cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23305805.v3
title: Supplementary Material for: Risk Factors of Progression to Cognitive Frailty: Singapore Longitudinal Ageing Study 2

description: Introduction: Cognitive frailty is associated with higher risk of dementia and adverse health outcomes. However, multidimensional factors that influence cognitive frailty transitions are not known. We aim to investigate risk factors of incident cognitive frailty.
Methods: Prospective cohort study participants were community-dwelling adults without dementia and other degenerative disorders and baseline and follow-up, including N=1054 participants aged ≥55 free of cognitive frailty at baseline, with complete baseline (March 6, 2009, to June 11, 2013) and follow-up data at 3–5 years later (January 16, 2013 to August 24, 2018). Incident cognitive frailty, defined by one or more criteria of the physical frailty phenotype and &lt;26 of Mini-Mental State Examination (MMSE) score. Potential risk factors assessed at baseline included demographic, socioeconomic, medical, psychological and social factors, and biochemical markers. Data were analysed using Least Absolute Shrinkage Selection Operator (LASSO) multivariable logistic regression models.
Results: A total of 51(4.8%) participants, including 21(3.5%) of the cognitively normal and physically robust participants, 20(4.7%) of the prefrail/frail only and 10(45.4%) of cognitively impaired only, transited to cognitive frailty at follow-up. Risk factors for transition to cognitive frailty were having eye problem (OR=2.6, 95%CI 1.24–5.43) and low HDL-cholesterol (OR=4.1, 95%CI 2.03–8.40), while protective factors for cognitive frailty transition were higher levels of education (OR=0.3, 95%CI 0.10–0.74) and participation in cognitive stimulating activities (OR=0.4, 95%CI 0.17–0.82).
Discussion/Conclusion: Multi-domain modifiable factors especially related to leisure activities predict cognitive frailty transition and may be targeted for prevention of dementia and associated adverse health outcomes.
DOI: 10.6084/m9.figshare.13698188
title: Additional file 3 of Genome-wide identification and functional analysis of the ERF2 gene family in response to disease resistance against Stemphylium lycopersici in tomato

description: Additional file 3: Table S2. Primers used in the text
DOI: 10.6084/m9.figshare.19111438
title: Two-Dimensional Functional Principal Component Analysis for Image Feature Extraction

description: Methodologies for functional principal component analysis are well established in the one-dimensional setting. However, for two-dimensional surfaces, for example, images, conducting functional principal component analysis is complicated and challenging, because the conventional eigendecomposition approach would require the estimation of a four-dimensional covariance function, which may incur high cost in terms of time and machine memory. To circumvent such computational difficulties, we propose a novel two-dimensional functional principal component analysis for extracting functional principal components and achieving dimensionality reduction for images. Different from the conventional eigendecomposition approach, our proposed method is based on the direct estimation of the optimal two-dimensional functional principal components via tensor product B-spline, which opens up a new avenue for estimating functional principal components. We present theoretical results that prove the consistency of the proposed approach. Our method is illustrated by analyzing brain images of subjects with the Alzheimer’s Disease and the handwritten digits images. The finite sample performance of our method is further assessed with some simulation studies. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.19111438.v1
title: Two-Dimensional Functional Principal Component Analysis for Image Feature Extraction

description: Methodologies for functional principal component analysis are well established in the one-dimensional setting. However, for two-dimensional surfaces, for example, images, conducting functional principal component analysis is complicated and challenging, because the conventional eigendecomposition approach would require the estimation of a four-dimensional covariance function, which may incur high cost in terms of time and machine memory. To circumvent such computational difficulties, we propose a novel two-dimensional functional principal component analysis for extracting functional principal components and achieving dimensionality reduction for images. Different from the conventional eigendecomposition approach, our proposed method is based on the direct estimation of the optimal two-dimensional functional principal components via tensor product B-spline, which opens up a new avenue for estimating functional principal components. We present theoretical results that prove the consistency of the proposed approach. Our method is illustrated by analyzing brain images of subjects with the Alzheimer’s Disease and the handwritten digits images. The finite sample performance of our method is further assessed with some simulation studies. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.7577453.v1
title: Splicing and gene expression signatures for splicing factors

description: DAS events and DEGs analyzed for RNA-Seq datasets with perturbed SFs.
DOI: 10.6084/m9.figshare.14393133.v1
title: Pediatric myeloid sarcoma: a single institution clinicopathologic and molecular analysis

description: Myeloid sarcoma (MS) is a neoplastic condition composed of immature myeloid cells involving an extramedullary site. We investigated underlying chromosomal and molecular alterations to assess potential molecular markers of prognosis and outcome in this rare pediatric disease. We conducted a retrospective review of clinicopathologic and cytogenetic data from 33 pediatric patients with MS (ages 1 month–18 years) at our institution over a 32 year period (1984–2016). Tissue-based cancer microarray and targeted next-generation sequencing analysis were performed on six cases. The median age at diagnosis was 2.8 years with a male-to-female ratio of 2.6:1. MS is commonly presented with concomitant marrow involvement (<i>n</i> = 12, 36.4%) or as a recurrence of acute myeloid leukemia (AML; <i>n</i> = 14, 42.4%). The skin (<i>n</i> = 18, 54.5%) and soft tissue (<i>n</i> = 9, 27.3%) were the most common sites of involvement. Twenty-one of 25 samples (84.0%) harbored chromosomal aberrations; <i>KMT2A</i> alterations (<i>n</i> = 10, 40.0%) or complex cytogenetics (<i>n</i> = 7, 28.0%) were most frequent. Mutations in RAS, tyrosine kinase, cell signaling, and chromatin remodeling genes were detected. When compared to pediatric patients with AML without extramedullary involvement (EMI), inferior overall survival (OS) was observed (18.8 months vs. 89.3 months, <i>p</i> = .008). Pediatric patients with MS with non-favorable cytogenetics [abnormalities other than t(8;21), inv(16)/t(16;16), or t(15;17)] had a significantly lower OS compared to patients with AML with non-favorable cytogenetics and no extramedullary involvement (8.0 months vs. 28.1 months, <i>p</i> &lt; .001). Pediatric MS is a rare disease with diverse clinical presentations. Non-favorable cytogenetics may be a poor prognostic marker for pediatric patients with MS and molecular diagnostics can assist with risk stratification and identify potentially actionable targets.
DOI: 10.6084/m9.figshare.13698188.v1
title: Additional file 3 of Genome-wide identification and functional analysis of the ERF2 gene family in response to disease resistance against Stemphylium lycopersici in tomato

description: Additional file 3: Table S2. Primers used in the text
DOI: 10.6084/m9.figshare.21732800
title: upload.7z

description: The dataset used to train the DLALNet.
DOI: 10.6084/m9.figshare.21732800.v1
title: upload.7z

description: The dataset used to train the DLALNet.
DOI: 10.6084/m9.figshare.23306110.v1
title: Genetic diversity and population genetic structure in <i>Kadsura coccinea</i> (Schisandraceae), an evergreen woody vine from Hunan, China

description: Kadsura coccinea is an evergreen woody vine species indigenous to Southeast Asia and south China with great promise in medicine, food, and ornamental gardening. Its natural resources have decreased dramatically due to irrational fruits and roots harvesting in two decades recently, which may result in heavy erosion of its genetic resources, especially in Hunan Province, China. Here 406 individuals of K. coccinea were collected from 11 natural populations in Hunan Province, and were analyzed for genetic variation using 17 polymorphic microsatellite markers. A total of 163 alleles were amplified with a mean of 9.588 alleles per locus. The mean effective number of alleles per locus, allele richness and the expected heterozygosity of these populations were 2.910, 4.171 and 0.558 on average, respectively, indicating a bit low level of genetic diversity. The among-population differentiation (F<sub>ST</sub>) accounted for 13.63% of the total genetic variation, and analysis of molecular variance also showed 13.38% of genetic variation existed among populations, representing a high genetic differentiation and a bit limited gene flow (N<sub>m</sub> = 1.813) among these populations. The results of Bayesian clustering analysis and neighbor-joining clustering analysis showed that populations GD and YZ were specific, and CB and HT were assigned into a cluster. The mantel test demonstrated that the genetic distances revealed by pairwise F<sub>ST</sub> between populations were remarkably correlated to geographic distances. It is the first report on genetic diversity of species in genus Kadsura using molecular markers, and the findings provide fundamental base for genetic resources conservation and breeding of this species.
DOI: 10.6084/m9.figshare.7577453
title: Splicing and gene expression signatures for splicing factors

description: DAS events and DEGs analyzed for RNA-Seq datasets with perturbed SFs.
DOI: 10.6084/m9.figshare.23306110
title: Genetic diversity and population genetic structure in <i>Kadsura coccinea</i> (Schisandraceae), an evergreen woody vine from Hunan, China

description: Kadsura coccinea is an evergreen woody vine species indigenous to Southeast Asia and south China with great promise in medicine, food, and ornamental gardening. Its natural resources have decreased dramatically due to irrational fruits and roots harvesting in two decades recently, which may result in heavy erosion of its genetic resources, especially in Hunan Province, China. Here 406 individuals of K. coccinea were collected from 11 natural populations in Hunan Province, and were analyzed for genetic variation using 17 polymorphic microsatellite markers. A total of 163 alleles were amplified with a mean of 9.588 alleles per locus. The mean effective number of alleles per locus, allele richness and the expected heterozygosity of these populations were 2.910, 4.171 and 0.558 on average, respectively, indicating a bit low level of genetic diversity. The among-population differentiation (F<sub>ST</sub>) accounted for 13.63% of the total genetic variation, and analysis of molecular variance also showed 13.38% of genetic variation existed among populations, representing a high genetic differentiation and a bit limited gene flow (N<sub>m</sub> = 1.813) among these populations. The results of Bayesian clustering analysis and neighbor-joining clustering analysis showed that populations GD and YZ were specific, and CB and HT were assigned into a cluster. The mantel test demonstrated that the genetic distances revealed by pairwise F<sub>ST</sub> between populations were remarkably correlated to geographic distances. It is the first report on genetic diversity of species in genus Kadsura using molecular markers, and the findings provide fundamental base for genetic resources conservation and breeding of this species.
DOI: 10.6084/m9.figshare.11405709
title: MOESM12 of Maternal milk and fecal microbes guide the spatiotemporal development of mucosa-associated microbiota and barrier function in the porcine neonatal gut

description: Additional file 12: Table S5. Relative expression of intestinal function-related genes using the whole statistical model.
DOI: 10.6084/m9.figshare.11405709.v1
title: MOESM12 of Maternal milk and fecal microbes guide the spatiotemporal development of mucosa-associated microbiota and barrier function in the porcine neonatal gut

description: Additional file 12: Table S5. Relative expression of intestinal function-related genes using the whole statistical model.
DOI: 10.6084/m9.figshare.7654346
title: Additional file 11: of Comparison of splenocyte microRNA expression profiles of pigs during acute and chronic toxoplasmosis

description: Table S8. DEMs induced by T. gondii at 50 DPI regulating the gene expression in BCR signaling pathway. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7654355.v1
title: Additional file 1: of Comparison of splenocyte microRNA expression profiles of pigs during acute and chronic toxoplasmosis

description: Table S1. Top 20 most abundant miRNAs of each sample. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7654361.v1
title: Additional file 2: of Comparison of splenocyte microRNA expression profiles of pigs during acute and chronic toxoplasmosis

description: Table S2. DEMs between SI-10 and SC-10 samples. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.17004479
title: Additional file 2 of Tube-dwelling in early animals exemplified by Cambrian scalidophoran worms

description: Additional file 2: Excel S1. Measurement of the complete tube of Selkirkia sinica and Selkirkia transita sp. nov.
DOI: 10.6084/m9.figshare.19101659
title: Additional file 7 of FIONA1 is an RNA N6-methyladenosine methyltransferase affecting Arabidopsis photomorphogenesis and flowering

description: Additional file 7: Table S5. Differentially expressed genes identified in fiona1-1 compared to WT by RNA-seq.
DOI: 10.5281/zenodo.1033803
title: Mt15434 Tph-1(Mg280)Ii | 2009-12-14T14:47:42+00:00

description: This experiment is part of the <em>C.elegans behavioural database</em>. For more information and the complete collection of experiments visit http://movement.openworm.org



<b>preview link</b> : https://www.youtube.com/watch?v=p7x6SQwC9AE
<b>strain</b> : MT15434
<b>timestamp</b> : 2009-12-14T14:47:42+00:00
<b>gene</b> : tph-1
<b>chromosome</b> : II
<b>allele</b> : mg280
<b>strain_description</b> : tph-1(mg280)II
<b>sex</b> : hermaphrodite
<b>stage</b> : adult
<b>ventral_side</b> : anticlockwise
<b>media</b> : NGM agar low peptone
<b>arena</b> :   
  <b>style</b> : petri
  <b>size</b> : 35
  <b>orientation</b> : away
  

<b>food</b> : OP50
<b>habituation</b> : 30m wait
<b>who</b> : Laura Grundy
<b>protocol</b> : Method in E. Yemini et al. doi:10.1038/nmeth.2560. Worm transferred to arena 30 minutes before recording starts.
<b>lab</b> :   
  <b>name</b> : William R Schafer
  <b>location</b> : MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK
  

<b>software</b> :   
  <b>name</b> : tierpsy (https://github.com/ver228/tierpsy-tracker)
  <b>version</b> : cbfc23eb4f1ac2f29be75ade7a937eed58a5b219
  <b>featureID</b> : @OMG
  

<b>base_name</b> : tph-1 superoutcrossed on food R_2009_12_14__14_47_42___2___10
<b>total time (s)</b> : 899.691
<b>frames per second</b> : 25.5754
<b>video micrometers per pixel</b> : 4.67931
<b>number of segmented skeletons</b> : 19460
DOI: 10.5281/zenodo.1013576
title: Cb755 Unc-43(E755)Iv | 2010-09-16T12:28:15+01:00

description: This experiment is part of the <em>C.elegans behavioural database</em>. For more information and the complete collection of experiments visit http://movement.openworm.org



<b>preview link</b> : https://www.youtube.com/watch?v=nhnEDj_J-Cs
<b>strain</b> : CB755
<b>timestamp</b> : 2010-09-16T12:28:15+01:00
<b>gene</b> : unc-43
<b>chromosome</b> : IV
<b>allele</b> : e755
<b>strain_description</b> : unc-43(e755)IV
<b>sex</b> : hermaphrodite
<b>stage</b> : adult
<b>ventral_side</b> : anticlockwise
<b>media</b> : NGM agar low peptone
<b>arena</b> :   
  <b>style</b> : petri
  <b>size</b> : 35
  <b>orientation</b> : away
  

<b>food</b> : OP50
<b>habituation</b> : 30m wait
<b>who</b> : Laura Grundy
<b>protocol</b> : Method in E. Yemini et al. doi:10.1038/nmeth.2560. Worm transferred to arena 30 minutes before recording starts.
<b>lab</b> :   
  <b>name</b> : William R Schafer
  <b>location</b> : MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK
  

<b>software</b> :   
  <b>name</b> : tierpsy (https://github.com/ver228/tierpsy-tracker)
  <b>version</b> : cbfc23eb4f1ac2f29be75ade7a937eed58a5b219
  <b>featureID</b> : @OMG
  

<b>base_name</b> : unc-43 (e755)IV on food R_2010_09_16__12_28_15___7___4
<b>total time (s)</b> : 899.0
<b>frames per second</b> : 30.03
<b>video micrometers per pixel</b> : 4.14723
<b>number of segmented skeletons</b> : 13568
DOI: 10.5281/zenodo.1013577
title: Cb755 Unc-43(E755)Iv | 2010-09-16T12:28:15+01:00

description: This experiment is part of the <em>C.elegans behavioural database</em>. For more information and the complete collection of experiments visit http://movement.openworm.org



<b>preview link</b> : https://www.youtube.com/watch?v=nhnEDj_J-Cs
<b>strain</b> : CB755
<b>timestamp</b> : 2010-09-16T12:28:15+01:00
<b>gene</b> : unc-43
<b>chromosome</b> : IV
<b>allele</b> : e755
<b>strain_description</b> : unc-43(e755)IV
<b>sex</b> : hermaphrodite
<b>stage</b> : adult
<b>ventral_side</b> : anticlockwise
<b>media</b> : NGM agar low peptone
<b>arena</b> :   
  <b>style</b> : petri
  <b>size</b> : 35
  <b>orientation</b> : away
  

<b>food</b> : OP50
<b>habituation</b> : 30m wait
<b>who</b> : Laura Grundy
<b>protocol</b> : Method in E. Yemini et al. doi:10.1038/nmeth.2560. Worm transferred to arena 30 minutes before recording starts.
<b>lab</b> :   
  <b>name</b> : William R Schafer
  <b>location</b> : MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK
  

<b>software</b> :   
  <b>name</b> : tierpsy (https://github.com/ver228/tierpsy-tracker)
  <b>version</b> : cbfc23eb4f1ac2f29be75ade7a937eed58a5b219
  <b>featureID</b> : @OMG
  

<b>base_name</b> : unc-43 (e755)IV on food R_2010_09_16__12_28_15___7___4
<b>total time (s)</b> : 899.0
<b>frames per second</b> : 30.03
<b>video micrometers per pixel</b> : 4.14723
<b>number of segmented skeletons</b> : 13568
DOI: 10.5281/zenodo.1014605
title: Cb120 Unc-4(E120)Ii | 2010-09-16T12:48:26+01:00

description: This experiment is part of the <em>C.elegans behavioural database</em>. For more information and the complete collection of experiments visit http://movement.openworm.org



<b>preview link</b> : https://www.youtube.com/watch?v=ciAriPvnfr8
<b>strain</b> : CB120
<b>timestamp</b> : 2010-09-16T12:48:26+01:00
<b>gene</b> : unc-4
<b>chromosome</b> : II
<b>allele</b> : e120
<b>strain_description</b> : unc-4(e120)II
<b>sex</b> : hermaphrodite
<b>stage</b> : adult
<b>ventral_side</b> : anticlockwise
<b>media</b> : NGM agar low peptone
<b>arena</b> :   
  <b>style</b> : petri
  <b>size</b> : 35
  <b>orientation</b> : away
  

<b>food</b> : OP50
<b>habituation</b> : 30m wait
<b>who</b> : Laura Grundy
<b>protocol</b> : Method in E. Yemini et al. doi:10.1038/nmeth.2560. Worm transferred to arena 30 minutes before recording starts.
<b>lab</b> :   
  <b>name</b> : William R Schafer
  <b>location</b> : MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK
  

<b>software</b> :   
  <b>name</b> : tierpsy (https://github.com/ver228/tierpsy-tracker)
  <b>version</b> : cbfc23eb4f1ac2f29be75ade7a937eed58a5b219
  <b>featureID</b> : @OMG
  

<b>base_name</b> : unc-4 (e120)III on food R_2010_09_16__12_48_26___7___5
<b>total time (s)</b> : 899.0
<b>frames per second</b> : 30.03
<b>video micrometers per pixel</b> : 4.14723
<b>number of segmented skeletons</b> : 26998
DOI: 10.5281/zenodo.1014606
title: Cb120 Unc-4(E120)Ii | 2010-09-16T12:48:26+01:00

description: This experiment is part of the <em>C.elegans behavioural database</em>. For more information and the complete collection of experiments visit http://movement.openworm.org



<b>preview link</b> : https://www.youtube.com/watch?v=ciAriPvnfr8
<b>strain</b> : CB120
<b>timestamp</b> : 2010-09-16T12:48:26+01:00
<b>gene</b> : unc-4
<b>chromosome</b> : II
<b>allele</b> : e120
<b>strain_description</b> : unc-4(e120)II
<b>sex</b> : hermaphrodite
<b>stage</b> : adult
<b>ventral_side</b> : anticlockwise
<b>media</b> : NGM agar low peptone
<b>arena</b> :   
  <b>style</b> : petri
  <b>size</b> : 35
  <b>orientation</b> : away
  

<b>food</b> : OP50
<b>habituation</b> : 30m wait
<b>who</b> : Laura Grundy
<b>protocol</b> : Method in E. Yemini et al. doi:10.1038/nmeth.2560. Worm transferred to arena 30 minutes before recording starts.
<b>lab</b> :   
  <b>name</b> : William R Schafer
  <b>location</b> : MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK
  

<b>software</b> :   
  <b>name</b> : tierpsy (https://github.com/ver228/tierpsy-tracker)
  <b>version</b> : cbfc23eb4f1ac2f29be75ade7a937eed58a5b219
  <b>featureID</b> : @OMG
  

<b>base_name</b> : unc-4 (e120)III on food R_2010_09_16__12_48_26___7___5
<b>total time (s)</b> : 899.0
<b>frames per second</b> : 30.03
<b>video micrometers per pixel</b> : 4.14723
<b>number of segmented skeletons</b> : 26998
DOI: 10.5281/zenodo.1019210
title: Cb1597 Unc-103(E1597)Iii | 2010-09-16T12:08:32+01:00

description: This experiment is part of the <em>C.elegans behavioural database</em>. For more information and the complete collection of experiments visit http://movement.openworm.org



<b>preview link</b> : https://www.youtube.com/watch?v=Vgqc5TbGGIY
<b>strain</b> : CB1597
<b>timestamp</b> : 2010-09-16T12:08:32+01:00
<b>gene</b> : unc-103
<b>chromosome</b> : III
<b>allele</b> : e1597
<b>strain_description</b> : unc-103(e1597)III
<b>sex</b> : hermaphrodite
<b>stage</b> : adult
<b>ventral_side</b> : clockwise
<b>media</b> : NGM agar low peptone
<b>arena</b> :   
  <b>style</b> : petri
  <b>size</b> : 35
  <b>orientation</b> : away
  

<b>food</b> : OP50
<b>habituation</b> : 30m wait
<b>who</b> : Laura Grundy
<b>protocol</b> : Method in E. Yemini et al. doi:10.1038/nmeth.2560. Worm transferred to arena 30 minutes before recording starts.
<b>lab</b> :   
  <b>name</b> : William R Schafer
  <b>location</b> : MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK
  

<b>software</b> :   
  <b>name</b> : tierpsy (https://github.com/ver228/tierpsy-tracker)
  <b>version</b> : cbfc23eb4f1ac2f29be75ade7a937eed58a5b219
  <b>featureID</b> : @OMG
  

<b>base_name</b> : unc-103 (e1597)II on food L_2010_09_16__12_08_32___7___3
<b>total time (s)</b> : 899.033
<b>frames per second</b> : 30.03
<b>video micrometers per pixel</b> : 4.14723
<b>number of segmented skeletons</b> : 26700