Find research datasets worth reusing

opencc-by-3.0Nov 2020View details →

A heterometallic [LnLn'Ln] lanthanide complex as a qubit with embedded quantum error correction. Open data set

Includes data relevant for publication with DOI <a href="https://doi.org/10.1021/acsnano.0c03167">10.1039/d0sc03107k</a> plus a table with information on how the data were obtained and processed.

opencc-by-4.0Dec 2019View details →

Data sets supporting "Report on EU socio-ecological systems" (MAGIC Deliverable 4.2)

Description: Report on EU socio-ecological systems (Deliverable 4.2; WP4; EU H2020 MAGIC Project) Subject and Keywords: nexus (i.e. food, water, energy, land use, climate and environment); quantitative story telling (QST); metabolic pattern; robustness of narratives; EU’ sustainability strategy Abstract: The sustainability agenda builds on key components (i.e. food, water, energy, land use, climate and environment) that are inherently interconnected in a Nexus. MAGIC uses an innovative approach to test the robustness of narratives about the Nexus in Europe and focuses on the EU sustainable strategy. The aim of this deliverable is to operationalize and test a tool-kit to structure the quantitative analysis of the metabolic pattern of social-ecological systems in relation to their sustainability and the Nexus, at different levels of aggregation and spatial scales (EU, country or regional level). We use “quantitative story telling” as an alternative approach to use scientific information generated and better inform policy-makers. This deliverable build on the methodological approach and the basic features of the theoretical framework of accounting called Multi-Scale Integrated Analysis of Societal and Ecosystem Metabolism (MuSIASEM). The application of the tool-kit in this deliverable has the only goal of illustrating the potentiality of the approach. In a series of chapters we i) present the theoretical background and features of the tool-kit used to characterize the state-of-the-play (diagnostic analysis) with regard to the sustainability of SES; ii) provide an overview of the results obtained in the analysis of 8 EU countries (i.e. France, Germany, Italy, Netherlands, Romania, Spain, Sweden and United Kingdom); iii) demonstrate the capability of the toolkit to perform the analysis at different scales (in this case, at a lower aggregated level -NUTS2-); and iv) highlight the methodological breakthrough provided by relational analysis and its relevance for policy making with regard to the water-energy-food-environment Nexus Publisher:          MAGIC Contributors:     18 co-authors from 4 organisations Citation: Ripoll-Bosch and Giampietro (Editors). 2019. Report on EU socio-ecological systems. MAGIC (H2020–GA 689669) Project Deliverable 4.2, Revision Date:    March/18 Language:         English Rights Management:       The access is open

opencc-by-4.0Jun 2020View details →

Supplementary material (individual data set): Egeler, G.-A. & Baur, P. (2020). Menüwahl in der Hochschulmensa: Fleisch oder Vegi? Ergebnisse eines 12-wöchigen Feldexperiments (NOVANIMAL Working Paper No. 5). ZHAW. https://doi.org/10.21256/zhaw-1405

Meal choice at two university canteens in a field experiment during 12 weeks: anonymised individual menu sales data How do canteen visitors respond to a revised offer of meat-based and plant-based meals? Selected innovations were simultaneously implemented and tested in a transdisciplinary field experiment in two university canteens over a 12-week period in the autumn semester 2017. Throughout this time, the meat dishes and ‘veg-meals’ (ovo-lacto-vegetarian and vegan meals) were randomly distributed among the three menu lines, the veg-meals were not marketed and advertised as such and the previous vegetarian menu line was abolished. Weeks where the usual number of meat dishes were on offer (the ‘base weeks’) alternated with weeks where the share of veg-meals was increased (the ‘intervention weeks’).  The field experiment did not have a negative impact on the number of meals sold or the turnover compared to the two previous years. Women choose meat dishes less often than men. This connection applies in the base weeks and intervention weeks, in all age groups, among both students and among staff. Remarkably, the share of (non-labelled) vegan dishes is comparable for women and men over all age groups, independent of university affiliation (student, staff). Authentic vegan dishes were particularly welcome. Veg-meals could also be sold on the more expensive menu line. There was a better correlation between meal choice, eating habits and attitudes (health, environment, animal welfare, social aspects) than expected.  The dataset the dataset contains over 21'000 anonymised individual menu sales. The analyses and results are summarized in the working paper No. 5 <a href="https://doi.org/10.21256/zhaw-1405">https://doi.org/10.21256/zhaw-1405</a> The corresponding scripts are:  - <a href="http://doi.org/10.5281/zenodo.4034686">10.5281/zenodo.4034686</a> - <a href="http://doi.org/10.5281/zenodo.4034698">10.5281/zenodo.4034698</a> - <a href="http://doi.org/10.5281/zenodo.4244258">10.5281/zenodo.4244258</a> (newer Version) For more information visit the <a href="http://novanimal.ch">novanimal.ch</a> website.

openother-ncNov 2020View details →

Augmentation Via Registration: AutoImplant 2020 Augmented Data Set

Augmented data derived from the AutoImplant 2020 Challenge. Data has been augmented via non-linear SyN registrations using Advanced Normalization Tools (ANTs). This data was used to obtain first place in the AutoImplant 2020 challenge. The AutoImplant 2020 Challenge data was derived from the QC500 dataset from qure.ai. The original dataset is licensed under the CC BY-NC-SA 4.0 license (Attribution-NonCommercial-ShareAlike) and complies with the End User License Agreement (EULA) which are both detailed in the "LICENSE" file in this folder. Please refer to the "LICENSE" file for terms of use. If you use this data, please cite the following paper: Ellis D.G., Aizenberg M.R. (2020) Deep Learning Using Augmentation via Registration: 1st Place Solution to the AutoImplant 2020 Challenge. In: Li J., Egger J. (eds) Towards the Automatization of Cranial Implant Design in Cranioplasty. AutoImplant 2020. Lecture Notes in Computer Science, vol 12439. Springer, Cham. <a href="https://doi.org/10.1007/978-3-030-64327-0_6">https://doi.org/10.1007/978-3-030-64327-0_6</a>

opencc-byOct 2016View details →

Data Set htwddKogRob-InfDynSim for Localization in Highly Crowded Environments

This data set presents a major challenge for robot localization in highly crowded environments. The total distance travelled over all runs is 113.3 km. 50 dynamic obstacles (see htwddKogRob-InfDynSim_dynObstacles.png) were inserted into the map (see htwddKogRob-InfDynSim.png | 1px \(\widehat{=}\) 0.1m). The work was first presented in: <ul> <li>A Fuzzy-based Adaptive Environment Model for Indoor Robot Localization</li> <li>Authors: Frank Bahrmann, Sven Hellbach, Hans-Joachim Böhme</li> <li>Date of Publication: 2016/10/6</li> <li>Conference: Telehealth and Assistive Technology / 847: Intelligent Systems and Robotics</li> <li>Publisher: ACTA Press</li> </ul> Additionally, we present a video with the proposed algorithm and an insight of this dataset under: <ul> <li>youtube.com/AugustDerSmarte</li> <li>https://www.youtube.com/watch?v=26NBFN_XeQg</li> </ul> Instructions for use The zip archives contain ascii files, which hold the log files of the robot observations and robot poses. Since this data set was recorded in a simulated environment, the logfiles include both a changed starting position and a ground-truth pose. For further information, please refer to the header of the logfile. To simplify the parsing of the files, you can use these two Java snippets:   Laser Range Measurements: <pre><code class="language-java"> List<Double> ranges = new ArrayList<>(numOfLaserRays); List<Error> errors = new ArrayList<>(numOfLaserRays); String s = line.substring(4); String delimiter = "()"; StringTokenizer tokenizer = new StringTokenizer(s, delimiter); while(tokenizer.hasMoreElements()){ String[] arr = tokenizer.nextToken().split(";"); boolean usable = (arr[0].equals("0")?false:true); double range = Double.parseDouble(arr[1]); ranges.add(range); errors.add(usable?Error.OKAY:Error.INVALID_MEASUREMENT); }</code></pre> Poses: <pre><code class="language-java"> String poseString = line.split(":")[2]; String[] elements = poseString.substring(1, poseString.length()-1).split(";"); double x = Double.parseDouble(elements[0]); double y = Double.parseDouble(elements[1]); double phi = Double.parseDouble(elements[2]);</code></pre>

opencc-by-4.0Nov 2020View details →

Appendix: Refactoring Data Set

A large-scale data set containing refactorings mined from 92.800 open-source Java projects enriched with code metrics. Additionally, the data set contains Stable-Instances of the Class-, Method-, Variable- and Field-Level. The source code of the data collection tool can be found on GitHub: https://github.com/refactoring-ai/Data-Collection.

openeupl-1.2Apr 2020View details →

Data set for validation of a Python script for computation of Protein-Ligand Interaction Fingerprints

1. Data set for  for validation of the Protein-Ligand Interaction Fingerprints, which includes examples of protein structures  (original PDB and equilibrated) and molecular dynamics trajectories (equilibration and ligand dissociation generated using Random Acceleration MD simulations, RAMD) mdifp_validation_data.tar.gz - archive that contains benchmark dataset for evaluation of the protein-ligand IFP protocol (PDB structures of protonated complexes, ligands, and MOL2 files of ligands) published in  D. B. Kokha, B. Doser, S. Richter, F. Ormersbach, X. Cheng, R. C. Wade "A Workflow for Exploring Ligand Dissociation from a Macromolecule: Efficient Random Acceleration Molecular Dynamics Simulation and Interaction Fingerprints Analysis of Ligand Trajectories" J. Chem. Phys. 153, 125102 (2020); <a href="https://doi.org/10.1063/5.0019088">https://doi.org/10.1063/5.0019088</a> (2020) <a href="https://arxiv.org/abs/2006.11066">arXiv:2006.11066</a>   2YKI - protein-ligand complex , PDB ID 2YKI    - 2yki_MOE.pdb complex with hydrogen added and energy minimized using MOE software (https://www.chemcomp.com/)    -  ligand_2yki_MOE.mol2 and ligand_2yki_MOE.pdb - ligand structure with hydrogens prepered by MOE software (https://www.chemcomp.com/) 6EI5 - MD trajectory of the protein-ligand complex generated from PDB ID 6EI5    - ref-min.pdb  minimized structure    - ref.prmtop topology file    - moe.mol2 - ligand structure in mol2 format    - amber2namd2.dcd generated MD trajectory  SAD_3-RAMD-03-2020.pkl - a pkl dataset with IFPs generated from RAMD dissociation trajectory of the complex PDB ID: 5LQ9 (trajectories from the paper Front. Mol. Biosci., 2019 DOI:10.3389/fmolb.2019.00036) HSP90_Gromacs.zip - an archive that contains three pkl data sets of protein-ligand IFPs (for three HSP90 complexes; PDB ID: 5J64, 5J86, 5LQ9) generated from RAMD dissociation trajectories simulated using new Gromacs-RAMD engine (https://github.com/HITS-MCM/gromacs-ramd) The rest of the files contains data obtained from simulation of the complex of GPCR muscarinic receptor M2 (PDB ID:4MQT); immersed in a mixed membrane: 50% CHL, 30% POPC, 20% POPE)  with a small molecule agonist iperoxo.     - IXO.pdb and moe.mol2 - PDBand MOL2 structure of iperoxo    - AMBER_eq.tar.gz - structure of the equilibrated complex generated using AMBER software    - NAMD_eq.tar.gz - two equilibration trajectories in dcd format generated using NAMD software     - RAMD_eq.tar.gz - dissociation tarjectoris of iprtoxo from the M2 protein generated from the last snapshot of two NAMD equilibration trajectories (for each case 2 RAMD dissociaiton trajectories are available)  ( *csv files were added erroneously and do not belong to the project)

opencc-by-4.0Nov 2020View details →

Data set - Lagrangian observations and modelling of turbulence along a tidally influenced river - Refined model

The 'Dataset_Kaipara_Lagrangian_refined.mat' file contains Lagrangian observations collected in the Kaipara river and corresponding model predictions, after refinement of the model.    The 'Kaipara_model_refined.mat' files contains the grid and bathymetry of a model of the Kaipara River, New Zealand, created notably in order to study turbulence in a Lagrangian frame of reference.

opencc-by-4.0Dec 2020View details →

MER Opportunity and Spirit Rovers Pancam Images Labeled Data Set

Introduction The data set is based on 3,004 images collected by the Pancam instruments mounted on the Opportunity and Spirit rovers from NASA's Mars Exploration Rovers (MER) mission. We used rotation, skewing, and shearing augmentation methods to increase the total collection to 70,864 (see Image Augmentation section for more information). Based on the <a href="https://merdatacatalog.com/survey">MER Data Catalog User Survey</a> [1], we identified 25 classes of both scientific (e.g. soil trench, float rocks, etc.) and engineering (e.g. rover deck, Pancam calibration target, etc.) interests (see Classes section for more information). The 3,004 images were labeled on <a href="https://www.zooniverse.org/">Zooniverse platform</a>, and each image is allowed to be assigned with multiple labels. The images are either 512 x 512 or 1024 x 1024 pixels in size (see Image Sampling section for more information). Classes There is a total of 25 classes for this data set. See the list below for class names, counts, and percentages (the percentages are computed as count divided by 3,004). Note that the total counts don't sum up to 3,004 and the percentages don't sum up to 1.0 because each image may be assigned with more than one class.  <ul> <li>Class name, count, percentage of dataset</li> <li>Rover Deck, 222, 7.39%</li> <li>Pancam Calibration Target, 14, 0.47%</li> <li>Arm Hardware, 4, 0.13%</li> <li>Other Hardware, 116, 3.86%</li> <li>Rover Tracks, 301, 10.02%</li> <li>Soil Trench, 34, 1.13%</li> <li>RAT Brushed Target, 17, 0.57%</li> <li>RAT Hole, 30, 1.00%</li> <li>Rock Outcrop, 1915, 63.75%</li> <li>Float Rocks, 860, 28.63%</li> <li>Clasts, 1676, 55.79%</li> <li>Rocks (misc), 249, 8.29%</li> <li>Bright Soil, 122, 4.06%</li> <li>Dunes/Ripples, 1000, 33.29%</li> <li>Rock (Linear Features), 943, 31.39%</li> <li>Rock (Round Features), 219, 7.29%</li> <li>Soil, 2891, 96.24%</li> <li>Astronomy, 12, 0.40%</li> <li>Spherules, 868, 28.89%</li> <li>Distant Vista, 903, 30.23%</li> <li>Sky, 954, 31.76%</li> <li>Close-up Rock, 23, 0.77%</li> <li>Nearby Surface, 2006, 66.78%</li> <li>Rover Parts, 301, 10.02%</li> <li>Artifacts, 28, 0.93%</li> </ul> Image Sampling Images in the MER rover Pancam archive are of sizes ranging from 64x64 to 1024x1024 pixels. The largest size, 1024x1024, was by far the most common size in the archive. For the deep learning dataset, we elected to sample only 1024x1024 and 512x512 images as the higher resolution would be beneficial to feature extraction. In order to ensure that the data set is representative of the total image archive of 4.3 million images, we elected to sample via "site code". Each Pancam image has a corresponding two-digit alphanumeric "site code" which is used to track location throughout its mission. Since each "site code" corresponds to a different general location, sampling a fixed proportion of images taken from each site  ensure that the data set contained some images from each location. In this way, we could ensure that a model performing well on this dataset would generalize well to the unlabeled archive data as a whole. We randomly sampled 20% of the images at each site within the subset of Pancam data fitting all other image criteria, applying a floor function to non-whole number sample sizes, resulting in a dataset of 3,004 images. Train/validation/test sets split The 3,004 images were split into train, validation, and test data sets. The split was done so that roughly 60, 15, and 25 percent of the 3,004 images would end up as train, validation, and test data sets respectively, while ensuing that images from a given site are not split between train/validaiton/test data sets. This resulted in 1,806 train images, 456 validation images, and 742 test images.  Augmentation To augment the images in train and validation data sets (note that images in the test data set were not augmented), three augmentation methods were chosen that best represent transformations that could be realistically seen in Pancam images.  The three augmentations methods are rotation, skew, and shear. The augmentation methods were applied with random magnitude, followed by a random horizontal flipping, to create 30 augmented images for each image. Since each transformation is followed by a square crop in order to keep input shape consistent, we had to constrict the magnitude limits of each augmentation to avoid cropping out important features at the edges of input images. Thus, rotations were limited to 15 degrees in either direction, the 3-dimensional skew was limited to 45 degrees in any direction, and shearing was limited to 10 degrees in either direction. Note that augmentation was done only on training and validation images.  Directory Contents <ul> <li>images: contains all 70,864 images</li> <li>train-set-v1.1.0.txt: label file for the training data set</li> <li>val-set-v1.1.0.txt: label file for the validation data set</li> <li>test-set-v1.1.0.txt: label file for the testing data set</li> </ul> Images with relatively short file names (e.g., 1p128287181mrd0000p2303l2m1.img.jpg) are original images, and images with long file names (e.g., 1p128287181mrd0000p2303l2m1.img.jpg_04140167-5781-49bd-a913-6d4d0a61dab1.jpg) are augmented images. The label files are formatted as "Image name, Class1, Class2, ..., ClassN".   Reference [1] S.B. Cole, J.C. Aubele, B.A. Cohen, S.M. Milkovich, and S.A. Shields, Identifying Community Needs for a Mars Exploration Rovers (MER), Daata Catalog, 51st Lunar and Planetary Science Conference (LPSC), 2020.

opencc-by-4.0Dec 2020View details →

Data set for study '"Optimal intervention strategies to mitigate the COVID-19 pandemic effects"

Data associated with the findings presented in the study '"Optimal intervention strategies to mitigate the COVID-19 pandemic effects"

Data from: Comparison of taxon-specific versus general locus sets for targeted sequence capture for plant phylogenomics

Premise of the study: Targeted sequence capture can be used to efficiently gather sequence data for large numbers of loci, such as single-copy nuclear loci. Most published studies in plants have used taxon-specific locus sets developed individually for a clade using multiple genomic and transcriptomic resources. General locus sets can also be developed from loci that have been identified as single-copy and having orthologs in large clades of plants. Methods: We identify and compare a taxon-specific locus set and three general locus sets (COSII, APVO SSC, PPR) for targeted sequence capture in Buddleja (Scrophulariaceae) and outgroups. We evaluate their performance in terms of assembly success, sequence variability, and resolution and support of inferred phylogenetic trees. Results: The taxon-specific locus set had the most target loci. Assembly success was high for all locus sets in Buddleja samples. For outgroups, general locus sets had greater assembly success. Taxon-specific and PPR loci had the highest average variability. The taxon-specific dataset produced the best supported tree, but all datasets showed improved resolution over previous non-sequence capture datasets. Discussion: General loci can be a useful source of sequence capture targets, especially if multiple genomic resources are not available for a taxon.

opencc-zeroDec 2015View details →

Data from: The third dimension: a novel set-up for filming coelacanths in their natural environment

Here, we describe a novel design to obtain three-dimensional data on the movements of aquatic organisms at depths of up to 140 m. The set-up consists of two synchronized high-speed cameras fixed to two articulated arms. The set-up was successfully used to film and quantify the locomotion of coelacanths Latimeria chalumnae living at a depth of about 120 m in Sodwana Bay, South Africa. As an example, the detailed motion of the dorsal fin is presented here. This set-up can be used for any underwater applications that require synchronized video recordings of medium- to large-sized animals.

opencc-by-nc-1.0Jun 2021View details →

River Erpe (Berlin, Germany) groundwater levels, temperature and 222-radon data set, June 2019

Time series of groundwater levels and temperature, chloride concentrations as well as 222-radon activities in piezometers P0 to P9 and P11 located close to Heidemühle at the River Erpe, Berlin, Germany, collected between June and November 2019. In "Rn_eql_incubations.csv", "mea" denotes the mean activity and "sdd" the associated standard deviation.

opencc-zeroDec 2016View details →

Data from: Squamate Conserved Loci (SqCL): a unified set of conserved loci for phylogenomics and population genetics of squamate reptiles

The identification of conserved loci across genomes, along with advances in target capture methods and high-throughput sequencing, has helped spur a phylogenomics revolution by enabling researchers to gather large numbers of homologous loci across clades of interest with minimal upfront investment in locus design. Target capture for vertebrate animals is currently dominated by two approaches – anchored hybrid enrichment (AHE) and ultraconserved elements (UCE) – and both approaches have proven useful for addressing questions in phylogenomics, phylogeography, and population genomics. However, these two sets of loci have minimal overlap with each other; moreover, they do not include many traditional loci that that have been used for phylogenetics. Here, we combine across UCE, AHE, and traditional phylogenetic gene locus sets to generate the Squamate Conserved Loci (SqCL) set, a single integrated probe set that can generate high-quality and highly complete data across all three loci types. We use these probes to generate data for 44 phylogenetically-disparate taxa that collectively span approximately 33% of terrestrial vertebrate diversity. Our results generated an average of 4.29 Mb across 4709 loci per individual, of which an average of 2.99 Mb was sequenced to high enough coverage (≥10×) to use for population genetic analyses. We validate the utility of these loci for both phylogenomic and population genomic questions, provide a comparison among these locus sets of their relative usefulness, and suggest areas for future improvement.

Data from: Effect of ecological momentary assessment, goal-setting and personalized phone-calls on adherence to interval walking training using the InterWalk application among patients with type 2 diabetes – a pilot randomized controlled trial

Objectives: The objective was to investigate the feasibility and usability of structured text-messages, goal-setting and phone-calls on adherence to a 12-week self-conducted interval walking training (IWT) program, delivered by the InterWalk smartphone among patients with type 2 diabetes (T2D). Methods: In a two-arm pilot randomized controlled trial (Denmark, March 2014 to February 2015), patients with T2D (18-80 years with a Body Mass Index of 18 and 40 kg/m2) were randomly allocated to 12 weeks of IWT with (intervention) or without additional support (control). The primary outcome was the difference between groups in accumulated time of interval walking training across 12 weeks. All patients were encouraged to use the InterWalk application to perform IWT for ≥90 minute/week. Patients in the intervention group made individual goals regarding lifestyle change, received automated text-messages once a week, inquiring about exercise adherence. In case of consistent non-adherence, the patients would receive a phone-call inquiring about the reason for non-adherence. The control group did not receive additional support. Information about training adherence was assessed objectively. Usability of structured text-messages was assessed based on response rates and self-reported satisfaction after 12-weeks. Results: Thirty-seven patients with T2D (66 years, 65% female, hemoglobin 1Ac 50.3 mmol/mol) where included (n=18 and n=19 in intervention and control group, respectively). The retention rate was 83%. The intervention group accumulated [95%CI] 345 -7, 698 minutes of IWT more than the control group. The response rate for the text-messages was 83% (68% for males and 90% for females). Forty-one percent of the intervention and 25% of the control group were very satisfied with their participation. Conclusion: The combination of structured text-messages, goal-setting with the possibility of follow-up phone calls are considered feasible interventions to attain training adherence when using the InterWalk app during a 12-week period in patients with T2D. Some uncertainty about the effect size of adherence remains.

Data from: Phylogenetics of moth-like butterflies (Papilionoidea: Hedylidae) based on a new 13-locus target capture probe set

The Neotropical moth-like butterflies (Hedylidae) are perhaps the most unusual butterfly family. In addition to being species-poor, this family is predominantly nocturnal and has anti-bat ultrasound hearing organs. Evolutionary relationships among the 36 described species are largely unexplored. A 13-gene anchored hybrid enrichment probe set ('BUTTERFLY2.0'), that includes standard markers used in butterfly phylogenetics, captured sequences from decades-old museum specimens, and appears to be a cost-effective technique to infer phylogenetic relationships of the butterfly tree of life. Our dataset comprises up to 10,898 aligned base pairs from each of the 22 species of Hedylidae and 19 outgroups. Eleven of the thirteen loci were captured from 100% of the taxa, and the remaining loci were captured from ≥94% of taxa. The inferred phylogeny had robust support at 80% of nodes. Our results are consistent with morphological work, with Macrosoma tipulata sister to all remaining hedylids, followed by M. semiermis sister to the remaining species in the genus. We tested the hypothesis that nocturnality evolved only once from diurnality in Hedylidae, and showed that the ancestral condition was likely diurnal, with a shift to nocturnality early in the diversification of this family.

Data from: Small volume plasma exchange for Guillain-Barré syndrome in resource-limited settings: a phase II safety and feasibility study

OBJECTIVE: To assess the safety and feasibility of small volume plasma exchange (SVPE) as an alternative to standard plasma exchange (PE) or intravenous immunoglobulin (IVIg) for Guillain-Barré syndrome (GBS) patients. DESIGN: Non-randomized, single arm, interventional trial. SETTING: National Institute of Neurosciences and Hospital, Dhaka, Bangladesh. PARTICIPANTS: Twenty adult (>18 years) patients with GBS presented within 2 weeks of onset of weakness who were unable to walk unaided for more than 10 meters. INTERVENTIONS: SVPE involves blood cell sedimentation in a blood bag and removal of supernatant plasma after blood cells are re-transfused. This procedure was repeated three to six times a day, for eight consecutive days. OUTCOME MEASURES: Serious adverse events (SAE) were defined as severe sepsis and deep venous thrombosis related to the central vein catheter (CVC) used during SVPE. SVPE was considered safe if less than 5/20 patients experienced a SAE, and feasible if 8 L plasma could be removed within 8 days in at least 15/20 patients. RESULTS Median patient age 33 years (IQR 23-46; range 18-55); 13 (65%) were male. Median MRC sum score was 20 (IQR 0-29; range 0-36); three (15%) patients required mechanical ventilation. One patient developed SAE (severe sepsis, possibly related to CVC). Minor adverse effects were transient hypotension in 10 (50%) patients; CVC-associated bleeding in 10 (50%); transfusion reaction to fresh frozen plasma in 4 (20%); and hypo-albuminemia, anaemia or electrolyte imbalance in 4 (20%). Removal of 8 L plasma was possible in 15 (75%) patients. GBS disability score improved by at least one grade in 14 (70%) patients four weeks after SVPE started. No patients died. CONCLUSION: SVPE seems a safe and feasible alternative treatment to standard PE or IVIg for GBS; further studies of clinical efficacy in low-resource developing countries are warranted. TRIAL REGISTRATION: Clinicaltrials.gov NCT02780570 on May 23, 2016. Strength and limitations of the study: 1. The strength of this study underlies the novel and simple technique of SVPE, which is much less expensive than conventional immunotherapies (plasma exchange and intravenous immunoglobulin). 2. SVPE is corroborated as safe and feasible for the first time in a prospective and standardized cohort of patients with Guillain-Barré syndrome (GBS). 3. The intrinsic limitations of this study are its non-randomized, single arm nature, which is conducted in a single center with a limited sample size of GBS patients. 4. Clinical efficacy of SVPE on patients with GBS was a secondary end-point assessment and therefore deserves a randomized controlled trial in future to assess the clinical efficacy of SVPE for the patients with GBS.

opencc-zeroDec 2014View details →

Data from: Collecting in collections: a PCR strategy and primer set for DNA barcoding of decades-old dried museum specimens

Natural history museums are vastly underutilized as a source of material for DNA analysis because of perceptions about the limitations of DNA degradation in older specimens. Despite very few exceptions, most DNA barcoding projects, which aim to obtain sequence data from all species, generally use specimens collected specifically for that purpose, instead of the wealth of identified material in museums, constrained by the lack of suitable PCR methods. Any techniques that extend the utility of museum specimens for DNA analysis therefore are highly valuable. This study first tested the effects of specimen age and PCR amplicon size on PCR success rates in pinned insect specimens, then developed a PCR primer set and amplification strategy allowing greatly increased utilization of older museum specimens for DNA barcoding. PCR success rates compare favourably with the few published studies utilizing similar aged specimens, and this new strategy has the advantage of being easily automated for high-throughput laboratory workflows. The strategy uses hemi-nested, degenerate, M13-tailed PCR primers to amplify two overlapping amplicons, using two PCRs per amplicon (i.e. four PCRs per DNA sample). Initial PCR products are reamplified using an internal primer and a M13 primer. Together the two PCR amplicons yield 559 bp of the COI gene from Coleoptera, Lepidoptera, Diptera, Hemiptera, Odonata and presumably also other insects. BARCODE standard-compliant data were recovered from 67% (56 of 84) of specimens up to 25 years old, and 51% (102 of 197) of specimens up to 55 years old. Given the time, cost and specialist expertise required for fieldwork and identification, 'collecting in collections' is a viable alternative allowing researchers to capitalize on the knowledge captured by curation work in decades past.

opencc-zeroDec 2012View details →

Data from: A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents

Introduction: The PCR-based analysis of homologous genes has become one of the most powerful approaches for species detection and identification, particularly with the recent availability of Next Generation Sequencing platforms (NGS) making it possible to identify species composition from a broad range of environmental samples. Identifying species from these samples relies on the ability to match sequences with reference barcodes for taxonomic identification. Unfortunately, most studies of environmental samples have targeted ribosomal markers, despite the fact that the mitochondrial Cytochrome c Oxidase subunit I gene (COI) is by far the most widely available sequence region in public reference libraries. This is largely because the available versatile ("universal") COI primers target the 658 barcoding region, whose size is considered too large for many NGS applications. Moreover, traditional barcoding primers are known to be poorly conserved across some taxonomic groups. Results: We first design a new PCR primer within the highly variable mitochondrial COI region, the "mlCOIintF" primer. We then show that this newly designed forward primer combined with the "jgHCO2198" reverse primer to target a 313 bp fragment performs well across metazoan diversity, with higher success rates than versatile primer sets traditionally used for DNA barcoding (i.e. LCO1490/HCO2198). Finally, we demonstrate how the shorter COI fragment coupled with an efficient bioinformatics pipeline can be used to characterize species diversity from environmental samples by pyrosequencing. We examine the gut contents of three species of planktivorous and benthivorous coral reef fish (family: Apogonidae and Holocentridae). After the removal of dubious COI sequences, we obtained a total of 334 prey Operational Taxonomic Units (OTUs) belonging to 14 phyla from 16 fish guts. Of these, 52.5% matched a reference barcode (>98% sequence similarity) and an additional 32% could be assigned to a higher taxonomic level using Bayesian assignment. Conclusions: The molecular analysis of gut contents targeting the 313 COI fragment using the newly designed mlCOIintF primer in combination with the jgHCO2198 primer offers enormous promise for metazoan metabarcoding studies. We believe that this primer set will be a valuable asset for a range of applications from large-scale biodiversity assessments to food web studies.