cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20335428.v1
title: Additional file 8 of The ferroptosis-related long non-coding RNAs signature predicts biochemical recurrence and immune cell infiltration in prostate cancer

description: Additional file 8: Supplemental Table 3. Univariate Cox analysis was conducted and 183 lncRNAs were verified to be associated with BCR.
DOI: 10.6084/m9.figshare.20335425.v1
title: Additional file 7 of The ferroptosis-related long non-coding RNAs signature predicts biochemical recurrence and immune cell infiltration in prostate cancer

description: Additional file 7: Supplemental Table 2. A total of 669 frlncRNAs were identified by Pearson’s correlation analysis in 495 prostate patients with absolute correlation coefficient &gt;0.30 and P &lt; 0.001.
DOI: 10.6084/m9.figshare.25103738
title: <b>Metadata for the article "</b><b>Interplay of biotic and abiotic factors shapes tree seedling growth and root-associated microbial communities"</b>

description: Root-associated microbial communities can alleviate plant abiotic stresses, thus potentially supporting adaptation to a changing climate during range expansion. While climate change is extending plant species fundamental niches northward, the distribution and colonization of mutualists (e.g., arbuscular mycorrhizal fungi) and pathogens may constrain plant growth and regeneration. Yet, the degree to which biotic and abiotic factors impact plant performance and associated microbial communities at the edge of their distribution remains unclear. In this study, we used a combination of root microscopy and amplicon sequencing to characterize tree root microbial communities (soil and root mycorrhizae, bacteria, and fungi) of sugar maple seedlings. We also explored the affect of abiotic and biotic factors on root microbial communities and their relationship with seedling growth along two elevation gradients in Quebec, Canada.<br>Metadata:comm_16S_2023: Bacteria ASV table with sequence counts per sample comm_ITS_2023: Fungi ASV table with sequence counts per sample comm_AMF_2023: Arbuscular mycorrhiza fungi (AMF) ASV table with sequence counts per sample taxa_16s_2023: Bacteria taxonomy taxa_ITS_2023: Fungi taxonomytaxa_AMF_2023: AMF taxonomy fungi_guild_meg: Table containing functional assignments for fungi described from one of the elevation gradientsfungi_guild_sut: Table containing functional assignments for fungi described from one of the elevation gradientsMetadata_clean_2023: Table containing information on the variables used in the modelling. Contains numerical data behind Figure 2 in the article, such as seedling annual growth (ann_growth) and elevation (alt).
DOI: 10.6084/m9.figshare.11423283
title: MOESM2 of PIRCh-seq: functional classification of non-coding RNAs associated with distinct histone modifications

description: Additional file 2 Table S1. Chromatin enriched ncRNAs in all mouse samples.
DOI: 10.6084/m9.figshare.11423283.v1
title: MOESM2 of PIRCh-seq: functional classification of non-coding RNAs associated with distinct histone modifications

description: Additional file 2 Table S1. Chromatin enriched ncRNAs in all mouse samples.
DOI: 10.6084/m9.figshare.11423292
title: MOESM3 of PIRCh-seq: functional classification of non-coding RNAs associated with distinct histone modifications

description: Additional file 3 Table S2. Allele specific chromatin enrichment in NPC.
DOI: 10.6084/m9.figshare.11423292.v1
title: MOESM3 of PIRCh-seq: functional classification of non-coding RNAs associated with distinct histone modifications

description: Additional file 3 Table S2. Allele specific chromatin enrichment in NPC.
DOI: 10.6084/m9.figshare.11423310
title: Additional file 1 of Computing and graphing probability values of pearson distributions: a SAS/IML macro

description: SAS/IML macro program. The SAS/IML macro program for computing and graphing probability values of Pearson distributions is available as an additional file, PearsonDistributionProbfinal.sas
DOI: 10.6084/m9.figshare.11423310.v1
title: Additional file 1 of Computing and graphing probability values of pearson distributions: a SAS/IML macro

description: SAS/IML macro program. The SAS/IML macro program for computing and graphing probability values of Pearson distributions is available as an additional file, PearsonDistributionProbfinal.sas
DOI: 10.6084/m9.figshare.11423319
title: Additional file 2 of Computing and graphing probability values of pearson distributions: a SAS/IML macro

description: Sample dataset 1. The dataset dataI.sas7bdat was taken from [1].
DOI: 10.6084/m9.figshare.11423325
title: Additional file 3 of Computing and graphing probability values of pearson distributions: a SAS/IML macro

description: Sample dataset 2. The dataset dataIV.sas7bdat was taken from [1].
DOI: 10.6084/m9.figshare.11423325.v1
title: Additional file 3 of Computing and graphing probability values of pearson distributions: a SAS/IML macro

description: Sample dataset 2. The dataset dataIV.sas7bdat was taken from [1].
DOI: 10.6084/m9.figshare.11423340
title: MOESM1 of Challenges in proteogenomics: a comparison of analysis methods with the case study of the DREAM proteogenomics sub-challenge

description: Additional file 1. Supplementary Figures
DOI: 10.6084/m9.figshare.11423340.v1
title: MOESM1 of Challenges in proteogenomics: a comparison of analysis methods with the case study of the DREAM proteogenomics sub-challenge

description: Additional file 1. Supplementary Figures
DOI: 10.6084/m9.figshare.19287851
title: Structure of the Kir7.1 channel inner pore revealed by disease mutant T153I

description: Supplemental data for paper "Structure of the Kir7.1 channel inner pore revealed by disease mutant T153I"
DOI: 10.5281/zenodo.10696953
title: WHOISWALKING dataset - walking data from accelerometer

description: Raw accelerometer data of 4 subjects, collected during a walk. Data were recorded on an iPhone 13 device, using Arduino Science Journal app. 

The data from the accelerometer includes the acceleration along the x-axis, y-axis, and z-axis. These axes capture the horizontal movement of the user (x-axis), forward/backward movement (y-axis), and upward/downward movement (z-axis).Each subject carried the phone in their right pant pocket during the walk.

This dataset was used for a university project whose aim was to identify subjects by their walk using machine learning methods.
DOI: 10.5281/zenodo.10696954
title: WHOISWALKING dataset - walking data from accelerometer

description: Raw accelerometer data of 4 subjects, collected during a walk. Data were recorded on an iPhone 13 device, using Arduino Science Journal app. 

The data from the accelerometer includes the acceleration along the x-axis, y-axis, and z-axis. These axes capture the horizontal movement of the user (x-axis), forward/backward movement (y-axis), and upward/downward movement (z-axis).Each subject carried the phone in their right pant pocket during the walk.

This dataset was used for a university project whose aim was to identify subjects by their walk using machine learning methods.
DOI: 10.6084/m9.figshare.20335358.v1
title: Additional file 2 of Expression and activation of nuclear hormone receptors result in neuronal differentiation and favorable prognosis in neuroblastoma

description: Additional file 2.
DOI: 10.6084/m9.figshare.20335355
title: Additional file 1 of Expression and activation of nuclear hormone receptors result in neuronal differentiation and favorable prognosis in neuroblastoma

description: Additional file 1.
DOI: 10.6084/m9.figshare.20335355.v1
title: Additional file 1 of Expression and activation of nuclear hormone receptors result in neuronal differentiation and favorable prognosis in neuroblastoma

description: Additional file 1.
DOI: 10.6084/m9.figshare.20335358
title: Additional file 2 of Expression and activation of nuclear hormone receptors result in neuronal differentiation and favorable prognosis in neuroblastoma

description: Additional file 2.
DOI: 10.6084/m9.figshare.21384362
title: Additional file 5 of Dynamic changes in community structure and degradation performance of a bacterial consortium MMBC-1 during the subculturing revival reveal the potential decomposers of lignocellulose

description: Additional file 5: Table S4. Pearson correlations between OTU abundances and degradation activities.
DOI: 10.6084/m9.figshare.21384353
title: Additional file 2 of Dynamic changes in community structure and degradation performance of a bacterial consortium MMBC-1 during the subculturing revival reveal the potential decomposers of lignocellulose

description: Additional file 2: Table S1. The classification and abundance of all the OTUs.
DOI: 10.6084/m9.figshare.20335388
title: Additional file 1 of Protective effect of melatonin on alleviating early oxidative stress induced by DOX in mice spermatogenesis and sperm quality maintaining

description: Table S1. Lists of primary antibodies.
DOI: 10.6084/m9.figshare.21384362.v1
title: Additional file 5 of Dynamic changes in community structure and degradation performance of a bacterial consortium MMBC-1 during the subculturing revival reveal the potential decomposers of lignocellulose

description: Additional file 5: Table S4. Pearson correlations between OTU abundances and degradation activities.
DOI: 10.6084/m9.figshare.16665922.v1
title: Standing crops and nutrient attributes of litchi (<i>Litchi chinensis</i>) floral nectar in response to the removal of inflorescences

description: Litchi inflorescences bear hundreds of small flowers, but most flowers need to be removed to reduce the consumption of carbohydrates and increase fruit setting. The production and secretion of nectar are largely affected by the availability and metabolism of carbohydrates. However, the secretion pattern and constituents of litchi nectar in response to the removal of inflorescences are unclear. Here, we showed that the litchi nectar secretion amount ranged from 4 to 10 mg per flower with the cultivar ‘Nuomici’ having the strongest secretion ability. The concentration of total soluble solids in litchi nectar was approximately 30%. Fructose was present in the highest concentration in nectar, followed by glucose and sucrose. Cultivar, flower sex and inflorescence-removal treatment had no significant main effect on soluble sugars but had two-way interaction effects on sucrose. Twenty-seven amino acids were detected, including seven essential amino acids. The concentration of amino acids was significantly affected by cultivar and flower sex, with nectar from the cultivar ‘Guiwei’ and male flowers having a significantly higher concentration. Removal of inflorescences did not show the main effect on the nectar amount, total soluble solids, or protein contents, but had interactive effects on the concentration of sucrose and amino acids.
DOI: 10.6084/m9.figshare.8277182.v2
title: Optimal Sparse Linear Prediction for Block-missing Multi-modality Data Without Imputation

description: In modern scientific research, data are often collected from multiple modalities. Since different modalities could provide complementary information, statistical prediction methods using multimodality data could deliver better prediction performance than using single modality data. However, one special challenge for using multimodality data is related to block-missing data. In practice, due to dropouts or the high cost of measures, the observations of a certain modality can be missing completely for some subjects. In this paper, we propose a new direct sparse regression procedure using covariance from multimodality data (DISCOM). Our proposed DISCOM method includes two steps to find the optimal linear prediction of a continuous response variable using block-missing multimodality predictors. In the first step, rather than deleting or imputing missing data, we make use of all available information to estimate the covariance matrix of the predictors and the cross-covariance vector between the predictors and the response variable. The proposed new estimate of the covariance matrix is a linear combination of the identity matrix, the estimates of the intra-modality covariance matrix and the cross-modality covariance matrix. Flexible estimates for both the sub-Gaussian and heavy-tailed cases are considered. In the second step, based on the estimated covariance matrix and the estimated cross-covariance vector, an extended Lasso-type estimator is used to deliver a sparse estimate of the coefficients in the optimal linear prediction. The number of samples that are effectively used by DISCOM is the minimum number of samples with available observations from two modalities, which can be much larger than the number of samples with complete observations from all modalities. The effectiveness of the proposed method is demonstrated by theoretical studies, simulated examples, and a real application from the Alzheimer’s Disease Neuroimaging Initiative. The comparison between DISCOM and some existing methods also indicates the advantages of our proposed method.
DOI: 10.6084/m9.figshare.20335388.v1
title: Additional file 1 of Protective effect of melatonin on alleviating early oxidative stress induced by DOX in mice spermatogenesis and sperm quality maintaining

description: Table S1. Lists of primary antibodies.
DOI: 10.6084/m9.figshare.21384398.v1
title: Additional file 2 of Identification of DNA methylation-regulated differentially expressed genes in RA by integrated analysis of DNA methylation and RNA-Seq data

description: Additional file 2: R code.
DOI: 10.6084/m9.figshare.19287335
title: LINC01234 regulates microRNA-27b-5p to induce the migration, invasion and self-renewal of ovarian cancer stem cells through targeting SIRT5

description: LINC01234 has been suggested to correlate with the survival of ovarian cancer (OS), but its role in the properties of OC stem cells (OCSCs) has been rarely described. We aim to investigate the effect of LINC01234 on the differentiation and self-renewal of OCSCs through adsorption of microRNA (miR)-27b-5p to target sirtuins 5 (SIRT5). Expression of LINC01234 and SIRT5 in OC and normal samples included in TCGA and GTEx was searched through the GEPIA2 database. Bioinformatics analysis was conducted to predict the relation of LINC01234, miR-27b-5p and SIRT5. Expression of LINC01234, miR-27b-5p and SIRT5 in OC tissues and cells was detected. OCSCs were cultured and identified. CD133<sup>+</sup> OCSCs were introduced with related oligonucleotides or vectors of LINC01234 or miR-27b-5p and SIRT5 to figure out their roles in OCSCs progression and tumorigenesis <i>in vivo</i>. The interaction of miR-27b-5p with LINC01234 or SIRT5 was analyzed. Bioinformatics analysis suggested that LINC01234 was very likely to influence SIRT5 and regulate the development of OC through miR-27b-5p. Up-regulated LINC01234 exhibited in OC tissues and cells. Down-regulated LINC01234 or elevated miR-27b-5p suppressed OCSCs progression and tumorigenesis <i>in vivo</i>. LINC01234 could restore SIRT5 expression by binding to miR-27b-5p. Down-regulated miR-27b-5p reversed the effect of silenced LINC01234 on OCSCs development and tumorigenesis <i>in vivo</i>. Up-regulation of SIRT5 reduced the effects of elevated miR-27b-5p on OCSCs progression and tumorigenesis <i>in vivo</i>. LINC01234 regulates miR-27b-5p to induce the migration, invasion and self-renewal of OCSCs through targeting SIRT5.
DOI: 10.15468/uj96mh
title: Avifaunal diversity study of Pakhibitan, Ecopark, 2023(April-June)

description: The Avifaunal diversity study of Pakhibitan Ecopark is published by Nature Mates Nature Club under WBHIDCO Pakhibitan Project in Pakhibitan, Ecopark, Newtown, Kolkata, West Bengal, India.
This sampling event was performed in a selected point located in the marshlands covered with elephant grass (Typha sp.) of Pakhibitan surrounded by a forest patch.In the summer (April-May), the maximum temperature of the area reaches around 41°C. During the winter (December-February), the temperature drops to 9°C while the average rainfall is 1836.5 mm per year. The soil type is alluvial because it is located in the Indo-Gangetic plain.
This dataset includes all the birds recorded in a span of three months. All the species are identified up to the species or genus level. A total of 99 species of birds are recorded belonging to 45 families and 16 order so far.
This dataset also includes the life stage, activity and behaviour of the birds observed.
DOI: 10.6084/m9.figshare.16665922
title: Standing crops and nutrient attributes of litchi (<i>Litchi chinensis</i>) floral nectar in response to the removal of inflorescences

description: Litchi inflorescences bear hundreds of small flowers, but most flowers need to be removed to reduce the consumption of carbohydrates and increase fruit setting. The production and secretion of nectar are largely affected by the availability and metabolism of carbohydrates. However, the secretion pattern and constituents of litchi nectar in response to the removal of inflorescences are unclear. Here, we showed that the litchi nectar secretion amount ranged from 4 to 10 mg per flower with the cultivar ‘Nuomici’ having the strongest secretion ability. The concentration of total soluble solids in litchi nectar was approximately 30%. Fructose was present in the highest concentration in nectar, followed by glucose and sucrose. Cultivar, flower sex and inflorescence-removal treatment had no significant main effect on soluble sugars but had two-way interaction effects on sucrose. Twenty-seven amino acids were detected, including seven essential amino acids. The concentration of amino acids was significantly affected by cultivar and flower sex, with nectar from the cultivar ‘Guiwei’ and male flowers having a significantly higher concentration. Removal of inflorescences did not show the main effect on the nectar amount, total soluble solids, or protein contents, but had interactive effects on the concentration of sucrose and amino acids.
DOI: 10.6084/m9.figshare.8277182.v1
title: Optimal Sparse Linear Prediction for Block-missing Multi-modality Data without Imputation

description: In modern scientific research, data are often collected from multiple modalities. Since different modalities could provide complementary information, statistical prediction methods using multi-modality data could deliver better prediction performance than using single modality data. However, one special challenge for using multi-modality data is related to block-missing data. In practice, due to dropouts or the high cost of measures, the observations of a certain modality can be missing completely for some subjects. In this paper, we propose a new DIrect Sparse regression procedure using COvariance from Multi-modality data (DISCOM). Our proposed DISCOM method includes two steps to find the optimal linear prediction of a continuous response variable using block-missing multi-modality predictors. In the first step, rather than deleting or imputing missing data, we make use of all available information to estimate the covariance matrix of the predictors and the cross-covariance vector between the predictors and the response variable. The proposed new estimate of the covariance matrix is a linear combination of the identity matrix, the estimates of the intra-modality covariance matrix and the cross-modality covariance matrix. Flexible estimates for both the sub-Gaussian and heavy-tailed cases are considered. In the second step, based on the estimated covariance matrix and the estimated cross-covariance vector, an extended Lasso-type estimator is used to deliver a sparse estimate of the coefficients in the optimal linear prediction. The number of samples that are effectively used by DISCOM is the minimum number of samples with available observations from two modalities, which can be much larger than the number of samples with complete observations from all modalities. The effectiveness of the proposed method is demonstrated by theoretical studies, simulated examples, and a real application from the Alzheimer’s Disease Neuroimaging Initiative. The comparison between DISCOM and some existing methods also indicates the advantages of our proposed method.
DOI: 10.6084/m9.figshare.21384398
title: Additional file 2 of Identification of DNA methylation-regulated differentially expressed genes in RA by integrated analysis of DNA methylation and RNA-Seq data

description: Additional file 2: R code.
DOI: 10.6084/m9.figshare.19287335.v1
title: LINC01234 regulates microRNA-27b-5p to induce the migration, invasion and self-renewal of ovarian cancer stem cells through targeting SIRT5

description: LINC01234 has been suggested to correlate with the survival of ovarian cancer (OS), but its role in the properties of OC stem cells (OCSCs) has been rarely described. We aim to investigate the effect of LINC01234 on the differentiation and self-renewal of OCSCs through adsorption of microRNA (miR)-27b-5p to target sirtuins 5 (SIRT5). Expression of LINC01234 and SIRT5 in OC and normal samples included in TCGA and GTEx was searched through the GEPIA2 database. Bioinformatics analysis was conducted to predict the relation of LINC01234, miR-27b-5p and SIRT5. Expression of LINC01234, miR-27b-5p and SIRT5 in OC tissues and cells was detected. OCSCs were cultured and identified. CD133<sup>+</sup> OCSCs were introduced with related oligonucleotides or vectors of LINC01234 or miR-27b-5p and SIRT5 to figure out their roles in OCSCs progression and tumorigenesis <i>in vivo</i>. The interaction of miR-27b-5p with LINC01234 or SIRT5 was analyzed. Bioinformatics analysis suggested that LINC01234 was very likely to influence SIRT5 and regulate the development of OC through miR-27b-5p. Up-regulated LINC01234 exhibited in OC tissues and cells. Down-regulated LINC01234 or elevated miR-27b-5p suppressed OCSCs progression and tumorigenesis <i>in vivo</i>. LINC01234 could restore SIRT5 expression by binding to miR-27b-5p. Down-regulated miR-27b-5p reversed the effect of silenced LINC01234 on OCSCs development and tumorigenesis <i>in vivo</i>. Up-regulation of SIRT5 reduced the effects of elevated miR-27b-5p on OCSCs progression and tumorigenesis <i>in vivo</i>. LINC01234 regulates miR-27b-5p to induce the migration, invasion and self-renewal of OCSCs through targeting SIRT5.
DOI: 10.6084/m9.figshare.20335425
title: Additional file 7 of The ferroptosis-related long non-coding RNAs signature predicts biochemical recurrence and immune cell infiltration in prostate cancer

description: Additional file 7: Supplemental Table 2. A total of 669 frlncRNAs were identified by Pearson’s correlation analysis in 495 prostate patients with absolute correlation coefficient &gt;0.30 and P &lt; 0.001.