cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6946046.v1
title: Mitochondrial membrane protein-associated neurodegeneration: a case report and literature review

description: Mitochondrial membrane protein-associated neurodegeneration (MPAN) is an autosomal recessive disorder caused by mutation in the C19orf12 gene. We report a compound heterozygous c.[32C&gt;T];[205G&gt;A;424A&gt;G] (p.[Thr11Met];[Gly69Arg;Lys142Glu]) Czech patient who manifested with right foot dystonia, impaired handwriting, attention deficit, and signs of iron accumulation on brain MRI. Gradually, he developed dysarthria, spastic-dystonic gait, pedes cavi, and atrophy of leg muscles. Additionally, we report demographic parameters, clinical signs, and allelic frequencies of C19orf12 mutations of all published MPAN cases. We compared the most frequent mutations, p.Thr11Met and p.Gly69ArgfsX10; the latter was associated with younger age at onset and more frequent optic atrophy in homozygotes.
DOI: 10.6084/m9.figshare.6946040
title: Supplementary Table 10

description: Unrarefied fungal OTU table
DOI: 10.6084/m9.figshare.6946040.v1
title: Supplementary Table 10

description: Unrarefied fungal OTU table
DOI: 10.6084/m9.figshare.6946022
title: Supplementary Table 8

description: Unrarefied bacterial OTU table
DOI: 10.6084/m9.figshare.6946034
title: Supplementary Table 9

description: Bacterial taxonomic classification
DOI: 10.6084/m9.figshare.6946034.v1
title: Supplementary Table 9

description: Bacterial taxonomic classification
DOI: 10.6084/m9.figshare.6946004
title: Derived data of flow cytometry analyses of mycobacteria membrane

description: Raw and derived data of flow cytometry analyses of mycobacteria membrane
DOI: 10.6084/m9.figshare.6946022.v1
title: Supplementary Table 8

description: Unrarefied bacterial OTU table
DOI: 10.6084/m9.figshare.6945998
title: Derived data of thiols level under drugs treatment

description: Raw and calculated data describing derived data of thiols level under drugs treatment, study-2, method-2, replicate-1 and 2
DOI: 10.6084/m9.figshare.6946004.v1
title: Derived data of flow cytometry analyses of mycobacteria membrane

description: Raw and derived data of flow cytometry analyses of mycobacteria membrane
DOI: 10.6084/m9.figshare.6945998.v1
title: Derived data of thiols level under drugs treatment

description: Raw and calculated data describing derived data of thiols level under drugs treatment, study-2, method-2, replicate-1 and 2
DOI: 10.6084/m9.figshare.6945992
title: Raw and calculated data for ergothioneine, mycothiol, hercynine and thiol levels

description: Raw and calculated data describing the results
DOI: 10.6084/m9.figshare.6945992.v1
title: Raw and calculated data for ergothioneine, mycothiol, hercynine and thiol levels

description: Raw and calculated data describing the results
DOI: 10.6084/m9.figshare.6945989.v1
title: SUPPLEMENTARY TABLES.docx

description: Supplemental Material (Supplementary Tables 1 and 2) for: <b>Serum levels of activins, follistatins and growth factors in neoplasms of the breast: A case-control study</b>
DOI: 10.6084/m9.figshare.6945899
title: Supplementary Material for: Gene Co-Expression Network Analysis Implicates microRNA Processing in Parkinson’s Disease Pathogenesis

description: <b><i>Background:</i></b> Recent advances in genetics have provided insights into important inherited causes of Parkinson’s disease (PD), but the underlying biological mechanisms are still incompletely understood. Gene expression studies have pointed toward the dysregulation of neuroinflammation, mitochondrial function, and protein degradation pathways. <b><i>Objective:</i></b> We aimed to identify groups of dysregulated genes in PD. <b><i>Methods:</i></b> In order to increase statistical power and control for potential confounders, we re-analyzed transcriptomic data from PD patients and model systems, integrating additional genomic data using a systems biology approach. Using weighted gene co-expression network analysis, we partitioned genes into co-expressed modules. <b><i>Results:</i></b><i></i> One co-expression module, M13, had an expression trajectory that was highly correlated with PD, was not characterized by any specific cell type markers, and was enriched in PD genes identified by genome-wide association studies. Genes within M13 seemed to be related to global microRNA biogenesis, and <i>DICER1</i> and <i>AGO3</i> were highly connected within the module. The <i>NUCKS1</i> gene, previously identified as part of the PARK16 locus, was also a hub gene within M13. <b><i>Conclusion:</i></b> These results suggest that microRNA processing and function may play a role in the pathogenesis of PD, and thus may represent a useful target for future drug development.
DOI: 10.6084/m9.figshare.6945824
title: Task-evoked pupil responses reflect internal belief states: Behavior & pupil data

description: Behavioral data and pupil responses corresponding to the paper:<br><br>Colizoli, O., de Gee, J. W., Urai, A. E. & Donner, T. H. <b>Task-evoked pupil responses reflect internal belief states</b>. <i>Scientific Reports</i> 8, 13702 (2018).<br>Corresponding code can be found here: https://github.com/colizoli/pupil_belief_states
DOI: 10.6084/m9.figshare.6945824.v1
title: Task-evoked pupil responses reflect internal belief states: Behavior & pupil data (scalar averages)

description: Task-evoked pupil responses reflect internal belief states: Behavioral data and pupil responses (scalar averages) for all subjects. <br>See 'ReadMe_pupil_subjects.txt' file for explanation of conditions and headers.
DOI: 10.6084/m9.figshare.6945737
title: Handouts - Ten Lectures on Grammar in the Mind

description: This series of lectures presents a synthesis of cognitive linguistic theory and research on first and second language acquisition, language processing, individual differences in linguistic knowledge, and on the role of multi-word chunks and low-level schemas in language production and comprehension. It highlights the tension between “linguists’ grammars”, which are strongly influenced by principles such as economy and elegance, and “speakers’ grammars”, which are often messy, less than fully general, and sometimes inconsistent, and argues that cognitive linguistics is an empirical science which combines study of real usage events and experiments which rigorously test specific hypotheses.
DOI: 10.6084/m9.figshare.6945737.v2
title: Handouts - Ten Lectures on Grammar in the Mind

description: This series of lectures presents a synthesis of cognitive linguistic theory and research on first and second language acquisition, language processing, individual differences in linguistic knowledge, and on the role of multi-word chunks and low-level schemas in language production and comprehension. It highlights the tension between “linguists’ grammars”, which are strongly influenced by principles such as economy and elegance, and “speakers’ grammars”, which are often messy, less than fully general, and sometimes inconsistent, and argues that cognitive linguistics is an empirical science which combines study of real usage events and experiments which rigorously test specific hypotheses.
DOI: 10.6084/m9.figshare.6945824.v2
title: Task-evoked pupil responses reflect internal belief states: Behavior & pupil data (scalar averages)

description: Task-evoked pupil responses reflect internal belief states: Behavioral data and pupil responses (scalar averages) for all subjects. <br>See 'ReadMe_pupil_subjects.txt' file for explanation of conditions and headers.
DOI: 10.6084/m9.figshare.6945737.v1
title: Handouts - Ten Lectures on Grammar in the Mind

description: This series of lectures presents a synthesis of cognitive linguistic theory and research on first and second language acquisition, language processing, individual differences in linguistic knowledge, and on the role of multi-word chunks and low-level schemas in language production and comprehension. It highlights the tension between “linguists’ grammars”, which are strongly influenced by principles such as economy and elegance, and “speakers’ grammars”, which are often messy, less than fully general, and sometimes inconsistent, and argues that cognitive linguistics is an empirical science which combines study of real usage events and experiments which rigorously test specific hypotheses.
DOI: 10.6084/m9.figshare.6945824.v3
title: Task-evoked pupil responses reflect internal belief states: Behavior & pupil data

description: Task-evoked pupil responses reflect internal belief states: Behavioral data and pupil responses for all subjects. <br>See 'ReadMe_pupil_subjects.txt' file for explanation of conditions and headers for 'pupil_subjects.csv'.<br>See 'ReadMe_pupil_evoked.txt' file for explanation of conditions and headers for 'pupil_evoked_responses.zip'.<br><br><br><br>
DOI: 10.6084/m9.figshare.6945725
title: Appendix 3 from Chase et al. Embracing scale-dependence to achieve a deeper understanding of biodiversity and its change across communities. Contains raw data for the analyses of invertebrate and amphibian communities in nutrient addition and reference treatments presented in Figure 6.

description: Data are from Chase, JM. 2010. Stochastic community assembly causes higher biodiversity in more productive environments. Science. 328: 1388-1391.
DOI: 10.6084/m9.figshare.6945722
title: Appendix 2 from Chase et al. Embracing scale-dependence to achieve a deeper understanding of biodiversity and its change across communities. Contains effect sizes, metadata, and references for studies used in the scale-dependent meta-analysis presented in Figure 4.

description: Effect sizes, metadata, and references for studies used in the scale-dependent meta-analysis presented in Figure 4.
DOI: 10.6084/m9.figshare.6945725.v1
title: Appendix 3. Raw data for the analyses of invertebrate and amphibian communities in nutrient addition and reference treatments presented in Figure 6.

description: Data are from Chase, JM. 2010. Stochastic community assembly causes higher biodiversity in more productive environments. Science. 328: 1388-1391.
DOI: 10.6084/m9.figshare.6945722.v1
title: Appendix 2. Effect sizes, metadata, and references for studies used in the scale-dependent meta-analysis presented in Figure 4.

description: Effect sizes, metadata, and references for studies used in the scale-dependent meta-analysis presented in Figure 4.
DOI: 10.6084/m9.figshare.6945725.v3
title: Appendix 3 from Chase et al. Embracing scale-dependence to achieve a deeper understanding of biodiversity and its change across communities. Contains raw data for the analyses of invertebrate and amphibian communities in nutrient addition and reference treatments presented in Figure 6.

description: Data are from Chase, JM. 2010. Stochastic community assembly causes higher biodiversity in more productive environments. Science. 328: 1388-1391.
DOI: 10.6084/m9.figshare.6945725.v2
title: Appendix 3 from Chase et al. Embracing scale-dependence to achieve a deeper understanding of biodiversity and its change across communities. Contains raw data for the analyses of invertebrate and amphibian communities in nutrient addition and reference treatments presented in Figure 6.

description: Data are from Chase, JM. 2010. Stochastic community assembly causes higher biodiversity in more productive environments. Science. 328: 1388-1391.
DOI: 10.6084/m9.figshare.6945719
title: Prepared_for_Plos_repositoryDEF.sav

description: Dataset of the PRO Trauma Prediction model
DOI: 10.6084/m9.figshare.6945722.v2
title: Appendix 2 from Chase et al. Embracing scale-dependence to achieve a deeper understanding of biodiversity and its change across communities. Contains effect sizes, metadata, and references for studies used in the scale-dependent meta-analysis presented in Figure 4.

description: Effect sizes, metadata, and references for studies used in the scale-dependent meta-analysis presented in Figure 4.
DOI: 10.6084/m9.figshare.6945713
title: Supplementary Material for: Impaired Spermatogenesis due to Small Supernumerary Marker Chromosomes: The Reason for Infertility Is Only Reliably Ascertainable by Cytogenetics

description: Infertile male with small supernumerary marker chromosomes (sSMCs) were studied. Overall, 37 own patients and 166 cases from the literature were included. sSMCs of our own cases were characterized by multicolor-FISH probe sets. Available clinical data of the infertile males were also evaluated, and meta-analysis on suitability of molecular karyotyping for sSMC characterization was done. As a result, sSMCs can be optimally characterized by single-cell directed (molecular) cytogenetics. In infertile males, sSMCs derive predominantly from one of the acrocentric chromosomes, mainly chromosomes 15, 14, and 22. Interestingly, altered spermiograms were found in 62% of the males with an sSMC, while the remainder cases had infertility in connection with recurrent spontaneous abortions. Meta-analysis for detectability of sSMCs by aCGH revealed that 81-87% of the cases would have not been picked up by exclusive use of that approach. Thus, as impaired spermatogenesis is known to be indicative for gross chromosomal anomalies in infertile male patients, it can be concluded from this study that the presence of sSMCs also needs to be considered. However, sSMCs can only be reliably detected by standard karyotyping and not by modern high throughput approaches like aCGH and next-generation sequencing.
DOI: 10.6084/m9.figshare.6945713.v1
title: Supplementary Material for: Impaired Spermatogenesis due to Small Supernumerary Marker Chromosomes: The Reason for Infertility Is Only Reliably Ascertainable by Cytogenetics

description: Infertile male with small supernumerary marker chromosomes (sSMCs) were studied. Overall, 37 own patients and 166 cases from the literature were included. sSMCs of our own cases were characterized by multicolor-FISH probe sets. Available clinical data of the infertile males were also evaluated, and meta-analysis on suitability of molecular karyotyping for sSMC characterization was done. As a result, sSMCs can be optimally characterized by single-cell directed (molecular) cytogenetics. In infertile males, sSMCs derive predominantly from one of the acrocentric chromosomes, mainly chromosomes 15, 14, and 22. Interestingly, altered spermiograms were found in 62% of the males with an sSMC, while the remainder cases had infertility in connection with recurrent spontaneous abortions. Meta-analysis for detectability of sSMCs by aCGH revealed that 81-87% of the cases would have not been picked up by exclusive use of that approach. Thus, as impaired spermatogenesis is known to be indicative for gross chromosomal anomalies in infertile male patients, it can be concluded from this study that the presence of sSMCs also needs to be considered. However, sSMCs can only be reliably detected by standard karyotyping and not by modern high throughput approaches like aCGH and next-generation sequencing.
DOI: 10.6084/m9.figshare.6945719.v2
title: Prepared_for_Plos_repositoryDEF.sav

description: Dataset of the PRO Trauma Prediction model
DOI: 10.6084/m9.figshare.6945704
title: Appendix 1 from Chase et al. Embracing scale-dependence to achieve a deeper understanding of biodiversity and its change across communities. Contains raw data and references for rarefaction curves and analyses presented in Figures 2 and 3.

description: These data are a subset of those presented in:McGill, BJ. 2011. Species abundance distributions. In. A. Magurran and B. McGill (eds) Biological diversity: frontiers in measurement and assessment. Oxford University Press, Oxford (2011) 105-122.
DOI: 10.6084/m9.figshare.6945719.v1
title: Prepared_for_Plos_repositoryDEF.sav

description: Dataset of the PRO Trauma Prediction model
DOI: 10.15131/shef.data.6945638
title: Lower Band Chorus Wave Data

description: The data contains Lower Band Chorus Waves from four Cluster spacecraft, DoubleStar, and THEMIS A, D, and E. The data contains a time series of the wave amplitudes at the spacecraft position in Magnetic Local Time and L shell. The data was produced as part of the European Union's Horizon 2020 research and innovation programme under grant agreement No 637302 named PROGRESS.
DOI: 10.6084/m9.figshare.6945704.v1
title: Appendix 1. Raw data and references for rarefaction curves and analyses presented in Figures 2 and 3.

description: These data are a subset of those presented in:McGill, BJ. 2011. Species abundance distributions. In. A. Magurran and B. McGill (eds) Biological diversity: frontiers in measurement and assessment. Oxford University Press, Oxford (2011) 105-122.
DOI: 10.15131/shef.data.6945638.v1
title: Lower Band Chorus Wave Data

description: The data contains Lower Band Chorus Waves from four Cluster spacecraft, DoubleStar, and THEMIS A, D, and E. The data contains a time series of the wave amplitudes at the spacecraft position in Magnetic Local Time and L shell. The data was produced as part of the European Union's Horizon 2020 research and innovation programme under grant agreement No 637302 named PROGRESS.
DOI: 10.6084/m9.figshare.6945704.v2
title: Appendix 1 from Chase et al. Embracing scale-dependence to achieve a deeper understanding of biodiversity and its change across communities. Contains raw data and references for rarefaction curves and analyses presented in Figures 2 and 3.

description: These data are a subset of those presented in:McGill, BJ. 2011. Species abundance distributions. In. A. Magurran and B. McGill (eds) Biological diversity: frontiers in measurement and assessment. Oxford University Press, Oxford (2011) 105-122.
DOI: 10.6084/m9.figshare.6945605
title: Removal of arsenic by <i>Acidothiobacillus ferrooxidans</i> bacteria in bench scale fixed-bed bioreactor system

description: In the present study arsenic contaminated simulated water and groundwater was treated by the combination of biological oxidation of tri-valent arsenite [As (III)] to penta-valent arsenate [As (V)] in presence of <i>Acidothiobacillus ferrooxidans bacteria</i> and its removal by adsorptive filtration in a bioreactor system. This method includes the immobilisation of <i>A.ferrooxidans</i> on Granulated Activated Carbon (GAC) capable of oxidising ferrous [Fe (II)] to ferric [Fe (III)]. The Fe (III) significantly converts the As (III) to As (V) and ultimately removed greater than 95% by the bed of GAC, limestone, and sand. The significant influence of Fe (II) concentration (0.1–1.5 gL<sup>−1</sup>), flowrate (0.06–0.18 Lh<sup>−1</sup>), and initial As (III) concentration (100–1000 µgL<sup>−1</sup>) on the arsenic removal efficiency was investigated. The simulated water sample containing the different concentration of As (III) and other ions was used in the study. The removal of other co-existing ions present in contaminated water was also investigated in column study. The concentration of arsenic was found to be &lt;10 µgL<sup>−1</sup> which is below Maximum Contaminant Level (MCL) as per WHO in treated water. The results confirmed that the present system including adsorptive-filtration was successfully used for the treatment of contaminated water containing As (III) ions.
DOI: 10.6084/m9.figshare.6945605.v1
title: Removal of arsenic by <i>Acidothiobacillus ferrooxidans</i> bacteria in bench scale fixed-bed bioreactor system

description: In the present study arsenic contaminated simulated water and groundwater was treated by the combination of biological oxidation of tri-valent arsenite [As (III)] to penta-valent arsenate [As (V)] in presence of <i>Acidothiobacillus ferrooxidans bacteria</i> and its removal by adsorptive filtration in a bioreactor system. This method includes the immobilisation of <i>A.ferrooxidans</i> on Granulated Activated Carbon (GAC) capable of oxidising ferrous [Fe (II)] to ferric [Fe (III)]. The Fe (III) significantly converts the As (III) to As (V) and ultimately removed greater than 95% by the bed of GAC, limestone, and sand. The significant influence of Fe (II) concentration (0.1–1.5 gL<sup>−1</sup>), flowrate (0.06–0.18 Lh<sup>−1</sup>), and initial As (III) concentration (100–1000 µgL<sup>−1</sup>) on the arsenic removal efficiency was investigated. The simulated water sample containing the different concentration of As (III) and other ions was used in the study. The removal of other co-existing ions present in contaminated water was also investigated in column study. The concentration of arsenic was found to be &lt;10 µgL<sup>−1</sup> which is below Maximum Contaminant Level (MCL) as per WHO in treated water. The results confirmed that the present system including adsorptive-filtration was successfully used for the treatment of contaminated water containing As (III) ions.
DOI: 10.6084/m9.figshare.6945560
title: Supplementary Material for: Variations in Oxygen Saturation Targeting, and Retinopathy of Prematurity Screening and Treatment Criteria in Neonatal Intensive Care Units: An International Survey

description: <b><i>Background:</i></b> Rates of retinopathy of prematurity (ROP) and ROP treatment vary between neonatal intensive care units (NICUs). Neonatal care practices, including oxygen saturation (SpO<sub>2</sub>) targets and criteria for the screening and treatment of ROP, are potential contributing factors to the variations. <b><i>Objectives:</i></b><i></i> To survey variations in SpO<sub>2</sub> targets in 2015 (and whether there had been recent changes) and criteria for ROP screening and treatment across the networks of the International Network for Evaluating Outcomes in Neonates (iNeo). <b><i>Methods:</i></b> Online prepiloted questionnaires on treatment practices for preterm infants were sent to the directors of 390 NICUs in 10 collaborating iNeo networks. Nine questions were asked and the results were summarized and compared. <b><i>Results:</i></b> Overall, 329/390 (84%) NICUs responded, and a majority (60%) recently made changes in upper and lower SpO<sub>2</sub> target limits, with the median set higher than previously by 2–3% in 8 of 10 networks. After the changes, fewer NICUs (15 vs. 28%) set an upper SpO<sub>2</sub> target limit &gt; 95% and fewer (3 vs. 5%) a lower limit &lt; 85%. There were variations in ROP screening criteria, and only in the Swedish network did all NICUs follow a single guideline. The initial retinal examination was carried out by an ophthalmologist in all but 6 NICUs, and retinal photography was used in 20% but most commonly as an adjunct to indirect ophthalmoscopy. <b><i>Conclusions:</i></b> There is considerable variation in SpO<sub>2</sub> targets and ROP screening and treatment criteria, both within networks and between countries.