cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5537752.v1
title: Properties of Na<sub>2</sub>O–SiO<sub>2</sub> slags in Doré smelting

description: Solubilities of metals in sodium silicate slags have been studied at 1000–1300°C in oxygen pressures of <i>P</i>(O<sub>2</sub>) = 10<sup>−4</sup> to 0.5 atm, in Doré alloy smelting of copper anode slimes. The boundary conditions for the slags were silica saturation, magnesia saturation with about 10 wt% and without BaO. The trace elements studied were copper, gold, palladium, rhodium, and tellurium. The analytical methods used in the phase composition analyses of equilibrated samples, quenched in brine, were electron probe X-ray microanalysis and laser ablation-inductively coupled plasma-mass spectrometry. Thermodynamic features of the slags, trace element solubilities with the given constraints, and their oxidation mechanisms were determined. The data allow optimizing the anode slime-smelting for the metals’ maximum recovery in sodium silicate fluxing.
DOI: 10.6084/m9.figshare.5537788.v1
title: Definitive screening design enables optimization of LC–ESI–MS/MS parameters in proteomics

description: In proteomics, more than 100,000 peptides are generated from the digestion of human cell lysates. Proteome samples have a broad dynamic range in protein abundance; therefore, it is critical to optimize various parameters of LC–ESI–MS/MS to comprehensively identify these peptides. However, there are many parameters for LC–ESI–MS/MS analysis. In this study, we applied definitive screening design to simultaneously optimize 14 parameters in the operation of monolithic capillary LC–ESI–MS/MS to increase the number of identified proteins and/or the average peak area of MS1. The simultaneous optimization enabled the determination of two-factor interactions between LC and MS. Finally, we found two parameter sets of monolithic capillary LC–ESI–MS/MS that increased the number of identified proteins by 8.1% or the average peak area of MS1 by 67%. The definitive screening design would be highly useful for high-throughput analysis of the best parameter set in LC–ESI–MS/MS systems. Definitive screening design enables simultaneous optimization of LC-ESI-MS/MS parameters in proteomics.
DOI: 10.6084/m9.figshare.5537584
title: SNPdata.txt

description: Data from "Characterization of Population Genetic Structure of Procambarus clarkii in China". This SNP dataset was generated from 2b-RAD technique.
DOI: 10.6084/m9.figshare.5537584.v1
title: SNPdata.txt

description: Data from "Characterization of Population Genetic Structure of Procambarus clarkii in China". This SNP dataset was generated from 2b-RAD technique.
DOI: 10.6084/m9.figshare.5537566
title: WP3: Simulation Results

description: Simulation results for multiobjective optimization
DOI: 10.6084/m9.figshare.5537545
title: Supplementary Material for: Online Education and e-Consent for GeneScreen, a Preventive Genomic Screening Study

description: <b><i>Background:</i></b> Online study recruitment is increasingly popular, but we know little about the decision making that goes into joining studies in this manner. In GeneScreen, a genomic screening study that utilized online education and consent, we investigated participants' perceived ease when deciding to join and their understanding of key study features. <b><i>Methods:</i></b> Individuals were recruited via mailings that directed them to a website where they could learn more about GeneScreen, consent to participate, and complete a survey. <b><i>Results:</i></b> Participants found it easy to decide to join GeneScreen and had a good understanding of study features. Multiple regression analyses revealed that ease of deciding to join was related to confidence in one's genetic self-efficacy, limited concerns about genetic screening, trust in and lack of frustration using the website, and the ability to spend a limited time on the website. Understanding of study features was related to using the Internet more frequently and attaining more information about GeneScreen conditions. <b><i>Conclusions:</i></b> The ease of deciding to join a genomic screening study and comprehension of its key features should be treated as different phenomena in research and practice. There is a need for a more nuanced understanding of how individuals respond to web-based consent information.
DOI: 10.6084/m9.figshare.5537566.v2
title: WP3: Simulation Results

description: Simulation results for multiobjective optimization
DOI: 10.6084/m9.figshare.5537506
title: Supplementary Material for: Cyclosporine A Induces MicroRNAs Controlling Innate Immunity during Renal Bacterial Infection

description: Urinary tract infections (UTIs) mainly due to uropathogenic <i>Escherichia coli</i> (UPEC) are one of the most frequent complications in kidney-transplanted patients, causing significant morbidity. However, the mechanisms underlying UTI in renal grafts remain poorly understood. Here, we analysed the effects of the potent immunosuppressive agent cyclosporine A (CsA) on the activation of collecting duct cells that represent a preferential site of adhesion and translocation for UPEC. CsA induced the inhibition of lipopolysaccharide- induced activation of collecting duct cells due to the downregulation of the expression of TLR4 via the microRNA Let-7i. Using an experimental model of ascending UTI, we showed that the pretreatment of mice with CsA prior to infection induced a marked fall in cytokine production by collecting duct cells, neutrophil recruitment, and a dramatic rise of bacterial load, but not in infected TLR4-defective mice kidneys. This effect was also observed in CsA-treated infected kidneys, where the expression of Let-7i was increased. Treatment with a synthetic Let-7i mimic reproduced the effects of CsA. Conversely, pretreatment with an anti-Let-7i antagonised the effects of CsA and rescued the innate immune response of collecting duct cells against UPEC. Thus, the utilisation of an anti-Let-7i during kidney transplantation may protect CsA-treated patients from ascending bacterial infection.
DOI: 10.6084/m9.figshare.5537566.v1
title: WP3: Simulation Results

description: Simulation results for multiobjective optimization
DOI: 10.6084/m9.figshare.5537506.v1
title: Supplementary Material for: Cyclosporine A Induces MicroRNAs Controlling Innate Immunity during Renal Bacterial Infection

description: Urinary tract infections (UTIs) mainly due to uropathogenic <i>Escherichia coli</i> (UPEC) are one of the most frequent complications in kidney-transplanted patients, causing significant morbidity. However, the mechanisms underlying UTI in renal grafts remain poorly understood. Here, we analysed the effects of the potent immunosuppressive agent cyclosporine A (CsA) on the activation of collecting duct cells that represent a preferential site of adhesion and translocation for UPEC. CsA induced the inhibition of lipopolysaccharide- induced activation of collecting duct cells due to the downregulation of the expression of TLR4 via the microRNA Let-7i. Using an experimental model of ascending UTI, we showed that the pretreatment of mice with CsA prior to infection induced a marked fall in cytokine production by collecting duct cells, neutrophil recruitment, and a dramatic rise of bacterial load, but not in infected TLR4-defective mice kidneys. This effect was also observed in CsA-treated infected kidneys, where the expression of Let-7i was increased. Treatment with a synthetic Let-7i mimic reproduced the effects of CsA. Conversely, pretreatment with an anti-Let-7i antagonised the effects of CsA and rescued the innate immune response of collecting duct cells against UPEC. Thus, the utilisation of an anti-Let-7i during kidney transplantation may protect CsA-treated patients from ascending bacterial infection.
DOI: 10.6084/m9.figshare.5537485
title: Supplementary Material for: Diagnosis of Inherited Epidermolysis Bullosa in Resource-Limited Settings: Immunohistochemistry Revisited

description: <b><i>Background:</i></b> Immunofluorescence (IFM) antigen mapping is the most commonly used technique to diagnose and differentiate epidermolysis bullosa (EB). In India, IFM is limited to few research laboratories and is not readily available, making the diagnosis largely clinical and often inaccurate. <b><i>Ob</i></b><b><i> jective of the Study:</i></b> To examine the diagnostic usefulness of immunohistochemistry (IHC) as compared to IFM in resource-limited settings. <b><i>Methods:</i></b> Forty-four consecutive EB patients were included in this study. IHC and IFM were performed on 7-µm frozen tissue sections using standard laboratory protocols with a limited panel of antibodies. The kappa coefficient of agreement was calculated with genetic analysis as the gold standard. <b><i>Results:</i></b> IFM and IHC accurately identified the subtype of EB in 80.9% (<i>p</i> &lt; 0.001) of the cases, when a clear blister cavity was evident on biopsy. The sensitivities and specificities of IHC and IFM for diagnosing EB simplex, junctional EB, and dystrophic EB were 100, 100, and 60% and 82.4, 100, and 100%, respectively. IHC was equally effective (<i>p</i> &lt; 0.001) in establishing the type of EB as IFM. <b><i>Conclusions:</i></b> IHC staining and its interpretation were simple and comparable to IFM. IHC had an advantage of showing subtle changes in the epidermal architecture that could not be appreciated on IFM and hence can be considered useful in resource-limited settings.
DOI: 10.6084/m9.figshare.5537485.v1
title: Supplementary Material for: Diagnosis of Inherited Epidermolysis Bullosa in Resource-Limited Settings: Immunohistochemistry Revisited

description: <b><i>Background:</i></b> Immunofluorescence (IFM) antigen mapping is the most commonly used technique to diagnose and differentiate epidermolysis bullosa (EB). In India, IFM is limited to few research laboratories and is not readily available, making the diagnosis largely clinical and often inaccurate. <b><i>Ob</i></b><b><i> jective of the Study:</i></b> To examine the diagnostic usefulness of immunohistochemistry (IHC) as compared to IFM in resource-limited settings. <b><i>Methods:</i></b> Forty-four consecutive EB patients were included in this study. IHC and IFM were performed on 7-µm frozen tissue sections using standard laboratory protocols with a limited panel of antibodies. The kappa coefficient of agreement was calculated with genetic analysis as the gold standard. <b><i>Results:</i></b> IFM and IHC accurately identified the subtype of EB in 80.9% (<i>p</i> &lt; 0.001) of the cases, when a clear blister cavity was evident on biopsy. The sensitivities and specificities of IHC and IFM for diagnosing EB simplex, junctional EB, and dystrophic EB were 100, 100, and 60% and 82.4, 100, and 100%, respectively. IHC was equally effective (<i>p</i> &lt; 0.001) in establishing the type of EB as IFM. <b><i>Conclusions:</i></b> IHC staining and its interpretation were simple and comparable to IFM. IHC had an advantage of showing subtle changes in the epidermal architecture that could not be appreciated on IFM and hence can be considered useful in resource-limited settings.
DOI: 10.6084/m9.figshare.5537338
title: Myogenic Artifact Dry EEG Datasets

description: Datasets containing EEG.mat structures with raw (unprocesed) data, channel locations, and data characteristics. Data contains myogenic (jaw) artifacts used to train and test SVM classifier.
DOI: 10.6084/m9.figshare.5537323
title: Eye Movement Artifact Dry EEG Datasets

description: Datasets containing EEG.mat structures with raw (unprocesed) data, channel locations, and data characteristics. Data contains eye movement artifacts used to train and test SVM classifier.
DOI: 10.6084/m9.figshare.5537311
title: Raw data for research done on raw milk from Nakasongola district

description: This file consists of raw data obtained from Nakasongola district. A total of 100 raw milk samples were collected and analyzed.<br>
DOI: 10.6084/m9.figshare.5537326
title: Myogenic Artifact Wet EEG Datasets

description: Datasets containing EEG.mat structures with raw (unprocesed) data, channel locations, and data characteristics. Data contains myogenic (jaw) artifacts used to train and test SVM classifier.
DOI: 10.6084/m9.figshare.5537311.v1
title: Raw data for research done on raw milk from Nakasongola district

description: This file consists of raw data obtained from Nakasongola district. A total of 100 raw milk samples were collected and analyzed.<br>
DOI: 10.6084/m9.figshare.5537314
title: Eye Movement Artifact Wet EEG Datasets

description: Datasets containing EEG.mat structures with raw (unprocesed) data, channel locations, and data characteristics. Data contains eye movement artifacts used to train and test SVM classifier.
DOI: 10.6084/m9.figshare.5537314.v1
title: Eye Movement Artifact Wet EEG Datasets

description: Datasets containing EEG.mat structures with raw (unprocesed) data, channel locations, and data characteristics. Data contains eye movement artifacts used to train and test SVM classifier.
DOI: 10.6084/m9.figshare.5537281
title: complete data FOTS6639.xlsx

description: Data from: Seasonal variation in the thermal responses to changing environmental temperature in the world's northernmost landbird, by Nord A, Folkow LP. J Exp. Biol.<br>Abstract: Arctic homeotherms counter challenges at high latitudes using a combination of seasonal adjustments in pelage/plumage, fat deposition, and intricate thermoregulatory adaptations. However, there are still gaps in our understanding of their thermal responses to cold, particularly in Arctic birds. Here, we have studied the potential use of local heterothermy (i.e., tissue cooling that can contribute to lower heat loss rate) in Svalbard ptarmigan (Lagopus muta hyperborea), the world's northernmost landbird. We exposed birds kept under simulated Svalbard photoperiod to low ambient temperatures (Ta; between 0 and -30oC) during three seasons (early winter, late winter, summer), whilst recording resting metabolic rate (RMR), core temperature (Tc) and several cutaneous temperatures. Leg skin temperature varied the most, but still only by up to ~15oC, whereas body trunk skin temperature changed &lt; 1oC when Ta decreased from 0 to -30oC. At the same time, Tc increased by 0.9oC, concomitant with increased RMR. This was likely driven by triggering of cerebral thermosensors in response to cooling of the poorly insulated head, the skin of which was 5.4oC colder at -30oC than at 0oC. Thermal conductance in winter was higher in yearling birds, probably because they were time/resource constrained from acquiring a high-quality plumage and sufficient fat reserves due to concomitant body growth. In conclusion, Svalbard ptarmigan do not employ extensive local heterothermy for cold protection, but instead rely on efficient thermogenesis combined with excellent body insulation. Hence, cold defence in the world's northernmost landbird is not mechanistically much different from that of lower latitude relatives.
DOI: 10.6084/m9.figshare.5537275
title: Eyeblink Artifact Wet EEG Datasets

description: Datasets containing EEG.mat structures with raw (unprocesed) data, channel locations, and data characteristics. Data contains eyeblink artifacts used to train and test SVM classifier.
DOI: 10.6084/m9.figshare.5537293
title: Eyeblink Artifact Dry EEG Datasets

description: Datasets containing EEG.mat structures with raw (unprocesed) data, channel locations, and data characteristics. Data contains eyeblink artifacts used to train and test SVM classifier.
DOI: 10.6084/m9.figshare.5537281.v1
title: complete data FOTS6639.xlsx

description: Data from: Seasonal variation in the thermal responses to changing environmental temperature in the world's northernmost landbird, by Nord A, Folkow LP. J Exp. Biol.<br>Abstract: Arctic homeotherms counter challenges at high latitudes using a combination of seasonal adjustments in pelage/plumage, fat deposition, and intricate thermoregulatory adaptations. However, there are still gaps in our understanding of their thermal responses to cold, particularly in Arctic birds. Here, we have studied the potential use of local heterothermy (i.e., tissue cooling that can contribute to lower heat loss rate) in Svalbard ptarmigan (Lagopus muta hyperborea), the world's northernmost landbird. We exposed birds kept under simulated Svalbard photoperiod to low ambient temperatures (Ta; between 0 and -30oC) during three seasons (early winter, late winter, summer), whilst recording resting metabolic rate (RMR), core temperature (Tc) and several cutaneous temperatures. Leg skin temperature varied the most, but still only by up to ~15oC, whereas body trunk skin temperature changed &lt; 1oC when Ta decreased from 0 to -30oC. At the same time, Tc increased by 0.9oC, concomitant with increased RMR. This was likely driven by triggering of cerebral thermosensors in response to cooling of the poorly insulated head, the skin of which was 5.4oC colder at -30oC than at 0oC. Thermal conductance in winter was higher in yearling birds, probably because they were time/resource constrained from acquiring a high-quality plumage and sufficient fat reserves due to concomitant body growth. In conclusion, Svalbard ptarmigan do not employ extensive local heterothermy for cold protection, but instead rely on efficient thermogenesis combined with excellent body insulation. Hence, cold defence in the world's northernmost landbird is not mechanistically much different from that of lower latitude relatives.
DOI: 10.15131/shef.data.5537269
title: Supporting Open Research: the role of an academic library

description: My keynote presentation from the "Better Science Through Better Data" conference, Wednesday 25 October 2017.
DOI: 10.6084/m9.figshare.5537275.v1
title: Eyeblink Artifact Wet EEG Datasets

description: Datasets containing EEG.mat structures with raw (unprocesed) data, channel locations, and data characteristics. Data contains eyeblink artifacts used to train and test SVM classifier.
DOI: 10.6084/m9.figshare.5537260
title: New insights into the systematics of North Atlantic <i>Gaidropsarus</i> (Gadiformes, Gadidae): flagging synonymies and hidden diversity

description: <i>Gaidropsarus</i> Rafinesque, 1810 is a genus of marine fishes, commonly known as rocklings, comprising 14 living species and showing a high ecological diversity from the intertidal zone to the deep sea. The systematics of this group has been controversial due to a general lack of representative specimens and the conservative morphology exhibited. A multidisciplinary approach combining the analysis of meristic data and the DNA barcode standard was applied in a species delimitation approach. Individuals representing eight valid and three unnamed species were collected, morphologically identified and archived in several museum collections. Comparison of DNA sequences shows complex results, furthering the idea of the difficult identification of specimens based on traditional taxonomy. DNA barcoding supports synonymies, like <i>G. biscayensis</i>–<i>G. macrophthalmus</i> and <i>G. guttatus</i>–<i>G. mediterraneus</i>, agreeing with the extensive overlaps observed in the meristic variables analysed and suggesting a reduction in the number of species. Genetic distances showed pairs of closely related species like <i>G. granti</i>–<i>G. vulgaris</i> and <i>G. argentatus</i>–<i>G. ensis</i>, the latter being only distinguished by one main distinctive character. Four deep-water specimens, morphologically classified only to the genus level, constituted three independent taxa apart from the ones present in this study and with no barcode matches in the repository databases. They could represent new records for the North Atlantic or unknown species of this genus. The results obtained show that more studies will be necessary to solve the systematics of this branch of the Gadiformes.
DOI: 10.6084/m9.figshare.5537260.v1
title: New insights into the systematics of North Atlantic <i>Gaidropsarus</i> (Gadiformes, Gadidae): flagging synonymies and hidden diversity

description: <i>Gaidropsarus</i> Rafinesque, 1810 is a genus of marine fishes, commonly known as rocklings, comprising 14 living species and showing a high ecological diversity from the intertidal zone to the deep sea. The systematics of this group has been controversial due to a general lack of representative specimens and the conservative morphology exhibited. A multidisciplinary approach combining the analysis of meristic data and the DNA barcode standard was applied in a species delimitation approach. Individuals representing eight valid and three unnamed species were collected, morphologically identified and archived in several museum collections. Comparison of DNA sequences shows complex results, furthering the idea of the difficult identification of specimens based on traditional taxonomy. DNA barcoding supports synonymies, like <i>G. biscayensis</i>–<i>G. macrophthalmus</i> and <i>G. guttatus</i>–<i>G. mediterraneus</i>, agreeing with the extensive overlaps observed in the meristic variables analysed and suggesting a reduction in the number of species. Genetic distances showed pairs of closely related species like <i>G. granti</i>–<i>G. vulgaris</i> and <i>G. argentatus</i>–<i>G. ensis</i>, the latter being only distinguished by one main distinctive character. Four deep-water specimens, morphologically classified only to the genus level, constituted three independent taxa apart from the ones present in this study and with no barcode matches in the repository databases. They could represent new records for the North Atlantic or unknown species of this genus. The results obtained show that more studies will be necessary to solve the systematics of this branch of the Gadiformes.
DOI: 10.6084/m9.figshare.5537239
title: Lithium-induced gene expression alterations in two peripheral cell models of bipolar disorder

description: <b>Objectives:</b> The aim of our study was to investigate molecular mechanisms of lithium action by studying the gene expression profile of peripheral cell models generated from bipolar patients (BD) and healthy controls (HC). <b>Methods:</b> EBV-immortalised lymphoblastoid cells (LCLs) and fibroblast cells from BD and HC were incubated with either lithium chloride or plain medium for 3 weeks. We first conducted a microarray gene expression study. The most promising differentially regulated genes in terms of lithium-associated or disorder-associated pathways were then replicated by quantitative real-time PCR (qRT-PCR). <b>Results:</b> The pooled microarray analysis showed 459 genes to be differentially regulated in BD compared to HC and 58 due to lithium treatment in LCLs, and 295 genes to be differentially regulated in BD compared to HC and five due to lithium treatment in fibroblasts. After correction for multiple comparison, <i>EPHB1</i> disorder × treatment interactions remained significant in LCLs validated by qRT-PCR. In the control group, lithium influenced the expression of <i>ANP32E</i>, <i>PLEKHA2</i>, <i>KCNK1</i>, <i>PRKCH</i>, <i>ST3GAL6</i> and <i>AIF1</i>. In bipolar and control fibroblast cells lithium treatment decreased <i>FGF9</i> expression. <b>Conclusions:</b> The differentially regulated genes in our study add evidence for the relevance of inflammation, neuronal/glial development, phosphatidylinositol second-messenger pathway and ion channels in the mode of action of lithium.