cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7910/dvn/v1rjpf/0mrpmf
title: cbb20160821_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4162470
title: Blood group and prognosis in NPC

description: This dataset was freely available to other researchers.
DOI: 10.6084/m9.figshare.4162578.v1
title: Supplementary Material for: Outcome Comparison of Allogeneic versus Autologous Stem Cell Transplantation in Transformed Low-Grade Lymphoid Malignancies: A Systematic Review and Pooled Analysis of Comparative Studies

description: <b><i>Background:</i></b> Some patients<b> </b>with low-grade lymphoid malignancies develop transformed disease, requiring stem cell transplantation (SCT). SCT outcomes in transformed low-grade lymphoid malignancies may differ from those of nontransformed disease or other aggressive non-Hodgkin lymphomas. We conducted a pooled analysis of the clinical outcomes of allogeneic versus high-dose therapy (HDT) with autologous SCT in adult patients with transformed low-grade lymphoid malignancies. <b><i>Methods:</i></b> A PubMed, EMBASE, and Cochrane search yielded 4 comparative studies reporting allogeneic versus HDT with autologous SCT outcomes in adults (age ≥18) with transformed low-grade lymphoid malignancies, including follicular, chronic/small lymphocytic, and marginal zone lymphoma. Risk ratio (RR) and 95% CI were calculated using random-effects models. <b><i>Results:</i></b> Rates for overall survival (OS) were 51.0 versus 69.5% (RR = 1.55, 95% CI 1.19-2.02, p = 0.001), rates of relapse were 37.3 versus 35.3% (RR = 1.04, 95% CI 0.70-1.55, p = 0.84), and rates of transplant-related mortality (TRM) were 33.3 versus 7.2% (RR = 4.52, 95% CI 2.75-7.43, p &lt; 0.00001) for allogeneic versus autologous SCT. Previous rituximab treatment, reduced intensity conditioning regimen prior to SCT, or original pathology had no prognostic impact. <b><i>Conclusion:</i></b> HDT followed by autologous SCT was associated with lower TRM and a better OS, but there was no difference in relapse versus allogeneic SCT. Autologous SCT may be the better therapeutic option, considering the second chance of allogeneic SCT in the case of relapse.
DOI: 10.6084/m9.figshare.4162161
title: Supplementary Material for: Blood-Based Oxidative Stress Markers and Cognitive Performance in Early Old Age: The HAPIEE Study

description: <b><i>Background/Aims:</i></b> Oxidative stress is involved in Alzheimer disease pathology, but its impact on cognitive function in community-dwelling older adults remains unknown. We estimated associations between serum oxidative stress markers and cognitive function in early old age. <b><i>Methods:</i></b> Subjects aged 45-69 years recruited in urban centers in Central and Eastern Europe had memory, verbal fluency, and processing speed assessed at baseline (2002-2005) and 3 years later. Derivatives of reactive oxygen metabolites (d-ROMs), biological antioxidant potential (BAP), and total thiol levels (TTLs) were measured at baseline in a subsample. Linear regression was used to estimate associations of biomarkers with cognitive test scores cross-sectionally (<i>n</i> = 4,304) and prospectively (<i>n</i> = 2,882). <b><i>Results:</i></b> Increased d-ROM levels were inversely associated with global cognition and verbal fluency cross-sectionally and in prospective analysis; observed effects corresponded to 3-4 years' higher age. TTL was inconsistently associated with memory. BAP was not related to cognitive function. <b><i>Conclusion:</i></b> This study found modest evidence for a relationship between serum d-ROMs and cognitive function in a population sample of older adults.
DOI: 10.7910/dvn/v1rjpf/skkvta
title: cbb20160711_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4161822
title: The mRNA transportome of the BicD/Egl transport machinery

description: mRNA (mRNA) transport focuses the expression of encoded proteins to specific regions within cells providing them with the means to assume specific functions and even identities. BicD and the mRNA binding protein Egl interact with the microtubule motor dynein to localize mRNAs in <i>Drosophila</i>. Because relatively few mRNA cargos were known, we isolated and identified Egl::GFP associated mRNAs. The top candidates were validated by qPCR, <i>in situ</i> hybridization and genetically by showing that their localization requires <i>BicD</i>. In young embryos these Egl target mRNAs are preferentially localized apically, between the plasma membrane and the blastoderm nuclei, but also in the pole plasm at the posterior pole. Egl targets expressed in the ovary were mostly enriched in the oocyte and some were apically localized in follicle cells. The identification of a large group of novel mRNAs associated with BicD/Egl points to several novel developmental and physiological functions of this dynein dependent localization machinery. The verified dataset also allowed us to develop a tool that predicts conserved A'-form-like stem loops that serve as localization elements in 3′UTRs.
DOI: 10.6084/m9.figshare.4161849
title: Supplementary Material for: Encephalography Connectivity on Sources in Male Nonsmokers after Nicotine Administration during the Resting State

description: We present an encephalography (EEG) connectivity study where 30 healthy male nonsmokers were randomly allocated either to a nicotine group (14 subjects, 7 mg of transdermal nicotine) or to a placebo group. EEG activity was recorded in an eyes-open (EO) and eyes-closed (EC) condition before and after drug administration. This is a reanalysis of a previous dataset. Through a source reconstruction procedure, we extracted 13 time series representing 13 sources belonging to a resting-state network. Here, we conducted connectivity analysis (renormalized partial directed coherence; rPDC) on sources, focusing on the frequency range of 8.5-18.4 Hz, subdivided into 3 frequency bands (α<sub>1</sub>, α<sub>2</sub>, and β<sub>1</sub>) with the hypothesis that an increase in vigilance would modulate connectivity. Furthermore, a phase-amplitude coupling (mean resultant vector length; VL) analysis, was performed investigating whether an increase of vigilance would modulate phase-amplitude coupling. In the VL analysis we estimated the coupling of the phases of 3 low frequencies (α<sub>1</sub>, α<sub>2</sub>, and β<sub>1</sub>), respectively, with the amplitude of high-frequency oscillations (30-40 Hz, low γ). With rPDC we found that during the EC condition, nicotine decreased feedback connectivity (from the precentral gyrus to precuneus, angular gyrus, cuneus and superior occipital gyrus) at 10.5-12.4 Hz. The VL analysis showed nicotine-induced increases in coupling at 10.5-18.4 Hz in the precuneus, cuneus and superior occipital gyrus during the EC condition. During the EO condition, no significant results were found in connectivity or phase-amplitude coupling measures at any frequency range. In conclusion, the results suggest that nicotine potentially increases the level of vigilance in the EC condition.
DOI: 10.7910/dvn/v1rjpf/4x8dnx
title: cbb20160417_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4161822.v1
title: The mRNA transportome of the BicD/Egl transport machinery

description: mRNA (mRNA) transport focuses the expression of encoded proteins to specific regions within cells providing them with the means to assume specific functions and even identities. BicD and the mRNA binding protein Egl interact with the microtubule motor dynein to localize mRNAs in <i>Drosophila</i>. Because relatively few mRNA cargos were known, we isolated and identified Egl::GFP associated mRNAs. The top candidates were validated by qPCR, <i>in situ</i> hybridization and genetically by showing that their localization requires <i>BicD</i>. In young embryos these Egl target mRNAs are preferentially localized apically, between the plasma membrane and the blastoderm nuclei, but also in the pole plasm at the posterior pole. Egl targets expressed in the ovary were mostly enriched in the oocyte and some were apically localized in follicle cells. The identification of a large group of novel mRNAs associated with BicD/Egl points to several novel developmental and physiological functions of this dynein dependent localization machinery. The verified dataset also allowed us to develop a tool that predicts conserved A'-form-like stem loops that serve as localization elements in 3′UTRs.
DOI: 10.7910/dvn/v1rjpf/x3iren
title: cbb20160729_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4161462
title: Antlerogenic stem cells: molecular features and potential in rabbit bone regeneration

description: <b><i>Aim</i>:</b> (i) To assess the expression profiles of stem cell-associated markers including <i>Oct4, Sox2, Klf4, Nanog, C-myc, Stat3</i> and <i>Cd9</i>, (ii) analyze the nanotopography of the MIC-1 stem cells and (iii) evaluate the efficiency of live stem cell implants and stem cell culture derivatives on the regeneration of bone deficiencies in rabbit mandibles. <b><i>Materials and methods</i>:</b> The expression profiles of stem cell-associated genes, including <i>Oct4, Sox2, Klf4, Nanog, C-myc, Stat3</i> and <i>CD9</i> were assessed using reverse transcription polymerase chain reaction and flow cytometry. Nanotopography of the antlerogenic MIC-1 cell lineage was analyzed using atomic force microscopy. The effect of MIC-1 stem cells, their homogenate and supernatant on the regeneration of bone deficiencies in rabbit mandibles was evaluated using histological analysis. The effect of MIC-1 stem cells and stem cell-based derivatives on the immune responses of the animals was assessed by analyses of acute phase protein levels (haptoglobin and fibrinogen). <b><i>Results</i>:</b> We found that the MIC-1 cells isolated from the apical regions of growing antlers exhibited molecular features that were characteristics of pluripotent stem cells. Using atomic force microscopy, we determined the details of the cell surface morphologies with a particular emphasis on the patterns of formation of plasma extensions for interlinking adjacent cells. We also demonstrated that not only implanted stem cells but also cell homogenates and cell post-culture supernatants have potential in the regeneration of bone deficiencies in the rabbit mandible. <b><i>Conclusions</i>:</b> Our findings indicate that the use of both antlerogenic stem cell implants and the preparations derived from the cells offer alternative approaches to those based on autologous stem cells in the biological stimulation of osteogenesis and in bone regeneration.
DOI: 10.6084/m9.figshare.4161462.v1
title: Antlerogenic stem cells: molecular features and potential in rabbit bone regeneration

description: <b><i>Aim</i>:</b> (i) To assess the expression profiles of stem cell-associated markers including <i>Oct4, Sox2, Klf4, Nanog, C-myc, Stat3</i> and <i>Cd9</i>, (ii) analyze the nanotopography of the MIC-1 stem cells and (iii) evaluate the efficiency of live stem cell implants and stem cell culture derivatives on the regeneration of bone deficiencies in rabbit mandibles. <b><i>Materials and methods</i>:</b> The expression profiles of stem cell-associated genes, including <i>Oct4, Sox2, Klf4, Nanog, C-myc, Stat3</i> and <i>CD9</i> were assessed using reverse transcription polymerase chain reaction and flow cytometry. Nanotopography of the antlerogenic MIC-1 cell lineage was analyzed using atomic force microscopy. The effect of MIC-1 stem cells, their homogenate and supernatant on the regeneration of bone deficiencies in rabbit mandibles was evaluated using histological analysis. The effect of MIC-1 stem cells and stem cell-based derivatives on the immune responses of the animals was assessed by analyses of acute phase protein levels (haptoglobin and fibrinogen). <b><i>Results</i>:</b> We found that the MIC-1 cells isolated from the apical regions of growing antlers exhibited molecular features that were characteristics of pluripotent stem cells. Using atomic force microscopy, we determined the details of the cell surface morphologies with a particular emphasis on the patterns of formation of plasma extensions for interlinking adjacent cells. We also demonstrated that not only implanted stem cells but also cell homogenates and cell post-culture supernatants have potential in the regeneration of bone deficiencies in the rabbit mandible. <b><i>Conclusions</i>:</b> Our findings indicate that the use of both antlerogenic stem cell implants and the preparations derived from the cells offer alternative approaches to those based on autologous stem cells in the biological stimulation of osteogenesis and in bone regeneration.
DOI: 10.7910/dvn/v1rjpf/vxz4w7
title: cbb20160808_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/ogtyud
title: cbb20160512_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4159920
title: GSE59992_counts_table.txt.gz

description: Counts table of ATAC-seq peaks. Data is based on Lara-Astasio et al, Science, 2014 and was downloaded from NCBI GEO (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59992). Reads were mapped using bwa version 0.7.12-r1039. Duplicates were marked using bamUtil version 1.02. Peaks were called using MACS2 2.1.0.20140616 with default parameters. Peaks were merged to create a non-redundant peak set and centered at the summit of the highest peak. <br>
DOI: 10.7910/dvn/v1rjpf/gq9zjw
title: cbb20160403_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4159716
title: Compilation and appraisal of geochronological data from the North Atlantic Igneous Province (NAIP)

description: NAG-TEC Geochronological Database
DOI: 10.7910/dvn/v1rjpf/zb7bsq
title: cbb20160326_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/kbvqvu
title: cbb20160316_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4154271
title: Supplementary data from Goffin's cockatoos make the same tool type from different materials

description: This excel file contains raw data of the experiment
DOI: 10.7910/dvn/v1rjpf/deubr0
title: cbb20161014_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/cylv0b
title: cbb20161004_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4154262
title: Data set from Mood and personality interact to determine cognitive biases in pigs

description: Complete data set for the study
DOI: 10.7910/dvn/v1rjpf/rywic8
title: cbb20160208_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4154262.v1
title: Data set from Mood and personality interact to determine cognitive biases in pigs

description: Complete data set for the study
DOI: 10.7910/dvn/v1rjpf/kresri
title: cbb20160226_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4154253
title: Output from Mood and personality interact to determine cognitive biases in pigs

description: Full analysis output
DOI: 10.6084/m9.figshare.4154253.v1
title: Output from Mood and personality interact to determine cognitive biases in pigs

description: Full analysis output
DOI: 10.7910/dvn/v1rjpf/gpbs0e
title: cbb20160907_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4154244
title: R code from Mood and personality interact to determine cognitive biases in pigs

description: Complete R code for the analysis
DOI: 10.7910/dvn/v1rjpf/aeloni
title: cbb20161218_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/7fjfyi
title: cbb20160424_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/qmqvca
title: cbb20160306_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/hif1le
title: cbb20160801_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/he5hp6
title: cbb20160412_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/sap5cx
title: cbb20160219_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/cmeikm
title: cbb20160313_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4153497
title: ESM data from Cytoplasmic inheritance of parent-offspring cell structure in the clonal diatom <i>Cyclotella meneghiniana</i>

description: The data supporting our paper
DOI: 10.7910/dvn/v1rjpf/jej1fj
title: cbb20160920_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/gmpkxj
title: cbb20160919_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4150899
title: Changes in the bacterial community in the fermentation process of <i>kôso</i>, a Japanese sugar-vegetable fermented beverage

description: <i>Kôso</i> is a Japanese fermented beverage made with over 20 kinds of vegetables, mushrooms, and sugars. The changes in the bacterial population of <i>kôso</i> during fermentation at 25 °C over a period of 10 days were studied using 454 pyrosequencing of the 16S rRNA gene. The analysis detected 224 operational taxonomic units (OTUs) clustered from 8 DNA samples collected on days 0, 3, 7, and 10 from two fermentation batches. Proteobacteria were the dominant phylum in the starting community, but were replaced by Firmicutes within three days. Seventy-eight genera were identified from the 224 OTUs, in which <i>Bifidobacterium</i>, <i>Leuconostoc</i>, <i>Lactococcus</i>, and <i>Lactobacillus</i> dominated, accounting for over 96% of the total bacterial population after three days’ fermentation. UniFrac–Principal Coordinate Analysis of longitudinal fermented samples revealed dramatic changes in the bacterial community in <i>kôso</i>, resulting in significantly low diversity at the end of fermentation as compared with the complex starting community. Changes in the relative abundance of the 50 species in <i>kôso</i> communities during 10-day fermentation.
DOI: 10.6084/m9.figshare.4150899.v1
title: Changes in the bacterial community in the fermentation process of <i>kôso</i>, a Japanese sugar-vegetable fermented beverage

description: <i>Kôso</i> is a Japanese fermented beverage made with over 20 kinds of vegetables, mushrooms, and sugars. The changes in the bacterial population of <i>kôso</i> during fermentation at 25 °C over a period of 10 days were studied using 454 pyrosequencing of the 16S rRNA gene. The analysis detected 224 operational taxonomic units (OTUs) clustered from 8 DNA samples collected on days 0, 3, 7, and 10 from two fermentation batches. Proteobacteria were the dominant phylum in the starting community, but were replaced by Firmicutes within three days. Seventy-eight genera were identified from the 224 OTUs, in which <i>Bifidobacterium</i>, <i>Leuconostoc</i>, <i>Lactococcus</i>, and <i>Lactobacillus</i> dominated, accounting for over 96% of the total bacterial population after three days’ fermentation. UniFrac–Principal Coordinate Analysis of longitudinal fermented samples revealed dramatic changes in the bacterial community in <i>kôso</i>, resulting in significantly low diversity at the end of fermentation as compared with the complex starting community. Changes in the relative abundance of the 50 species in <i>kôso</i> communities during 10-day fermentation.
DOI: 10.7910/dvn/v1rjpf/mtwxvi
title: cbb20160320_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/7rvexs
title: cbb20161221_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4148307
title: PowerPoint Slides for: Cognitive Impairment in Advanced Chronic Kidney Disease: The Canadian Frailty Observation and Interventions Trial

description: <i>Background:</i> Chronic kidney disease (CKD) affects more than one third of older adults, and is a strong risk factor for vascular disease and cognitive impairment. Cognitive impairment can have detrimental effects on the quality of life through decreased treatment adherence and poor nutrition and results in increased costs of care and early mortality. Though widely studied in hemodialysis populations, little is known about cognitive impairment in patients with pre-dialysis CKD. <i>Methods:</i>Multicenter, cross-sectional, prospective cohort study including 385 patients with CKD stages G4-G5. Cognitive function was measured with a validated tool called the Montreal Cognitive Assessment (MoCA) as part of a comprehensive frailty assessment in the Canadian Frailty Observation and Interventions Trial. Cognitive impairment was defined as a MoCA score of ≤24. We determined the prevalence and risk factors for cognitive impairment in patients with CKD stages G4-G5, not on dialysis. <i>Results:</i> Two hundred and thirty seven participants (61%) with CKD stages G4-G5 had cognitive impairment at baseline assessment. When compared to a control group, this population scored lower in all domains of cognition, with the most pronounced deficits observed in recall, attention, and visual/executive function (p &lt; 0.01 for all comparisons). Older age, recent history of falls and history of stroke were independently associated with cognitive impairment. <i>Conclusions:</i> Our study uncovered a high rate of unrecognized cognitive impairment in an advanced CKD population. This impairment is global, affecting all aspects of cognition and is likely vascular in nature. The longitudinal trajectory of cognitive function and its effect on dialysis decision-making and outcomes deserves further study.
DOI: 10.7910/dvn/v1rjpf/kvemdl
title: cbb20161018_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4148307.v1
title: PowerPoint Slides for: Cognitive Impairment in Advanced Chronic Kidney Disease: The Canadian Frailty Observation and Interventions Trial

description: <i>Background:</i> Chronic kidney disease (CKD) affects more than one third of older adults, and is a strong risk factor for vascular disease and cognitive impairment. Cognitive impairment can have detrimental effects on the quality of life through decreased treatment adherence and poor nutrition and results in increased costs of care and early mortality. Though widely studied in hemodialysis populations, little is known about cognitive impairment in patients with pre-dialysis CKD. <i>Methods:</i>Multicenter, cross-sectional, prospective cohort study including 385 patients with CKD stages G4-G5. Cognitive function was measured with a validated tool called the Montreal Cognitive Assessment (MoCA) as part of a comprehensive frailty assessment in the Canadian Frailty Observation and Interventions Trial. Cognitive impairment was defined as a MoCA score of ≤24. We determined the prevalence and risk factors for cognitive impairment in patients with CKD stages G4-G5, not on dialysis. <i>Results:</i> Two hundred and thirty seven participants (61%) with CKD stages G4-G5 had cognitive impairment at baseline assessment. When compared to a control group, this population scored lower in all domains of cognition, with the most pronounced deficits observed in recall, attention, and visual/executive function (p &lt; 0.01 for all comparisons). Older age, recent history of falls and history of stroke were independently associated with cognitive impairment. <i>Conclusions:</i> Our study uncovered a high rate of unrecognized cognitive impairment in an advanced CKD population. This impairment is global, affecting all aspects of cognition and is likely vascular in nature. The longitudinal trajectory of cognitive function and its effect on dialysis decision-making and outcomes deserves further study.
DOI: 10.7910/dvn/v1rjpf/4w1kmx
title: cbb20160427_03.txt.gz

description: :unav