cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22609952.v1
title: Additional file 1 of Genomic features and its potential implication in bone oligometastatic NSCLC

description: Additional file 1: Table S1. Gene list of the 1021-gene panel.
DOI: 10.6084/m9.figshare.22609967.v1
title: Additional file 1 of Complete chloroplast genomes provide insights into evolution and phylogeny of Zingiber (Zingiberaceae)

description: Additional file 1: Fig. S1. Molecular phylogenetic tree based on 55 chloroplast genomes of Zingiberaceae. Species name in red color represent chloroplast genome obtained in this study. Table S1. List of RNA editing sites in fourteen Zingiber species by PREP program. Table S2. List of 14 species of Zingiber sequenced in this study.
DOI: 10.6084/m9.figshare.22610068
title: Additional file 2 of The study on interacting factors and functions of GASA6 in Jatropha curcas L.

description: Additional file 2.
DOI: 10.6084/m9.figshare.22610068.v1
title: Additional file 2 of The study on interacting factors and functions of GASA6 in Jatropha curcas L.

description: Additional file 2.
DOI: 10.5281/zenodo.10579340
title: DOM files, positive, raw, 2 of 2

description: DOM samples for Daniel, 20230807, pos mode, raw, 2 of 2
DOI: 10.5281/zenodo.10579341
title: DOM files, positive, raw, 2 of 2

description: DOM samples for Daniel, 20230807, pos mode, raw, 2 of 2
DOI: 10.6084/m9.figshare.22605695.v1
title: Additional file 5 of Integrated single-cell transcriptomics of cerebrospinal fluid cells in treatment-naïve multiple sclerosis

description: Additional file 5: Table S1. Subject demographics and technical information on scRNA-Seq. (Table 1.1) Composition of the three datasets, subject demographics of included multiple sclerosis (MS, n = 20) and control (IIH/HC = Ctrl, n = 11) patients, MRI features and CSF findings are listed. For dataset 3, non-included samples from Ramesh et al. [13] are listed (grayed out) and their exclusion criteria are shown. See methods for the primary source of the three datasets. Column legend: IIH = idiopathic intracranial hypertension, MS = multiple sclerosis, CIS = clinically isolated syndrome, f = female, m = male, rel_gd = relapse, lesions with gadolinium enhancement detected on magnetic resonance imaging (MRI), rel_nogd = relapse, no lesion with gadolinium enhancement on MRI, MS-typical MRI = MS-typical lesion pattern in characteristic locations (ovoid periventricular lesions/Dawson fingers, cortical or juxtacortical, infratentorial and spinal cord) (1) / no Ms-typical lesion pattern (0), active = active relapse, Gd +  = gadolinium detected (1) or not detected (0) in MRI lesion, months from onset = months from first symptoms until sample collection, cell = cell count/µL obtained via lumbar puncture, lympho = lymphocytes/µL of cerebrospinal fluid (CSF), granulo = granulocytes/µL of CSF, rbc = red blood cell count/µL CSF, protein = obtained protein concentration in mg/L CSF, lactate = CSF lactate in nmol/L, glucose = CSF glucose in mg/dL, OCB +  = any oligoclonal bands (OCB) detected in CSF (1) or not detectable (0). Barrier disruption = no barrier disruption (0) or present barrier disruption (1). CSF index = derived from the Reiber scheme [54] (IgG CSF/IgG serum index compared to the albumin CSF/albumin serum index), no barrier disruption (none), intrathecal immunoglobulin synthesis (Ig only), intrathecal immunoglobulin synthesis plus barrier disruption (barrier_and_Ig). IgG-index &gt; 0.7 = IgG synthesis in the CSF. All parameters were obtained within 24 h of CSF sampling. (Table 1.2) Technical information on scRNA-seq results of all patients (MS, n = 20) and healthy controls (Ctrl, n = 11) included in the study are listed. The sequencing technique for generation of the 10 × libraries is listed for the different datasets (10 × Genomics scRNA-seq kit version). Furthermore, the total number of measured cells after sequencing and genome alignment (total cells per sample) and the average number of detected genes per cells (average gene per cell) used for downstream analysis is depicted.
DOI: 10.6084/m9.figshare.22610090.v1
title: Additional file 2 of A survey of the full-length transcriptome of Gracilariopsis lemaneiformis using single-molecule long-read sequencing

description: Additional file 2: Table S1. Sequences of primers used for validation of splicing, alternative polyadenylation sites, predicted miRNAs and novel genes. Table S2. Fusion genes. Table S3. polyA summary. Table S4. miRNA analysis. Table S5. Novel genes annotated across seven databases. Table S6. Transcription factors present in novel genes. Table S7. The transcripts with DAS events of TFs in response to Cu and Cu + ACC in G.lemaneiformis. The number in each cell is the log2 fold change (log2FC). Table S8. The expression quantity and AS ratio of TFs in response to Cu and Cu + ACC in G.lemaneiformis.
DOI: 10.6084/m9.figshare.22610090
title: Additional file 2 of A survey of the full-length transcriptome of Gracilariopsis lemaneiformis using single-molecule long-read sequencing

description: Additional file 2: Table S1. Sequences of primers used for validation of splicing, alternative polyadenylation sites, predicted miRNAs and novel genes. Table S2. Fusion genes. Table S3. polyA summary. Table S4. miRNA analysis. Table S5. Novel genes annotated across seven databases. Table S6. Transcription factors present in novel genes. Table S7. The transcripts with DAS events of TFs in response to Cu and Cu + ACC in G.lemaneiformis. The number in each cell is the log2 fold change (log2FC). Table S8. The expression quantity and AS ratio of TFs in response to Cu and Cu + ACC in G.lemaneiformis.
DOI: 10.6084/m9.figshare.13172934.v1
title: Additional file 1 of Physiological and transcriptome changes induced by exogenous putrescine in anthurium under chilling stress

description: Additional file 1: Table S1. The primers of the target genes and the internal reference gene used for qRT-PCR. Table S2. Gene information of DEGs in anthurium seedlings treated with Put.
DOI: 10.6084/m9.figshare.22610194.v1
title: Additional file 7 of LINC00629 protects osteosarcoma cell from ER stress-induced apoptosis and facilitates tumour progression by elevating KLF4 stability

description: Additional file 7: Supplementary Table 1. The shRNAs used in the article.
DOI: 10.6084/m9.figshare.14745910.v1
title: Genome-wide comparison of the GRAS protein family in eight Rosaceae species and <i>GRAS</i> gene expression analysis in Chinese white pear (<i>Pyrus bretschneideri</i> Rehder)

description: The GRAS protein family encodes a family of plant-specific transcription factors that have diverse and significant functions in regulating plant development and anthocyanin biosynthesis. Our study represents the comprehensive identification and comparison of GRAS protein family genes in the Rosaceae. Here, 535 <i>GRAS</i> genes were screened from eight Rosaceae species. Phylogenetic analysis revealed that whole-genome duplication (WGD) events and dispersed duplication events were the major mechanisms promoting the expansion of the GRAS protein family in these Rosaceae species. Furthermore, selection pressure caused by different duplication events indicates that <i>GRAS</i> genes were mainly under purifying selection during the evolution process, suggesting that strong functional restriction affected the evolution of <i>GRAS</i> genes. Analysis of gene expression patterns and qRT-PCR assays showed that <i>GRAS</i> genes were widely participating in the development of pear and that expression could be tissue-specific. In particular, further analysis indicated that <i>Pbr010864.1</i> and <i>Pbr024549.1</i> might be two important candidate genes during anthocyanin biosynthesis in pear. Our study is the first to perform a comprehensive analysis of the <i>GRAS</i> genes in pear and other Rosaceae species. These results presented here provide profitable information for understanding the process of the <i>GRAS</i> genes evolution and the possible improvement of pear fruit quality.
DOI: 10.6084/m9.figshare.22610197
title: Additional file 8 of LINC00629 protects osteosarcoma cell from ER stress-induced apoptosis and facilitates tumour progression by elevating KLF4 stability

description: Additional file 8: Supplementary Table 2. The primers used in the article.
DOI: 10.5281/zenodo.10630679
title: Model-guided metabolic engineering of curcuminoid production in Pseudomonas putida

description: Supplementary data belonging to Chapter 2 of the PhD Thesis entiteled Model-Guided Strain Engineering: Bridges between Design and Learning in Bioprocess Development
DOI: 10.5281/zenodo.10630680
title: Model-guided metabolic engineering of curcuminoid production in Pseudomonas putida

description: Supplementary data belonging to Chapter 2 of the PhD Thesis entiteled Model-Guided Strain Engineering: Bridges between Design and Learning in Bioprocess Development
DOI: 10.6084/m9.figshare.22610200
title: Additional file 9 of LINC00629 protects osteosarcoma cell from ER stress-induced apoptosis and facilitates tumour progression by elevating KLF4 stability

description: Additional file 9: Supplementary Table 3. The altered LncRNAs under 3 μM TM treatment.
DOI: 10.6084/m9.figshare.13697326.v1
title: Preliminary evaluation of an automated robotic transfer assist device in the home setting

description: The purpose of this study was to examine the effects of six weeks of routine use of a novel robotic transfer device, the AgileLife Patient Transfer System, on mobility-related health outcomes, task demand, and satisfaction relative to previous transfer methods. Six end users and five caregivers used the system in their homes for six weeks. Participants completed several surveys examining perceived demands related to preparing and performing a transfer and mobility-related health outcomes pre and post intervention. Participants were also asked about their satisfaction with using the technology compared to previous transfer methods. Both end users and caregivers reported reduction in perceived physical demand (<i>p</i> = 0.007) and work (<i>p</i> ≤ 0.038) when preparing for and performing a transfer. End users indicated that the device intervention had a positive impact, indicating some improvements to health-related quality of life as well as improved competence, adaptability, and self-esteem post-intervention. All participants were highly likely to recommend the technology to others. The AgileLife Patient Transfer System is a promising new form of transfer technology that may improve the mobility and mobility-related health of individuals with disabilities and their caregivers in home settings.Implications for rehabilitationRobotic transfer assistance reduced physical demand and work among end users and caregivers.The robotic device had a positive impact on some quality of life outcomes after 6 weeks of use.Users were highly likely to recommend the robotic transfer device to others. Robotic transfer assistance reduced physical demand and work among end users and caregivers. The robotic device had a positive impact on some quality of life outcomes after 6 weeks of use. Users were highly likely to recommend the robotic transfer device to others.
DOI: 10.6084/m9.figshare.22610194
title: Additional file 7 of LINC00629 protects osteosarcoma cell from ER stress-induced apoptosis and facilitates tumour progression by elevating KLF4 stability

description: Additional file 7: Supplementary Table 1. The shRNAs used in the article.
DOI: 10.6084/m9.figshare.1466880
title: openSNP - BOSC15 Poster

description: The poster on openSNP for the 2015 Bioinformatics Open Source Conference (#BOSC15)
DOI: 10.6084/m9.figshare.1466884.v1
title: Intermittency as a transition state in combustor dynamics: An explanation for flame dynamics near lean blowout

description: The dynamic transitions preceding lean blowout were investigated experimentally in a laboratory scale turbulent combustor by systematically varying the flow Reynolds number . Previous studies on combustor dynamics have shown that the onset of large-amplitude, combustion-driven oscillations is, at times, presaged by intermittent bursts of high-amplitude periodic pressure pulsations that appear in a near random fashion amidst regions of aperiodic low-amplitude fluctuations, provided the underlying flow-field is turbulent. In the present study, we show that intermittent burst oscillations are also observed in combustors close to the lean blowout limit. We show that such intermittent oscillations emerge through the establishment of homoclinic orbits in the phase space of pressure oscillations. The formation of such orbits points to the complex nature of the interaction between the hydrodynamics and acoustic subsystems which operate over a range of different time scales. High-speed flame images reveal that the intermittent states observed prior to lean blowout correspond to aperiodic detachment of the flame from the bluff-body lip. These findings are consistent with other reports of possibly intermittent states in the literature.
DOI: 10.6084/m9.figshare.1466878
title: Data From: Multiple imputation for harmonizing longitudinal non-commensurate measures in individual participant data meta-analysis

description: There are many advantages to individual participant data meta-analysis for combining data from multiple studies. These advantages include greater power to detect effects, increased sample heterogeneity, and the ability to perform more sophisticated analyses than meta-analyses that rely on published results. However, a fundamental challenge is that it is unlikely that variables of interest are measured the same way in all of the studies to be combined. We propose that this situation can be viewed as a missing data problem in which some outcomes are entirely missing within some trials, and use multiple imputation to fill in missing measurements. We apply our method to 5 longitudinal adolescent depression trials where 4 studies used one depression measure and the fifth study used a different depression measure. None of the 5 studies contained both depression measures. We describe a multiple imputation approach for filling in missing depression measures that makes use of external calibration studies in which both depression measures were used. We discuss some practical issues in developing the imputation model including taking into account treatment group and study. We present diagnostics for checking the fit of the imputation model and investigating whether external information is appropriately incorporated into the imputed values.
DOI: 10.6084/m9.figshare.1466880.v3
title: openSNP - BOSC15 Poster

description: The poster on openSNP for the 2015 Bioinformatics Open Source Conference (#BOSC15)
DOI: 10.6084/m9.figshare.1466874
title: Transfer of egg white proteins with reference to lysozyme during the development of <i>Meleagris gallopavo</i> (Galliformes: Phasianidae) embryos

description: The egg white and egg yolk are the two main sources of nutrients for the developing avian embryo. The egg white should be transferred into the yolk in order to be consumed by the embryo. How the egg white ultimately reaches the egg yolk is largely unexplored in the turkey <i>Meleagris gallopavo</i>. Here, we explored the routes of egg white transfer in fertilized turkey eggs. Initially, we tested the electrophoretic pattern of the proteins in different egg compartments throughout development. Then, we used lysozyme as a reference protein to follow the egg white transfer, and we measured its activity using <i>Micrococcus lysodeikticus</i> as a substrate. We found that several presumptive egg white protein bands appeared in the different egg compartments. Also, the electrophoretic patterns in the intestinal fluid and thick yolk were marked by the disappearance of large bands and the appearance of small ones at late developmental stages. Moreover, we detected a chronological appearance of lysozyme activity in the different egg compartments. The activity appeared in the extraembryonic and amniotic fluids on day 15, in the intestinal fluid on day 16 and in the thick yolk on day 17, and it increased in general with the progress of development. Our results suggest that the main route of egg white transfer is albumen sac – extraembryonic cavity – amniotic cavity – intestinal lumen – egg yolk. Furthermore, the transferred egg white proteins seem to undergo digestion in the intestinal lumen and egg yolk at late developmental stages.
DOI: 10.6084/m9.figshare.1466878.v2
title: Data From: Multiple imputation for harmonizing longitudinal non-commensurate measures in individual participant data meta-analysis

description: There are many advantages to individual participant data meta-analysis for combining data from multiple studies. These advantages include greater power to detect effects, increased sample heterogeneity, and the ability to perform more sophisticated analyses than meta-analyses that rely on published results. However, a fundamental challenge is that it is unlikely that variables of interest are measured the same way in all of the studies to be combined. We propose that this situation can be viewed as a missing data problem in which some outcomes are entirely missing within some trials, and use multiple imputation to fill in missing measurements. We apply our method to 5 longitudinal adolescent depression trials where 4 studies used one depression measure and the fifth study used a different depression measure. None of the 5 studies contained both depression measures. We describe a multiple imputation approach for filling in missing depression measures that makes use of external calibration studies in which both depression measures were used. We discuss some practical issues in developing the imputation model including taking into account treatment group and study. We present diagnostics for checking the fit of the imputation model and investigating whether external information is appropriately incorporated into the imputed values.
DOI: 10.6084/m9.figshare.1466873
title: <i>Iris atrofusca</i> genetic and phenotypic variation, the role of habitat-specific selection in this variation structuring, and conservation implications using <i>quasi in situ</i> guidelines

description: Knowing the extent and structure of genetic variation in an endangered species is essential for establishing efficient conservation practices. However, the proper use of this information requires understanding the role of habitat-specific selection in genetic structuring. We present a study of population differentiation in an endangered species that utilizes guidelines of recently a proposed <i>quasi in situ</i> conservation approach, i.e. taking into account the scale and spatial pattern of local adaptation since if local adaptation is important, the introduced genotypes must be matched to the local biotic/abiotic conditions. Following this approach, we examined the extent and structure of genetic (AFLP) and phenotypic variation and tested for adaptive significance of this variation in critically endangered <i>Iris atrofusca</i> growing in Israel and Jordan. From these results we propose a sampling design that would (i) preserve species adaptive potential and (ii) insure environmental match of the plant material for relocation, reintroduction or enhancement.
DOI: 10.6084/m9.figshare.1466878.v1
title: Multiple imputation for harmonizing longitudinal non-commensurate measures in individual participant data meta-analysis

description: There are many advantages to individual participant data meta-analysis for combining data from multiple studies. These advantages include greater power to detect effects, increased sample heterogeneity, and the ability to perform more sophisticated analyses than meta-analyses that rely on published results. However, a fundamental challenge is that it is unlikely that variables of interest are measured the same way in all of the studies to be combined. We propose that this situation can be viewed as a missing data problem in which some outcomes are entirely missing within some trials, and use multiple imputation to fill in missing measurements. We apply our method to 5 longitudinal adolescent depression trials where 4 studies used one depression measure and the fifth study used a different depression measure. None of the 5 studies contained both depression measures. We describe a multiple imputation approach for filling in missing depression measures that makes use of external calibration studies in which both depression measures were used. We discuss some practical issues in developing the imputation model including taking into account treatment group and study. We present diagnostics for checking the fit of the imputation model and investigating whether external information is appropriately incorporated into the imputed values.
DOI: 10.6084/m9.figshare.1466872
title: Carabid beetle (Coleoptera: Carabidae) richness and functional traits in relation to differently managed grasslands in the Alps

description: SummarySpecies richness, composition, and functional traits of carabid beetle assemblages (Coleoptera: Carabidae) were studied in relation to different grassland management. Carabid beetles were sampled during the summers 2008 and 2009 by 165 traps located in 11 sites in the central-eastern Italian Alps. Using mixed effect models to account for potential spatial bias, we found that mown grasslands had significantly more species, a lower proportion of wingless species and a lower proportion of species with long larval development than grazed and natural grasslands. Within grazed and mown grasslands, neither cattle density nor number of cuts had any significant effect neither on species richness nor on any of the traits. The influence of grassland management can be summarised as follows: (1) grazing does not change community structure and functional traits compared to natural grasslands; (2) mowing negatively affects the carabid beetle assemblages; (3) the intensity of grazing and of cutting may not affect the structure of species assemblages of ground beetles. Our results support the hypothesis that agroecosystem practices in alpine grasslands influence carabid beetle communities. Specifically, the species with traits typical of undisturbed habitats (low dispersal abilities and long larval development) are more sensitive to perturbations (e.g. cutting). Our suggestion for agricultural and environmental planning and for conservation schemes is that the preservation of natural grasslands (e.g. forest gaps) and the implementation of grazing should be promoted during the planning of agroecosystem mosaics.
DOI: 10.6084/m9.figshare.1466873.v1
title: <i>Iris atrofusca</i> genetic and phenotypic variation, the role of habitat-specific selection in this variation structuring, and conservation implications using <i>quasi in situ</i> guidelines

description: Knowing the extent and structure of genetic variation in an endangered species is essential for establishing efficient conservation practices. However, the proper use of this information requires understanding the role of habitat-specific selection in genetic structuring. We present a study of population differentiation in an endangered species that utilizes guidelines of recently a proposed <i>quasi in situ</i> conservation approach, i.e. taking into account the scale and spatial pattern of local adaptation since if local adaptation is important, the introduced genotypes must be matched to the local biotic/abiotic conditions. Following this approach, we examined the extent and structure of genetic (AFLP) and phenotypic variation and tested for adaptive significance of this variation in critically endangered <i>Iris atrofusca</i> growing in Israel and Jordan. From these results we propose a sampling design that would (i) preserve species adaptive potential and (ii) insure environmental match of the plant material for relocation, reintroduction or enhancement.
DOI: 10.6084/m9.figshare.1466880.v4
title: openSNP - BOSC15 Poster

description: The poster on openSNP for the 2015 Bioinformatics Open Source Conference (#BOSC15)