cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12867341
title: LTP_BinocularRivalryModulation.xlsx

description: In this study, we induced binocular rivalry by dichoptically presenting orthogonal, sinusoidal gratings. Dichoptic presentation was achieved using red/green anaglyphs. The aim of our first experiment was to determine suitable grating parameters. Specifically, we aimed to identify a stimulus configuration that generated minimal time spent in piecemeal and stable alternation rates across trials. In our second experiment, we used this stimulus to assess whether monocular rapid visual stimulation modulates binocular rivalry dynamics and/or dominance durations in individuals with normal binocular vision, based on previous work showing that rapid visual stimulation induces LTP-like effects in human visual cortex (Teyler et al., 2005; Clapp et al., 2006a; Normann et al., 2007; Ross et al., 2008; Sanders et al., 2018). Our hypothesis was that rapid monocular visual stimulation would strengthen the cortical response to inputs from the stimulated eye and that this would increase the relative time spent perceiving the stimulus presented to the stimulated eye during binocular rivalry (i.e. increase the perceptual dominance of the stimulated eye). In a third experiment, we measured binocular rivalry before and after viewing a monocular static grating as a test of monocular visual adaptation.
DOI: 10.6084/m9.figshare.12867341.v1
title: LTP_BinocularRivalryModulation.xlsx

description: In this study, we induced binocular rivalry by dichoptically presenting orthogonal, sinusoidal gratings. Dichoptic presentation was achieved using red/green anaglyphs. The aim of our first experiment was to determine suitable grating parameters. Specifically, we aimed to identify a stimulus configuration that generated minimal time spent in piecemeal and stable alternation rates across trials. In our second experiment, we used this stimulus to assess whether monocular rapid visual stimulation modulates binocular rivalry dynamics and/or dominance durations in individuals with normal binocular vision, based on previous work showing that rapid visual stimulation induces LTP-like effects in human visual cortex (Teyler et al., 2005; Clapp et al., 2006a; Normann et al., 2007; Ross et al., 2008; Sanders et al., 2018). Our hypothesis was that rapid monocular visual stimulation would strengthen the cortical response to inputs from the stimulated eye and that this would increase the relative time spent perceiving the stimulus presented to the stimulated eye during binocular rivalry (i.e. increase the perceptual dominance of the stimulated eye). In a third experiment, we measured binocular rivalry before and after viewing a monocular static grating as a test of monocular visual adaptation.
DOI: 10.6084/m9.figshare.12874626
title: Additional file 3 of Microarray analysis and scale-free gene networks identify candidate regulators in drought-stressed roots of loblolly pine (P. taeda L.)

description: Additional file 3:This Excel file contains the complete PtGen2 master file including annotations and print tip information (3A), the list of duplicate spotted validation cDNAs and buffer blanks that were excluded from statistical analysis (3B), and 251 probes removed from statistical analysis since they mapped to contigs already represented by other cDNAs. 3A (PtGen2 Master Annotation File): Gene ID = unique probe address (metarow, metacolumn, row, column), UniScript = Fungen assembly contig ID, Clone_Name = cDNA clone ID. P_C_R actual = plate, column, and row or source print plates. P_C_R Virtual = plate_column_row with virtual plate 69 (actually a reprint of plate 10). Print Tip = print tip location on 48 pin head. All BlastX results are ordered by database name abbreviation followed by accession (BlastX), description (ID), and E-value (Exp). NCBI = NCBI non-redundant, SP = Swiss Prot, TR = TrEMBL, UREF = UniRef100, TAIR = Arabidopsis, MT2P = Medicago, OSA = rice. 3B (Plate 69 + Buffers) Gene IDs and clone names for duplicate spotted plate 69 (re-spot of source plate 10) used only for validation purposes and removed from statistical evaluation of experimental data. A correlation analysis was done on these 384 probes (see Additional File 5). 3C (251 Duplicate cDNAs): Gene IDs and clone names of 251 cDNAs removed from statistical evaluation of experimental data since these clones were duplicate probes that derived from cDNA clones that mapped to the same Uniscript (contig). (XLS 20 MB)
DOI: 10.6084/m9.figshare.12874638
title: Additional file 7 of Microarray analysis and scale-free gene networks identify candidate regulators in drought-stressed roots of loblolly pine (P. taeda L.)

description: Additional file 7:Expression Results for differentially expressed genes (DEGs) identified after interrogation of PtGen2. This Excel file contains three separate sheets that list the normalized log2 mean ratios for differentially expressed genes exhibiting at least a 1.5-fold difference obtained after pair wise comparisons for each of the three water availability treatments (drought stressed (DS), well-watered (WW), and drought recovered (DR). Note that each table can be sorted by either fold-increase or fold-decrease expression to coincide with results and discussion sections. 7A (DS versus WW) 2445 DEGs with at least 1.5 fold expression difference identified in the DS versus well-WW comparison. 7B (DR versus WW) 76 DEGs with at least 1.5 fold expression difference identified in the DR versus WW comparison. 7C (DS versus DR) 1918 DEGs with at least a 1.5-fold expression difference identified in the DS versus DR comparison. All three tables show Gene ID = the physical address of the spot on the array (metarow, metacolumn, row, column), UniScript = FUNGEN contig ID, Clone_Name = cDNA clone ID, Fold ↑, and Fold ↓values are displayed as normalized log2 mean ratios. All BlastX results are ordered by database name abbreviation followed by accession (BlastX), description (ID), and E-value (Exp). NCBI = NCBI non-redundant, SP = SwissProt. (XLS 1 MB)
DOI: 10.6084/m9.figshare.12874638.v1
title: Additional file 7 of Microarray analysis and scale-free gene networks identify candidate regulators in drought-stressed roots of loblolly pine (P. taeda L.)

description: Additional file 7:Expression Results for differentially expressed genes (DEGs) identified after interrogation of PtGen2. This Excel file contains three separate sheets that list the normalized log2 mean ratios for differentially expressed genes exhibiting at least a 1.5-fold difference obtained after pair wise comparisons for each of the three water availability treatments (drought stressed (DS), well-watered (WW), and drought recovered (DR). Note that each table can be sorted by either fold-increase or fold-decrease expression to coincide with results and discussion sections. 7A (DS versus WW) 2445 DEGs with at least 1.5 fold expression difference identified in the DS versus well-WW comparison. 7B (DR versus WW) 76 DEGs with at least 1.5 fold expression difference identified in the DR versus WW comparison. 7C (DS versus DR) 1918 DEGs with at least a 1.5-fold expression difference identified in the DS versus DR comparison. All three tables show Gene ID = the physical address of the spot on the array (metarow, metacolumn, row, column), UniScript = FUNGEN contig ID, Clone_Name = cDNA clone ID, Fold ↑, and Fold ↓values are displayed as normalized log2 mean ratios. All BlastX results are ordered by database name abbreviation followed by accession (BlastX), description (ID), and E-value (Exp). NCBI = NCBI non-redundant, SP = SwissProt. (XLS 1 MB)
DOI: 10.6084/m9.figshare.12874641
title: Additional file 8 of Microarray analysis and scale-free gene networks identify candidate regulators in drought-stressed roots of loblolly pine (P. taeda L.)

description: Additional file 8:Gene correlation analysis and module membership data generated using WGCNA. This file contains the WGCNA module memberships for the 2445 differentially expressed genes identified in the drought stressed versus well-watered analysis as well as log2 mean ratios and BlastX annotation information. Each module color represents a grouping of genes whose expression profiles are coordinately expressed. Module membership correlation values were used to generate the graphical representation of the pine root gene network. Gene ID = the physical address of the spot on the array (metarow, metacolumn, row, column), Fold ↑, and Fold ↓values for DS vs. WW comparison are displayed as normalized log2 mean ratios. Module color, MM = module membership correlation value, p.MM = probability of module membership. All BlastX results are ordered by database name abbreviation followed by accession (BlastX), description (ID), and E-value (Exp). NCBI = NCBI non-redundant, SP = Swiss Prot. (XLS 2 MB)
DOI: 10.6084/m9.figshare.12874647.v8
title: Additional file of Microarray analysis and scale-free gene networks identify candidate regulators in drought-stressed roots of loblolly pine (P. taeda L.)

description: Additional file of Microarray analysis and scale-free gene networks identify candidate regulators in drought-stressed roots of loblolly pine (P. taeda L.)
DOI: 10.6084/m9.figshare.12874641.v1
title: Additional file 8 of Microarray analysis and scale-free gene networks identify candidate regulators in drought-stressed roots of loblolly pine (P. taeda L.)

description: Additional file 8:Gene correlation analysis and module membership data generated using WGCNA. This file contains the WGCNA module memberships for the 2445 differentially expressed genes identified in the drought stressed versus well-watered analysis as well as log2 mean ratios and BlastX annotation information. Each module color represents a grouping of genes whose expression profiles are coordinately expressed. Module membership correlation values were used to generate the graphical representation of the pine root gene network. Gene ID = the physical address of the spot on the array (metarow, metacolumn, row, column), Fold ↑, and Fold ↓values for DS vs. WW comparison are displayed as normalized log2 mean ratios. Module color, MM = module membership correlation value, p.MM = probability of module membership. All BlastX results are ordered by database name abbreviation followed by accession (BlastX), description (ID), and E-value (Exp). NCBI = NCBI non-redundant, SP = Swiss Prot. (XLS 2 MB)
DOI: 10.6084/m9.figshare.12874626.v1
title: Additional file 3 of Microarray analysis and scale-free gene networks identify candidate regulators in drought-stressed roots of loblolly pine (P. taeda L.)

description: Additional file 3:This Excel file contains the complete PtGen2 master file including annotations and print tip information (3A), the list of duplicate spotted validation cDNAs and buffer blanks that were excluded from statistical analysis (3B), and 251 probes removed from statistical analysis since they mapped to contigs already represented by other cDNAs. 3A (PtGen2 Master Annotation File): Gene ID = unique probe address (metarow, metacolumn, row, column), UniScript = Fungen assembly contig ID, Clone_Name = cDNA clone ID. P_C_R actual = plate, column, and row or source print plates. P_C_R Virtual = plate_column_row with virtual plate 69 (actually a reprint of plate 10). Print Tip = print tip location on 48 pin head. All BlastX results are ordered by database name abbreviation followed by accession (BlastX), description (ID), and E-value (Exp). NCBI = NCBI non-redundant, SP = Swiss Prot, TR = TrEMBL, UREF = UniRef100, TAIR = Arabidopsis, MT2P = Medicago, OSA = rice. 3B (Plate 69 + Buffers) Gene IDs and clone names for duplicate spotted plate 69 (re-spot of source plate 10) used only for validation purposes and removed from statistical evaluation of experimental data. A correlation analysis was done on these 384 probes (see Additional File 5). 3C (251 Duplicate cDNAs): Gene IDs and clone names of 251 cDNAs removed from statistical evaluation of experimental data since these clones were duplicate probes that derived from cDNA clones that mapped to the same Uniscript (contig). (XLS 20 MB)
DOI: 10.6084/m9.figshare.7981889
title: Mesopassandrinae subfam. nov., a basal group of parasitic flat beetle (Coleoptera: Passandridae) from Cretaceous Burmese amber

description: †<i>Mesopassandra keyao</i> gen. et sp. nov., representing the first Mesozoic record of the family Passandridae (Coleoptera: Cucujoidea), is here described from Upper Cretaceous Burmese amber. Based on a phylogenetic analysis of 30 adult characters †<i>Mesopassandra</i> was recovered as the sister group to all remaining Passandridae, having a large labrum, bidentate mandibles and presumably 5-5-4 tarsi in the male. It is here placed in a new subfamily, †Mesopassandrinae subfam. nov. Ancestral area was reconstructed using the phylogeny and an ancient Gondwanan origin was inferred for the whole family. The Eocene species <i>Catogenus punctatus</i> Ramírez, Corsolini & Di Iorio, 2016 from Patagonia, Argentina is here transferred from Passandridae to Cucujidae Latreille, 1802, in the genus <i>Platisus</i> Erichson, 1842 as <i>Platisus punctatus</i> (Ramírez, Corsolini & Di Iorio, 2016) comb. nov. http://zoobank.org/urn:lsid:zoobank.org:pub:8F3FF954-B687-4FCF-BAA8-16562C53C7D0
DOI: 10.6084/m9.figshare.7981892
title: Transitional fossils illuminate early evolution of the ant-like stone beetle tribe Leptomastacini (Coleoptera: Staphylinidae: Scydmaeninae)

description: The ant-like stone beetle supertribe Mastigitae (Staphylinidae: Scydmaeninae) comprises nine extant and five extinct genera that exhibit unusual morphological specializations and ecological adaptions. Recent discoveries of mastigite fossils from Upper Cretaceous–middle Eocene deposits have significantly improved our knowledge of the evolutionary history of this group, yet a direct fossil record for two modern tribes of unclear affinities, i.e. Leptomastacini and Papusini, is lacking. Herein we describe a new genus and species, †<i>Archemastax divida</i> gen. et sp. nov., based on two well-preserved individuals entombed in mid-Cretaceous Burmese amber (<i>c</i>. 99 Ma), representing the earliest known representative of Leptomastacini. †<i>Archemastax</i> possesses both plesiomorphic and derived characters, with a few important traits shared with extant members of Papusini and Clidicini. A data set of 70 morphological characters scored for 29 species of Mastigitae was analysed using maximum parsimony and Bayesian inference; both analyses recovered a sister relationship between †<i>Archemastax</i> and extant leptomastacines. However, in the former analysis Leptomastacini was recovered as sister to the remaining Mastigitae, while the latter indicated an origin of Leptomastacini from within Clidicini. Although a close affinity between †<i>Archemastax</i> and Papusini was not supported by our analyses, similarities in some shared characters of these two groups are discussed. http://zoobank.org/urn:lsid:zoobank.org:pub:BB17DF86-25FC-48B5-8AFB-1DB27328280F
DOI: 10.6084/m9.figshare.7981889.v1
title: Mesopassandrinae subfam. nov., a basal group of parasitic flat beetle (Coleoptera: Passandridae) from Cretaceous Burmese amber

description: †<i>Mesopassandra keyao</i> gen. et sp. nov., representing the first Mesozoic record of the family Passandridae (Coleoptera: Cucujoidea), is here described from Upper Cretaceous Burmese amber. Based on a phylogenetic analysis of 30 adult characters †<i>Mesopassandra</i> was recovered as the sister group to all remaining Passandridae, having a large labrum, bidentate mandibles and presumably 5-5-4 tarsi in the male. It is here placed in a new subfamily, †Mesopassandrinae subfam. nov. Ancestral area was reconstructed using the phylogeny and an ancient Gondwanan origin was inferred for the whole family. The Eocene species <i>Catogenus punctatus</i> Ramírez, Corsolini & Di Iorio, 2016 from Patagonia, Argentina is here transferred from Passandridae to Cucujidae Latreille, 1802, in the genus <i>Platisus</i> Erichson, 1842 as <i>Platisus punctatus</i> (Ramírez, Corsolini & Di Iorio, 2016) comb. nov. http://zoobank.org/urn:lsid:zoobank.org:pub:8F3FF954-B687-4FCF-BAA8-16562C53C7D0
DOI: 10.6084/m9.figshare.12874647.v13
title: Additional file of Microarray analysis and scale-free gene networks identify candidate regulators in drought-stressed roots of loblolly pine (P. taeda L.)

description: Additional file of Microarray analysis and scale-free gene networks identify candidate regulators in drought-stressed roots of loblolly pine (P. taeda L.)
DOI: 10.6084/m9.figshare.7981892.v1
title: Transitional fossils illuminate early evolution of the ant-like stone beetle tribe Leptomastacini (Coleoptera: Staphylinidae: Scydmaeninae)

description: The ant-like stone beetle supertribe Mastigitae (Staphylinidae: Scydmaeninae) comprises nine extant and five extinct genera that exhibit unusual morphological specializations and ecological adaptions. Recent discoveries of mastigite fossils from Upper Cretaceous–middle Eocene deposits have significantly improved our knowledge of the evolutionary history of this group, yet a direct fossil record for two modern tribes of unclear affinities, i.e. Leptomastacini and Papusini, is lacking. Herein we describe a new genus and species, †<i>Archemastax divida</i> gen. et sp. nov., based on two well-preserved individuals entombed in mid-Cretaceous Burmese amber (<i>c</i>. 99 Ma), representing the earliest known representative of Leptomastacini. †<i>Archemastax</i> possesses both plesiomorphic and derived characters, with a few important traits shared with extant members of Papusini and Clidicini. A data set of 70 morphological characters scored for 29 species of Mastigitae was analysed using maximum parsimony and Bayesian inference; both analyses recovered a sister relationship between †<i>Archemastax</i> and extant leptomastacines. However, in the former analysis Leptomastacini was recovered as sister to the remaining Mastigitae, while the latter indicated an origin of Leptomastacini from within Clidicini. Although a close affinity between †<i>Archemastax</i> and Papusini was not supported by our analyses, similarities in some shared characters of these two groups are discussed. http://zoobank.org/urn:lsid:zoobank.org:pub:BB17DF86-25FC-48B5-8AFB-1DB27328280F
DOI: 10.6084/m9.figshare.12874647.v12
title: Additional file of Microarray analysis and scale-free gene networks identify candidate regulators in drought-stressed roots of loblolly pine (P. taeda L.)

description: Additional file of Microarray analysis and scale-free gene networks identify candidate regulators in drought-stressed roots of loblolly pine (P. taeda L.)
DOI: 10.6084/m9.figshare.7981856
title: The first three-dimensional fossils of Cretaceous sclerorhynchid sawfish: <i>Asflapristis cristadentis</i> gen. et sp. nov., and implications for the phylogenetic relations of the Sclerorhynchoidei (Chondrichthyes)

description: A new fossil batoid (ray), <i>Asflapristis cristadentis</i> gen. et sp. nov., is described from six exceptionally well-preserved, three-dimensional skeletal remains from the Turonian (Late Cretaceous) of Morocco. Mechanical and acid preparation and computed tomographic scanning of these specimens reveal details of much of the proximal skeleton, especially the skull, synarcual and pectoral skeleton, with only the more distal parts of the skeleton missing. These fossils represent a relatively large animal (62 cm preserved length, estimated total length approximately 2 metres) possessing a robust rostrum that lacks enlarged rostral denticles. It has a narrow and small chondrocranium with jaws that are relatively large compared to the rest of the skull and robust with highly ornamented teeth that lack cusps. The branchial skeleton shows a large second hypobranchial without an anterior process, which was probably fused to the basibranchial as in other sclerorhynchoids. The synarcual is large and lacks centra through its entire length, with no direct connection to the pectoral girdle observed. Pectoral fins probably possessed enlarged proximal elements (propterygium, mesopterygium and metapterygium); the articulation facet between the coracoid and the pectoral elements was reduced. A phylogenetic analysis using both parsimony and Bayesian methods was performed incorporating this new taxon. Both analyses recovered a phylogenetic topology that places the sclerorhynchoids in a close relation to rajoids and clearly separated from the morphologically similar Pristidae within the Rhinopristiformes. With respect to the extant taxa, the phylogenies generated are similar to that obtained from molecular analysis of modern batoids. The palaeoecological implication of this discovery suggests that the Asfla assemblage was not from a ‘normal’ open carbonate shelf but rather a restricted environment favouring a low-diversity chondrichthyan fauna. http://zoobank.org/urn:lsid:zoobank.org:pub:7752385F-817D-40BF-961C-1AF7B9093E14
DOI: 10.6084/m9.figshare.7981838
title: Identification and functional analysis of novel mutations in the <i>SOD1</i> gene in Chinese patients with amyotrophic lateral sclerosis

description: Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease characterized by selective involvement of motor neurons in the central nervous system (CNS). The most common causative gene of ALS in the Chinese population is the Cu/Zn <i>superoxide dismutase 1</i> (<i>SOD1)</i> gene, which accounts for 20–42.9% of familial ALS (FALS) and 1–2% of sporadic ALS (SALS) cases. In this study, we identify three novel <i>SOD1</i> mutations, Gly17Cys, Pro75Ser, and His121Gln, in four ALS pedigrees. A functional analysis was performed, and the results showed that all three mutations could lead to the formation of misfolded proteins. In addition, genotype–phenotype correlations in these patients are also described. Our study helps to characterize the genotype and phenotype of ALS with <i>SOD1</i> mutations.
DOI: 10.6084/m9.figshare.7981856.v2
title: The first three-dimensional fossils of Cretaceous sclerorhynchid sawfish: <i>Asflapristis cristadentis</i> gen. et sp. nov., and implications for the phylogenetic relations of the Sclerorhynchoidei (Chondrichthyes)

description: A new fossil batoid (ray), <i>Asflapristis cristadentis</i> gen. et sp. nov., is described from six exceptionally well-preserved, three-dimensional skeletal remains from the Turonian (Late Cretaceous) of Morocco. Mechanical and acid preparation and computed tomographic scanning of these specimens reveal details of much of the proximal skeleton, especially the skull, synarcual and pectoral skeleton, with only the more distal parts of the skeleton missing. These fossils represent a relatively large animal (62 cm preserved length, estimated total length approximately 2 metres) possessing a robust rostrum that lacks enlarged rostral denticles. It has a narrow and small chondrocranium with jaws that are relatively large compared to the rest of the skull and robust with highly ornamented teeth that lack cusps. The branchial skeleton shows a large second hypobranchial without an anterior process, which was probably fused to the basibranchial as in other sclerorhynchoids. The synarcual is large and lacks centra through its entire length, with no direct connection to the pectoral girdle observed. Pectoral fins probably possessed enlarged proximal elements (propterygium, mesopterygium and metapterygium); the articulation facet between the coracoid and the pectoral elements was reduced. A phylogenetic analysis using both parsimony and Bayesian methods was performed incorporating this new taxon. Both analyses recovered a phylogenetic topology that places the sclerorhynchoids in a close relation to rajoids and clearly separated from the morphologically similar Pristidae within the Rhinopristiformes. With respect to the extant taxa, the phylogenies generated are similar to that obtained from molecular analysis of modern batoids. The palaeoecological implication of this discovery suggests that the Asfla assemblage was not from a ‘normal’ open carbonate shelf but rather a restricted environment favouring a low-diversity chondrichthyan fauna. http://zoobank.org/urn:lsid:zoobank.org:pub:7752385F-817D-40BF-961C-1AF7B9093E14