Agrobacterium-mediated plant transformation, which enables the delivery of DNA using transfer DNA (T-DNA) binary vectors, is an essential technique in plant research. T-DNAs randomly integrate into the host genome and multiple T-DNAs can integrate in a single transformation event, necessitating the development of efficient, reliable tools to identify the T-DNA insertion sites (TISs). Here, we developed T-DNAreader to identify TISs from RNA-sequencing (RNA-seq) data with high precision, sensitivity, and speed, outperforming existing tools. T-DNAreader detected previously unknown TISs in characterized mutant plants. Overall, T-DNAreader enables the simple identification of TISs within transcribed regions and standardizes the characterization of T-DNA-containing transgenic plants.

opencc-by-4.0Jul 2021View details →

Figure 2 in Differences in the soil seed bank of a mining area and its surroundings: a case study inserted in the Cerrado domain

Figure 2. Curves of species accumulation for the seed bank of Vazante city, northwest of the state of Minas Gerais, Brazil. A. Accumulation curve for the seed bank and confidence interval in a mining area and surrounding area separated; B. Accumulation curve for the seed bank, confidence interval and first-order Jackknife richness estimator in a mining area and surrounding area together.

opencc-by-4.0Jul 2021View details →

Figure 3 in Differences in the soil seed bank of a mining area and its surroundings: a case study inserted in the Cerrado domain

Figure 3. Two-dimensional ordination diagram based on the nonmetric multidimensional scaling (nMDS) for species density of the seed bank from a mining pit and surrounding areas in Vazante municipality, northwest of the state of Minas Gerais, Brazil.

opencc-by-4.0Nov 2021View details →

Probing Ion Channel Functional Architecture and Domain Recombination Compatibility by Massively Parallel Domain Insertion Profiling

Supplementary Data for a large insertional profiling study described in Coyote-Maestas et al. (2021) Nature Communications.

opencc-by-4.0Mar 2022View details →

Insertion sequences and other mobile elements associated with antibiotic resistance genes in Enterococcus isolates from an inpatient with prolonged bacteremia.

Insertion sequences (ISs) and other transposable elements are associated with the mobilization of antibiotic resistance determinants and the modulation of pathogenic characteristics. In this work, we aimed to investigate the association between ISs and antibiotic resistance genes, and their role in dissemination and modification of the antibiotic resistant phenotype. To that end, we leveraged fully resolved Enterococcus faecium and Enterococcus faecalis genomes of isolates collected over five days from an inpatient with prolonged bacteremia. Isolates from both species harbored similar IS family content but showed significant species-dependent differences in copy number and arrangements of ISs throughout their replicons. Here, we describe two inter-specific IS-mediated recombination events and IS-mediated excision events in plasmids of E. faecium isolates. We also characterize a novel arrangement of the ISs in a Tn1546-like transposon in E. faecalis isolates likely implicated in a vancomycin genotype-phenotype discrepancy. Furthermore, an extended analysis revealed a novel association between daptomycin resistance mutations in liaSR genes and a putative composite transposon in E. faecium, offering a new paradigm for the study of daptomycin resistance and novel insights into the dissemination of daptomycin resistance. In conclusion, our study highlights the role ISs and other transposable elements play in the rapid adaptation and response to clinically relevant stresses such as aggressive antibiotic treatment in enterococci.

opencc-by-4.0Aug 2022View details →

Text-fig. 2. Nymphaea sp. from the Miocene Clarkia Lake flora, Locality P-33. a: Photograph of the fossil leaf. b: Sketch of leaf showing the salient features of shape, basal lobes and margin, eccentric insertion point of the abaxial petiole, and primary actinodromous venation. Dashed lines represent torn edge of lamina; dotted line is outline of right basal lobe. Line drawing by P. Martin Sander. Scale bar applies to both photo and drawing. in First Water Lily, A Leaf Of Nymphaea Sp., From The Miocene Clarkia Flora, Northern Idaho, Usa: Occurrence, Taphonomic Observations, Floristic Implications

Text-fig. 2. Nymphaea sp. from the Miocene Clarkia Lake flora, Locality P-33. a: Photograph of the fossil leaf. b: Sketch of leaf showing the salient features of shape, basal lobes and margin, eccentric insertion point of the abaxial petiole, and primary actinodromous venation. Dashed lines represent torn edge of lamina; dotted line is outline of right basal lobe. Line drawing by P. Martin Sander. Scale bar applies to both photo and drawing.

Fig. 4 in A new species of Hortipes (Araneae, Corinnidae), the Frst spider with an insertable retrolateral tibial apophysis on the male palp

Fig. 4. Hortipes gigapophysalis sp. nov. A. Male palp, retrolateral view. B. Male palpal patella and tibia, dorsal view. C. Male palp, ventral view. D. idem, dorsal view. E. Male palpal tibia and patella, dorsolateral view. F. Detail of previous. E: embolus, DTA: distal tegular apophysis, RTA: retrolateral tibial apophysis.

Fig. 3 in A new species of Hortipes (Araneae, Corinnidae), the Frst spider with an insertable retrolateral tibial apophysis on the male palp

Fig. 3. Hortipes gigapophysalis sp. nov. A. Epigyne cleared in methyl salicylate, ventral view. B. idem, dorsal view.

Fig. 1 in A new species of Hortipes (Araneae, Corinnidae), the Frst spider with an insertable retrolateral tibial apophysis on the male palp

Fig. 1. Hortipes gigapophysalis sp. nov. A. Male habitus, dorsal view. B. Male prosoma, ventral view. C. Male habitus, lateral view. D. Female habitus, dorsal view. E. Female prosoma, ventral view (epigyne removed). F. Male prosoma, ventrolateral view.

Fig. 2 in A new species of Hortipes (Araneae, Corinnidae), the Frst spider with an insertable retrolateral tibial apophysis on the male palp

Fig. 2. Hortipes gigapophysalis sp. nov. A. Male palp, lateral view. B. idem, ventral view. C. Epigyne, ventral view. D. Epigyne, cleared, dorsal view, second system omitted. E. idem, primary system omitted. F. idem, both systems combined. E: embolus, ent1: entrance of insemination duct, ent2: entrance of secondary duct system, dv: dorso-ventral stretch of secondary duct system, pdv: position of dorsoventral stretch, RTA: retrolateral tibial apophysis, st1: spermathecae 1, st2: spermatheca 2. Scale bars: 100 µm.