cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12878552
title: Additional file 3 of Sequential analysis of global gene expression profiles in immature and in vitro matured bovine oocytes: potential molecular markers of oocyte maturation

description: Additional file 3:Table S1: Transcripts over-expressed in IVM oocytes compared to immature oocytes (GV). (XLS 169 KB)
DOI: 10.6084/m9.figshare.12878555.v1
title: Additional file 4 of Sequential analysis of global gene expression profiles in immature and in vitro matured bovine oocytes: potential molecular markers of oocyte maturation

description: Additional file 4:Table S2: Transcripts under-expressed in IVM oocytes compared to immature oocytes (GV). (XLS 378 KB)
DOI: 10.6084/m9.figshare.7956404
title: MOESM1 of Automated peak detection method for behavioral event identification: detecting Balaenoptera musculus and Grampus griseus feeding attempts

description: Additional file 1. Data spreadsheets displaying the detection statistics and tag deployment information for all animal individuals used in this study.
DOI: 10.6084/m9.figshare.7956404.v1
title: MOESM1 of Automated peak detection method for behavioral event identification: detecting Balaenoptera musculus and Grampus griseus feeding attempts

description: Additional file 1. Data spreadsheets displaying the detection statistics and tag deployment information for all animal individuals used in this study.
DOI: 10.6084/m9.figshare.7956377
title: MOESM1 of Alternative methods of estimating the water potential at turgor loss point in Acer genotypes

description: Additional file 1. All data, P-V curves raw data, WP4, Vapro, & P-V TLP values.
DOI: 10.6084/m9.figshare.7956377.v1
title: MOESM1 of Alternative methods of estimating the water potential at turgor loss point in Acer genotypes

description: Additional file 1. All data, P-V curves raw data, WP4, Vapro, & P-V TLP values.
DOI: 10.6084/m9.figshare.7956233
title: The Simulation Optimization and Experimental Study of the Air Distribution Chamber Structure of Straw-based Nutrient Seeding-growing Tray Microwave Hot Air Coupling Dryers

description: In order to improve the flow field structure of the air distribution chamber of the straw-based nutrient seeding-growing tray microwave hot air coupling dryer, and enhance the uniformity of the outlet gas velocity distribution, the computational fluid dynamics software is used to simulate the flow field of the air distribution chamber, on the basis of the gas motion differential equation and the renormalization group (RNG) k~ε turbulence model. Using the front panel height, the upper apex angle and the side wall inclination angle as the factors, and the speed non-uniformity coefficient as the index, we carried out the quadratic regression orthogonal rotation combination simulation test which was combined with the design theory of Central Composite Design to obtain the optimal structural parameter of the air distribution chamber. On this basis, the spoiler was constructed for the air distribution chamber with optimized structural parameters, and the internal flow field was spoiled to further improve the uniformity of the outlet airflow velocity distribution. At the same time, the predicted value and experimental data of the optimal model flow field were compared. The research results show that when the air distribution chamber front panel height is 33mm, the upper apex angle is 108°, the side wall inclination angle is 78°, the heights of two spoilers are 40mm, the outlet airflow speed varies from 5.36 m/s to 5.71m/s, and the speed unevenness coefficient is reduced from 13.95% of the original model to 6.05%. The maximum deviation between the numerical simulation results and the test data is less than 4%, which can meet the uniformity of the outlet airflow speed of the dryer. The research results can provide theoretical support for the design and industrial production of the microwave hot air coupling dryer, and provide technical support for the industrial production of straw-based nutrient seeding-growing tray.
DOI: 10.6084/m9.figshare.7956227
title: Intraspecific variability in isotopic composition of a monomorphic seabird, the Common Tern (<i>Sterna hirundo</i>), at wintering grounds

description: Understanding sex differences in foraging behaviour has important implications for breeding biology and population ecology. This requires the evaluation of segregation throughout the annual cycle, including the non-breeding period. We studied the diet and foraging strategies of the Common Tern (<i>Sterna hirundo</i>) at an intraspecific level by sampling birds during two consecutive non-breeding periods in Punta Rasa, Buenos Aires Province, Argentina. Blood samples were taken for sex determination and carbon and nitrogen stable isotope analysis. No isotopic difference was observed between years, but higher isotopic values occurred during late non-breeding period. Carbon and nitrogen isotopic values were similar between sexes; however, differences were observed in standard ellipse analyses, considered to represent isotopic niches. Even though the Bayesian ellipse areas overlapped, females showed wider isotopic niches throughout the non-breeding period. This could be related to different feeding strategies, foraging areas or migratory stopover sites at either intraspecific or individual levels. Diet contributions of different prey categories estimated through mixing model analyses suggested a higher contribution of estuarine fish than of marine pelagic species. These results highlight the importance of stable isotope analyses as a complementary methodology to traditional diet studies, particularly during the non-breeding period.
DOI: 10.6084/m9.figshare.7956233.v2
title: The Simulation Optimization and Experimental Study of the Air Distribution Chamber Structure of Straw-based Nutrient Seeding-growing Tray Microwave Hot Air Coupling Dryers

description: In order to improve the flow field structure of the air distribution chamber of the straw-based nutrient seeding-growing tray microwave hot air coupling dryer, and enhance the uniformity of the outlet gas velocity distribution, the computational fluid dynamics software is used to simulate the flow field of the air distribution chamber, on the basis of the gas motion differential equation and the renormalization group (RNG) k~ε turbulence model. Using the front panel height, the upper apex angle and the side wall inclination angle as the factors, and the speed non-uniformity coefficient as the index, we carried out the quadratic regression orthogonal rotation combination simulation test which was combined with the design theory of Central Composite Design to obtain the optimal structural parameter of the air distribution chamber. On this basis, the spoiler was constructed for the air distribution chamber with optimized structural parameters, and the internal flow field was spoiled to further improve the uniformity of the outlet airflow velocity distribution. At the same time, the predicted value and experimental data of the optimal model flow field were compared. The research results show that when the air distribution chamber front panel height is 33mm, the upper apex angle is 108°, the side wall inclination angle is 78°, the heights of two spoilers are 40mm, the outlet airflow speed varies from 5.36 m/s to 5.71m/s, and the speed unevenness coefficient is reduced from 13.95% of the original model to 6.05%. The maximum deviation between the numerical simulation results and the test data is less than 4%, which can meet the uniformity of the outlet airflow speed of the dryer. The research results can provide theoretical support for the design and industrial production of the microwave hot air coupling dryer, and provide technical support for the industrial production of straw-based nutrient seeding-growing tray.
DOI: 10.6084/m9.figshare.7956227.v1
title: Intraspecific variability in isotopic composition of a monomorphic seabird, the Common Tern (<i>Sterna hirundo</i>), at wintering grounds

description: Understanding sex differences in foraging behaviour has important implications for breeding biology and population ecology. This requires the evaluation of segregation throughout the annual cycle, including the non-breeding period. We studied the diet and foraging strategies of the Common Tern (<i>Sterna hirundo</i>) at an intraspecific level by sampling birds during two consecutive non-breeding periods in Punta Rasa, Buenos Aires Province, Argentina. Blood samples were taken for sex determination and carbon and nitrogen stable isotope analysis. No isotopic difference was observed between years, but higher isotopic values occurred during late non-breeding period. Carbon and nitrogen isotopic values were similar between sexes; however, differences were observed in standard ellipse analyses, considered to represent isotopic niches. Even though the Bayesian ellipse areas overlapped, females showed wider isotopic niches throughout the non-breeding period. This could be related to different feeding strategies, foraging areas or migratory stopover sites at either intraspecific or individual levels. Diet contributions of different prey categories estimated through mixing model analyses suggested a higher contribution of estuarine fish than of marine pelagic species. These results highlight the importance of stable isotope analyses as a complementary methodology to traditional diet studies, particularly during the non-breeding period.
DOI: 10.6084/m9.figshare.7956233.v1
title: The Simulation Optimization and Experimental Study of the Air Distribution Chamber Structure of Straw-based Nutrient Seeding-growing Tray Microwave Hot Air Coupling Dryers

description: In order to improve the flow field structure of the air distribution chamber of the straw-based nutrient seeding-growing tray microwave hot air coupling dryer, and enhance the uniformity of the outlet gas velocity distribution, the computational fluid dynamics software is used to simulate the flow field of the air distribution chamber, on the basis of the gas motion differential equation and the renormalization group (RNG) k~ε turbulence model. Using the front panel height, the upper apex angle and the side wall inclination angle as the factors, and the speed non-uniformity coefficient as the index, we carried out the quadratic regression orthogonal rotation combination simulation test which was combined with the design theory of Central Composite Design to obtain the optimal structural parameter of the air distribution chamber. On this basis, the spoiler was constructed for the air distribution chamber with optimized structural parameters, and the internal flow field was spoiled to further improve the uniformity of the outlet airflow velocity distribution. At the same time, the predicted value and experimental data of the optimal model flow field were compared. The research results show that when the air distribution chamber front panel height is 33mm, the upper apex angle is 108°, the side wall inclination angle is 78°, the heights of two spoilers are 40mm, the outlet airflow speed varies from 5.36 m/s to 5.71m/s, and the speed unevenness coefficient is reduced from 13.95% of the original model to 6.05%. The maximum deviation between the numerical simulation results and the test data is less than 4%, which can meet the uniformity of the outlet airflow speed of the dryer. The research results can provide theoretical support for the design and industrial production of the microwave hot air coupling dryer, and provide technical support for the industrial production of straw-based nutrient seeding-growing tray.
DOI: 10.6084/m9.figshare.7956203
title: ImageJ_data Figures 1,3,&4 Supp Figures 2,3,&25 Supp tables 1&3

description: All processed images used in 2D fractal analysis, related tables, and files.<br><br>The zip folder includes all 2D fractal analysis for:<br>Figures:<br>1, 3, and 4<br>Supp Figures:<br>2, 3 and 25<br>Supp Tables:1 and 3<br>
DOI: 10.6084/m9.figshare.7956197
title: Table 2 - Summary Genetic Variants

description: Summary of genetic variants identified between 12 paired, isogenic non-typeable <i>Haemophilus influenzae</i> isolates retrieved from the nasopharynx vs. lower airways.
DOI: 10.6084/m9.figshare.7956203.v1
title: ImageJ_data Figures 1,3,&4 Supp Figures 2,3,&25 Supp tables 1&3

description: All processed images used in 2D fractal analysis, related tables, and files.<br><br>The zip folder includes all 2D fractal analysis for:<br>Figures:<br>1, 3, and 4<br>Supp Figures:<br>2, 3 and 25<br>Supp Tables:1 and 3<br>
DOI: 10.6084/m9.figshare.7956194
title: Table S2 - WGS and RNAseq summary information

description: Whole-genome sequencing and RNA sequencing summary information.
DOI: 10.6084/m9.figshare.7956197.v1
title: Table 2 - Summary Genetic Variants

description: Summary of genetic variants identified between 12 paired, isogenic non-typeable <i>Haemophilus influenzae</i> isolates retrieved from the nasopharynx vs. lower airways.
DOI: 10.6084/m9.figshare.7956212
title: Data for: Machine Source Localization of Tursiops truncatus Whistle-like Sounds in a Reverberant Aquatic Environment

description: Each file is one tonal "snippet," as described in our paper (https://www.biorxiv.org/content/10.1101/606673v11). In brief, a snippet is a 2-s, 16-channel, 192-kHz WAV file for 16 hydrophones listening to an artificial tonal sound played at a particular source location in the Exhibit Pool (EP) of the National Aquarium in Baltimore, Maryland. The specific geometries of the hydrophones and tonal source locations are given in the paper (refer to Figure 1, Table 1, and Table 3).<br>Each filename string consists of several sub-strings separated by underscores. In general, tonal parameter names are followed by their snippet-specific values. Below, we clarify segments of the string in turn, where X's denote variable value characters. See Table 2 and the accompanying text for further explanation of the tonals and their parameters.<br>"extracted_whistle_XXXXX": Common file header followed by date of snippet collection, given in a MMDDYY format.<br>"ptXX": Indicates the source location inside the EP where the tonal was played. XX takes values 01 to 14. See Table 3 of the attached paper for corresponding three-dimensional source coordinates.<br>"count_XXX": Discrete identifier of which of the 127 created tonals was played (which is characterized by the subsequent parameter values). XXX takes values 000 to 127.<br>"cycles_X": Number of a tonal's cycles in time-frequency space. X takes a value from {1, 2}.<br><br>"dur_X": Duration of a tonal in seconds. X takes a value from {0.3, 1}.<br>"oscamp_XXXX": Amplitude of a tonal's frequency sweep in Hertz. X takes a value from {2000, 5000}.<br>"centerfreq_XXXX[X]": Center/average frequency of a tonal in Hertz. X takes a value from {6000, 105000}.<br>"tailpercent_XXX[X]": Percentage of a tonal's beginning and end over which tonal intensity onset and offset, respectively, occurred. X takes a value from {0.1, 0.25}.<br><br>"phase_XXXXXX[X]": A tonal's phase at onset. X takes a value from {-1.5708, 1.5708}.<br>"shift_000000": Obsolete parameter.<br>Lastly, we note that the order of the 16 channels in the snippet WAV's do not map directly to the hydrophone numbers given in Table 1. The mapping is as follows:<br>Hydrophone 1 Channel 8 Hydrophone 2 Channel 6 Hydrophone 3 Channel 7 Hydrophone 4 Channel 5 Hydrophone 5 Channel 1 Hydrophone 6 Channel 3 Hydrophone 7 Channel 2 Hydrophone 8 Channel 4 Hydrophone 9 Channel 12 Hydrophone 10 Channel 10 Hydrophone 11 Channel 11 Hydrophone 12 Channel 9 Hydrophone 13 Channel 16 Hydrophone 14 Channel 15 Hydrophone 15 Channel 14 Hydrophone 16 Channel 13<br>
DOI: 10.6084/m9.figshare.7956191
title: Table S1 - Updated COG terms for NTHi strain 86-028NP

description: Updated Cluster of Orthologous Group terms for non-typeable <i>Haemophilus influenzae </i>strain 86-028NP.
DOI: 10.6084/m9.figshare.7956185
title: Table 1 - Summary Patient

description: Summary of genomic and transcriptomic differences between paired, isogenic NTHi isolates obtained from the nasopharynx (NP) and lower airways (bronchoalveolar lavage; BAL) of 11 Australian children with chronic lung disease.<br>
DOI: 10.6084/m9.figshare.7956191.v1
title: Table S1 - Updated COG terms for NTHi strain 86-028NP

description: Updated Cluster of Orthologous Group terms for non-typeable <i>Haemophilus influenzae </i>strain 86-028NP.
DOI: 10.6084/m9.figshare.7956161
title: Dataset S2

description: RNA sequencing raw read counts against Non-typeable <i>Haemophilus influenzae </i>strain 86-028NP.
DOI: 10.6084/m9.figshare.7956113
title: Figure 3: Assembly formation and characterization with Helium Ion Microscopy (HIM), Atomic Force Microscopy (AFM), and Transmission Electron Microscopy (TEM)

description: <b>Figure 3: Assembly formation and characterization with Helium Ion Microscopy (HIM), Atomic Force Microscopy (AFM), and Transmission Electron Microscopy (TEM)</b>, all reveal fractal-like topologies on a surface, (<b>A to G</b>) Longer fractal-like structures, branch-like, and flower-like structures are seen in HIM (<b>A</b> to <b>C</b>) and AFM (<b>D</b>). (<b>E</b>) Representative HIM images for assemblies obtained at different concentrations of pY-AtzAM1 (250 nM- 3 µM) while maintaining a fixed concentration of AtzCM1-SH2 (2 µM). Increasing concentrations of pY-AtzM1 result in larger assemblies with higher fractal dimensions. (<b>F</b>) D<sub>f</sub> and l, the fractal dimension and lacunarity of the images, are similar for images obtained from different microscopy techniques. HIM images show fractal-like assembly formation with pY-AtzAM1 and AtzCM1-SH2 (<b>G</b>), while the Gly-Ser-rich linker-containing variants form globular assemblies under these conditions (<b>H</b>).
DOI: 10.6084/m9.figshare.7956149
title: Figure 5: Fractal assemblies capture and release greater amounts of cargo compared to globular assemblies

description: <b>Figure 5: Fractal assemblies capture and release greater amounts of cargo compared to globular assemblies. </b>Scheme for the envisioned reversible capture of cargo proteins for the (<b>A</b>) fractal and (<b>B</b>) globular structures. The red stars denote an example cargo protein (antibody). (<b>C</b>) % protein capture was measured for 3:2 fractal (assemblies obtained with 3 AtzA-pY: 2 AtzC-SH2), 3:2 GS linker (globular assemblies obtained at the same stoichiometry with fusion proteins containing long GS-rich linkers), and 3:1 fractal (assemblies obtained with 3 AtzA-pY: 1 AtzC-SH2). The 3:2 fractal captured more IgG antibody (red bars) and GFP-SH2 (green barss), and degraded more substrate TCP (purple bar; reflecting the higher capture efficiency of enzyme DhaA-Sh2) than the 3:2 GS linker assemblies. In addition, 3:2 fractal released more captured antibody compared to the 3:2 GS linker when incubated with YopH phosphatase (blue bars). (<b>D</b>, <b>E</b>) Confocal fluorescence microscopy images of the 3-component assembly with GFP-SH2 showing the topology of incorporation of GFP-SH2 in fractal and (<b>F-G</b>) the incorporation of GFP-SH2 into the globular assemblies. (<b>H-I</b>) the IgG antibody Alexa Fluor 568 incorporation into the fractal assembly and (<b>J-K</b>) the incorporation into the globular assembly.<b></b>
DOI: 10.6084/m9.figshare.7956158
title: Dataset S1

description: Within-patient Non-typeable Haemophilus influenzae differential expression analysis comparing nasopharynx against bronchoalveolar isolates
DOI: 10.6084/m9.figshare.7956161.v1
title: Dataset S2

description: RNA sequencing raw read counts against Non-typeable <i>Haemophilus influenzae </i>strain 86-028NP.
DOI: 10.6084/m9.figshare.7956113.v1
title: Figure 3: Assembly formation and characterization with Helium Ion Microscopy (HIM), Atomic Force Microscopy (AFM), and Transmission Electron Microscopy (TEM)

description: <b>Figure 3: Assembly formation and characterization with Helium Ion Microscopy (HIM), Atomic Force Microscopy (AFM), and Transmission Electron Microscopy (TEM)</b>, all reveal fractal-like topologies on a surface, (<b>A to G</b>) Longer fractal-like structures, branch-like, and flower-like structures are seen in HIM (<b>A</b> to <b>C</b>) and AFM (<b>D</b>). (<b>E</b>) Representative HIM images for assemblies obtained at different concentrations of pY-AtzAM1 (250 nM- 3 µM) while maintaining a fixed concentration of AtzCM1-SH2 (2 µM). Increasing concentrations of pY-AtzM1 result in larger assemblies with higher fractal dimensions. (<b>F</b>) D<sub>f</sub> and l, the fractal dimension and lacunarity of the images, are similar for images obtained from different microscopy techniques. HIM images show fractal-like assembly formation with pY-AtzAM1 and AtzCM1-SH2 (<b>G</b>), while the Gly-Ser-rich linker-containing variants form globular assemblies under these conditions (<b>H</b>).
DOI: 10.6084/m9.figshare.7956104
title: Supplementary Figure 35, 36, and 37 Enzymatic activity of the three-component atrazine-degradation assembly and comparison of fractal vs globular assembly

description: Supp Figure 35: (A) Atrazine degradation pathway, enzymatic conversion of atrazine to cyanuric acid, and further enzymatic conversion to NH3 and CO2. (B) AtzB was added as an SH2-domain fusion to the two-component (AtzA-AtzC) assembly. c and d, Three-component assembly formation was validated using HIM (C), and the incorporation of AtzB was confirmed with fluorescence microscopy (using an Alexa-658-labeled AtzB) (D). (E) and (F), Assemblies were found to be more thermotolerant, as detected by incubation at a given temperature for 30 min followed by activity assays, and more robust to mechanical shearing forces, as detected by ability to withstand shaking. (G), <b>Assemblies and free enzymes were incorporated into a Basotect® polymer foam with different TEOS % layers, to trap proteins, and assayed for cyanuric acid production. </b>Proteins can be lost during the wash step after crosslinking and the % of protein lost under each condition is indicated on top of the bars. Supp Figure 36: <b>Phase contrast micrographs of the Basotect® polymer foam with and without assemblies for the AtzAM1, AtzBSH2, and AtzCM1 components. </b>(A and B) The microporous polymer foam with no assemblies. (C and D) The assemblies have been immobilized into the polymer foam, red arrows depict locations with assemblies. Images were taken with a Leica DM4000 B LED microscope, 10X objective (100X total magnification). Supp Figure 37: <b>The fractal-like assemblies (Reg-Assembly) and the extended linker globular assemblies (ExtLinker-Assembly) enzymatic conversion of atrazine to cyanuric acid demonstrates no enzymatic benefit of a globular assembly. </b>(A) AtzB was incorporated into the two-component assembly as an SH2-domain fusion as previously described to create the three-component assembly for both the fractal and globular assemblies. The activity of the fractal assembly was similar than the extended linker assemblies (GS linker) under different shaking speeds. Note: All enzymatic data from excel is then taken into graph pad for analyses, converted to Relative Yield %, addition of error bars, exported in vector format, and edited in Illustrator for final figure.<br>