cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12683822
title: Thesis (Dr. med.) - Exome sequencing in hereditary nephropathies - Supplementary Table

description: Supplementary Table for the thesis (Dr. med.) "Exome sequencing in hereditary nephropathies" by Korbinian Maria Riedhammer, Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany. <br><br>The aim of this thesis is to evaluate the application of ES in hereditary kidney disease in a cohort of 260 phenotypically well-ascertained index cases featuring children, adolescents, and adults. Each index case had either a phenotype in accordance with/the clinical tentative diagnosis of a specific hereditary nephropathy or had renal disease and fulfilled specific criteria such as positive family history or syndromic disease pointing towards a hereditary nephropathy. Furthermore, this thesis intends to delineate the utility of ES in uncovering phenocopies in hereditary nephropathies and prioritizing novel disease-associated genes and to improve clinical decision-making in patients with a presumed hereditary nephropathy.<br>The Supplementary Table features phenotypic and genotypic information on all 260 index cases included in this thesis with applied inclusion criteria and also information on all excluded cases of a larger ES cohort (called "NephroGen") of the Institute of Human Genetics Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.<br><br>
DOI: 10.6084/m9.figshare.12683822.v1
title: Thesis (Dr. med.) - Exome sequencing in hereditary nephropathies - Supplementary Table

description: Supplementary Table for the thesis (Dr. med.) "Exome sequencing in hereditary nephropathies" by Korbinian Maria Riedhammer, Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany. <br><br>The aim of this thesis is to evaluate the application of ES in hereditary kidney disease in a cohort of 260 phenotypically well-ascertained index cases featuring children, adolescents, and adults. Each index case had either a phenotype in accordance with/the clinical tentative diagnosis of a specific hereditary nephropathy or had renal disease and fulfilled specific criteria such as positive family history or syndromic disease pointing towards a hereditary nephropathy. Furthermore, this thesis intends to delineate the utility of ES in uncovering phenocopies in hereditary nephropathies and prioritizing novel disease-associated genes and to improve clinical decision-making in patients with a presumed hereditary nephropathy.<br>The Supplementary Table features phenotypic and genotypic information on all 260 index cases included in this thesis with applied inclusion criteria and also information on all excluded cases of a larger ES cohort (called "NephroGen") of the Institute of Human Genetics Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.<br><br>
DOI: 10.6084/m9.figshare.12683057
title: e_coli.10kb.n50000.sim.fasta.gz

description: 10,000 simulated error-free long reads, each of length 50,000 basepairs, based off a 100kb region of the E. coli genome.
DOI: 10.6084/m9.figshare.12683057.v1
title: e_coli.10kb.n50000.sim.fasta.gz

description: 10,000 simulated error-free long reads, each of length 50,000 basepairs, based off a 100kb region of the E. coli genome.
DOI: 10.23641/asha.12682874
title: Neural indices of nonword rhyme in stuttering (Hampton Wray & Spray, 2020)

description: <b>Purpose: </b>Phonological skills have been associated with developmental stuttering. The current study aimed to determine whether the neural processes underlying phonology, specifically for nonword rhyming, differentiated stuttering persistence and recovery.<b>Method:</b> Twenty-six children who stutter (CWS) and 18 children who do not stutter, aged 5 years, completed an auditory nonword rhyming task. Event-related brain potentials were elicited by prime, rhyming, and nonrhyming targets. CWS were followed longitudinally to determine eventual persistence (<i>n</i> = 14) or recovery (<i>n</i> = 12). This is a retrospective analysis of data acquired when all CWS presented as stuttering.<b>Results:</b> CWS who eventually recovered and children who do not stutter exhibited the expected rhyme effect, with larger event-related brain potential amplitudes elicited by nonrhyme targets compared to rhyme targets. In contrast, CWS who eventually persisted exhibited a reverse rhyme effect, with larger responses to rhyme than nonrhyme targets.<b>Conclusions:</b> These findings suggest that CWS who eventually persisted are not receiving the same benefit of phonological priming as CWS who eventually recovered for complex nonword rhyming tasks. These results indicate divergent patterns of phonological processing in young CWS who eventually persisted, especially for difficult tasks with limited semantic context, and suggest that the age of 5 years may be an important developmental period for phonology in CWS.<br><b>Supplemental Material S1.</b> List of rhyme word pairs. <br>Hampton Wray, A., & Spray, G. (2020). Neural processes underlying nonword rhyme differentiate eventual stuttering persistence and recovery. <i>Journal of Speech, Language, and Hearing Research.</i> Advance online publication. https://doi.org/10.1044/2020_JSLHR-19-00320
DOI: 10.6084/m9.figshare.12683321.v1
title: Whole-genome SNP markers reveal conservation status, signatures of selection and introgression in Chinese Laiwu pigs

description: Laiwu pigs are a Chinese indigenous breed that is renowned for its exceptionally high intramuscular fat content (average greater than 6%), providing an excellent genetic resource for the genetic improvement of meat quality of modern commercial pigs. To uncover genetic diversity, population structure, signature of selection and potential exotic introgression in this breed, we sampled 238 Laiwu pigs from a state-supported conservation population and genotyped these individuals using GeneSeek 80K SNP BeadChip. We then conducted in-depth population genetics analyses for the Laiwu pig in a context of 1116 pigs from 42 Eurasian diverse breeds. First, we show that the current Laiwu population has more abundant genetic diversity than the population of 18 years ago likely due to gene flow from European commercial breeds. Both neighbor-joining (NJ) and principal component analyses indicate the introgression of European haplotypes into Laiwu pigs. The admixture analysis reveals that an average 26.66% of Laiwu genetic components are of European origin. Then, we assigned the tested individuals to different families according to their clustering patterns in the NJ tree, and proposed a family-based conservation strategy to reduce the risk of inbreeding depression in Laiwu pigs. Next, we explored three statistics (ROH and iHS and EigenGWAS) to identify a list of candidate genes for fat deposition, reproduction and growth in Laiwu pigs. Last, we detected a strong signature of introgression from European pigs into Laiwu pigs at the <i>GPC6</i> locus that regulates the growth of developing long bones. Further association analyses indicate that the introgressed <i>GPC6</i> haplotype contributed to the improvement of growth performance in Laiwu pigs. Altogether, this study not only benefits the better conservation of the Laiwu pig, but also advances our knowledge of the poorly understood effect of human-mediated introgression on phenotypic traits in Chinese indigenous pigs.
DOI: 10.23641/asha.12682874.v1
title: Neural indices of nonword rhyme in stuttering (Hampton Wray & Spray, 2020)

description: <b>Purpose: </b>Phonological skills have been associated with developmental stuttering. The current study aimed to determine whether the neural processes underlying phonology, specifically for nonword rhyming, differentiated stuttering persistence and recovery.<b>Method:</b> Twenty-six children who stutter (CWS) and 18 children who do not stutter, aged 5 years, completed an auditory nonword rhyming task. Event-related brain potentials were elicited by prime, rhyming, and nonrhyming targets. CWS were followed longitudinally to determine eventual persistence (<i>n</i> = 14) or recovery (<i>n</i> = 12). This is a retrospective analysis of data acquired when all CWS presented as stuttering.<b>Results:</b> CWS who eventually recovered and children who do not stutter exhibited the expected rhyme effect, with larger event-related brain potential amplitudes elicited by nonrhyme targets compared to rhyme targets. In contrast, CWS who eventually persisted exhibited a reverse rhyme effect, with larger responses to rhyme than nonrhyme targets.<b>Conclusions:</b> These findings suggest that CWS who eventually persisted are not receiving the same benefit of phonological priming as CWS who eventually recovered for complex nonword rhyming tasks. These results indicate divergent patterns of phonological processing in young CWS who eventually persisted, especially for difficult tasks with limited semantic context, and suggest that the age of 5 years may be an important developmental period for phonology in CWS.<br><b>Supplemental Material S1.</b> List of rhyme word pairs. <br>Hampton Wray, A., & Spray, G. (2020). Neural processes underlying nonword rhyme differentiate eventual stuttering persistence and recovery. <i>Journal of Speech, Language, and Hearing Research.</i> Advance online publication. https://doi.org/10.1044/2020_JSLHR-19-00320
DOI: 10.6084/m9.figshare.12682331
title: Table S6. Analysis of Chinese domestic yak WGS data set DYY31 for B. taurus sequences

description: Using triallelic SNPs for determining parentage in North American yak (<i>Bos grunniens</i>) and estimating cattle (<i>B. taurus</i>) introgression<br>
DOI: 10.6084/m9.figshare.12682331.v1
title: Table S6. Analysis of Chinese domestic yak WGS data set DYY31 for B. taurus sequences

description: Using triallelic SNPs for determining parentage in North American yak (<i>Bos grunniens</i>) and estimating cattle (<i>B. taurus</i>) introgression<br>
DOI: 10.5281/zenodo.3999204
title: GPS 50 Hz data set for the case study. Part 2 (Version sbf)

description: GPS 50 Hz data set for the case study entitled "Comparison of TEC calculations based on Trimble, Javad, Leica and Septentrio GNSS receiver data". Part 2 (Septentrio dataset).
DOI: 10.6084/m9.figshare.12682253
title: fmcad20-material.zip

description: Supplementary material to the FMCAD'20 paper "SWITSS: Computing Small Witnessing Subsystems"<br>
DOI: 10.5281/zenodo.3996442
title: GPS 50 Hz data set for the case study entitled "Comparison of TEC calculations based on Trimble, Javad, Leica and Septentrio GNSS receiver data". Part 1

description: This dataset contains 50 Hz GPS data to explore JAVAD and Leica receivers quality to reconstruct slant TEC. GNSS receiver is to some extent a “black box” when its data is used for ionospheric studies. The results based on Javad, Septentrio, Trimble and Leica GNSS receivers (which is placed in this data set) proved that the accuracy of the slant Total Electron Content (TEC) calculation can differ significantly if data used for its calculation is from different GNSS receiver make/type. This is because TEC measurements depend on the carrier phase tracking technique applied in a receiver. Based on this data it was found that: 1) Correlation coefficient between carrier phase noises in L1 and L2 channel outputs may be considered as an indicator showing whether the L1-aided tracking technique or independent tracking is applied. 2) The empirical model of TEC noise component was provided to determine TEC noise value in GNSS receivers of different make/type.
DOI: 10.5281/zenodo.3999203
title: GPS 50 Hz data set for the case study. Part 2 (Version sbf)

description: GPS 50 Hz data set for the case study entitled "Comparison of TEC calculations based on Trimble, Javad, Leica and Septentrio GNSS receiver data". Part 2 (Septentrio dataset).
DOI: 10.6084/m9.figshare.12682220
title: replication_package.zip

description: Questionnaires, example models, result data, analysis scripts<br>
DOI: 10.5281/zenodo.3996441
title: GPS 50 Hz data set for the case study entitled "Comparison of TEC calculations based on Trimble, Javad, Leica and Septentrio GNSS receiver data". Part 1

description: This dataset contains 50 Hz GPS data to explore JAVAD and Leica receivers quality to reconstruct slant TEC. GNSS receiver is to some extent a “black box” when its data is used for ionospheric studies. The results based on Javad, Septentrio, Trimble and Leica GNSS receivers (which is placed in this data set) proved that the accuracy of the slant Total Electron Content (TEC) calculation can differ significantly if data used for its calculation is from different GNSS receiver make/type. This is because TEC measurements depend on the carrier phase tracking technique applied in a receiver. Based on this data it was found that: 1) Correlation coefficient between carrier phase noises in L1 and L2 channel outputs may be considered as an indicator showing whether the L1-aided tracking technique or independent tracking is applied. 2) The empirical model of TEC noise component was provided to determine TEC noise value in GNSS receivers of different make/type.
DOI: 10.6084/m9.figshare.12682220.v1
title: replication_package.zip

description: Questionnaires, example models, result data, analysis scripts<br>
DOI: 10.6084/m9.figshare.12682253.v2
title: fmcad20-material.zip

description: Supplementary material to the FMCAD'20 paper "SWITSS: Computing Small Witnessing Subsystems"<br>
DOI: 10.6084/m9.figshare.12682382.v1
title: Soil-microbes-mediated invasional meltdown in plants

description: This is the data, codes and reports of the paper 'Soil-microbes-mediated invasional meltdown in plants' by Zhijie Zhang, Yanjie Liu, Caroline Brunel and Mark van Kleunen, which was accepted in Nature Ecology and Evolution in 2020.<br>We experimentally tested whether and how a third plant species affected the competitive outcomes between alien and native plants through its soil legacy. We first conditioned soil with one of ten species (six natives and four aliens) or without plants. Then, we grew on these 11 soils, five aliens and five natives without competition, or with intra- or interspecific competition.<br>It is also deposited at GitHub (https://github.com/ecozhang/Invasional-meltdown).
DOI: 10.6084/m9.figshare.12682253.v1
title: fmcad20-material.zip

description: Supplementary material to the FMCAD'20 paper "SWITSS: Computing Small Witnessing Subsystems"<br>
DOI: 10.6084/m9.figshare.12682382.v2
title: Soil-microbes-mediated invasional meltdown in plants

description: This is the data, codes and reports of the paper 'Soil-microbes-mediated invasional meltdown in plants' by Zhijie Zhang, Yanjie Liu, Caroline Brunel and Mark van Kleunen, which was accepted in Nature Ecology and Evolution in 2020.<br>We experimentally tested whether and how a third plant species affected the competitive outcomes between alien and native plants through its soil legacy. We first conditioned soil with one of ten species (six natives and four aliens) or without plants. Then, we grew on these 11 soils, five aliens and five natives without competition, or with intra- or interspecific competition.<br>It is also deposited at GitHub (https://github.com/ecozhang/Invasional-meltdown).
DOI: 10.6084/m9.figshare.12682067
title: Fruit fly foraging data in optogenetic closed loop set-up

description: The Gr5a-Chr2 is a mat file structure array that stores X and Y position tracking and stimulation events. When loaded into the matlab workspace as FD file It has multiple fields. First is the P - probability conditions [0.05, 0.15, 0.3, 0.45, 0.6, 0.75, 1] that correspond to one sided stimulation for indexes from 1-7. indexes 8-9 correspond to two sided stimulaton with 0.05 and 0.15. index 10 corresponds to no stimulation periods.The P structure array stores multiple variables: like X and Y position, timestamps that animal spends in Trigger zone (InTZ) and into the Reset zone (InRZ), Returns, Trigger events and etc. Variable Arena has two cell arrays for each animal and each session that correspond to the events for the left and right side. The mat file GeneticControls has the same structure as Gr5a-ChR2 file and it stores probability stimulation data for genetic control lines. For LexAop-Chrimson/+ flies 0.05 and for Gr5a-LexA/+ 0.05, 0.3 and 0.6 probability stimulation data.
DOI: 10.6084/m9.figshare.12682073
title: Supplementary Material for: Comparative Acoustic Analyses of L2 English: The Search for Systematic Variation

description: <b><i>Background/Aims:</i></b> Previous research has shown that exposure to multiple foreign accents facilitates adaptation to an untrained novel accent. One explanation is that L2 speech varies systematically such that there are commonalities in the productions of nonnative speakers, regardless of their language background. <b><i>Methods:</i></b> A systematic acoustic comparison was conducted between 3 native English speakers and 6 nonnative accents. Voice onset time, unstressed vowel duration, and formant values of stressed and unstressed vowels were analyzed, comparing each nonnative accent to the native English talkers. A subsequent perception experiment tests what effect training on regionally accented voices has on the participant’s comprehension of nonnative accented speech to investigate the importance of within-speaker variation on attunement and generalization. <b><i>Results:</i></b> Data for each measure show substantial variability across speakers, reflecting phonetic transfer from individual L1s, as well as substantial inconsistency and variability in pronunciation, rather than commonalities in their productions. Training on native English varieties did not improve participants’ accuracy in understanding nonnative speech. <b><i>Conclusion:</i></b> These findings are more consistent with a hypothesis of accent attune­ment wherein listeners track general patterns of nonnative speech rather than relying on overlapping acoustic signals between speakers.
DOI: 10.6084/m9.figshare.12682058
title: Supplementary Material for: Effects of White Matter Hyperintensities on 90-Day Functional Outcome after Large Vessel and Non-Large Vessel Stroke

description: <b><i>Introduction:</i></b> White matter hyperintensity (WMH) burden is a critically important cerebrovascular phenotype related to the diagnosis and prognosis of acute ischemic stroke. The effect of WMH burden on functional outcome in large vessel occlusion (LVO) stroke has only been sparsely assessed, and direct LVO and non-LVO comparisons are currently lacking. <b><i>Material and Methods:</i></b> We reviewed acute ischemic stroke patients admitted between 2009 and 2017 at a large healthcare system in the USA. Patients with LVO were identified and clinical characteristics, including 90-day functional outcomes, were assessed. Clinical brain MRIs obtained at the time of the stroke underwent quantification of WMH using a fully automated algorithm. The pipeline incorporated automated brain extraction, intensity normalization, and WMH segmentation. <b><i>Results:</i></b> A total of 1,601 acute ischemic strokes with documented 90-day mRS were identified, including 353 (22%) with LVO. Among those strokes, WMH volume was available in 1,285 (80.3%) who had a brain MRI suitable for WMH quantification. Increasing WMH volume from 0 to 4 mL, age, female gender, a number of stroke risk factors, presence of LVO, and higher NIHSS at presentation all decreased the odds for a favorable outcome. Increasing WMH above 4 mL, however, was not associated with decreasing odds of favorable outcome. While WMH volume was associated with functional outcome in non-LVO stroke (<i>p</i> = 0.0009), this association between WMH and functional status was not statistically significant in the complete case multivariable model of LVO stroke (<i>p</i> = 0.0637). <b><i>Conclusion:</i></b> The burden of WMH has effects on 90-day functional outcome after LVO and non-LVO strokes. Particularly, increases from no measurable WMH to 4 mL of WMH correlate strongly with the outcome. Whether this relationship of increasing WMH to worse outcome is more pronounced in non-LVO than LVO strokes deserves additional investigation.
DOI: 10.6084/m9.figshare.12682046
title: Supplementary Material for: The Association of Low Hemoglobin Levels with IgA Nephropathy Progression: A Two-Center Cohort Study of 1,828 Cases

description: <b><i>Aim:</i></b> To investigate the relationship between hemoglobin levels and the progression of IgA nephropathy (IgAN). <b><i>Methods:</i></b> In a two-center cohort of 1,828 cases with biopsy-proven IgAN, we examined the association of hemoglobin levels with the primary outcome of a composite of all-cause mortality or kidney failure defined as a 40% decline in eGFR, or ESKD (defined as eGFR &lt;15 mL/min/1.73 m<sup>2</sup> or need for kidney replacement therapy including hemodialysis, peritoneal dialysis, or kidney transplantation), or the outcome of kidney failure, assessed using Cox and logistic regression models, respectively, with adjustment for confounders. <b><i>Results:</i></b> At baseline, mean age, eGFR, and hemoglobin levels were 33.75 ± 11.03 years, 99.70 ± 30.40 mL/min/1.73 m<sup>2</sup>, and 123.47 ± 18.36 g/L, respectively. During a median of approximately 7-year follow-up, 183 cases reached the composite outcome. After adjustment for demographic and IgAN-specific covariates and treatments, a lower quartile of hemoglobin was nonlinearly associated with an increased risk of the primary outcome or kidney failure in the Cox proportional hazards models (primary outcome: HR for quartile 3 vs. 4, 1.37; 95% CI, 0.83–2.25; HR for quartile 2 vs. 4, 1.18; 95% CI, 0.68–2.07; HR for quartile 1 vs. 4, 1.91; 95% CI, 1.15–3.17; kidney failure: HR for quartile 3 vs. 4, 1.39; 95% CI, 0.84–2.31; HR for quartile 2 vs. 4, 1.20; 95% CI, 0.68–2.11; HR for quartile 1 vs. 4, 1.83; 95% CI, 1.09–3.07) in the fully adjusted model. Then, hemoglobin levels were transformed to a binary variable for fitting the model according to the criteria for anemia of 110 g/L in the women and 120 g/L in men in China. The participants in the anemia group had an increased risk of developing outcomes compared with the nonanemia group in both genders (primary outcome: male: HR, 1.64; 95% CI, 1.01–2.68; female: HR, 1.68; 95% CI, 1.02–2.76; kidney failure: male: HR, 1.60; 95% CI, 0.97–2.64; female: HR, 1.58; 95% CI, 0.95–2.61) in the fully adjusted model. <b><i>Conclusions:</i></b> A low level of hemoglobin was nonlinearly associated with IgAN progression. The anemic IgAN patients presented a higher risk of developing poor outcomes compared with the nonanemic patients.