cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7583909.v6
title: Supplementary material for article "Analyzing Groups of Replications in Software Engineering: a Procedure and Guidelines"

description: -Code.R: file containing the R code to analyze SE groups of replications<br>-Raw Data.xlsx: file containing the raw data <br>-Characteristics.xlsx: file containing the experiment-level characteristics of the replications<br>-Rnotebook.Rmd: R notebook that applies Code.R to analyze the raw data in Raw Data.xlsx<br>-R tutorial: tutorial with embedded R code, mathematical formulae, and datasets descriptions, to ease the understanding of the analysis procedure
DOI: 10.7284/121580
title: TSG (Thermosalinograph) data collected during research cruise FK160305 using a Sea-Bird SBE-45 instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/121585
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise FK160320 using a Hawaii UHDAS instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/121583
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise FK160320 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/121584
title: Expendable Probe data collected during research cruise FK160320 using a Turo Quoll instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/121586
title: Fluorometer data collected during research cruise FK160320 using a WET Labs ECO-FLNTU instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/121582
title: GNSS (Global Navigation Satellite System) data collected during research cruise FK160320 using a C&C C-Nav 3050 instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/121581
title: Gyrocompass data collected during research cruise FK160320 using a Raytheon STD 22 instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/121590
title: INS (Inertial Navigation System) data collected during research cruise FK160320 using a Kongsberg Seapath 320 instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/121588
title: Meteorological Station data collected during research cruise FK160320 using a Gill MetPak Pro instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7583723
title: Epidemiological simulation

description: Random realisation of a simulated spread of plant epidemics in a randomly-generated landscape. A square 100km<sup>2</sup> landscape is generated with 2,500 randomly distributed plants and each plant is assumed to be equally susceptible to the disease. We assume there is no latent phase, that plants remain infectious once they become infected and that infectious plants show disease symptoms. At time step t = 0, an initial infection is seeded in the most centrally located host. A number of time steps are then performed in which a susceptible host either remains susceptible or becomes infected until all hosts are infected. Infection occurs due to the spread of the pathogen from an infected to a susceptible host within the known landscape. The probability that a susceptible host becomes infected in a single time step is determined by the total inoculum that the host receives from all currently infected hosts and the transmission rate parameter<i>.</i> The total inoculum that a susceptible host receives depends upon the distance between each infected host from the susceptible host under consideration. The proportion of inoculum emitted from an infected host that is received by a susceptible host is determined by an exponential dispersal kernel. Two scenarios are explored with two different dispersal kernels.
DOI: 10.7284/121587
title: Multibeam Echosounder data collected during research cruise FK160320 using a Kongsberg EM302 instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7583699
title: The <i>Acinetobacter</i> trimeric autotransporter adhesin Ata controls key virulence traits of <i>Acinetobacter baumannii</i>

description: <i>Acinetobacter baumannii</i> is a Gram-negative pathogen that causes a multitude of nosocomial infections. The <i>Acinetobacter</i> trimeric autotransporter adhesin (Ata) belongs to the superfamily of trimeric autotransporter adhesins which are important virulence factors in many Gram-negative species. Phylogenetic profiling revealed that <i>ata</i> is present in 78% of all sequenced <i>A. baumannii</i> isolates but only in 2% of the closely related species <i>A. calcoaceticus</i> and <i>A. pittii</i>. Employing a markerless <i>ata</i> deletion mutant of <i>A. baumannii</i> ATCC 19606 we show that adhesion to and invasion into human endothelial and epithelial cells depend on Ata. Infection of primary human umbilical cord vein endothelial cells (HUVECs) with <i>A. baumannii</i> led to the secretion of interleukin (IL)-6 and IL-8 in a time- and Ata-dependent manner. Furthermore, infection of HUVECs by WT <i>A. baumannii</i> was associated with higher rates of apoptosis via activation of caspases-3 and caspase-7, but not necrosis, in comparison to ∆<i>ata</i>. Ata deletion mutants were furthermore attenuated in their ability to kill larvae of <i>Galleria mellonella</i> and to survive in larvae when injected at sublethal doses. This indicates that Ata is an important multifunctional virulence factor in <i>A. baumannii</i> that mediates adhesion and invasion, induces apoptosis and contributes to pathogenicity <i>in vivo</i>.
DOI: 10.6084/m9.figshare.7583711
title: Health literacy among asthma patients and treatment expectations: results of a Belgian survey

description: <b>Objectives</b>: Non-adherence to asthma medication can lead to lower disease control and asthma exacerbations that may be fatal. This survey assessed the attitude and expectations of Belgian asthma patients towards their treatment. <b>Methods</b>: This cross-sectional survey was conducted between June 2015 and February 2016 in 70 Belgian pharmacies. Participants completing the survey had to be ≥15 years, diagnosed with asthma, and on inhaled corticosteroid-based treatment. The analysis included 80 completed questionnaires. <b>Results</b>: Participants comprehended well that controller drugs are intended to prevent the occurrence of asthma symptoms and complications, and their long-term daily use should be maintained. Twenty seven percent of participants indicated fear of side effects concerning long-term daily use of a controller inhaler. Participants had a good understanding that quick-relief drugs are intended to (quickly) relieve asthma symptoms and do not need to be used on a systematic, daily basis. Out of 73 participants on long-term controller drugs, 33 (45%) were ‘non-adherent’ (used less frequently than prescribed). Suboptimal adherence to maintenance treatment appeared to increase nightly awakenings and the risk of restrictions in activities due to asthma. Out of 54 participants with available quick-relief drug adherence data, 18 (33%) were non-adherent (used their quick-relief drug more frequently than prescribed). <b>Discussion</b>: This survey confirms suboptimal adherence to maintenance controller therapy and overuse of short-acting reliever medications among Belgian patients, which affects asthma control and quality of life. A substantial proportion of patients expressed fear about their chronic therapy, indicating the need for patient education about their disease and its management.
DOI: 10.6084/m9.figshare.7583723.v1
title: Epidemiological simulation

description: Random realisation of a simulated spread of plant epidemics in a randomly-generated landscape. A square 100km<sup>2</sup> landscape is generated with 2,500 randomly distributed plants and each plant is assumed to be equally susceptible to the disease. We assume there is no latent phase, that plants remain infectious once they become infected and that infectious plants show disease symptoms. At time step t = 0, an initial infection is seeded in the most centrally located host. A number of time steps are then performed in which a susceptible host either remains susceptible or becomes infected until all hosts are infected. Infection occurs due to the spread of the pathogen from an infected to a susceptible host within the known landscape. The probability that a susceptible host becomes infected in a single time step is determined by the total inoculum that the host receives from all currently infected hosts and the transmission rate parameter<i>.</i> The total inoculum that a susceptible host receives depends upon the distance between each infected host from the susceptible host under consideration. The proportion of inoculum emitted from an infected host that is received by a susceptible host is determined by an exponential dispersal kernel. Two scenarios are explored with two different dispersal kernels.
DOI: 10.6084/m9.figshare.7583711.v1
title: Health literacy among asthma patients and treatment expectations: results of a Belgian survey

description: <b>Objectives</b>: Non-adherence to asthma medication can lead to lower disease control and asthma exacerbations that may be fatal. This survey assessed the attitude and expectations of Belgian asthma patients towards their treatment. <b>Methods</b>: This cross-sectional survey was conducted between June 2015 and February 2016 in 70 Belgian pharmacies. Participants completing the survey had to be ≥15 years, diagnosed with asthma, and on inhaled corticosteroid-based treatment. The analysis included 80 completed questionnaires. <b>Results</b>: Participants comprehended well that controller drugs are intended to prevent the occurrence of asthma symptoms and complications, and their long-term daily use should be maintained. Twenty seven percent of participants indicated fear of side effects concerning long-term daily use of a controller inhaler. Participants had a good understanding that quick-relief drugs are intended to (quickly) relieve asthma symptoms and do not need to be used on a systematic, daily basis. Out of 73 participants on long-term controller drugs, 33 (45%) were ‘non-adherent’ (used less frequently than prescribed). Suboptimal adherence to maintenance treatment appeared to increase nightly awakenings and the risk of restrictions in activities due to asthma. Out of 54 participants with available quick-relief drug adherence data, 18 (33%) were non-adherent (used their quick-relief drug more frequently than prescribed). <b>Discussion</b>: This survey confirms suboptimal adherence to maintenance controller therapy and overuse of short-acting reliever medications among Belgian patients, which affects asthma control and quality of life. A substantial proportion of patients expressed fear about their chronic therapy, indicating the need for patient education about their disease and its management.
DOI: 10.7284/121589
title: SSV (Sound Speed Velocimeter) data collected during research cruise FK160320 using a Valeport MiniSVS instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7583672
title: MAKER configuration files for Brassica cretica individual A

description: Configuration files used for MAKER annotation of genome assembly GCA_003260655.1.
DOI: 10.6084/m9.figshare.7583672.v1
title: MAKER configuration files for Brassica cretica individual A

description: Configuration files used for MAKER annotation of genome assembly GCA_003260655.1.
DOI: 10.6084/m9.figshare.7583699.v2
title: The <i>Acinetobacter</i> trimeric autotransporter adhesin Ata controls key virulence traits of <i>Acinetobacter baumannii</i>

description: <i>Acinetobacter baumannii</i> is a Gram-negative pathogen that causes a multitude of nosocomial infections. The <i>Acinetobacter</i> trimeric autotransporter adhesin (Ata) belongs to the superfamily of trimeric autotransporter adhesins which are important virulence factors in many Gram-negative species. Phylogenetic profiling revealed that <i>ata</i> is present in 78% of all sequenced <i>A. baumannii</i> isolates but only in 2% of the closely related species <i>A. calcoaceticus</i> and <i>A. pittii</i>. Employing a markerless <i>ata</i> deletion mutant of <i>A. baumannii</i> ATCC 19606 we show that adhesion to and invasion into human endothelial and epithelial cells depend on Ata. Infection of primary human umbilical cord vein endothelial cells (HUVECs) with <i>A. baumannii</i> led to the secretion of interleukin (IL)-6 and IL-8 in a time- and Ata-dependent manner. Furthermore, infection of HUVECs by WT <i>A. baumannii</i> was associated with higher rates of apoptosis via activation of caspases-3 and caspase-7, but not necrosis, in comparison to ∆<i>ata</i>. Ata deletion mutants were furthermore attenuated in their ability to kill larvae of <i>Galleria mellonella</i> and to survive in larvae when injected at sublethal doses. This indicates that Ata is an important multifunctional virulence factor in <i>A. baumannii</i> that mediates adhesion and invasion, induces apoptosis and contributes to pathogenicity <i>in vivo</i>.
DOI: 10.7284/121591
title: TSG (Thermosalinograph) data collected during research cruise FK160320 using a Sea-Bird SBE-45 instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7583699.v1
title: The <i>Acinetobacter</i> trimeric autotransporter adhesin Ata controls key virulence traits of <i>Acinetobacter baumannii</i>

description: <i>Acinetobacter baumannii</i> is a Gram-negative pathogen that causes a multitude of nosocomial infections. The <i>Acinetobacter</i> trimeric autotransporter adhesin (Ata) belongs to the superfamily of trimeric autotransporter adhesins which are important virulence factors in many Gram-negative species. Phylogenetic profiling revealed that <i>ata</i> is present in 78% of all sequenced <i>A. baumannii</i> isolates but only in 2% of the closely related species <i>A. calcoaceticus</i> and <i>A. pittii</i>. Employing a markerless <i>ata</i> deletion mutant of <i>A. baumannii</i> ATCC 19606 we show that adhesion to and invasion into human endothelial and epithelial cells depend on Ata. Infection of primary human umbilical cord vein endothelial cells (HUVECs) with <i>A. baumannii</i> led to the secretion of interleukin (IL)-6 and IL-8 in a time- and Ata-dependent manner. Furthermore, infection of HUVECs by WT <i>A. baumannii</i> was associated with higher rates of apoptosis via activation of caspases-3 and caspase-7, but not necrosis, in comparison to ∆<i>ata</i>. Ata deletion mutants were furthermore attenuated in their ability to kill larvae of <i>Galleria mellonella</i> and to survive in larvae when injected at sublethal doses. This indicates that Ata is an important multifunctional virulence factor in <i>A. baumannii</i> that mediates adhesion and invasion, induces apoptosis and contributes to pathogenicity <i>in vivo</i>.
DOI: 10.7284/121595
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise FK160407 using a Hawaii UHDAS instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/121594
title: Expendable Probe data collected during research cruise FK160407 using a Turo Quoll instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7583387
title: TKOv1 Data

description: Reformatted data using TKOv1 library as used in JACKS 2019 paper. Please see README.txt for more information about each file and where it comes from.
DOI: 10.6084/m9.figshare.7583396
title: Configuration files for SOAPdenovo2 assembly of Brassica cretica

description: Configuration files for SOAPdenovo2
DOI: 10.7284/121596
title: Fluorometer data collected during research cruise FK160407 using a WET Labs ECO-FLNTU instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7583387.v1
title: TKOv1 Data

description: Reformatted data using TKOv1 library as used in JACKS 2019 paper. Please see README.txt for more information about each file and where it comes from.
DOI: 10.6084/m9.figshare.7583366
title: Supplementary Material for: Resistance Exercise Improves Mitochondrial Quality Control in a Rat Model of Sporadic Inclusion Body Myositis

description: <b><i>Background:</i></b> Mitochondrial dysfunction is implicated in the pathogenesis of multiple muscular diseases, including sporadic inclusion body myositis (s-IBM), the most common aging-related muscle disease. However, the factors causing mitochondrial dysfunction in s-IBM are unknown. <b><i>Objective:</i></b> We hypothesized that resistance exercise (RE) may alleviate muscle impairment by improving mitochondrial function via reducing amyloid-beta (Aβ) accumulation. <b><i>Methods:</i></b> Twenty-four male Wistar rats were randomized to a saline-injection control group (sham, <i>n</i> = 8), a chloroquine (CQ) control group (CQ-CON, <i>n</i> = 8), and a CQ plus RE group (CQ-RE, <i>n</i> = 8) in which rats climbed a ladder with weight attached to their tails 9 weeks after starting CQ treatment. <b><i>Results:</i></b> RE markedly inhibited soleus muscle atrophy and muscle damage. RE reduced CQ-induced Aβ accumulation, which resulted in decreased formation of rimmed vacuoles and mitochondrial-mediated apoptosis. Most importantly, the decreased Aβ accumulation improved both mitochondrial quality control (MQC) through increased mitochondrial biogenesis and mitophagy, and mitochondrial dynamics. Furthermore, RE-mediated reduction of Aβ accumulation elevated mitochondrial oxidative capacity by upregulating superoxide dismutase-2, catalase, and citrate synthase via activating sirtuin 3 signaling. <b><i>Conclusion:</i></b> RE enhances mitochondrial function by improving MQC and mitochondrial oxidative capacity via reducing Aβ accumulation, thereby inhibiting CQ-induced muscle impairment, in a rat model of s-IBM.
DOI: 10.6084/m9.figshare.7583369
title: Whitehead Data

description: Reformatted data using Whitehead library as used in JACKS 2019 paper. Please see README.txt for more information about each file and where it comes from.
DOI: 10.7284/121593
title: GNSS (Global Navigation Satellite System) data collected during research cruise FK160407 using a C&C C-Nav 3050 instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7583366.v1
title: Supplementary Material for: Resistance Exercise Improves Mitochondrial Quality Control in a Rat Model of Sporadic Inclusion Body Myositis

description: <b><i>Background:</i></b> Mitochondrial dysfunction is implicated in the pathogenesis of multiple muscular diseases, including sporadic inclusion body myositis (s-IBM), the most common aging-related muscle disease. However, the factors causing mitochondrial dysfunction in s-IBM are unknown. <b><i>Objective:</i></b> We hypothesized that resistance exercise (RE) may alleviate muscle impairment by improving mitochondrial function via reducing amyloid-beta (Aβ) accumulation. <b><i>Methods:</i></b> Twenty-four male Wistar rats were randomized to a saline-injection control group (sham, <i>n</i> = 8), a chloroquine (CQ) control group (CQ-CON, <i>n</i> = 8), and a CQ plus RE group (CQ-RE, <i>n</i> = 8) in which rats climbed a ladder with weight attached to their tails 9 weeks after starting CQ treatment. <b><i>Results:</i></b> RE markedly inhibited soleus muscle atrophy and muscle damage. RE reduced CQ-induced Aβ accumulation, which resulted in decreased formation of rimmed vacuoles and mitochondrial-mediated apoptosis. Most importantly, the decreased Aβ accumulation improved both mitochondrial quality control (MQC) through increased mitochondrial biogenesis and mitophagy, and mitochondrial dynamics. Furthermore, RE-mediated reduction of Aβ accumulation elevated mitochondrial oxidative capacity by upregulating superoxide dismutase-2, catalase, and citrate synthase via activating sirtuin 3 signaling. <b><i>Conclusion:</i></b> RE enhances mitochondrial function by improving MQC and mitochondrial oxidative capacity via reducing Aβ accumulation, thereby inhibiting CQ-induced muscle impairment, in a rat model of s-IBM.
DOI: 10.6084/m9.figshare.7583396.v1
title: Configuration files for SOAPdenovo2

description: Configuration files for SOAPdenovo2
DOI: 10.6084/m9.figshare.7583348
title: Long-term neuropathy and quality of life in colorectal cancer patients treated with oxaliplatin containing adjuvant chemotherapy

description: <b>Background:</b> Oxaliplatin, combined with capecitabine (CAPOX) or infused 5-fluorouracil (FOLFOX), is standard of care in the adjuvant treatment of colorectal cancer (CRC). Prospective data on prevalence of oxaliplatin induced acute and long-term neuropathy in a real-life patient population and its effects on quality of life (QOL) and survival is limited, and scarce in CAPOX versus FOLFOX treated, especially in a subarctic climate. <b>Methods:</b> One hundred forty-four adjuvant CRC patients (all 72 CAPOX cases and 72 matched FOLFOX controls) were analyzed regarding oxaliplatin induced sensory neuropathy, which was graded according to NCI-CTCAEv3.0. Ninety-two long-term survivors responded to the QOL (EORTC QLQ-C30) and Chemotherapy-Induced Peripheral Neuropathy (EORTC CIPN20) questionnaires and were interviewed regarding long-term neuropathy. <b>Results:</b> Acute neurotoxicity was present in 94% (136/144) during adjuvant therapy and there was a significant association between acute neurotoxicity and long-term neuropathy (<i>p</i> p = .031), decreased role functioning (<i>p</i> = .040), and more diarrhea (<i>p</i> = .021) in QLQ-C30 items. There were no differences in acute neurotoxicity, long-term neuropathy, or in QOL between CAPOX and FOLFOX treated. Neuropathy showed no pattern of variation according to starting and stopping month or treatment during winter. <b>Conclusions:</b> Neuropathy following oxaliplatin containing adjuvant chemotherapy is present in two-thirds, years after cessation, and impairs some QOL scales. There is no difference in severity of acute or long-term neuropathy between CAPOX and FOLFOX treated and QOL is similar. No seasonal variation in neuropathy was noted.
DOI: 10.7284/121592
title: Gyrocompass data collected during research cruise FK160407 using a Raytheon STD 22 instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition