cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5558626.v1
title: Preparation and biological activities of anti-HER2 monoclonal antibodies with fully core-fucosylated homogeneous bi-antennary complex-type glycans

description: Recently, the absence of a core-fucose residue in the N-glycan has been implicated to be important for enhancing antibody-dependent cellular cytotoxicity (ADCC) activity of immunoglobulin G monoclonal antibodies (mAbs). Here, we first prepared anti-HER2 mAbs having two core-fucosylated N-glycan chains with the single G2F, G1aF, G1bF, or G0F structure, together with those having two N-glycan chains with a single non-core-fucosylated corresponding structure for comparison, and determined their biological activities. Dissociation constants of mAbs with core-fucosylated N-glycans bound to recombinant Fcγ-receptor type IIIa variant were 10 times higher than those with the non-core-fucosylated N-glycans, regardless of core glycan structures. mAbs with the core-fucosylated N-glycans had markedly reduced ADCC activities, while those with the non-core-fucosylated N-glycans had high activities. These results indicate that the presence of a core-fucose residue in the N-glycan suppresses the binding to the Fc-receptor and the induction of ADCC of anti-HER2 mAbs. Dramatic decreases in ADCC activity brought by core-fucosylation (red-colored) of N-glycans attached to anti-HER2 mAbs as illustrated with outline.
DOI: 10.6084/m9.figshare.5558611
title: Expiratory muscle strength training improves swallowing and respiratory outcomes in people with dysphagia: A systematic review

description: <i>Purpose</i>: To investigate the effects of expiratory muscle strength training on communication and swallowing outcomes in adults with acquired motor based communication and/or swallowing difficulties of any aetiology. <i>Method</i>: A systematic review was conducted. Six databases (CINAHL, MEDLINE, EMBASE, SPEECHBYTE, AMED and PUBMED) were searched from inception until end of May 2016. Randomised and non-randomised controlled studies and pre-test/post-test studies published in English that investigated the effects of expiratory muscle strength training were included. Study quality was assessed using the PEDro scale. Data were analysed descriptively and effect sizes and associated 95% confidence intervals were calculated. <i>Result</i>: Seven articles reporting data from five studies were included. Preliminary data suggests expiratory muscle strength training improved airway safety during swallowing in people with dysphagia and increased the strength of the expiratory muscles in all patient groups. There was little evidence to suggest changes in communication outcomes after expiratory muscle strength training. <i>Conclusion</i>: Speech–language pathologists might consider using expiratory muscle strength training to improve airway safety in adults with swallowing disorders.
DOI: 10.6084/m9.figshare.5558620
title: Heterologous expression of two minor laccase isozyme cDNAs from the edible mushroom <i>Grifola frondosa</i>

description: Two cDNAs encoding the minor laccase isozymes (Lac2 and Lac3) of <i>Grifola frondosa</i> were cloned, characterized, and expressed in <i>Pichia pastoris.</i> The recombinant Lac2 (rLac2) was stable at pH 6.0, whereas the recombinant Lac3 (rLac3) was stable in a broad pH range (pH 4.0–8.0). In addition, rLac2 and rLac3 showed the highest catalytic efficiency (<i>k</i><sub>cat</sub>/<i>K</i><sub>m</sub>) for 2,2′-azino-bis-(3-ethylbenzthiazoline-6-sulfonic acid).
DOI: 10.6084/m9.figshare.5558635.v1
title: Genetic structure of wild and domesticated grasscutters (<i>Thryonomys swinderianus</i>) from south-western Nigeria

description: Grasscutter (<i>Thryonomys swinderianus</i>) is a large rodent distributed across sub-Saharan Africa that is highly valued as a source of protein. There has been little effort to evaluate the genetic structure of grasscutters despite long-term harvesting pressure and over 40 years of grasscutter domestication in West Africa. Our objectives were to quantify the genetic structure of wild grasscutters, and to compare genetic variation from wild samples to those from various farmed samples within south-western Nigeria. We genotyped 145 wild and 88 domesticated individuals at 11 microsatellite loci and present results quantifying regional genetic structuring and the relative patterns of diversity among wild and domesticated grasscutter populations. Our data reflect high differentiation between wild and domesticated grasscutters, and significantly greater allelic richness and gene diversity in the former. Despite this, domesticated populations appear to have similar levels of observed heterozygosity and comparable levels of differentiation among domesticated samples relative to wild samples. This may be the result of high turnover within captive colonies, or frequent infusion of new animals. More detailed molecular and quantitative genetic studies are recommended on this species to be able to understand their natural variation, degree of connectivity and to improve strategies for domestication.
DOI: 10.6084/m9.figshare.5558587
title: Accompanying Data for paper: How Effective Mutation Testing Tools Are? An Empirical Analysis of Java Mutation Testing Tools with Manual Analysis and Real Faults

description: Mutation analysis is a well-studied, fault-based testing technique. It requires testers to design tests based on a set of artificial defects. The defects help in performing testing activities by measuring the ratio that is revealed by the candidate tests. Unfortunately, applying mutation to real-world programs requires automated tools due to the vast number of defects involved. In such a case, the effectiveness of the method strongly depends on the peculiarities of the employed tools. Thus, when using automated tools, their implementation inadequacies can lead to inaccurate results. To deal with this issue, we cross-evaluate four mutation testing tools for Java, namely PIT, MUJAVA, MAJOR and the research version of PIT, PITRV, with respect to their fault-detection capabilities. We investigate the strengths of the tools based on: a) a set of real faults and b) manual analysis of the mutants they introduce. We find that there are large differences between the tools’ effectiveness and demonstrate that no tool is able to subsume the others. We also provide results indicating the application cost of the method. Overall, we find that PITRV achieves the best results. In particular, PITRV outperforms the other tools by finding 6% more faults than the other tools combined.
DOI: 10.6084/m9.figshare.5558620.v1
title: Heterologous expression of two minor laccase isozyme cDNAs from the edible mushroom <i>Grifola frondosa</i>

description: Two cDNAs encoding the minor laccase isozymes (Lac2 and Lac3) of <i>Grifola frondosa</i> were cloned, characterized, and expressed in <i>Pichia pastoris.</i> The recombinant Lac2 (rLac2) was stable at pH 6.0, whereas the recombinant Lac3 (rLac3) was stable in a broad pH range (pH 4.0–8.0). In addition, rLac2 and rLac3 showed the highest catalytic efficiency (<i>k</i><sub>cat</sub>/<i>K</i><sub>m</sub>) for 2,2′-azino-bis-(3-ethylbenzthiazoline-6-sulfonic acid).
DOI: 10.6084/m9.figshare.5558611.v2
title: Expiratory muscle strength training improves swallowing and respiratory outcomes in people with dysphagia: A systematic review

description: <i>Purpose</i>: To investigate the effects of expiratory muscle strength training on communication and swallowing outcomes in adults with acquired motor based communication and/or swallowing difficulties of any aetiology. <i>Method</i>: A systematic review was conducted. Six databases (CINAHL, MEDLINE, EMBASE, SPEECHBYTE, AMED and PUBMED) were searched from inception until end of May 2016. Randomised and non-randomised controlled studies and pre-test/post-test studies published in English that investigated the effects of expiratory muscle strength training were included. Study quality was assessed using the PEDro scale. Data were analysed descriptively and effect sizes and associated 95% confidence intervals were calculated. <i>Result</i>: Seven articles reporting data from five studies were included. Preliminary data suggests expiratory muscle strength training improved airway safety during swallowing in people with dysphagia and increased the strength of the expiratory muscles in all patient groups. There was little evidence to suggest changes in communication outcomes after expiratory muscle strength training. <i>Conclusion</i>: Speech–language pathologists might consider using expiratory muscle strength training to improve airway safety in adults with swallowing disorders.
DOI: 10.6084/m9.figshare.5558587.v1
title: Accompanying Data for paper: How Effective Mutation Testing Tools Are? An Empirical Analysis of Java Mutation Testing Tools with Manual Analysis and Real Faults

description: Mutation analysis is a well-studied, fault-based testing technique. It requires testers to design tests based on a set of artificial defects. The defects help in performing testing activities by measuring the ratio that is revealed by the candidate tests. Unfortunately, applying mutation to real-world programs requires automated tools due to the vast number of defects involved. In such a case, the effectiveness of the method strongly depends on the peculiarities of the employed tools. Thus, when using automated tools, their implementation inadequacies can lead to inaccurate results. To deal with this issue, we cross-evaluate four mutation testing tools for Java, namely PIT, MUJAVA, MAJOR and the research version of PIT, PITRV, with respect to their fault-detection capabilities. We investigate the strengths of the tools based on: a) a set of real faults and b) manual analysis of the mutants they introduce. We find that there are large differences between the tools’ effectiveness and demonstrate that no tool is able to subsume the others. We also provide results indicating the application cost of the method. Overall, we find that PITRV achieves the best results. In particular, PITRV outperforms the other tools by finding 6% more faults than the other tools combined.
DOI: 10.6084/m9.figshare.5558611.v1
title: Expiratory muscle strength training improves swallowing and respiratory outcomes in people with dysphagia: a systematic review

description: <i>Purpose</i>: To investigate the effects of expiratory muscle strength training on communication and swallowing outcomes in adults with acquired motor based communication and/or swallowing difficulties of any aetiology. <i>Method</i>: A systematic review was conducted. Six databases (CINAHL, MEDLINE, EMBASE, SPEECHBYTE, AMED and PUBMED) were searched from inception until end of May 2016. Randomised and non-randomised controlled studies and pre-test/post-test studies published in English that investigated the effects of expiratory muscle strength training were included. Study quality was assessed using the PEDro scale. Data were analysed descriptively and effect sizes and associated 95% confidence intervals were calculated. <i>Result</i>: Seven articles reporting data from five studies were included. Preliminary data suggests expiratory muscle strength training improved airway safety during swallowing in people with dysphagia and increased the strength of the expiratory muscles in all patient groups. There was little evidence to suggest changes in communication outcomes after expiratory muscle strength training. <i>Conclusion</i>: Speech–language pathologists might consider using expiratory muscle strength training to improve airway safety in adults with swallowing disorders.
DOI: 10.6084/m9.figshare.5558557
title: Alpha shapes MATLAB code

description: MATLAB code to accompany the paper "Alpha shapes: Determining 3D shape complexity across morphologically diverse structures"
DOI: 10.6084/m9.figshare.5558530
title: Table 1

description: List of AIC, -2 log-likelihood and P-value for the hypothesis models.
DOI: 10.6084/m9.figshare.5558539
title: Quality evaluation of RNA-Seq

description: There is a representative statistic summary for quality evaluation of the RNA-Seq raw reads (statistical_evaluation_raw_reads.txt). We also provide the correspondences between the sequenced sample ID and NCBI SRA run accession number (run_accession_number.xlsx).
DOI: 10.6084/m9.figshare.5558527
title: Sample preparation, transcriptome and 16S rRNA sequencing, and analysis results

description: Five files are included in this dataset, which describe the phenotype scoring of rabbits, RNA quality, 16s rRNA amplicon content, count of raw and clean sequencing reads, and mapping results of reads against the reference genome for each sample (sample_sequencing_mapping.xlsx), the chromosome information (gene_information.txt) and expression levels (gene_quantification.txt) for these assembled genes from RNA-Seq, and the taxonomically annotated results (otu_annotation.txt) and estimated abundances (otu_abundances.txt) of OTUs.
DOI: 10.6084/m9.figshare.5558518
title: ob3lyp.txt from A DFT investigation of the blue bottle experiment: <i>E</i>°<sub>halfcell</sub> analysis of autoxidation catalysed by redox indicators

description: Optimised geometries at B3LYP/6-311++G**
DOI: 10.6084/m9.figshare.5558521
title: The designed ingredients and nutritive values for fibre-deficiency and standard diets

description: The designed ingredients and nutritive values for fibre-deficiency and standard diets, which is fed to rabbit to investigate the effects on host gene expression and gut microbiota composition.
DOI: 10.6084/m9.figshare.5558515
title: calculations.xlsx from A DFT investigation of the blue bottle experiment: <i>E</i>°<sub>halfcell</sub> analysis of autoxidation catalysed by redox indicators

description: Energies of all structures and reactions and graphs
DOI: 10.6084/m9.figshare.5558518.v1
title: ob3lyp.txt from A DFT investigation of the blue bottle experiment: <i>E</i>°<sub>halfcell</sub> analysis of autoxidation catalysed by redox indicators

description: Optimised geometries at B3LYP/6-311++G**
DOI: 10.6084/m9.figshare.5558521.v1
title: The designed ingredients and nutritive values for fibre-deficiency and standard diets

description: The designed ingredients and nutritive values for fibre-deficiency and standard diets, which is fed to rabbit to investigate the effects on host gene expression and gut microbiota composition.
DOI: 10.6084/m9.figshare.5558515.v1
title: calculations.xlsx from A DFT investigation of the blue bottle experiment: <i>E</i>°<sub>halfcell</sub> analysis of autoxidation catalysed by redox indicators

description: Energies of all structures and reactions and graphs
DOI: 10.6084/m9.figshare.5558512
title: omp2.txt from A DFT investigation of the blue bottle experiment: <i>E</i>°<sub>halfcell</sub> analysis of autoxidation catalysed by redox indicators

description: Optimised geometries at MP2/cc-pVDZ
DOI: 10.6084/m9.figshare.5558506
title: output.zip from A DFT investigation of the blue bottle experiment: <i>E</i>°<sub>halfcell</sub> analysis of autoxidation catalysed by redox indicators

description: All Q-CHEM output files
DOI: 10.6084/m9.figshare.5558506.v1
title: output.zip from A DFT investigation of the blue bottle experiment: <i>E</i>°<sub>halfcell</sub> analysis of autoxidation catalysed by redox indicators

description: All Q-CHEM output files
DOI: 10.6084/m9.figshare.5558512.v1
title: omp2.txt from A DFT investigation of the blue bottle experiment: <i>E</i>°<sub>halfcell</sub> analysis of autoxidation catalysed by redox indicators

description: Optimised geometries at MP2/cc-pVDZ
DOI: 10.6084/m9.figshare.5558500
title: Adult plant resistance to leaf rust and stem rust of wheat in a newly developed recombinant inbred line population

description: Leaf rust caused by <i>Puccinia triticina</i> and stem rust by <i>P. graminis</i> f. sp. <i>tritici</i> are the most destructive diseases of wheat (<i>Triticum aestivum</i> L.), resulting in substantial yield losses globally. A continuous search for new sources of effective rust resistance genes is necessary to develop improved cultivars with durable resistance. This study aimed to investigate inheritance of adult-plant resistance in a recombinant inbred line (RIL) population of a cross between wheat cultivars ‘Popo’ and ‘Kariega’, and to identify breeding lines possessing both leaf rust and stem rust resistance. A panel of 179 RILs, two parental cultivars and three checks were evaluated in South Africa at two localities, Cedara and Tygerhoek, in 2014 and 2015. Disease response ranged from highly resistant to highly susceptible. Analysis of variance indicated highly significant (<i>p</i>
DOI: 10.6084/m9.figshare.5558491
title: Data Figure 4

description: Fitting of different hypothesis models to PHO2 data.
DOI: 10.6084/m9.figshare.5558494
title: Data Figure 5

description: Observed and predicted profiles of PHO2 and IPS1 under Pi-depletion and repletion conditions
DOI: 10.6084/m9.figshare.5558485
title: Data Figure 1

description: Expression profiles of PHO2, IPS1 and miR399 in Pi-starved rice seedling (cv. Nippobare) roots.
DOI: 10.6084/m9.figshare.5558488
title: Data Figure 3

description: Model fitting to time-course data at different prediction intervals.
DOI: 10.6084/m9.figshare.5558488.v1
title: Data Figure 3

description: Model fitting to time-course data at different prediction intervals.
DOI: 10.6084/m9.figshare.5558500.v2
title: Adult plant resistance to leaf rust and stem rust of wheat in a newly developed recombinant inbred line population

description: Leaf rust caused by <i>Puccinia triticina</i> and stem rust by <i>P. graminis</i> f. sp. <i>tritici</i> are the most destructive diseases of wheat (<i>Triticum aestivum</i> L.), resulting in substantial yield losses globally. A continuous search for new sources of effective rust resistance genes is necessary to develop improved cultivars with durable resistance. This study aimed to investigate inheritance of adult-plant resistance in a recombinant inbred line (RIL) population of a cross between wheat cultivars ‘Popo’ and ‘Kariega’, and to identify breeding lines possessing both leaf rust and stem rust resistance. A panel of 179 RILs, two parental cultivars and three checks were evaluated in South Africa at two localities, Cedara and Tygerhoek, in 2014 and 2015. Disease response ranged from highly resistant to highly susceptible. Analysis of variance indicated highly significant (<i>p</i>
DOI: 10.6084/m9.figshare.5558128
title: Data and code to reproduce Evans et al. 2018 "Carry-over effects of urban larval environments on the transmission potential of dengue-2 virus"

description: This dataset contains the code and data to reproduce the analysis from Evans et al. 2018 "Carry-over effects of urban larval environments on the transmission potential of dengue-2 virus". <i>Parasites and Vectors</i>.<br>View the full repository on github at https://github.com/mvevans89/dengue-carryover.<br><br>To run code, extract the zip file and name this top repository 'denguePaper'. Set the working directory to the directory above denguePaper. Code should be run in numbered order to process raw data into clean, run analyses, and create figures. <br>Information on individual data files is in metadata.md file in `data` folder.<br>
DOI: 10.6084/m9.figshare.5558113
title: Pearmanetal_HiddenMajority_COI_metadata.xlsx

description: The table contains all the metadata associated with the benthic coral reef samples collected in the Red Sea. Primer and adaptor sequences are provided for each sample.
DOI: 10.6084/m9.figshare.5558128.v2
title: Data and code to reproduce Evans et al. 2018 "Carry-over effects of urban larval environments on the transmission potential of dengue-2 virus"

description: This dataset contains the code and data to reproduce the analysis from Evans et al. 2018 "Carry-over effects of urban larval environments on the transmission potential of dengue-2 virus". <i>Parasites and Vectors</i>.<br>View the full repository on github at https://github.com/mvevans89/dengue-carryover.<br><br>To run code, extract the zip file and name this top repository 'denguePaper'. Set the working directory to the directory above denguePaper. Code should be run in numbered order to process raw data into clean, run analyses, and create figures. <br>Information on individual data files is in metadata.md file in `data` folder.<br>
DOI: 10.6084/m9.figshare.5558077
title: data_distributional_graph_sampling

description: This fileset contains 4 triples and 2 quad structure files. Triple files are genes, biomarkers chemicals and diseases triples, quads file have pathways and co-occurrence information
DOI: 10.6084/m9.figshare.5558113.v1
title: Pearmanetal_HiddenMajority_COI_metadata.xlsx

description: The table contains all the metadata associated with the benthic coral reef samples collected in the Red Sea. Primer and adaptor sequences are provided for each sample.
DOI: 10.17608/k6.auckland.5558062
title: Maximise research impact using social media, Doctoral Skills Programme workshop, University of Auckland.

description: <i>Maximise research impact using social media </i>is a 2hr workshop provided within the University of Auckland's Doctoral Skills Programme. It introduces doctoral candidates to the various opportunities offered by social media to increase the impact of their to their research.<br><br>Fileset includes:<br>- slide deck<br>- 'Quick guide: social media platforms' handout<br>- 'My social media plan' exercise sheet (used progressively through the session)<br><br>Workshop has been compiled in 2017 with contributions from Research Support Services (RSS) and Subject Librarian (SL) teams, Libraries and Learning Services, and by the Research Office. Coordinated by the Research Support Services team, the workshop has been delivered several times throughout 2017 by a variety of RSS and SL presenters. <br>
DOI: 10.6084/m9.figshare.5558077.v1
title: data_distributional_graph_sampling

description: This fileset contains 4 triples and 2 quad structure files. Triple files are genes, biomarkers chemicals and diseases triples, quads file have pathways and co-occurrence information
DOI: 10.6084/m9.figshare.5558128.v1
title: Data and code to reproduce Evans et al. 2018 "Carry-over effects of urban larval environments on the transmission potential of dengue-2 virus"

description: This dataset contains the code and data to reproduce the analysis from Evans et al. 2018 "Carry-over effects of urban larval environments on the transmission potential of dengue-2 virus". <i>Parasites and Vectors</i>.<br>Code should be run in numbered order to process raw data into clean, run analyses, and create figures.<br>Information on individual data files is in metadata.md file in `data` folder.<br>
DOI: 10.25373/ctsnet.5557981
title: Preventing Recurrence: Optimal Surgical and Medical Management of Catamenial Pneumothorax

description: The authors describe the successful surgical and medical management of a young woman with recurrent catamenial pneumothoraxes. A 34-year-old woman was referred to thoracic surgery clinic for recurrent episodes of dyspnea. She stopped taking oral contraceptive pills at the age of 30, shortly after which she began having recurrent episodes of dyspnea, cough, and dysmenorrhea. She underwent a diagnostic laparoscopy with evidence of pelvic endometriosis. She was found to have a right pneumothorax and had a chest tube placed. The pneumothorax persisted and she underwent a VATS blebectomy and decortication at an outside hospital.Full article available at:<br>https://www.ctsnet.org/article/preventing-recurrence-optimal-surgical-and-medical-management-catamenial-pneumothorax<b>Images:</b><br><b>Figure 1.</b> Selected images of the patient’s preoperative computed tomography imaging showing her right apical and basilar pneumothoraxes and pigtail thoracostomy tube.<br><b>Figure 2.</b> The patient’s 14-month postoperative chest x-ray showing no recurrence of her pneumothorax.<br>
DOI: 10.6084/m9.figshare.5557966
title: 3-gene_phylogeny_ML.result

description: This is the resulting 3-gene_phylogeny_ML.result file of the Maximum Likelihood phylogenetic reconstruction using the three-gene dataset (SSU+ITS+LSU) as input.