cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25550/1-sxs0
title: Somnath Datta. Exploratory Statistical Analysis of Differential Network Behaviors Based on Gene Expression Atlas of Palate Development

description: An extensive gene expression atlas for craniofacial development including that of the murine palate in mice has been constructed and validated by the research team of Steven Potter as part of the FaceBase Consortium. Since genes act in consort during a biological process, a network analysis is essential for a system-wide understanding. To the best of our knowledge, such a system-wide network and differential network analysis has not been conducted in the literature for the murine palate development. The goal of this R03 proposal is to mine these data for the E14.5 palate to explore further into the collective workings of the genes for various compartments at this stage. This will be achieved by reverse engineering of gene-gene association/interaction networks and their differential analysis. In the process, exiting and novel modern statistical techniques will be employed and tools (R packages) will be developed that will be freely available to the scientific community for other similar studies involving microarray and next generation sequencing based data collected across multiple experimental conditions. Thus, the following two broad interconnected aims (and sub-aims) all leading to better understanding of craniofacial palate development in mice will be undertaken. We will explore suitable measures for detecting gene-gene association/interaction using RNA-seq expression data and construct gene-gene association/interaction networks for palate development using these association measures (Aim 1). We will conduct a differential network analysis based on the gene expressions between two regions; this will show how the connected components vary in different regions of the palate indicating changes in collective activities of the corresponding genes (Aim 2). Also, we will identify genes paying important cross compartment roles by integrating ranked lists of differentially connected genes between multiple pairwise comparisons. It is also anticipated that the proposed research will lead to some novel bioinformatics tools (R packages/codes) which will be freely distributed through the Comprehensive R Archive Network and/or Bioconductor.
DOI: 10.5281/zenodo.3953639
title: TestData_tools21cm

description: Data from the PRACE4LOFAR reionization simulation 244Mpc_f2_0_250 for redshift z=7.059. At this stage, the volume-averaged ionization fraction is 0.4073 and the mass-averaged ionization fraction 0.5018.
DOI: 10.5281/zenodo.3953638
title: TestData_tools21cm

description: Data from the PRACE4LOFAR reionization simulation 244Mpc_f2_0_250 for redshift z=7.059. At this stage, the volume-averaged ionization fraction is 0.4073 and the mass-averaged ionization fraction 0.5018.
DOI: 10.5281/zenodo.3953749
title: From dome dune to barchan dune: airflow structure changes measured with particle image velocimetry in a wind tunnel

description: data of Fig. 3
DOI: 10.5525/gla.researchdata.1010
title: aBravo is a novel Aedes aegypti antiviral protein that interacts with, but acts independently of, the exogenous siRNA pathway effector Dicer 2

description: These datasets contain luciferase data contained in the paper.
DOI: 10.24377/ljmu.d.00000077
title: Clarity of Task Difficulty Moderates the Impact of the Explicit Achievement Motive on Physical Effort in Hand Grip Tasks - Data and Script Files

description: This dataset includes data and script files from two studies (N = 80) in which we examined the joint impact of clarity of task difficulty and explicit achievement motive on exerted force in an isometric hand grip task.
description: experiment; lab study;
DOI: 10.25345/c5wx8x
title: MassIVE MSV000085796 - Phosphoproteomics of the developing heart identifies PERM1 - an outer mitochondrial membrane protein
title: Heart development relies on PTMs that control cardiomyocyte proliferation, differentiation and cardiac morphogenesis. We generated a map of phosphorylation sites during the early stages of cardiac postnatal development in mice; we quantified over 10,000 phosphorylation sites and 5000 proteins that were assigned to different pathways. Analysis of mitochondrial proteins led to the identification of PGC-1- and ERR-induced regulator in muscle 1 (PERM1), which is specifically expressed in skeletal muscle and heart tissue and associates with the outer mitochondrial membrane. We demonstrate PERM1 is subject to rapid changes mediated by the UPS through phosphorylation of its PEST motif by casein kinase 2. Ablation of Perm1 in mice results in reduced protein expression of lipin-1 accompanied by accumulation of specific phospholipid species. Isolation of Perm1-deficient mitochondria revealed significant downregulation of mitochondrial transport proteins for amino acids and carnitines, including SLC25A12/13/29/34 and CPT2. Consistently, we observed altered levels of various lipid species, amino acids and acylcarnitines in Perm1-/- mitochondria. We conclude that the outer mitochondrial membrane protein PERM1 regulates homeostasis of lipid and amino acid metabolites in mitochondria.
DOI: 10.5285/82907459c1c74495874df13503053e3c
title: NERC-ARF 2014_303 - RG13_06 Flight: Airborne remote sensing measurements

description: Airborne remote sensing measurements collected on 30 October 2014 onboard the Natural Environment Research Council Airborne Research Facility (NERC-ARF) Dornier Do228-101 D-CALM Aircraft for the Biodiversity and Land-use Impacts on Tropical Ecosystem function (BALI) (RG13_06) project (flight reference: 2014_303). This dataset comprises: digital photography data collected using a Leica RCD105 camera, hyperspectral data collected using a Specim Aisa FENIX imager, full-waveform airborne LiDAR data collected using a Leica ALS50II LiDAR and hyperspectral data collected using a Specim Aisa OWL imager. Data were collected over the Maliau Basin, Malaysia area.
DOI: 10.5285/acbe9091dc4249fb94f02aa9064582fe
title: NERC-ARF 2014_302a - RG13_06 Flight: Airborne remote sensing measurements

description: Airborne remote sensing measurements collected on 29 October 2014 onboard the Natural Environment Research Council Airborne Research Facility (NERC-ARF) Dornier Do228-101 D-CALM Aircraft for the Biodiversity and Land-use Impacts on Tropical Ecosystem function (BALI) (RG13_06) project (flight reference: 2014_302a). This dataset comprises: full-waveform airborne LiDAR data collected using a Leica ALS50II LiDAR. Data were collected over the Maliau Basin, Malaysia area.
DOI: 10.5285/3f7d71a981d341708bcb4db1edbff62e
title: NERC-ARF 2014_298 - RG13_06 Flight: Airborne remote sensing measurements

description: Airborne remote sensing measurements collected on 25 October 2014 onboard the Natural Environment Research Council Airborne Research Facility (NERC-ARF) Dornier Do228-101 D-CALM Aircraft for the Biodiversity and Land-use Impacts on Tropical Ecosystem function (BALI) (RG13_06) project (flight reference: 2014_298). This dataset comprises: digital photography data collected using a Leica RCD105 camera, hyperspectral data collected using a Specim Aisa FENIX imager and full-waveform airborne LiDAR data collected using a Leica ALS50II LiDAR. Data were collected over the Danum Valley, Malaysia area.
DOI: 10.25345/c5s45x
title: MassIVE MSV000085797 - GNPS_Discovery of unusual cyanobacterial tryptophan-containing anabaenopeptins by MS/MS based molecular networking
title: Heterocytous cyanobacteria are among the most prolific source of bioactive secondary metabolites, including anabaenopeptins. A terrestrial filamentous Brasilonema sp. CT11 collected in Costa Rica bamboo forest, as black mat was studied using a multidisciplinary approach: genome mining and HPLC-HRMS/MS coupled with bionformatic analyses. Herein, we report the nearly complete genome consisting 8.79 Mbp with a GC content of 42.4%. Moreover, we report on three novel tryptophane-containing APTs; anabaenopeptin 788 (1), anabaenopeptin 802 (2) and anabaenopeptin 816 (3). Further, the structure of two homologues, i.e., anabaenopeptin 802 (2a) and anabaenopeptin 802 (2b) was determined by spectroscopic analysis (NMR and MS). Both compounds were shown to exert weak to moderate antiproliferative activity against HeLa cell lines. This study also provides the biosynthetic diversity of biosynthetic gene clusters and an assessment of the predicted chemical space yet to be discovered from this genus.
DOI: 10.5285/ca81ecd6acd441ac89fc5b505a355102
title: NERC-ARF 2014_297 - RG13_06 Flight: Airborne remote sensing measurements

description: Airborne remote sensing measurements collected on 24 October 2014 onboard the Natural Environment Research Council Airborne Research Facility (NERC-ARF) Dornier Do228-101 D-CALM Aircraft for the Biodiversity and Land-use Impacts on Tropical Ecosystem function (BALI) (RG13_06) project (flight reference: 2014_297). This dataset comprises: digital photography data collected using a Leica RCD105 camera, hyperspectral data collected using a Specim Aisa FENIX imager and full-waveform airborne LiDAR data collected using a Leica ALS50II LiDAR. Data were collected over the Danum Valley, Malaysia area.
DOI: 10.5285/4b30bf7c8f1243bcbc70c4816356a8d6
title: NERC-ARF 2014_295 - RG13_06 Flight: Airborne remote sensing measurements

description: Airborne remote sensing measurements collected on 22 October 2014 onboard the Natural Environment Research Council Airborne Research Facility (NERC-ARF) Dornier Do228-101 D-CALM Aircraft for the Biodiversity and Land-use Impacts on Tropical Ecosystem function (BALI) (RG13_06) project (flight reference: 2014_295). This dataset comprises: digital photography data collected using a Leica RCD105 camera, hyperspectral data collected using a Specim Aisa FENIX imager and full-waveform airborne LiDAR data collected using a Leica ALS50II LiDAR. Data were collected over the Danum Valley, Malaysia area.
DOI: 10.5285/eb49848446ef41dcad6c45658b8c644a
title: NERC-ARF 2014_294 - RG13_06 Flight: Airborne remote sensing measurements

description: Airborne remote sensing measurements collected on 21 October 2014 onboard the Natural Environment Research Council Airborne Research Facility (NERC-ARF) Dornier Do228-101 D-CALM Aircraft for the Biodiversity and Land-use Impacts on Tropical Ecosystem function (BALI) (RG13_06) project (flight reference: 2014_294). This dataset comprises: digital photography data collected using a Leica RCD105 camera, hyperspectral data collected using a Specim Aisa FENIX imager and full-waveform airborne LiDAR data collected using a Leica ALS50II LiDAR. Data were collected over the Danum Valley, Malaysia. area.
DOI: 10.5285/1a072df93a19434e85b4fff7fabfdafa
title: NERC-ARF 2014_289 - RG13_06 Flight: Airborne remote sensing measurements

description: Airborne remote sensing measurements collected on 16 October 2014 onboard the Natural Environment Research Council Airborne Research Facility (NERC-ARF) Dornier Do228-101 D-CALM Aircraft for the Biodiversity and Land-use Impacts on Tropical Ecosystem function (BALI) (RG13_06) project (flight reference: 2014_289). This dataset comprises: digital photography data collected using a Leica RCD105 camera, hyperspectral data collected using a Specim Aisa FENIX imager and full-waveform airborne LiDAR data collected using a Leica ALS50II LiDAR. Data were collected over the Danum Valley, Malaysia. Maliau Basin, Malaysia area.
DOI: 10.17037/data.00001811
title: The WOMAN (World Maternal Antifibrinolytic) Trial Dataset

description: The WOMAN trial was a large, pragmatic, randomised, double blind, placebo controlled trial to quantify the effects of the early administration of tranexamic acid on death, hysterectomy and other relevant outcomes. This dataset includes the data for 20,060 adult women, who had clinically diagnosed postpartum haemorrhage and who fulfilled the eligibility criteria, who were randomised to receive either TXA or placebo. Relevant data on an entry form was collected before randomisation to assess eligibility and then the woman was randomised. Outcome data was completed at death, discharge from the randomising hospital or 6 weeks (42 days) after randomisation, whichever occurred first. Each row in the dataset represents the full entry and outcome data collected for one woman. Additional information was collected on the sequence of events leading to death to confirm the cause of death.
description: This trial was coordinated from LSHTM and conducted in hospitals from 21 countries worldwide. Data was collected at each site by local investigators and transmitted to the CTU either as a paper form (by fax or email) or by entering the data directly into the trial database. Data outlined on the entry, outcome and adverse event forms was collected for this trial. The data was collected from the woman’s and her baby/ies routine medical records; no special tests were required.
DOI: 10.5285/a88dca766a6f4059bf60a866258f4903
title: NERC-ARF 2014_290 - RG13_06 Flight: Airborne remote sensing measurements

description: Airborne remote sensing measurements collected on 17 October 2014 onboard the Natural Environment Research Council Airborne Research Facility (NERC-ARF) Dornier Do228-101 D-CALM Aircraft for the Biodiversity and Land-use Impacts on Tropical Ecosystem function (BALI) (RG13_06) project (flight reference: 2014_290). This dataset comprises: digital photography data collected using a Leica RCD105 camera, hyperspectral data collected using a Specim Aisa FENIX imager and full-waveform airborne LiDAR data collected using a Leica ALS50II LiDAR. Data were collected over the Danum Valley, Malaysia area.
DOI: 10.5285/340711b723124764bd42f39c4465d728
title: NERC-ARF 2014_291 - RG13_06 Flight: Airborne remote sensing measurements

description: Airborne remote sensing measurements collected on 18 October 2014 onboard the Natural Environment Research Council Airborne Research Facility (NERC-ARF) Dornier Do228-101 D-CALM Aircraft for the Biodiversity and Land-use Impacts on Tropical Ecosystem function (BALI) (RG13_06) project (flight reference: 2014_291). This dataset comprises: digital photography data collected using a Leica RCD105 camera, hyperspectral data collected using a Specim Aisa FENIX imager and full-waveform airborne LiDAR data collected using a Leica ALS50II LiDAR. Data were collected over the Danum Valley, Malaysia area.
DOI: 10.5285/2ffddce56f01468b888b01942eba75dc
title: NERC-ARF 2014_293 - RG13_06 Flight: Airborne remote sensing measurements

description: Airborne remote sensing measurements collected on 20 October 2014 onboard the Natural Environment Research Council Airborne Research Facility (NERC-ARF) Dornier Do228-101 D-CALM Aircraft for the Biodiversity and Land-use Impacts on Tropical Ecosystem function (BALI) (RG13_06) project (flight reference: 2014_293). This dataset comprises: digital photography data collected using a Leica RCD105 camera, hyperspectral data collected using a Specim Aisa FENIX imager and full-waveform airborne LiDAR data collected using a Leica ALS50II LiDAR. Data were collected over the Danum Valley, Malaysia area.
DOI: 10.5281/zenodo.3953938
title: An empirical study of automatically-generated tests from the perspective of test smells

description: Developing software test code can be as or more expensive than developing software production code. Commonly, developers use automated unit test generators to speed up software testing. The purpose of such tools is to shorten production time without decreasing code quality. Nonetheless, unit tests usually do not have a quality check layer above testing code, which might be hard to guarantee the quality of the generated tests. An emerging strategy to verify the tests quality is to analyze the presence of test smells in software test code. Test smells are characteristics in the test code that possibly indicate weaknesses in test design and implementation. The presence of test smells in unit test code could be used as an indicator of unit test quality. In this paper, we present an empirical study aimed to analyze the quality of unit test code generated by automated test tools. We compare the tests generated by two tools (Randoop and EvoSuite) with the existing unit test suite of open-source software projects. We analyze the unit test code of twenty-one open-source Java projects and detected the presence of nineteen types of test smells. The results indicated significant differences in the unit test quality when comparing data from both automated unit test generators and existing unit test suites.
DOI: 10.5281/zenodo.3783477
title: Fundplatzdatenbank Siedlungskammer Kilikien

description: In der für das Projekt "Siedlungskammer Kilikien" erstellten Fundplatzdatenbank (FDB) sind die in den Survey- und Forschungsberichten erwähnten Fundplätze des Ebenen Kilikien mit ihren Koordinaten und den dokumentierten Nutzungsphasen erfasst. Dafür wurde die bis Mitte 2015 publizierte Literatur berücksichtigt.
DOI: 10.5281/zenodo.3953494
title: Switch to second-line versus continued first-line antiretroviral therapy for patients with low-level HIV-1 viremia: an open-label randomized controlled trial in Lesotho

description: These are pseudo-anonymised data from the SESOTHO randomised trial: "Switch to second-line versus WHO-guided standard of care for unsuppressed patients on first-line ART with viremia below 1000 copies/mL – a multicenter, parallel-group, open-label, randomized clinical study in rural Lesotho". There are two datasets, one containing baseline data (one row per participant) and one containing longitudinal viral load data (one row per participant per visit). The data dictionary explains the data available in each dataset. Between August 2017 and August 2019, 80 eligible and consenting participants were enrolled from eight health facilities in four districts of Lesotho, and followed up for nine months. The protocol was published, DOI: 10.1186/s12879-018-2979-y
DOI: 10.5281/zenodo.3953493
title: Switch to second-line versus continued first-line antiretroviral therapy for patients with low-level HIV-1 viremia: an open-label randomized controlled trial in Lesotho

description: These are pseudo-anonymised data from the SESOTHO randomised trial: "Switch to second-line versus WHO-guided standard of care for unsuppressed patients on first-line ART with viremia below 1000 copies/mL – a multicenter, parallel-group, open-label, randomized clinical study in rural Lesotho". There are two datasets, one containing baseline data (one row per participant) and one containing longitudinal viral load data (one row per participant per visit). The data dictionary explains the data available in each dataset. Between August 2017 and August 2019, 80 eligible and consenting participants were enrolled from eight health facilities in four districts of Lesotho, and followed up for nine months. The protocol was published, DOI: 10.1186/s12879-018-2979-y
DOI: 10.5281/zenodo.3953965
title: Output_ranking_PPI_DeepRank

description: Results of training DeepRank to rank PPIs.
DOI: 10.5281/zenodo.3953964
title: Output_ranking_PPI_DeepRank

description: Results of training DeepRank to rank PPIs.
DOI: 10.15468/4abnwp
title: Taxonomic studies of Diospyros L. (Ebenaceae) from the Malagasy region. IV. Synoptic revision of the Squamosa group in Madagascar and the Comoro Islands

description: This dataset contains the digitized treatments in Plazi based on the original journal article Schatz, George E., Lowry II, Porter P. (2020): Taxonomic studies of Diospyros L. (Ebenaceae) from the Malagasy region. IV. Synoptic revision of the Squamosa group in Madagascar and the Comoro Islands. Adansonia sér. 3 42 (9): 201-218, DOI: 10.5252/adansonia2020v42a10
DOI: 10.5285/aaa4dab8-7c9d-0cca-e053-6c86abc00b1d
title: Iodide to iodate oxidation by laboratory cultures of nitrifying bacteria between August-September 2017.

description: The dataset presented here is from two experiments demonstrating the oxidation of iodide to iodate by marine ammonium oxidising bacteria <em>Nitrosomonas sp.</em> (Nm51) and <em>Nitrosoccocus oceani</em> (Nc10). In each experiment there were three replicates of bacterial culture and three replicates of media only control. Cultures grown in the dark at 25 degrees C in nutrient enriched artificial seawater (ESAW) supplemented with 7-8 mM ammonium and 9-10 mM iodide. Aliquots were removed from cultures and controls at intervals through the course of the experiment, and analysed for iodine and nitrogen speciation, pH and cell count. This dataset includes iodide, iodate, nitrite and ammonium concentrations, pH and cell counts over the duration of each experiment. The data presented here were generated by Dr Helmke Hepach (University of York, now at GEOMAR Helmholtz Centre for Ocean Research, Kiel) and Eleanor Barton, under the supervision of Dr Claire Hughes (University of York) and with additional guidance from Dr Rosie Chance (University of York). These experiments were part of the NERC project "Iodide in the ocean: distribution and impact on iodine flux and ozone loss" (NE/N009983/1, PI: Prof Lucy Carpenter, University of York).
DOI: 10.18112/openneuro.ds002905.v1.0.1
title: simpcomp_rawdata
DOI: 10.5281/zenodo.3954024
title: Data for: Hand muscles attachments: A Geometrical model

description: Dataset to be linked with not yet published manuscript "Hand muscles attachments: A Geometrical model" In musculoskeletal modelling, parameters identification, such as the exact position and trajectories of muscle attachments, is a crucial issue. The main goal of this study was to calculate the position, attachment dimensions and cross section areas of twenty-five extrinsic and intrinsic hand muscle complexes. We integrated measurements taken from cadaveric preparations, magnetic resonance imaging and mathematical theory. Sixteen cadaveric preparations were dissected to draw up the anatomical maps including the position of muscle attachments, dimensions, shapes, cross section areas and variations. The magnetic resonance imaging of cadaveric upper extremity was performed to reconstruct the geometry of all bones and hand muscles. Using these outcomes, the muscle attachments and cross section areas were extracted and verified using the obtained morphological and morphometric analysis. The exact trajectories of muscle lines of action were computed using the modified weighted k-means method and Hungary algorithm. This work introduces a new approach to acquiring musculoskeletal modelling data in general and contributes extensive dataset to the hand musculature modelling in particular. <strong>Acknowledgments</strong> This work was supported by the project n. 182 “Obstetrics 2.0 - Virtual models for the prevention of injuries during childbirth” realised within the frame of the Program INTERREG V-A: Cross- border cooperation between the Czech Republic and the Federal State of Germany Bavaria, Aim European Cross-border cooperation 2014-2020. The realisation is supported by financial means of the European Regional Development Fund (85 % of the costs) and the state budget of the Czech Republic (5 %). KI is part-funded by project No. CZ.02.1.01/0.0/0.0/16_019/0000787 “Fighting INfectious Diseases“, awarded by the Ministry of Education, Youth and Sports of the Czech Republic, financed from The European Regional Development Fund.
DOI: 10.5281/zenodo.3954023
title: Successful mating and hybridisation in two closely related flatworm species despite significant differences in reproductive morphology and behaviour

description: Dataset of Article 'Successful mating and hybridisation in two closely related flatworm species despite significant differences in reproductive morphology and behaviour' (DOI : 10.1038/s41598-020-69767-5)
DOI: 10.5281/zenodo.3954022
title: Successful mating and hybridisation in two closely related flatworm species despite significant differences in reproductive morphology and behaviour

description: Dataset of Article 'Successful mating and hybridisation in two closely related flatworm species despite significant differences in reproductive morphology and behaviour' (DOI : 10.1038/s41598-020-69767-5)