cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1266267.v3
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.1266267.v2
title: Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms ()

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.v273
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 to be 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.
DOI: 10.6084/m9.figshare.1266194
title: Gene expression analysis in the adult zebrafish pallium

description: Dataset 1 Expression of eomesb in the embryonic brain and the adult pallium in zebrafish.<br>Raw data of Figure S2 and additional image files of eomesb expression in the embryo and the adult pallium. Dataset 2 Images of negative control.<br>No signal was detected in the absence of the riboprobe, demonstrating that the antibody reacts specifically with the synthetic RNA. Dataset 3 Expression of eomesa in the zebrafish pallium.<br>Raw data of Figure 1 and additional image files of eomesa expression in the adult pallium. Dataset 4 Expression of emx1, emx2 and emx3 in the zebrafish larval brain. Raw data of Figure S3 and additional image files of emx gene expression in the zebrafish larvae. Dataset 5 Expression of emx1, emx2 and emx3 in the zebrafish pallium.<br>Raw data of Figure 2 and additional image files of emx gene expression in the adult pallium. Dataset 6 Expression of Prox1 in the zebrafish pallium.<br>Raw data of Figure 3 and additional image files of Prox1 expression in the adult pallium. Dataset 7 Expression of ascl1a in the zebrafish pallium.<br>Raw data of Figure 4 and additional image files of ascl1a expression in the adult pallium.
DOI: 10.6084/m9.figshare.1266197.v1
title: Interoperability for Data Repositories. Machine Methods for Retrieving Data for Display or Mining Utilising Persistent (data-DOI) Identifiers

description: Use of a persistent identifier for access to journal articles (the DOI) is now almost universal amongst researchers. It directs to the journal landing page where the human has to then take over navigation (or payment). Recently, the deposition of data into open access repositories and the resulting assignment of a data-DOI to the data or fileset has started to be increasingly adopted, and in the near future probably mandated by funders. Unfortunately, mechanisms for the retrieval and application of the data from such sources are still inherited from those developed for journal articles. We argue these mechanisms are not fit for (data) purpose. In these three demonstrations, we show how existing standards can be used to automate the data retrieval process, starting purely from the DOI assigned to the objects. The first of these utilises the 10320/loc method (see doi:10.1021/ci500302p) which is flexible and efficient, but is not supported by the DataCite registry. The next two schemes were developed to achieve such interoperability, the first using the DataCite Media API and the second exploiting added metadata such as relatedMetadataScheme = ORE to use the repository ORE resource map. We have embedded these methods into a Javascript-based data viewing demonstrator (JSmol), which is designed to display molecular information. Handlers for other types of data could be readily incorporated, and the system could also be exploited for data-mining. Examples of recently published journal articles which use such data-DOI handling will be cited.
DOI: 10.6084/m9.figshare.1266216.v1
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.1266194.v1
title: Gene expression analysis in the adult zebrafish pallium

description: Dataset 1 Expression of eomesb in the embryonic brain and the adult pallium in zebrafish.<br>Raw data of Figure S2 and additional image files of eomesb expression in the embryo and the adult pallium. Dataset 2 Images of negative control.<br>No signal was detected in the absence of the riboprobe, demonstrating that the antibody reacts specifically with the synthetic RNA. Dataset 3 Expression of eomesa in the zebrafish pallium.<br>Raw data of Figure 1 and additional image files of eomesa expression in the adult pallium. Dataset 4 Expression of emx1, emx2 and emx3 in the zebrafish larval brain. Raw data of Figure S3 and additional image files of emx gene expression in the zebrafish larvae. Dataset 5 Expression of emx1, emx2 and emx3 in the zebrafish pallium.<br>Raw data of Figure 2 and additional image files of emx gene expression in the adult pallium. Dataset 6 Expression of Prox1 in the zebrafish pallium.<br>Raw data of Figure 3 and additional image files of Prox1 expression in the adult pallium. Dataset 7 Expression of ascl1a in the zebrafish pallium.<br>Raw data of Figure 4 and additional image files of ascl1a expression in the adult pallium.
DOI: 10.6084/m9.figshare.1279394.v274
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.
DOI: 10.6084/m9.figshare.1266216.v2
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.1279394.v275
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, initiate the process of growth inhibition through enzyme-substrate competition with subsequent trans-species <i>O</i>-GalNAc-glycosylations.
DOI: 10.6084/m9.figshare.1279394.v276
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 antibody, which is complementary to the <i>O</i>-GalNAc glycan expressed by syngeneic ovarian glycolipids, appears serologically identical to the human innate anti-A isoagglutinin. 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 human blood group O, an A-allelic, phenotype-specific GalNAc glycosylation of plasma proteins does not occur and affect the levels of the anti-Tn antibody, which may function as a growth regulator and depending on its levels, initiate the process of growth inhibition through enzyme-substrate competition with subsequent trans-species <i>O</i>-GalNAc-glycosylations. <br>
DOI: 10.6084/m9.figshare.1266183
title: Behavior of the Amazonian damselfly <i>Chalcopteryx scintillans</i> McLachlan (Zygoptera: Polythoridae) and comments on its morphological distinction from <i>C. rutilans</i> (Rambur)

description: Polythorid damselflies are Neotropical stream dwellers, whose behavior has rarely been recorded. Here we describe the territorial and courtship behavior of <i>Chalcopteryx scintillans</i> McLachlan, an Amazonian damselfly with shiny copper-colored hind wings. Territorial behavior consists of aerial contests, when males engage in threat displays and mutual pursuits in ascending and rocking flights. During courtship, males hold their coppery hind wings still while hovering with their forewings, showing the hind wings to females, which hover in front of the male in response. After copulation, the male exhibits the courtship flight again by hovering over the oviposition resource (i.e. fallen tree trunk) on the stream. The females oviposit on the trunk while the males guard them by perching near and hovering around them constantly. We also present behavioral notes on reproductive and oviposition behavior, and comments on the differentiation between <i>C. scintillans</i> and <i>C. rutilans</i> (Rambur).
DOI: 10.6084/m9.figshare.1266216.v3
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.1266176
title: Changes of enological variables, metal ions, and aromas in Fenjiu during 3 years of ceramic and glass bottle ageing

description: Changes in enological variables, metal ions, and aromas of Fenjiu were examined after 3 years of ageing in ceramic and glass bottles. Container type and ageing time showed significant effects on six enological variables, all metal ions, and most of the aromas. A principal component analysis was performed for aromas exhibiting simultaneous dependence on the container type and ageing time at the <i>p</i>
DOI: 10.6084/m9.figshare.1266183.v3
title: Behavior of the Amazonian damselfly <i>Chalcopteryx scintillans</i> McLachlan (Zygoptera: Polythoridae) and comments on its morphological distinction from <i>C. rutilans</i> (Rambur)

description: Polythorid damselflies are Neotropical stream dwellers, whose behavior has rarely been recorded. Here we describe the territorial and courtship behavior of <i>Chalcopteryx scintillans</i> McLachlan, an Amazonian damselfly with shiny copper-colored hind wings. Territorial behavior consists of aerial contests, when males engage in threat displays and mutual pursuits in ascending and rocking flights. During courtship, males hold their coppery hind wings still while hovering with their forewings, showing the hind wings to females, which hover in front of the male in response. After copulation, the male exhibits the courtship flight again by hovering over the oviposition resource (i.e. fallen tree trunk) on the stream. The females oviposit on the trunk while the males guard them by perching near and hovering around them constantly. We also present behavioral notes on reproductive and oviposition behavior, and comments on the differentiation between <i>C. scintillans</i> and <i>C. rutilans</i> (Rambur).
DOI: 10.6084/m9.figshare.1266216.v4
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.1279394.v277
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 antibody, which is complementary to the <i>O</i>-GalNAc glycan expressed by syngeneic ovarian glycolipids, appears serologically identical to the human innate anti-A isoagglutinin. 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 human blood group O, an A-allelic, phenotype-specific GalNAc glycosylation of plasma proteins does not occur and affect the levels of the anti-Tn antibody, which may function as a growth regulator and depending on its levels, initiate the process of growth inhibition through enzyme-substrate competition with subsequent trans-species <i>O</i>-GalNAc-glycosylations. <br>
DOI: 10.6084/m9.figshare.1266183.v2
title: Behavior of the Amazonian damselfly <i>Chalcopteryx scintillans</i> McLachlan (Zygoptera: Polythoridae) and comments on its morphological distinction from <i>C. rutilans</i> (Rambur)

description: Polythorid damselflies are Neotropical stream dwellers, whose behavior has rarely been recorded. Here we describe the territorial and courtship behavior of <i>Chalcopteryx scintillans</i> McLachlan, an Amazonian damselfly with shiny copper-colored hind wings. Territorial behavior consists of aerial contests, when males engage in threat displays and mutual pursuits in ascending and rocking flights. During courtship, males hold their coppery hind wings still while hovering with their forewings, showing the hind wings to females, which hover in front of the male in response. After copulation, the male exhibits the courtship flight again by hovering over the oviposition resource (i.e. fallen tree trunk) on the stream. The females oviposit on the trunk while the males guard them by perching near and hovering around them constantly. We also present behavioral notes on reproductive and oviposition behavior, and comments on the differentiation between <i>C. scintillans</i> and <i>C. rutilans</i> (Rambur).