cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15131/shef.data.12327560.v1
title: Data and figures related to publication: Investigation of a novel AlZnN semiconductor alloy

description: The data provided here is related to the publication:<br>"Investigation of a novel AlZnN semiconductor alloy"<br>Materials Letters: X (2020); https://doi.org/10.1016/j.mlblux.2020.100052<br><br>The study reported in this paper was funded by the EPSRC (Fund code EP/M507611/1) and Johson Matthey PLC. The financial support by these parties is highly appreciated.<br><br>The data required to reproduce each figure panel is provided in different text files. Columns are separated by a space character. The first line in each column describes the dataset. The complete figures are also included as .tif files.<br><br>With the added context of the paper, it should be easy to reproduce the figures.<br><br><b>Figure 1:</b> (a) Zn and Al peaks in EDS spectra, (b) AlN fraction plotted against the Zn<sub>3</sub>N<sub>2</sub> fraction, and (c) GIXRD measurements of samples ZN and AZN-1 to AZN-4. The dashed line in (b) indicates the stoichiometric ratio of Al<sub>2x</sub>Zn<sub>3(1-x)</sub>N<sub>2</sub>.<br><b><br>Figure 2:</b> (a) Extinction coefficient and (b) refractive index of AlZnN films obtained from ellipsometry measurements. (c) Cody plot analysis used to measure the optical bandgap of AlZnN films.<br><br><b>Figure 3:</b> (a) Optical bandgap, (b) refractive index, (c) resistivity, and (d) carrier concentration of different AlZnN films. The star (☆) in (a) shows the intrinsic bandgap of Zn<sub>3</sub>N<sub>2</sub> as reported by Kumagai <i>et al</i>.<sup>3</sup> The dashed lines are intended as guides to the eye.<br>
DOI: 10.6084/m9.figshare.12327596.v1
title: Discerning Solution Concepts for Discrete Games

description: The empirical analysis of discrete complete-information games has relied on behavioral restrictions in the form of solution concepts, such as Nash equilibrium. Choosing the right solution concept is crucial not just for the identification of payoff parameters, but also for the validity and informativeness of counterfactual exercises and policy implications. We say that a solution concept is discernible if it is possible to determine whether it generated the observed data on the players’ behavior and covariates. We propose a set of conditions that make it possible to discern solution concepts. In particular, our conditions are sufficient to tell whether the players’ choices emerged from Nash equilibria. We can also discriminate between rationalizable behavior, maxmin behavior, and collusive behavior. Finally, we identify the correlation structure of unobserved shocks in our model using a novel approach.
DOI: 10.6084/m9.figshare.12327602.v1
title: genome fasta sequence and annotation files

description: cultivated alfalfa genome sequence, CDS sequence, protein sequence and gff files.
DOI: 10.6084/m9.figshare.12327602.v2
title: genome fasta sequence and annotation files

description: cultivated alfalfa genome sequence, CDS sequence, protein sequence and gff files.
DOI: 10.6084/m9.figshare.12326612
title: Metadata record for: Genome sequence of Kobresia littledalei, the first chromosome-level genome in the family Cyperaceae

description: This dataset contains key characteristics about the data described in the Data Descriptor Genome sequence of Kobresia littledalei, the first chromosome-level genome in the family Cyperaceae. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format
DOI: 10.6084/m9.figshare.12326612.v1
title: Metadata record for: Genome sequence of Kobresia littledalei, the first chromosome-level genome in the family Cyperaceae

description: This dataset contains key characteristics about the data described in the Data Descriptor Genome sequence of Kobresia littledalei, the first chromosome-level genome in the family Cyperaceae. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format
DOI: 10.6084/m9.figshare.12326519
title: Metadata record for: Neural and physiological data from participants listening to affective music

description: This dataset contains key characteristics about the data described in the Data Descriptor Neural and physiological data from participants listening to affective music. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format <br> <br> <br>
DOI: 10.6084/m9.figshare.12326489
title: Supplementary data on virus-like particles in the brainstem of Parkinson’s disease patients and controls

description: In this study, we present 84 transmission electron microscopy (TEM) images of human brainstem tissue from 11 cases of late onset Parkinson’s disease. The tissues were fixed, embedded, sectioned, and stained for TEM application. In addition, we present 14 images from autopsy specimens of 1 case of human poliomyelitis infection as positive controls and 14 images from 8 cases of autopsy specimens of other conditions as negative controls.
DOI: 10.6084/m9.figshare.12326519.v1
title: Metadata record for: Neural and physiological data from participants listening to affective music

description: This dataset contains key characteristics about the data described in the Data Descriptor Neural and physiological data from participants listening to affective music. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format <br> <br> <br>
DOI: 10.6084/m9.figshare.12326489.v1
title: Supplementary data on virus-like particles in the brainstem of Parkinson’s disease patients and controls

description: In this study, we present 84 transmission electron microscopy (TEM) images of human brainstem tissue from 11 cases of late onset Parkinson’s disease. The tissues were fixed, embedded, sectioned, and stained for TEM application. In addition, we present 14 images from autopsy specimens of 1 case of human poliomyelitis infection as positive controls and 14 images from 8 cases of autopsy specimens of other conditions as negative controls.
DOI: 10.6084/m9.figshare.12326471
title: Metadata record for: Multicenter intracranial EEG dataset for classification of graphoelements and artifactual signals

description: This dataset contains key characteristics about the data described in the Data Descriptor Multicenter intracranial EEG dataset for classification of graphoelements and artifactual signals. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format
DOI: 10.6084/m9.figshare.12326441
title: ActDES – a Curated Actinobacterial Database for Evolutionary Studies - Microreact input files and links

description: <i>Actinobacteria</i> are a large and diverse phylum of bacteria that contains medically and ecologically relevant organisms. Many members are valuable sources of bioactive natural products and chemical precursors that are exploited in the clinic. These are made using the enzyme pathways encoded in their complex genomes. Whilst the number of sequenced genomes has increased rapidly in the last twenty years, the large size and complexity of many Actinobacterial genomes means that the sequences remain incomplete and consist of large numbers of contigs with poor annotation, which hinders large scale comparative genomics and evolutionary studies. To enable greater understanding and exploitation of Actinobacterial genomes, specialist genomic databases must be linked to high-quality genome sequences. Here we provide a curated database of 612 high quality actinobacterial genomes from 80 genera, chosen to represent a broad phylogenetic group with equivalent genome re-annotation. Utilising this database will provide researchers with a framework for evolutionary and metabolic studies, to enable a foundation for genome and metabolic engineering, to facilitate discovery of novel bioactive therapeutics and studies on gene family evolution. <br>Interactive trees in Microreact for GlcP tree https://microreact.org/project/VBUdiQ5_k/0fc4622b and associated files are here<br>Interactive trees in Microreact for Glk tree https://microreact.org/project/w_KDfn1xA/90e6759e and associated files are here <br><br>Reference for Microreact here<b>Argimón S, Abudahab K, Goater RJE, Fedosejev A, Bhai J, <i>et al.</i></b> Microreact: visualizing and sharing data for genomic epidemiology and phylogeography. <i>Microb Genom</i>;2. Epub ahead of print 2016. DOI: 10.1099/mgen.0.000093.<br>
DOI: 10.6084/m9.figshare.12326471.v1
title: Metadata record for: Multicenter intracranial EEG dataset for classification of graphoelements and artifactual signals

description: This dataset contains key characteristics about the data described in the Data Descriptor Multicenter intracranial EEG dataset for classification of graphoelements and artifactual signals. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format
DOI: 10.6084/m9.figshare.12326420
title: S5 File.docx

description: Torsion Tables. a) 6M0J Vina Autodock results, b) 6WKP Vina Autodock results.
DOI: 10.6084/m9.figshare.12326423
title: S4 File.pdf

description: RCSB 6JX7 PDB results.
DOI: 10.6084/m9.figshare.12326438
title: Raw Data of Awarness and Panic-buying behavior.xlsx

description: The relationship between the level of awareness and the level of panic-buying behavior among Jordanians
DOI: 10.6084/m9.figshare.12326423.v1
title: S4 File.pdf

description: RCSB 6JX7 PDB results.
DOI: 10.6084/m9.figshare.12326414
title: S6 File.zip

description: 6M0J SWISSDOCK results.
DOI: 10.6084/m9.figshare.12326417
title: S3 File .pdf

description: I-TASSER analysis results.
DOI: 10.6084/m9.figshare.12326420.v1
title: S5 File.docx

description: Torsion Tables. a) 6M0J Vina Autodock results, b) 6WKP Vina Autodock results.
DOI: 10.6084/m9.figshare.12326438.v1
title: Raw Data of Awarness and Panic-buying behavior.xlsx

description: The relationship between the level of awareness and the level of panic-buying behavior among Jordanians
DOI: 10.6084/m9.figshare.12326411
title: S7 File.zip

description: 6WKP SWISSDOCK results.
DOI: 10.6084/m9.figshare.12326414.v1
title: S6 File.zip

description: 6M0J SWISSDOCK results.
DOI: 10.6084/m9.figshare.12326402
title: S2a File.pdf

description: MAUVE genetic phylogenetic analysis
DOI: 10.6084/m9.figshare.12326405
title: S2b File.pdf

description: Clustal W genetic phylogenetic analysis.<b></b>
DOI: 10.6084/m9.figshare.12326408
title: S1 File .xls

description: The genome sequences downloaded from GISAID.
DOI: 10.6084/m9.figshare.12326417.v1
title: S3 File .pdf

description: I-TASSER analysis results.
DOI: 10.6084/m9.figshare.12326402.v1
title: S2a File.pdf

description: MAUVE genetic phylogenetic analysis
DOI: 10.6084/m9.figshare.12326408.v1
title: S1 File .xls

description: The genome sequences downloaded from GISAID.
DOI: 10.6084/m9.figshare.12326294
title: Bile acid supplementation improves murine pancreatitis in association with the gut microbiota

description: 16S rDNA
DOI: 10.6084/m9.figshare.12326330
title: Supporting datasets for the manuscript: Press disturbance alters community structure and assembly mechanisms of bacterial taxa and functional genes in mesocosm-scale bioreactors

description: Supporting datasets accompanying the manuscript titled "Press disturbance alters community structure and assembly mechanisms of bacterial taxa and functional genes in mesocosm-scale bioreactors". R-script, data and a graphic schematic of the null model used in the manuscript is included, so as to reproduce Figs. 6 and 7 as well as Tables S3-S5.
DOI: 10.6084/m9.figshare.12326330.v1
title: Supporting datasets for the manuscript: Press disturbance alters community structure and assembly mechanisms of bacterial taxa and functional genes in mesocosm-scale bioreactors

description: Supporting datasets accompanying the manuscript titled "Press disturbance alters community structure and assembly mechanisms of bacterial taxa and functional genes in mesocosm-scale bioreactors". R-script, data and a graphic schematic of the null model used in the manuscript is included, so as to reproduce Figs. 6 and 7 as well as Tables S3-S5.
DOI: 10.6084/m9.figshare.12326294.v1
title: Bile acid supplementation improves murine pancreatitis in association with the gut microbiota

description: 16S rDNA
DOI: 10.6084/m9.figshare.12326294.v2
title: Bile acid supplementation improves murine pancreatitis in association with the gut microbiota

description: 16S rDNA
DOI: 10.6084/m9.figshare.12326219
title: Dataset: Contrasting exposure effects on copepod respiration

description: Includes main data "Respiration and predation.csv" and blank measurements "normBlanks_respiration and predation.csv".<br>We exposed two species of copepods (Tigriopus brevicornis and Calanus finmarchicus) to the treatments predation risk, copper, combined predation risk and copper, or control. We measured incubation chamber oxygen levels continuously throughout a 12 hour exposure period and calculated the median per dry weight respiration rates per replicate. Thus, only one time-point is included (i.e. TimeHours=1.125), but medians are extracted for all relevant exposure intervals for investigation.<br>Dataset column explanations<br>UniqueID - a per replicate unique ID based on well plate positioning, treatment and series.Well.ID - replicate position on 24 well cell culture plates used for incubation.TimeHours - time (hours) into exposure period. We removed the first hour due to acclimation.Series - we conducted four experimental rounds which we refer to as series.SDR - refer to Sensor Dish Reader (SDR) units used for measuring oxygen. We used four SDR-units per series.Treatment - we exposed copepods to predation risk, copper, combined predation risk and copper, or control.RespRate_corr.nlm_0to12h - extracted median of influx-corrected negated oxygen difference (i.e. oxygen consumption rates) per replicate well for the full exposure period 0-12 h. Medians were similarly extracted for the time-intervals 0-3 h, 3-6 h, 6-9 h and 9-12 h. Oxygen consumption rates are given as µmol O2 per replicate well per h.Well - replicate position on 24 well cell culture plate used for incubationPredation risk - three-spined stickleback chemical cue exposure, 0 = no, 1 = yes.Cu - copper exposure, 0 = no, 1 = yes.Species - copepod, Tigriopus brevicornis, Calanus finmarchicusmale - number of individuals.female - number of individuals.juveniles - number of individuals.DmgAntenna - registered external physical injuries post exposure.WhiteDot - registered external physical abnormalities post exposure.Alive - number of surviving individuals post exposure.Dead - number of dead individuals post exposure.BigBubble - registered potentially confounding gas bubble.length.um - copepod prosome length, µm.DWeight - ash-free dry weight, calculated from prosome length.DWResp_0to12h - equals RespRate_corr.nlm_0to12h normalized by biomass to µmol O2 per µg.dw per h. Similarly calculated for the time-intervals 0-3 h, 3-6 h, 6-9 h and 9-12 h.
DOI: 10.6084/m9.figshare.12326246
title: Supplementary Material for: The p.R206C Mutation in <b><i>MYO7A</i></b> Leads to Autosomal Dominant Nonsyndromic Hearing Loss

description: <b><i>Background:</i></b> Dominant mutations in <i>MYO7A</i> may lead to nonsyndromic deafness DFNA11. A p.R206C variant in <i>MYO7A</i> has previously been reported in a small deaf family from Taiwan but with ambiguous pathogenicity and inheritance pattern. <b><i>Aims/Objectives:</i></b> Our study aims to clarify the pathogenicity of this variant by clinical characterization and genetic analysis of a separate autosomal dominant deaf family harboring this variant in mainland China. <b><i>Materials and Methods:</i></b> Auditory features of hearing loss were characterized in representative affected family members. Mutation screening was performed by targeted next-generation sequencing of 138 known deafness genes in the proband. Candidate pathogenic mutations were confirmed by Sanger sequencing in family members and ethnically matched controls. <b><i>Results:</i></b> Consistent with typical DFNA11 phenotype, the affected family members in this study showed delayed-onset, progressive hearing loss affecting mostly high frequencies. Targeted next-generation sequencing identified a p.R206C mutation in <i>MYO7A</i> as the only candidate pathogenic mutation cosegregating with the hearing phenotype. This mutation is not seen in 200 Chinese Han normal-hearing controls. <b><i>Conclusions and Significance:</i></b> The recurrent p.R206C variant in <i>MYO7A</i> is pathogenic and is likely in a mutation hot spot or due to a founder effect. Reports of such rare variants in multiple patients or families may facilitate exploitation of its pathogenicity.
DOI: 10.6084/m9.figshare.12326219.v1
title: Dataset: Contrasting exposure effects on copepod respiration

description: Includes main data "Respiration and predation.csv" and blank measurements "normBlanks_respiration and predation.csv".<br>We exposed two species of copepods (Tigriopus brevicornis and Calanus finmarchicus) to the treatments predation risk, copper, combined predation risk and copper, or control. We measured incubation chamber oxygen levels continuously throughout a 12 hour exposure period and calculated the median per dry weight respiration rates per replicate. Thus, only one time-point is included (i.e. TimeHours=1.125), but medians are extracted for all relevant exposure intervals for investigation.<br>Dataset column explanations<br>UniqueID - a per replicate unique ID based on well plate positioning, treatment and series.Well.ID - replicate position on 24 well cell culture plates used for incubation.TimeHours - time (hours) into exposure period. We removed the first hour due to acclimation.Series - we conducted four experimental rounds which we refer to as series.SDR - refer to Sensor Dish Reader (SDR) units used for measuring oxygen. We used four SDR-units per series.Treatment - we exposed copepods to predation risk, copper, combined predation risk and copper, or control.RespRate_corr.nlm_0to12h - extracted median of influx-corrected negated oxygen difference (i.e. oxygen consumption rates) per replicate well for the full exposure period 0-12 h. Medians were similarly extracted for the time-intervals 0-3 h, 3-6 h, 6-9 h and 9-12 h. Oxygen consumption rates are given as µmol O2 per replicate well per h.Well - replicate position on 24 well cell culture plate used for incubationPredation risk - three-spined stickleback chemical cue exposure, 0 = no, 1 = yes.Cu - copper exposure, 0 = no, 1 = yes.Species - copepod, Tigriopus brevicornis, Calanus finmarchicusmale - number of individuals.female - number of individuals.juveniles - number of individuals.DmgAntenna - registered external physical injuries post exposure.WhiteDot - registered external physical abnormalities post exposure.Alive - number of surviving individuals post exposure.Dead - number of dead individuals post exposure.BigBubble - registered potentially confounding gas bubble.length.um - copepod prosome length, µm.DWeight - ash-free dry weight, calculated from prosome length.DWResp_0to12h - equals RespRate_corr.nlm_0to12h normalized by biomass to µmol O2 per µg.dw per h. Similarly calculated for the time-intervals 0-3 h, 3-6 h, 6-9 h and 9-12 h.
DOI: 10.6084/m9.figshare.12326246.v1
title: Supplementary Material for: The p.R206C Mutation in <b><i>MYO7A</i></b> Leads to Autosomal Dominant Nonsyndromic Hearing Loss

description: <b><i>Background:</i></b> Dominant mutations in <i>MYO7A</i> may lead to nonsyndromic deafness DFNA11. A p.R206C variant in <i>MYO7A</i> has previously been reported in a small deaf family from Taiwan but with ambiguous pathogenicity and inheritance pattern. <b><i>Aims/Objectives:</i></b> Our study aims to clarify the pathogenicity of this variant by clinical characterization and genetic analysis of a separate autosomal dominant deaf family harboring this variant in mainland China. <b><i>Materials and Methods:</i></b> Auditory features of hearing loss were characterized in representative affected family members. Mutation screening was performed by targeted next-generation sequencing of 138 known deafness genes in the proband. Candidate pathogenic mutations were confirmed by Sanger sequencing in family members and ethnically matched controls. <b><i>Results:</i></b> Consistent with typical DFNA11 phenotype, the affected family members in this study showed delayed-onset, progressive hearing loss affecting mostly high frequencies. Targeted next-generation sequencing identified a p.R206C mutation in <i>MYO7A</i> as the only candidate pathogenic mutation cosegregating with the hearing phenotype. This mutation is not seen in 200 Chinese Han normal-hearing controls. <b><i>Conclusions and Significance:</i></b> The recurrent p.R206C variant in <i>MYO7A</i> is pathogenic and is likely in a mutation hot spot or due to a founder effect. Reports of such rare variants in multiple patients or families may facilitate exploitation of its pathogenicity.
DOI: 10.6084/m9.figshare.12326177
title: De novo assembly of transcriptome dataset from leaves of Dryobalanops aromatica (Syn. Dryobalanops sumatrensis) seedlings grown in two contrasting potting media

description: The RNA transcriptome data of <i>D. aromatica’</i>s seedlings derived from young leaves extracted from three seedlings of one year old planted in dry mineral soil media and peat media were generated by Illumina HiSeq 4000 platform in NovogenAIT, Singapore. Our data, as the first transcriptome dataset for <i>D. aromatica,</i> is of great importance for understanding the molecular mechanism and the involving genes of <i>D. aromatica</i> responses to contrasting growing potting media condition and could be useful to generate molecular markers.<br><br>
DOI: 10.6084/m9.figshare.12326168
title: Supplementary Material for: Identification of <b><i>Transient Receptor Potential Channel 4-Associated Protein</i></b> as a Novel Candidate Gene Causing Congenital Primary Hypothyroidism

description: <b><i>Background:</i></b> Congenital primary hypothyroidism (CH) is the most common endocrine disorder in neonates. <b><i>Methods:</i></b> To identify novel genes, we performed whole exome sequencing (WES) in 6 patients with CH due to thyroid dysgenesis (TD). The potential effects of the most relevant variants were analyzed using in silico prediction tools. The most promising candidate gene, transient receptor potential channel 4-associated protein (<i>TRPC4AP</i>), was sequenced in 179 further patients with TD. Expression of <i>TRPC4AP</i> in human thyroid was investigated using RT-PCR. <i>Trpc4ap</i>- functional analysis was performed in <i>Xenopus laevis</i> using Morpholino (MO) antisense oligomers. <b><i>Results:</i></b> WES identified a likely damaging mutation in <i>TRPC4AP</i> leading to a de novo stop codon p.Q552*. Targeted sequencing of <i>TRPC4AP</i> demonstrated gene variants with predicted damaging potential in 5 patients resulting each in an amino acid exchange (p.P706S, p.F729L, p.S777C, and p.N229S). We demonstrated that <i>TRPC4AP</i> is expressed in human thyroid gland tissue. Using <i>Xenopus laevis</i>, we showed that the volume of the tadpole thyroid anlage was reduced by 20% in <i>Trpc4ap</i> MO knockdowns compared to controls and by 41% in “Clustered Regularly Interspaced Short Palindromic Repeats”/Cas9-mediated gene knockout experiments. <b><i>Discussion:</i></b> A recognized interaction of TRPC4AP and the NF-kappa-B-essential-modulator encoded by <i>IKBKG</i> gene was identified by IPA analysis. IKBKG plays a role in activation of the NF-κB-signaling pathway and regulates genes involved in proliferation and survival of thyrocytes and expression of key enzymes of thyroid hormone synthesis. <b><i>Conclusion:</i></b> <i>TRPC4AP</i> was identified as a novel candidate gene in TD, but further studies are needed to validate its role in thyroid function.