cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1266375.v1
title: Visualising gait symmetry/asymmetry from acceleration data

description: Accelerometry-based quantification of gait symmetry/asymmetry is a promising approach for objectively evaluating gait dysfunctions. An important step in the application of this method in clinical settings is to develop reliable gait asymmetry measures and tools for visualising them to create easy-to-understand presentations for both clinicians and patients. This paper describes a new self-adaptive algorithm for estimating motion trajectory from acceleration data and visualising the degree of its asymmetry in 3D space. Two new parameters are introduced to capture asymmetric walking patterns based on the assessment of 3D autocorrelation and biphasicity of the motion trajectory. The performance of our algorithm is confirmed by analysing gait data collected from 245 healthy subjects. The proposed method may be clinically useful in tracking the process of recovering from pathology or injury after rehabilitation.
DOI: 10.6084/m9.figshare.1266346
title: I-LM-1A-1HNMR-400MHzOzric_data

description: 1H NMR data acquired in CDCl3 of 1,3-bis(dec-9-en-1-yl)urea to allow reprocessing.
DOI: 10.6084/m9.figshare.1279394.v267
title: Germline encoded anti-A-reactive IgM arising from growth-dependent and aberrant O-GalNAc glycosylations*

description: The germline encoding of a mammalian immunoglobulin M (IgM) molecule was experimentally documented for the first time in C57BL/10 mice subjected to an ovariectomy prior to the onset of puberty. The target of this innate antibody is a trans-species developmental antigen that signifies malignancy when accumulating in non-developmental tissues. This murine anti-A, which is complementary to the GalNAc glycan expressed by syngeneic ovarian glycolipids and distinct from cross-reactive adaptive anti-A antibody, did not appear in the plasma of animals subjected to ovariectomy at the age of 20 days. In mouse and man, this molecule most likely gets its complementary footprint from the early growth-dependent, trans-species <i>O</i>-GalNAc glycosylations of proteins in connection with the subsequent transferase depletions, which result in the formation and release of glycan-depleted proteins that through specific binding sites and reactivity might establish this process and reveal the structure and quality of the volatilely expressed, “lost” glycans. Consequently, these <i>O</i>-GalNAc-glycosylations of proteins, involving serine/threonine residues, are either identical or metabolically related with those of the mucin-type, “aberrant” monosaccharide GalNAcα1-<i>O</i>-Ser/Thr-R or Tn antigen and explain the anti-Tn cross-reactivity of anti-A specific immunoglobulins and the pronounced occurrence of cross-reactive anti-Tn antibody in the plasma of human histo (blood) group O. In fact, in the blood group O, an A-allelic, phenotype-specific GalNAc glycosylation of plasma proteins does not occur and affect the reactivity of the anti-Tn antibody, which may occur in appearance as a growth regulator and depending on its level, initiates the process of growth inhibition through substrate competition with subsequent trans-species <i>O</i>-GalNAc-glycosylations.
DOI: 10.6084/m9.figshare.1266346.v1
title: I-LM-1A-1HNMR-400MHzOzric_data

description: 1H NMR data acquired in CDCl3 of 1,3-bis(dec-9-en-1-yl)urea to allow reprocessing.
DOI: 10.6084/m9.figshare.1279394.v268
title: Germline encoded anti-A-reactive IgM arising from growth-dependent and aberrant O-GalNAc glycosylations*

description: The germline encoding of a mammalian immunoglobulin M (IgM) molecule was experimentally documented for the first time in C57BL/10 mice subjected to an ovariectomy prior to the onset of puberty. The target of this innate antibody is a trans-species developmental antigen that signifies malignancy when accumulating in non-developmental tissues. This murine anti-A, which is complementary to the GalNAc glycan expressed by syngeneic ovarian glycolipids and distinct from cross-reactive adaptive anti-A antibody, did not appear in the plasma of animals subjected to ovariectomy at the age of 20 days. In mouse and man, this molecule most likely gets its complementary footprint from the early growth-dependent, trans-species <i>O</i>-GalNAc glycosylations of proteins in connection with the subsequent transferase depletions, which result in the formation and release of glycan-depleted proteins that through specific binding sites and reactivity might establish this process and reveal the structure and quality of the volatilely expressed, “lost” glycans. Consequently, these <i>O</i>-GalNAc-glycosylations of proteins, involving serine/threonine residues, are either identical or metabolically related with those of the mucin-type, “aberrant” monosaccharide GalNAcα1-<i>O</i>-Ser/Thr-R or Tn antigen and explain the anti-Tn cross-reactivity of anti-A specific immunoglobulins and the pronounced occurrence of cross-reactive anti-Tn antibody in the plasma of human histo (blood) group O. In fact, in the blood group O, an A-allelic, phenotype-specific GalNAc glycosylation of plasma proteins does not occur and affect the reactivity of the anti-Tn antibody, which may occur in appearance as a growth regulator and depending on its level, initiates the process of growth inhibition through substrate competition with subsequent trans-species <i>O</i>-GalNAc-glycosylations.
DOI: 10.6084/m9.figshare.1266298.v1
title: Atlantic salmon %P and ecosystem flux

description: These datafiles are used in analyses contained in the manuscript Ebel, J.D., S.J. Leroux, M.J. Robertson, J.B. Dempson. 2015. Ontogenetic differences in Atlantic salmon phosphorus concentration and its implications for cross-ecosystem fluxes. Ecosphere 6(8):136. http://dx.doi.org/10.1890/ES14-00516.1<br> These data include biological characteristics of three distinct Atlantic salmon populations over a 20 year period (1993-2012): Campbellton River, Conne River, and Western Arm Brook, Newfoundland Canada. These data were collected by Fisheries and Oceans Canada and posted with the permission of collaborating researchers. Additionally, this set of files includes the concentrations of 7 elements in whole Atlantic salmon of three life stages. The R code used for analyses contained in the manuscript is also included [Ebel_et_al_Rcode.R]. Please read Metadata file carefully before using any of this data.
DOI: 10.6084/m9.figshare.1279394.v269
title: Germline encoded anti-A-reactive IgM arising from growth-dependent and aberrant O-GalNAc glycosylations*

description: echanism The germline encoding of a mammalian immunoglobulin M (IgM) molecule was experimentally documented for the first time in C57BL/10 mice subjected to an ovariectomy prior to the onset of puberty. The target of this innate antibody is a trans-species developmental antigen that signifies malignancy when accumulating in non-developmental tissues. This murine anti-A, which is complementary to the GalNAc glycan expressed by syngeneic ovarian glycolipids and distinct from cross-reactive adaptive anti-A antibody, did not appear in the plasma of animals subjected to ovariectomy at the age of 20 days. In mouse and man, this molecule most likely gets its complementary footprint from the early growth-dependent, trans-species <i>O</i>-GalNAc glycosylations of proteins in connection with the subsequent transferase depletions, which result in the formation and release of glycan-depleted proteins that through specific binding sites and reactivity might establish this mechanism and reveal the structure and quality of the volatilely expressed “lost” glycans. Consequently, these <i>O</i>-GalNAc-glycosylations of proteins, involving serine/threonine residues, are either identical or metabolically related with those of the mucin-type, “aberrant” monosaccharide GalNAcα1-<i>O</i>-Ser/Thr-R or Tn antigen and explain the anti-Tn cross-reactivity of anti-A specific immunoglobulins and the pronounced occurrence of cross-reactive anti-Tn antibody in the plasma of human histo (blood) group O. In fact, in the blood group O, an A-allelic, phenotype-specific GalNAc glycosylation of plasma proteins does not occur and affect the reactivity of the anti-Tn antibody, which may occur in appearance as a growth regulator and depending on its level, initiates the process of growth inhibition through substrate competition with subsequent trans-species <i>O</i>-GalNAc-glycosylations.
DOI: 10.6084/m9.figshare.1279394.v270
title: Germline encoded anti-A-reactive IgM arising from growth-dependent and aberrant O-GalNAc glycosylations*

description: <br> The germline encoding of a mammalian immunoglobulin M (IgM) molecule was experimentally documented for the first time in C57BL/10 mice subjected to an ovariectomy prior to the onset of puberty. The target of this innate antibody is a trans-species developmental antigen that signifies malignancy when accumulating in non-developmental tissues. This murine anti-A, which is complementary to the GalNAc glycan expressed by syngeneic ovarian glycolipids and distinct from cross-reactive adaptive anti-A antibody, did not appear in the plasma of animals subjected to ovariectomy at the age of 20 days. In mouse and man, this molecule most likely gets its complementary footprint from the early growth-dependent, trans-species <i>O</i>-GalNAc glycosylations of proteins in connection with the subsequent transferase depletions, which result in the formation and release of glycan-depleted proteins that through specific binding sites and reactivity might establish this mechanism and reveal the structure and quality of the volatilely expressed “lost” glycans. Consequently, these <i>O</i>-GalNAc-glycosylations of proteins, involving serine/threonine residues, are either identical or metabolically related with those of the mucin-type, “aberrant” monosaccharide GalNAcα1-<i>O</i>-Ser/Thr-R or Tn antigen and explain the anti-Tn cross-reactivity of anti-A specific immunoglobulins and the pronounced occurrence of cross-reactive anti-Tn antibody in the plasma of human histo (blood) group O. In fact, in the blood group O, an A-allelic, phenotype-specific GalNAc glycosylation of plasma proteins does not occur and affect the reactivity of the anti-Tn antibody, which may function as a growth regulator and depending on its level, initiates the process of growth inhibition through substrate competition with subsequent trans-species <i>O</i>-GalNAc-glycosylations.
DOI: 10.6084/m9.figshare.1266267
title: Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms (file : Novel_diversity_V4_BIOM_DNA.fasta)

description: file : Novel_diversity_V4_BIOM_DNA.fasta see details in Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms (file : readme_Forster_et_al_BMC) http://dx.doi.org/10.6084/m9.figshare.1264013 Background: High-throughput sequencing technologies are lifting major limitations to molecular-based ecological studies of eukaryotic microbial diversity, but in silico analyses of the resulting millions of short amplicons remain a major bottleneck for these approaches. Here, we introduced the analytical and statistical framework of sequence similarity networks, increasingly used in evolutionary studies and graph theory, into the field of ecology to analyze novel pyrosequenced V4 SSU-rDNA sequence data sets in the context of previous studies, including SSU-rDNA Sanger sequence data from cultured ciliates and from previous environmental diversity inventories.<br>Results: Our broadly applicable protocol quantified progress in the description of genetic diversity of ciliates by environmental rRNA amplicons studies, detected a fundamental historical bias, the tendency to recover already known groups, in these surveys, and revealed substantial amounts of hidden microbial diversity. Moreover, network measures demonstrated that ciliates are not globally dispersed, but present strong local patterns at intermediate geographical scale, as observed for bacteria, plants, and animals.<br>Conclusions: Although currently available ‘universal’ primers used for local in-depth sequencing surveys provide little hope to exhaust the significantly higher ciliate (and most likely microbial) diversity than previously thought, sequence similarity networks, since they identify groups of divergence sequences sharing distinctive similarities, offer a promising way to guide the design of novel primers and to further explore such a vast and structured microbial diversity.
DOI: 10.6084/m9.figshare.1279394.v271
title: Germline encoded anti-A-reactive IgM arising from growth-dependent and aberrant O-GalNAc glycosylations*

description: <br> The germline encoding of a mammalian immunoglobulin M (IgM) molecule was experimentally documented for the first time in C57BL/10 mice subjected to an ovariectomy prior to the onset of puberty. The target of this innate antibody is a trans-species developmental antigen that signifies malignancy when accumulating in non-developmental tissues. This murine anti-A, which is complementary to the GalNAc glycan expressed by syngeneic ovarian glycolipids and distinct from cross-reactive adaptive anti-A antibody, did not appear in the plasma of animals subjected to an ovariectomy at the age of 20 days. In mouse and man, this molecule most likely gets its complementary footprint from the early growth-dependent, trans-species <i>O</i>-GalNAc glycosylations of proteins in connection with the subsequent transferase depletions, which result in the formation and release of glycan-depleted proteins that through specific binding sites and reactivity might establish this mechanism and reveal the structure and quality of the volatilely expressed “lost” glycans. Consequently, these <i>O</i>-GalNAc-glycosylations of proteins, involving serine/threonine residues, are either identical or metabolically related with those of the mucin-type, “aberrant” monosaccharide GalNAcα1-<i>O</i>-Ser/Thr-R or Tn antigen and explain the anti-Tn cross-reactivity of anti-A specific immunoglobulins and the pronounced occurrence of cross-reactive anti-Tn antibody in the plasma of human histo (blood) group O. In fact, in the blood group O, an A-allelic, phenotype-specific GalNAc glycosylation of plasma proteins does not occur and affect the reactivity of the anti-Tn antibody, which may function as a growth regulator and depending on its level, initiates the process of growth inhibition through enzyme-substrate competition with subsequent trans-species <i>O</i>-GalNAc-glycosylations.
DOI: 10.6084/m9.figshare.1266266.v2
title: Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms (file : Novel_diversity_V4_BIOM_cDNA.fasta)

description: file : Novel_diversity_V4_BIOM_cDNA.fasta see details in Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms (file : readme_Forster_et_al_BMC) http://dx.doi.org/10.6084/m9.figshare.1264013 Background: High-throughput sequencing technologies are lifting major limitations to molecular-based ecological studies of eukaryotic microbial diversity, but in silico analyses of the resulting millions of short amplicons remain a major bottleneck for these approaches. Here, we introduced the analytical and statistical framework of sequence similarity networks, increasingly used in evolutionary studies and graph theory, into the field of ecology to analyze novel pyrosequenced V4 SSU-rDNA sequence data sets in the context of previous studies, including SSU-rDNA Sanger sequence data from cultured ciliates and from previous environmental diversity inventories.<br>Results: Our broadly applicable protocol quantified progress in the description of genetic diversity of ciliates by environmental rRNA amplicons studies, detected a fundamental historical bias, the tendency to recover already known groups, in these surveys, and revealed substantial amounts of hidden microbial diversity. Moreover, network measures demonstrated that ciliates are not globally dispersed, but present strong local patterns at intermediate geographical scale, as observed for bacteria, plants, and animals.<br>Conclusions: Although currently available ‘universal’ primers used for local in-depth sequencing surveys provide little hope to exhaust the significantly higher ciliate (and most likely microbial) diversity than previously thought, sequence similarity networks, since they identify groups of divergence sequences sharing distinctive similarities, offer a promising way to guide the design of novel primers and to further explore such a vast and structured microbial diversity.
DOI: 10.6084/m9.figshare.1266266.v1
title: Novel_diversity_V4_BIOM_cDNA.fasta

description: Background: High-throughput sequencing technologies are lifting major limitations to molecular-based ecological studies of eukaryotic microbial diversity, but in silico analyses of the resulting millions of short amplicons remain a major bottleneck for these approaches. Here, we introduced the analytical and statistical framework of sequence similarity networks, increasingly used in evolutionary studies and graph theory, into the field of ecology to analyze novel pyrosequenced V4 SSU-rDNA sequence data sets in the context of previous studies, including SSU-rDNA Sanger sequence data from cultured ciliates and from previous environmental diversity inventories.<br>Results: Our broadly applicable protocol quantified progress in the description of genetic diversity of ciliates by environmental rRNA amplicons studies, detected a fundamental historical bias, the tendency to recover already known groups, in these surveys, and revealed substantial amounts of hidden microbial diversity. Moreover, network measures demonstrated that ciliates are not globally dispersed, but present strong local patterns at intermediate geographical scale, as observed for bacteria, plants, and animals.<br>Conclusions: Although currently available ‘universal’ primers used for local in-depth sequencing surveys provide little hope to exhaust the significantly higher ciliate (and most likely microbial) diversity than previously thought, sequence similarity networks, since they identify groups of divergence sequences sharing distinctive similarities, offer a promising way to guide the design of novel primers and to further explore such a vast and structured microbial diversity.
DOI: 10.6084/m9.figshare.1266216
title: An electroencephalography network and connectivity analysis for deception in instructed lying tasks

description: The uploaded files are the experimental datasets for an electroencephalography network and connectivity analysis for deception in instructed lying tasks
DOI: 10.6084/m9.figshare.1266267.v1
title: Novel_diversity_V4_BIOM_DNA.fasta

description: Background: High-throughput sequencing technologies are lifting major limitations to molecular-based ecological studies of eukaryotic microbial diversity, but in silico analyses of the resulting millions of short amplicons remain a major bottleneck for these approaches. Here, we introduced the analytical and statistical framework of sequence similarity networks, increasingly used in evolutionary studies and graph theory, into the field of ecology to analyze novel pyrosequenced V4 SSU-rDNA sequence data sets in the context of previous studies, including SSU-rDNA Sanger sequence data from cultured ciliates and from previous environmental diversity inventories.<br>Results: Our broadly applicable protocol quantified progress in the description of genetic diversity of ciliates by environmental rRNA amplicons studies, detected a fundamental historical bias, the tendency to recover already known groups, in these surveys, and revealed substantial amounts of hidden microbial diversity. Moreover, network measures demonstrated that ciliates are not globally dispersed, but present strong local patterns at intermediate geographical scale, as observed for bacteria, plants, and animals.<br>Conclusions: Although currently available ‘universal’ primers used for local in-depth sequencing surveys provide little hope to exhaust the significantly higher ciliate (and most likely microbial) diversity than previously thought, sequence similarity networks, since they identify groups of divergence sequences sharing distinctive similarities, offer a promising way to guide the design of novel primers and to further explore such a vast and structured microbial diversity.
DOI: 10.6084/m9.figshare.1279394.v272
title: Germline encoded anti-A-reactive IgM arising from growth-dependent and aberrant O-GalNAc glycosylations*

description: <br> The germline encoding of a mammalian immunoglobulin M (IgM) molecule was experimentally documented for the first time in C57BL/10 mice subjected to an ovariectomy prior to the onset of puberty. The target of this innate antibody is a trans-species developmental antigen that signifies malignancy when accumulating in non-developmental tissues. This murine anti-A antibody, which appears serologically identical to the human innate anti-A isoagglutinin is complementary to the GalNAc glycan expressed by syngeneic ovarian glycolipids and does not appear in the plasma of animals subjected to an ovariectomy at the age of 20 days. In mouse and man, this molecule most likely gets its complementary footprint from the early growth-dependent, trans-species <i>O</i>-GalNAc glycosylations of proteins in connection with the subsequent transferase depletions, which result in the formation and release of glycan-depleted proteins that through specific binding sites and reactivity might establish this mechanism and reveal the structure and quality of the volatilely expressed “lost” glycans. Consequently, these <i>O</i>-GalNAc-glycosylations of proteins, involving serine/threonine residues, are either identical or metabolically related with those of the mucin-type, “aberrant” monosaccharide GalNAcα1-<i>O</i>-Ser/Thr-R or Tn antigen and explain the anti-Tn cross-reactivity of anti-A specific immunoglobulins and the pronounced occurrence of cross-reactive anti-Tn antibody in the plasma of human histo (blood) group O. In fact, in the blood group O, an A-allelic, phenotype-specific GalNAc glycosylation of plasma proteins does not occur and affect the reactivity of the anti-Tn antibody, which may function as a growth regulator and depending on its level, initiates the process of growth inhibition through enzyme-substrate competition with subsequent trans-species <i>O</i>-GalNAc-glycosylations.