cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13357544
title: Additional file 7 of Longitudinal data in peripheral blood confirm that PM20D1 is a quantitative trait locus (QTL) for Alzheimer’s disease and implicate its dynamic role in disease progression

description: Additional file 7. Table S7: P values and regression coefficients for the correlation between DNA methylation in blood with four brain regions (prefrontal cortex, entorhinal cortex, superior temporal gyrus and cerebellum) from 71 to 75 matched samples for all the 8 CpG probes. The data are taken from the Blood Brain DNA Methylation Comparison Tool [17].
DOI: 10.6084/m9.figshare.13357547.v1
title: Additional file 8 of Longitudinal data in peripheral blood confirm that PM20D1 is a quantitative trait locus (QTL) for Alzheimer’s disease and implicate its dynamic role in disease progression

description: Additional file 8. Table S8: Mean β values and their standard deviations (SD) at baseline measurements for the sex and age matched samples at the 10 CpG probes stratified by the allelic dose of rs708727. Control and MCI samples were obtained by matching AD samples’ sex and age using ‘matchControls’ command in the R package ‘e1071.’
DOI: 10.6084/m9.figshare.13357532.v1
title: Additional file 3 of Longitudinal data in peripheral blood confirm that PM20D1 is a quantitative trait locus (QTL) for Alzheimer’s disease and implicate its dynamic role in disease progression

description: Additional file 3. Table S3: P values and significant slopes for the regression lines modeled by linear mixed effect modeling between age or p-tau181 and β values for the 10 CpG probes at PM20D1 promoter region in the different diagnosis groups.
DOI: 10.6084/m9.figshare.13357535
title: Additional file 4 of Longitudinal data in peripheral blood confirm that PM20D1 is a quantitative trait locus (QTL) for Alzheimer’s disease and implicate its dynamic role in disease progression

description: Additional file 4. Table S4: P values for the regression lines between the β values of the 10 CpG probes and the gene expression of PM20D1.
DOI: 10.6084/m9.figshare.13357535.v1
title: Additional file 4 of Longitudinal data in peripheral blood confirm that PM20D1 is a quantitative trait locus (QTL) for Alzheimer’s disease and implicate its dynamic role in disease progression

description: Additional file 4. Table S4: P values for the regression lines between the β values of the 10 CpG probes and the gene expression of PM20D1.
DOI: 10.6084/m9.figshare.13357541.v1
title: Additional file 6 of Longitudinal data in peripheral blood confirm that PM20D1 is a quantitative trait locus (QTL) for Alzheimer’s disease and implicate its dynamic role in disease progression

description: Additional file 6. Table S6: P values for the regression lines between the β values of the 8 CpG probes and the gene expression of PM20D1 from the ROSMAP cohort brain samples.
DOI: 10.5281/zenodo.10654706
title: (AD-POLARIS) Polarization Imaging through Turbid Media

description: This open-access dataset provides polarized images captured through turbid media with annotations of human and mannequin bounding boxes. The dataset allows researchers to develop and evaluate vision algorithms in challenging scenarios where traditional RGB vision is ineffective. The inclusion of both humans and mannequins provides opportunities for differentiating real people from objects mimicking human shapes, crucial for applications like security and search and rescue. The dataset also includes YOLO-like bounding boxes for both people and mannequins.
DOI: 10.5281/zenodo.10654707
title: (AD-POLARIS) Polarization Imaging through Turbid Media

description: This open-access dataset provides polarized images captured through turbid media with annotations of human and mannequin bounding boxes. The dataset allows researchers to develop and evaluate vision algorithms in challenging scenarios where traditional RGB vision is ineffective. The inclusion of both humans and mannequins provides opportunities for differentiating real people from objects mimicking human shapes, crucial for applications like security and search and rescue. The dataset also includes YOLO-like bounding boxes for both people and mannequins.
DOI: 10.6084/m9.figshare.13357544.v1
title: Additional file 7 of Longitudinal data in peripheral blood confirm that PM20D1 is a quantitative trait locus (QTL) for Alzheimer’s disease and implicate its dynamic role in disease progression

description: Additional file 7. Table S7: P values and regression coefficients for the correlation between DNA methylation in blood with four brain regions (prefrontal cortex, entorhinal cortex, superior temporal gyrus and cerebellum) from 71 to 75 matched samples for all the 8 CpG probes. The data are taken from the Blood Brain DNA Methylation Comparison Tool [17].
DOI: 10.6084/m9.figshare.13357526
title: Additional file 1 of Longitudinal data in peripheral blood confirm that PM20D1 is a quantitative trait locus (QTL) for Alzheimer’s disease and implicate its dynamic role in disease progression

description: Additional file 1. Table S1: The differentially methylated regions (DMRs) as detected by the comparisons among control, MCI and AD. Each tab shows the significant regions as ranked by the p values for each comparison.
DOI: 10.6084/m9.figshare.9163508
title: Heterogeneous mantle melting and magmatic processes at the East Pacific Rise (2.6–3.1°S): Evidence from mid-ocean ridge basalt geochemistry and Sr–Nd–Pb isotopes

description: We present the major and trace elements and Sr, Nd, and Pb isotopes in mid-ocean ridge basalts (MORB) from the East Pacific Rise (EPR) at 2.6–3.1°S. These samples are low-K tholeiites and show significant variation in their major element compositions (e.g. 4.60–8.18 wt% MgO, 8.34–12.12 wt% CaO, 9.78–14.25 wt% Fe<sub>2</sub>O<sub>3</sub>, and 0.06–0.34 K<sub>2</sub>O wt%). Trace element abundances of the 2.6–3.1°S MORB are variably depleted (e.g. (La/Sm), <sub>N</sub> = 0.51–0.78, Zr/Y = 2.35–3.42, Th/La = 0.035–0.056, and Ce/Yb = 2.38–3.96) but closely resemble the average N-MORB. In the compatible elements (Ni and Cr) against incompatible element Zr plots, the 2.6–3.1°S MORB show well-defined negative correlations, together with a liquid line of descent (LLD) modelling and petrographic observations, implying a significant role of olivine, plagioclase and clinopyroxene fractionation during magma evolution. When compared to global MORB and peridotites, the 2.6–3.1°S MORB and most of the other axial lavas from the South EPR show similar Zn/Fe, Zn/Mn, and Fe/Mn ratios, attesting to a peridotite-dominated mantle lithology. However, the relationships between incompatible trace element ratios, such as Zr/Rb and Nb/Sm, and the negative correlation between Zr/Nb and <sup>87</sup>Sr/<sup>86</sup>Sr indicate a geochemically heterogeneous mantle source. The mantle beneath the South EPR likely consists of two components, with the enriched component residing as physically distinct domains (e.g. veins or dikes) in the depleted peridotite matrix. In the Sr–Nd–Pb isotope space, the South EPR MORB lie along the mixing lines between the depleted MORB mantle (DMM) and the ‘C’-like Pukapuka endmember. We infer that low-F melts derived from these enriched materials may cause localized mantle heterogeneity (veins or dikes) via an infiltration process. Subsequent melting of the refertilized mantle may impart an isotopically distinct characteristic to South EPR MORB.
DOI: 10.23641/asha.24970302
title: Loud speech in children with cerebral palsy (Nip, 2024)

description: <b>Purpose:</b> Speech motor control changes underlying louder speech are poorly understood in children with cerebral palsy (CP). The current study evaluates changes in the oral articulatory and laryngeal subsystems in children with CP and their typically developing (TD) peers during louder speech.<b>Method:</b> Nine children with CP and nine age- and sex-matched TD peers produced sentence repetitions in two conditions: (a) with their habitual rate and loudness and (b) with louder speech. Lip and jaw movements were recorded with optical motion capture. Acoustic recordings were obtained to evaluate vocal fold articulation.<b>Results:</b> Children with CP had smaller jaw movements, larger lower lip movements, slower jaw speeds, faster lip speeds, reduced interarticulator coordination, reduced low-frequency spectral tilt, and lower cepstral peak prominences (CPP) in comparison to their TD peers. Both groups produced louder speech with larger lip and jaw movements, faster lip and jaw speeds, increased temporal coordination, reduced movement variability, reduced spectral tilt, and increased CPP.<b>Conclusions:</b> Children with CP differ from their TD peers in the speech motor control of both the oral articulatory and laryngeal subsystems. Both groups alter oral articulatory and vocal fold movements when cued to speak loudly, which may contribute to the increased intelligibility associated with louder speech.<b>Supplemental Material S1.</b> Individual means and standard deviations for each dependent variable during habitual and loud speaking tasks.Nip, I. S. B. (2024). Articulatory and vocal fold movement patterns during loud speech in children with cerebral palsy. <i>Journal of Speech, Language, and Hearing Research, 67</i>(2), 477–493. https://doi.org/10.1044/2023_JSLHR-23-00411
DOI: 10.23641/asha.24970302.v1
title: Loud speech in children with cerebral palsy (Nip, 2024)

description: <b>Purpose:</b> Speech motor control changes underlying louder speech are poorly understood in children with cerebral palsy (CP). The current study evaluates changes in the oral articulatory and laryngeal subsystems in children with CP and their typically developing (TD) peers during louder speech.<b>Method:</b> Nine children with CP and nine age- and sex-matched TD peers produced sentence repetitions in two conditions: (a) with their habitual rate and loudness and (b) with louder speech. Lip and jaw movements were recorded with optical motion capture. Acoustic recordings were obtained to evaluate vocal fold articulation.<b>Results:</b> Children with CP had smaller jaw movements, larger lower lip movements, slower jaw speeds, faster lip speeds, reduced interarticulator coordination, reduced low-frequency spectral tilt, and lower cepstral peak prominences (CPP) in comparison to their TD peers. Both groups produced louder speech with larger lip and jaw movements, faster lip and jaw speeds, increased temporal coordination, reduced movement variability, reduced spectral tilt, and increased CPP.<b>Conclusions:</b> Children with CP differ from their TD peers in the speech motor control of both the oral articulatory and laryngeal subsystems. Both groups alter oral articulatory and vocal fold movements when cued to speak loudly, which may contribute to the increased intelligibility associated with louder speech.<b>Supplemental Material S1.</b> Individual means and standard deviations for each dependent variable during habitual and loud speaking tasks.Nip, I. S. B. (2024). Articulatory and vocal fold movement patterns during loud speech in children with cerebral palsy. <i>Journal of Speech, Language, and Hearing Research, 67</i>(2), 477–493. https://doi.org/10.1044/2023_JSLHR-23-00411
DOI: 10.6084/m9.figshare.13357649
title: Additional file 2 of A quantitative proteomics analysis for small molecule Stemazole’s effect on human neural stem cells

description: Additional file 2: Table S1. Summary analysis results of differentially abundant proteins.
DOI: 10.6084/m9.figshare.13357652.v1
title: Additional file 3 of A quantitative proteomics analysis for small molecule Stemazole’s effect on human neural stem cells

description: Additional file 3: Table S2. Summary results of KEGG enrichment analysis.
DOI: 10.6084/m9.figshare.13357649.v1
title: Additional file 2 of A quantitative proteomics analysis for small molecule Stemazole’s effect on human neural stem cells

description: Additional file 2: Table S1. Summary analysis results of differentially abundant proteins.
DOI: 10.6084/m9.figshare.13357818.v1
title: Additional file 8 of Germline variation networks in the PI3K/AKT pathway corresponding to familial high-incidence lung cancer pedigrees

description: Additional file 8: Table S5. Shared germline mutations of probands.
DOI: 10.6084/m9.figshare.13357821
title: Additional file 9 of Germline variation networks in the PI3K/AKT pathway corresponding to familial high-incidence lung cancer pedigrees

description: Additional file 9: Table S6. Top 10 KEGG pathways of the non-synonymous mutated genes of the individuals.
DOI: 10.6084/m9.figshare.9163508.v1
title: Heterogeneous mantle melting and magmatic processes at the East Pacific Rise (2.6–3.1°S): Evidence from mid-ocean ridge basalt geochemistry and Sr–Nd–Pb isotopes

description: We present the major and trace elements and Sr, Nd, and Pb isotopes in mid-ocean ridge basalts (MORB) from the East Pacific Rise (EPR) at 2.6–3.1°S. These samples are low-K tholeiites and show significant variation in their major element compositions (e.g. 4.60–8.18 wt% MgO, 8.34–12.12 wt% CaO, 9.78–14.25 wt% Fe<sub>2</sub>O<sub>3</sub>, and 0.06–0.34 K<sub>2</sub>O wt%). Trace element abundances of the 2.6–3.1°S MORB are variably depleted (e.g. (La/Sm), <sub>N</sub> = 0.51–0.78, Zr/Y = 2.35–3.42, Th/La = 0.035–0.056, and Ce/Yb = 2.38–3.96) but closely resemble the average N-MORB. In the compatible elements (Ni and Cr) against incompatible element Zr plots, the 2.6–3.1°S MORB show well-defined negative correlations, together with a liquid line of descent (LLD) modelling and petrographic observations, implying a significant role of olivine, plagioclase and clinopyroxene fractionation during magma evolution. When compared to global MORB and peridotites, the 2.6–3.1°S MORB and most of the other axial lavas from the South EPR show similar Zn/Fe, Zn/Mn, and Fe/Mn ratios, attesting to a peridotite-dominated mantle lithology. However, the relationships between incompatible trace element ratios, such as Zr/Rb and Nb/Sm, and the negative correlation between Zr/Nb and <sup>87</sup>Sr/<sup>86</sup>Sr indicate a geochemically heterogeneous mantle source. The mantle beneath the South EPR likely consists of two components, with the enriched component residing as physically distinct domains (e.g. veins or dikes) in the depleted peridotite matrix. In the Sr–Nd–Pb isotope space, the South EPR MORB lie along the mixing lines between the depleted MORB mantle (DMM) and the ‘C’-like Pukapuka endmember. We infer that low-F melts derived from these enriched materials may cause localized mantle heterogeneity (veins or dikes) via an infiltration process. Subsequent melting of the refertilized mantle may impart an isotopically distinct characteristic to South EPR MORB.
DOI: 10.6084/m9.figshare.23305036
title: Additional file 8 of Mitochondrial folate pathway regulates myofibroblast differentiation and silica-induced pulmonary fibrosis

description: Additional file 8: Table S2. Proteins identified by quantitative mass spectrometry. Table S3 Mitochondrial inventory combining MitoCarta3.0 and MitoCoP. Table S4 Mitochondrial proteins identified by quantitative mass spectrometry. Table S5 Proteins involved in mitochondrial central dogma identified by quantitative mass spectrometry.
DOI: 10.34740/kaggle/dsv/7626529
title: On-Time Delivery
DOI: 10.23641/asha.25015979
title: Efficacy of amplification for tinnitus relief (Kam, 2024)

description: <b>Purpose:</b> The study aimed to evaluate the efficacy of amplification with hearing aids for people with chronic subjective tinnitus and mild hearing loss.<b>Method:</b> In this randomized, controlled, three-arm trial, 38 subjects with a primary complaint of tinnitus were randomly assigned to one of the three treatment groups. Twelve subjects received informational counselling (IC) only, 13 received IC with hearing aid fitting, and 13 subjects received IC with individualized music stimulation for 12 months. The primary efficacy analysis in tinnitus severity was based on the change from baseline to 12 months after the 1st day of the intervention. Secondary outcome measures included tinnitus impact, psychological and mental health effects, subjective ratings, and psychoacoustically measured tinnitus loudness.<b>Results:</b> A statistically significant treatment difference among the three groups in the Chinese Tinnitus Functional Index (TFI-CH) total score at the predefined end point in Month 12 was observed (<i>F</i> = 3.34, <i>p</i> = .04, partial η<sup>2</sup> = .16). Reductions in the TFI-CH scores in both the hearing aid and the customized music group were more prominent than in the IC-only group. Only the hearing aid group showed a significantly greater treatment effect than the IC-only group.<b>Conclusion:</b> Results from this study support that a combination of hearing aid use and IC can help improve tinnitus in people with mild hearing loss.<b>Supplemental Material S1. </b>Individual outcome results.Kam, A. C. S. (2024). Efficacy of amplification for tinnitus relief in people with mild hearing loss. <i>Journal of Speech, Language, and Hearing Research, 67</i>(2), 606–617. https://doi.org/10.1044/2023_JSLHR-23-00031
DOI: 10.6084/m9.figshare.13357815
title: Additional file 7 of Germline variation networks in the PI3K/AKT pathway corresponding to familial high-incidence lung cancer pedigrees

description: Additional file 7: Table S4. Somatic mutations of probands.
DOI: 10.6084/m9.figshare.13357818
title: Additional file 8 of Germline variation networks in the PI3K/AKT pathway corresponding to familial high-incidence lung cancer pedigrees

description: Additional file 8: Table S5. Shared germline mutations of probands.
DOI: 10.6084/m9.figshare.13357821.v1
title: Additional file 9 of Germline variation networks in the PI3K/AKT pathway corresponding to familial high-incidence lung cancer pedigrees

description: Additional file 9: Table S6. Top 10 KEGG pathways of the non-synonymous mutated genes of the individuals.
DOI: 10.6084/m9.figshare.23305073.v1
title: Additional file 3 of Single-cell and spatial transcriptomics reveal changes in cell heterogeneity during progression of human tendinopathy

description: Additional file 3: Table S2. Differentially expressed genes of each cluster.
DOI: 10.6084/m9.figshare.23305082.v1
title: Additional file 5 of Single-cell and spatial transcriptomics reveal changes in cell heterogeneity during progression of human tendinopathy

description: Additional file 5: Table S4. Enrichment analysis of differentially expressed genes in normal and disease tenocytes.
DOI: 10.6084/m9.figshare.23305079.v1
title: Additional file 4 of Single-cell and spatial transcriptomics reveal changes in cell heterogeneity during progression of human tendinopathy

description: Additional file 4: Table S3. Differentially expressed genes of different tenocyte subcluster.
DOI: 10.6084/m9.figshare.23305067
title: Additional file 1 of Single-cell and spatial transcriptomics reveal changes in cell heterogeneity during progression of human tendinopathy

description: Additional file 1: Table S1. Donor and sample information.
DOI: 10.6084/m9.figshare.7590857.v3
title: BET on Independence

description: We study the problem of nonparametric dependence detection. Many existing methods may suffer severe power loss due to nonuniform consistency, which we illustrate with a paradox. To avoid such power loss, we approach the nonparametric test of independence through the new framework of binary expansion statistics (BEStat) and binary expansion testing (BET), which examine dependence through a novel binary expansion filtration approximation of the copula. Through a Hadamard transform, we find that the symmetry statistics in the filtration are complete sufficient statistics for dependence. These statistics are also uncorrelated under the null. By using symmetry statistics, the BET avoids the problem of nonuniform consistency and improves upon a wide class of commonly used methods (a) by achieving the minimax rate in sample size requirement for reliable power and (b) by providing clear interpretations of global relationships upon rejection of independence. The binary expansion approach also connects the symmetry statistics with the current computing system to facilitate efficient bitwise implementation. We illustrate the BET with a study of the distribution of stars in the night sky and with an exploratory data analysis of the TCGA breast cancer data. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.7590866.v3
title: Cauchy Combination Test: A Powerful Test With Analytic <i>p</i>-Value Calculation Under Arbitrary Dependency Structures

description: <b><i>Abstract–</i>Combining individual <i>p</i>-values to aggregate multiple small effects has a long-standing interest in statistics, dating back to the classic Fisher’s combination test. In modern large-scale data analysis, correlation and sparsity are common features and efficient computation is a necessary requirement for dealing with massive data. To overcome these challenges, we propose a new test that takes advantage of the Cauchy distribution. Our test statistic has a simple form and is defined as a weighted sum of Cauchy transformation of individual <i>p</i>-values. We prove a nonasymptotic result that the tail of the null distribution of our proposed test statistic can be well approximated by a Cauchy distribution under arbitrary dependency structures. Based on this theoretical result, the <i>p</i>-value calculation of our proposed test is not only accurate, but also as simple as the classic <i>z</i>-test or <i>t</i>-test, making our test well suited for analyzing massive data. We further show that the power of the proposed test is asymptotically optimal in a strong sparsity setting. Extensive simulations demonstrate that the proposed test has both strong power against sparse alternatives and a good accuracy with respect to <i>p</i>-value calculations, especially for very small <i>p</i>-values. The proposed test has also been applied to a genome-wide association study of Crohn’s disease and compared with several existing tests. Supplementary materials for this article are available online.</b>
DOI: 10.6084/m9.figshare.13357815.v1
title: Additional file 7 of Germline variation networks in the PI3K/AKT pathway corresponding to familial high-incidence lung cancer pedigrees

description: Additional file 7: Table S4. Somatic mutations of probands.
DOI: 10.6084/m9.figshare.7590857.v4
title: BET on Independence

description: We study the problem of nonparametric dependence detection. Many existing methods may suffer severe power loss due to nonuniform consistency, which we illustrate with a paradox. To avoid such power loss, we approach the nonparametric test of independence through the new framework of binary expansion statistics (BEStat) and binary expansion testing (BET), which examine dependence through a novel binary expansion filtration approximation of the copula. Through a Hadamard transform, we find that the symmetry statistics in the filtration are complete sufficient statistics for dependence. These statistics are also uncorrelated under the null. By using symmetry statistics, the BET avoids the problem of nonuniform consistency and improves upon a wide class of commonly used methods (a) by achieving the minimax rate in sample size requirement for reliable power and (b) by providing clear interpretations of global relationships upon rejection of independence. The binary expansion approach also connects the symmetry statistics with the current computing system to facilitate efficient bitwise implementation. We illustrate the BET with a study of the distribution of stars in the night sky and with an exploratory data analysis of the TCGA breast cancer data. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.23305079
title: Additional file 4 of Single-cell and spatial transcriptomics reveal changes in cell heterogeneity during progression of human tendinopathy

description: Additional file 4: Table S3. Differentially expressed genes of different tenocyte subcluster.