cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6865571
title: Supplementary Material for: MicroRNA-126 Deficiency Affects the Development of Thymus CD4<sup>+</sup> Single-Positive Cells through Elevating IRS-1

description: <b><i>Background:</i></b> MicroRNA-126 (miR-126), a distinct miRNA family member, has been reported to be involved in the development and function of some types of immune cells. However, the potential role of miR-126 in the development of CD4<sup>+</sup> T cells remains to be elucidated. <b><i>Objectives:</i></b> To investigate the potential role of miR-126 in the development of CD4<sup>+</sup> T cells in the thymus and explore its significance. <b><i>Methods:</i></b> The relative expression level of miR-126 in thymus CD4<sup>+</sup> single-positive (SP) cells was detected by Real-Time PCR assay. The possible change in thymus tissue was assessed by histopathology. The total cell number of thymocytes and the expression of activation-associated molecules including CD62L, CD69, and CD44, as well as proliferation-associated nuclear antigen Ki-67, in CD4<sup>+</sup> SP cells were assessed by flow cytometric analysis. The expression of IRS-1 and related signaling pathways including Akt and Erk were determined by flow cytometric analysis. <b><i>Results:</i></b> Compared with that in wild-type (WT) mice,<i></i> the total cell number of thymocytes in miR-126 knockdown (KD) mice increased significantly. Moreover, the proportion and absolute cell number of thymic CD4<sup>+</sup> SP cells decreased significantly in miR-126 KD mice. Further analysis showed that the frequencies of activation-associated molecules including CD62L, CD69, and CD44, as well as proliferation-associated nuclear antigen Ki-67 in CD4<sup>+</sup> SP cells also changed significantly, respectively. Mechanism aspect, the expression level of IRS-1, a putative target of miR-126, increased significantly in CD4<sup>+</sup> SP cells in miR-126 KD mice. Moreover, the expression levels of the signaling molecules phosphorylated (p)-Akt and p-Erk also changed significantly. <b><i>Conclusions:</i></b> Our work is the first to reveal a previously unknown role of miR-126 in the development of CD4<sup>+</sup> SP cells in the thymus, which might ultimately benefit studies on development of thymocytes.
DOI: 10.6084/m9.figshare.6865571.v1
title: Supplementary Material for: MicroRNA-126 Deficiency Affects the Development of Thymus CD4<sup>+</sup> Single-Positive Cells through Elevating IRS-1

description: <b><i>Background:</i></b> MicroRNA-126 (miR-126), a distinct miRNA family member, has been reported to be involved in the development and function of some types of immune cells. However, the potential role of miR-126 in the development of CD4<sup>+</sup> T cells remains to be elucidated. <b><i>Objectives:</i></b> To investigate the potential role of miR-126 in the development of CD4<sup>+</sup> T cells in the thymus and explore its significance. <b><i>Methods:</i></b> The relative expression level of miR-126 in thymus CD4<sup>+</sup> single-positive (SP) cells was detected by Real-Time PCR assay. The possible change in thymus tissue was assessed by histopathology. The total cell number of thymocytes and the expression of activation-associated molecules including CD62L, CD69, and CD44, as well as proliferation-associated nuclear antigen Ki-67, in CD4<sup>+</sup> SP cells were assessed by flow cytometric analysis. The expression of IRS-1 and related signaling pathways including Akt and Erk were determined by flow cytometric analysis. <b><i>Results:</i></b> Compared with that in wild-type (WT) mice,<i></i> the total cell number of thymocytes in miR-126 knockdown (KD) mice increased significantly. Moreover, the proportion and absolute cell number of thymic CD4<sup>+</sup> SP cells decreased significantly in miR-126 KD mice. Further analysis showed that the frequencies of activation-associated molecules including CD62L, CD69, and CD44, as well as proliferation-associated nuclear antigen Ki-67 in CD4<sup>+</sup> SP cells also changed significantly, respectively. Mechanism aspect, the expression level of IRS-1, a putative target of miR-126, increased significantly in CD4<sup>+</sup> SP cells in miR-126 KD mice. Moreover, the expression levels of the signaling molecules phosphorylated (p)-Akt and p-Erk also changed significantly. <b><i>Conclusions:</i></b> Our work is the first to reveal a previously unknown role of miR-126 in the development of CD4<sup>+</sup> SP cells in the thymus, which might ultimately benefit studies on development of thymocytes.
DOI: 10.6084/m9.figshare.6865484
title: Introduced ants (Hymenoptera: Formicidae) of mainland France and Belgium, with a focus on greenhouses

description: The monitoring of introduced species is becoming more important as global trade intensifies. Although ants make up a larger proportion of species on the list of the most invasive species in the world compared with other groups, little is known about the occurrence of those introduced in France, especially inside heated buildings. Here we review the literature available for mainland France and Belgium and report the results of a survey conducted with the help of tropical building managers between 2014 and 2016. We report for the first time in France the presence of <i>Technomyrmex vitiensis</i> and <i>Plagiolepis alluaudi</i> in multiple greenhouses. <i>Technomyrmex difficilis</i> was also found in one greenhouse for the first time in Europe. The diversity of introduced ants in greenhouses is very low, and these buildings are most often dominated by one or two species. We compared the most recent data and those collected throughout the twentieth century and showed that ant communities have changed substantially. Greenhouses could be responsible for the introduction of invasive species because they regularly import exotic plants, but we found no evidence that the three species of invasive ants present outdoors in France were introduced from greenhouses, where they rarely occur. We also report that introduced ants are pests in greenhouses because they disperse scale insects and kill biological control agents. The suppression of these ants could ease the maintenance of plants inside greenhouses.
DOI: 10.6084/m9.figshare.6865484.v1
title: Introduced ants (Hymenoptera: Formicidae) of mainland France and Belgium, with a focus on greenhouses

description: The monitoring of introduced species is becoming more important as global trade intensifies. Although ants make up a larger proportion of species on the list of the most invasive species in the world compared with other groups, little is known about the occurrence of those introduced in France, especially inside heated buildings. Here we review the literature available for mainland France and Belgium and report the results of a survey conducted with the help of tropical building managers between 2014 and 2016. We report for the first time in France the presence of <i>Technomyrmex vitiensis</i> and <i>Plagiolepis alluaudi</i> in multiple greenhouses. <i>Technomyrmex difficilis</i> was also found in one greenhouse for the first time in Europe. The diversity of introduced ants in greenhouses is very low, and these buildings are most often dominated by one or two species. We compared the most recent data and those collected throughout the twentieth century and showed that ant communities have changed substantially. Greenhouses could be responsible for the introduction of invasive species because they regularly import exotic plants, but we found no evidence that the three species of invasive ants present outdoors in France were introduced from greenhouses, where they rarely occur. We also report that introduced ants are pests in greenhouses because they disperse scale insects and kill biological control agents. The suppression of these ants could ease the maintenance of plants inside greenhouses.
DOI: 10.6084/m9.figshare.6865463
title: Tables colorectal cancer

description: Table 1. Patients characteristics Table 2. Relationship between the occurrence of mutations in the <i>KRAS</i>, <i>NRAS</i> or <i>BRAF</i> genes and sex, age, and tumor localization in CRC patients. Table 3. Relationship between the occurrence of mutations in the <i>KRAS</i>, <i>NRAS</i> or <i>BRAF</i> genes and tumor localization in CRC patients. *lack of any examined mutations (wild type)
DOI: 10.18112/openneuro.ds003097.v1.0.0
title: AOMIC-ID1000
DOI: 10.6084/m9.figshare.6865463.v1
title: Tables colorectal cancer

description: Table 1. Patients characteristics Table 2. Relationship between the occurrence of mutations in the <i>KRAS</i>, <i>NRAS</i> or <i>BRAF</i> genes and sex, age, and tumor localization in CRC patients. Table 3. Relationship between the occurrence of mutations in the <i>KRAS</i>, <i>NRAS</i> or <i>BRAF</i> genes and tumor localization in CRC patients. *lack of any examined mutations (wild type)
DOI: 10.6084/m9.figshare.6865418
title: Cranial and mandibular morphology of Middle Pleistocene cave bears (<i>Ursus deningeri</i>): implications for diet and evolution

description: Deninger’s bears (<i>Ursus deningeri</i>) have been studied less frequently than <i>Ursus spelaeus</i> <i>s.l.</i> Our objective is to present, for the first time, an analysis of the skull shape of <i>U. deningeri</i>. Bear crania and mandibles were digitised with a Microscribe or CT-scanned and the surface models subsequently landmarked. The landmarks were chosen based on a compromise between functional morphology and sample size. Results show that <i>U. deningeri</i> and <i>U. spelaeus</i> mandibles display very similar morphologies and allometric trajectories, both to each other and to <i>Ailuropoda melanoleuca</i>. It is inferred that masticatory adaptations to a herbivorous diet were already present in the Middle Pleistocene. <i>U. deningeri</i> displays a cranial morphology that is similar to that of <i>U. spelaeus</i> when comparing all species, but <i>U. deningeri</i> has a relatively narrower and dorsoventrally lower zygomatic arch than <i>U. spelaeus</i>, although the masticatory signal is less strong in the skull. We observe intraspecific differences between different populations of <i>U. deningeri</i>, which could parallel the genetic diversity found in <i>U. spelaeus</i>. The intraspecific differences found within <i>U. deningeri</i> may be temporal and/or geographical in nature and could be related to the evolution of the Late Pleistocene cave bear, but this hypothesis remains to be tested.
DOI: 10.6084/m9.figshare.6865415
title: Phylogenetic analysis of symbiont transmission mechanisms reveal evolutionary patterns in thermotolerance and host specificity that enhance bleaching resistance among vertically transmitted <i>Symbiodinium</i>

description: Vertical transmission of <i>Symbiodinium</i> symbionts between generations of coral hosts has been hypothesized to result in superior matches between host and symbiont physiologies, and to form holobionts that are generally more resistant to thermal stress. Alternatively, horizontal transmission, with its greater potential for assembling physiologically diverse associations as well as being capable of substituting symbionts in response to stimuli, may result in holobionts that are generally more resistant to thermal stress. While the most common mode of transmission among Scleractinia–<i>Symbiodinium</i> symbioses is horizontal, mixed-modes transmission only occurs in vertically transmitting corals, allowing the maintenance of highly specialized associations across generations as well as transiently critical relationships. These advantages of mixed-modes transmission may serve to rescue otherwise susceptible corals, or alternatively, reinforce otherwise resistant corals, depending upon the other attributes of vertically transmitted <i>Symbiodinium</i> phylotypes. Here we ask if vertically transmitted symbionts tend to be more thermotolerant and specific. Because significant relationships between traits can be overestimated or obscured by patterns of shared evolutionary history, we inferred a novel molecular phylogeny for 97 <i>Symbiodinium</i> phylotypes representing clades A–F to evaluate the relationship between phylotype transmission-mode, thermotolerance and specificity to coral hosts. Thermotolerance and specificity have been independently derived multiple times during the evolutionary history of <i>Symbiodinium</i>, and cannot be predicted by clade membership. The probability of phylotype transmission being predominantly vertical increased by more than 200% across the observed ranges of increase of thermotolerance and specificity, even though phylotype thermotolerance is not correlated with host specificity. Higher thermotolerance and specificity of vertically transmitted <i>Symbiodinium</i> may contribute to robust bleaching resistance among vertically transmitting corals that could reinforce the potential benefits of mixed-modes transmission.
DOI: 10.6084/m9.figshare.6865418.v1
title: Cranial and mandibular morphology of Middle Pleistocene cave bears (<i>Ursus deningeri</i>): implications for diet and evolution

description: Deninger’s bears (<i>Ursus deningeri</i>) have been studied less frequently than <i>Ursus spelaeus</i> <i>s.l.</i> Our objective is to present, for the first time, an analysis of the skull shape of <i>U. deningeri</i>. Bear crania and mandibles were digitised with a Microscribe or CT-scanned and the surface models subsequently landmarked. The landmarks were chosen based on a compromise between functional morphology and sample size. Results show that <i>U. deningeri</i> and <i>U. spelaeus</i> mandibles display very similar morphologies and allometric trajectories, both to each other and to <i>Ailuropoda melanoleuca</i>. It is inferred that masticatory adaptations to a herbivorous diet were already present in the Middle Pleistocene. <i>U. deningeri</i> displays a cranial morphology that is similar to that of <i>U. spelaeus</i> when comparing all species, but <i>U. deningeri</i> has a relatively narrower and dorsoventrally lower zygomatic arch than <i>U. spelaeus</i>, although the masticatory signal is less strong in the skull. We observe intraspecific differences between different populations of <i>U. deningeri</i>, which could parallel the genetic diversity found in <i>U. spelaeus</i>. The intraspecific differences found within <i>U. deningeri</i> may be temporal and/or geographical in nature and could be related to the evolution of the Late Pleistocene cave bear, but this hypothesis remains to be tested.
DOI: 10.6084/m9.figshare.6865391
title: Figures colorectal cancer

description: Figure 1. Location of CRC in the studied group Figure 2. The frequency of mutations in particular codons of the <i>KRAS</i> gene<br> Figure 3. The frequency of mutations in particular codons of the <i>NRAS</i> gene Figure 4. Differences in CRC localization in patients without <i>KRAS</i>, <i>NRAS</i> or <i>BRAF</i> genes mutations (A) and in patients with mutations in the <i>KRAS</i>, <i>NRAS</i> or <i>BRAF</i> genes (B) Figure 5. Differences in CRC localization in female (A) and male (B) patients with <i>KRAS</i> gene mutations<br>
DOI: 10.6084/m9.figshare.6865391.v1
title: Figures colorectal cancer

description: Figure 1. Location of CRC in the studied group Figure 2. The frequency of mutations in particular codons of the <i>KRAS</i> gene<br> Figure 3. The frequency of mutations in particular codons of the <i>NRAS</i> gene Figure 4. Differences in CRC localization in patients without <i>KRAS</i>, <i>NRAS</i> or <i>BRAF</i> genes mutations (A) and in patients with mutations in the <i>KRAS</i>, <i>NRAS</i> or <i>BRAF</i> genes (B) Figure 5. Differences in CRC localization in female (A) and male (B) patients with <i>KRAS</i> gene mutations<br>
DOI: 10.21954/ou.rd.6865298
title: Citation-Context Dataset (C2D)

description: We have released the first version of a citation-context based dataset called C2D, created while doing an experiment in the work which will be published in RecSys 2018 as a short paper.<br><br>C2D dataset is created by using 2 million full-text open-source research publications obtained from CORE. It contains 53 million unique records of citation-information. To construct C2D, we extracted citation information from each publication. Information such as cited document's title, author(s), published date and citation-context. We will describe the assumption of extracting citation-context in a bit more detail below:<br>First of all, we extracted positions of citations where they are mentioned including citation-contexts which are texts around the cited documents. For our purpose, we created a citation-context using three sentences; the sentence where the reference has been cited, the preceding, and the following sentence. Additionally, at the start or end of a paragraph, the preceding or following sentence is not extracted respectively.<br>Therefore, the attributes of the dataset contain:Attributes:<strong>ReferenceID</strong> - unique identifier of cited reference in a citing document<strong>SourceID</strong> - unique identifier of a citing document.<strong>ChapterNumber</strong> - Chapter number of the citing document where the <b>ReferenceID</b> has mentioned.<strong>ParagraphNumber</strong> - paragraph number of the citing document where the reference <strong>ReferenceID</strong> has mentioned.<strong>SentenceNumber</strong> - sentence number of the citing document where the reference <strong>ReferencedID</strong> has mentioned.<strong>Title</strong> - Title of the reference <strong>ReferenceID.</strong><strong>PublishedDate</strong> - Publication date when the reference <strong>ReferenceID </strong>was published.<strong>Authors</strong> - Author(s) of the reference <strong>ReferenceID</strong><strong>TextBeforeRefMention</strong> - Sentence just before the sentence where the reference <strong>ReferenceID</strong> has been cited.<strong> TextWhereRefMention</strong> - Sentence where the reference <strong>ReferenceID</strong> has been cited.<strong>TextAfterRefMention</strong> - Sentence just after the sentence where the reference <strong>ReferenceID</strong> has been cited.Please cite our paper if you use this dataset. <br>Note:<br>The actual size of the dataset is ~40gb however compressed size is ~6.7gb.Requirements of different users may be different therefore we have released the raw version of the dataset. Please note, data cleansing (such as special character and stop-word removal) has not been performed.
DOI: 10.6084/m9.figshare.6865289
title: Supplementary Material for: A 2018 Italian and Romanian Survey on Subclinical Hypothyroidism in Pregnancy

description: <b><i>Objectives:</i></b> Pregnancy induces changes in thyroid function, and thyroid dysfunction during gestation is associated with adverse outcomes. We examined the management of subclinical hypothyroidism and chronic autoimmune thyroiditis in pregnancy among Italian and Romanian endocrinologists. <b><i>Methods:</i></b> Members of the Associazione Medici Endocrinologi (AME) and Romanian Society of Endocrinology (RSE) were invited to participate in a web-based survey investigating the topic. <b><i>Results:</i></b> A total of 902 individuals participated in the survey, 759 of whom completed all sections. Among the respondents, 85.1% were aware of the 2017 American Thyroid Association guidelines about thyroid disease and pregnancy, and 82.9% declared that thyroid-stimulating hormone (TSH) screening at the beginning of pregnancy should be warranted. In a patient negative for peroxidase antibodies, 53.6% considered 2.5 mIU/L and 26.2% considered 4.0 mIU/L as the upper normal limit of TSH, and 50% would treat a patient with TSH 3.5 mIU/L with levothyroxine. About 20% did not suggest iodine supplementation. Isolated hypothyroxinemia detected in the first trimester would be treated by 40.8%. In patients undergoing ovarian stimulation, a TSH &lt; 2.5 mIU/L would be targeted by 70%. <b><i>Conclusions:</i></b> Respondents globally appeared well informed about the management of thyroid autoimmunity and subclinical hypothyroidism in pregnancy. A more aggressive attitude in implementing iodine supplementation would be desirable. Most endocrinologists were convinced about an evident association between mild thyroid impairment and adverse outcomes in pregnancy, thus using a TSH value of 2.5 mIU/L as the threshold for diagnosing hypothyroidism and starting levothyroxine in pregnant women.
DOI: 10.21954/ou.rd.6865298.v1
title: Citation-Context Dataset (C2D)

description: C2D dataset is created by using 2 million full-text open-source research publications obtained from CORE. It contains 53 million unique records of citation-information. To construct C2D, we extracted citation information from each publication. Information such as cited document's title, author(s), published date and citation-context. We will describe the assumption of extracting citation-context in a bit more detail below:<br>First of all, we extracted positions of citations where they are mentioned including citation-contexts which are texts around the cited documents. For our purpose, we created a citation-context using three sentences; the sentence where the reference has been cited, the preceding, and the following sentence. Additionally, at the start or end of a paragraph, the preceding or following sentence is not extracted respectively.<br>Therefore, the attributes of the dataset contain:Attributes:<strong>ReferenceID</strong> - unique identifier of cited reference in a citing document<strong>SourceID</strong> - unique identifier of a citing document.<strong>ChapterNumber</strong> - Chapter number of the citing document where the <b>ReferenceID</b> has mentioned.<strong>ParagraphNumber</strong> - paragraph number of the citing document where the reference <strong>ReferenceID</strong> has mentioned.<strong>SentenceNumber</strong> - sentence number of the citing document where the reference <strong>ReferencedID</strong> has mentioned.<strong>Title</strong> - Title of the reference <strong>ReferenceID.</strong><strong>PublishedDate</strong> - Publication date when the reference <strong>ReferenceID </strong>was published.<strong>Authors</strong> - Author(s) of the reference <strong>ReferenceID</strong><strong>TextBeforeRefMention</strong> - Sentence just before the sentence where the reference <strong>ReferenceID</strong> has been cited.<strong> TextWhereRefMention</strong> - Sentence where the reference <strong>ReferenceID</strong> has been cited.<strong>TextAfterRefMention</strong> - Sentence just after the sentence where the reference <strong>ReferenceID</strong> has been cited.Note:<br>The actual size of the dataset is ~40gb however compressed size is ~6.7gb.Requirements of different users may be different therefore we have released the raw version of the dataset. Please note, data cleansing (such as special character and stop-word removal) has not been performed.