cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6324815.v1
title: Supplementary Material for: A de novo <b><i>KCNA1</i></b> Mutation in a Patient with Tetany and Hypomagnesemia

description: Mutations in the <i>KCNA1</i> gene encoding the voltage-gated potassium (K<sup>+</sup>) channel Kv1.1 have been linked to rare neurological syndromes, episodic ataxia type 1 (EA1) and myokymia. In 2009, a <i>KCNA1</i> mutation was identified in a large family with autosomal dominant hypomagnesemia. Despite efforts in establishing a genotype-phenotype correlation for the wide variety of symptoms in EA1, little is known on the serum magnesium (Mg<sup>2+</sup>) levels in these patients. In the present study, we describe a new de novo <i>KCNA1</i> mutation in a Polish patient with tetany and hypomagnesemia. Electrophysiological and biochemical analyses were performed to determine the pathogenicity of the mutation. A female patient presented with low serum Mg<sup>2+</sup> levels, renal Mg<sup>2+</sup> wasting, muscle cramps, and tetanic episodes. Whole exome sequencing identified a p.Leu328Val mutation in <i>KCNA1</i> encoding the Kv1.1 K<sup>+</sup> channel. Electrophysiological examinations demonstrated that the p.Leu328Val mutation caused a dominant-negative loss of function of the encoded Kv1.1 channel. Cell surface biotinylation showed normal plasma membrane expression. Taken together, this is the second report linking <i>KCNA1</i> with hypomagnesemia, thereby emphasizing the need for further evaluation of the clinical phenotypes observed in patients carrying <i>KCNA1</i> mutations.
DOI: 10.6084/m9.figshare.6324629
title: Metabolite profiling of shoot extract, root extract, and root exudate of rice under nitrogen and phosphorus deficiency

description: Root exudate is derived from plant metabolites and its composition is affected by plant nutrient status. A deficiency of mineral nutrients, such as nitrogen (N) and phosphorus (P), strongly affects the type and amount of plant metabolites. We applied a metabolite profiling technique to investigate root exudates of rice plants under N and P deficiency. <i>Oryza sativa</i> was grown in culture solution containing two N levels (0 and 60 mg N L<sup>−1</sup>) or two P levels (0 and 8 mg P L<sup>−1</sup>). Shoot extracts, root extracts, and root exudates were obtained from the rice plants 5 and 15 days after transplanting and their metabolites were determined by capillary electrophoresis/time-of-flight mass spectrometry. Shoot N concentration and dry weight of rice plants grown at −N level were lower than those of plants grown at +N level. Shoot P concentration and dry weight of rice plants grown at −P level were lower than those of plants grown at +P level. One hundred and thirty-two, 127, and 98 metabolites were identified in shoot extracts, root extracts, and root exudates, respectively, at the two N levels. One hundred and thirty-two, 128, and 99 metabolites were identified in shoot extracts, root extracts, and root exudates, respectively, at the two P levels. Seventy-seven percent of the metabolites were exuded to the rhizosphere. The concentrations of betaine, gamma-aminobutyric acid, and glutarate in root exudates were higher at both −N and −P levels than at their respective high levels. The concentration of spermidine in root exudates was lower at both −N and −P levels than at their respective high levels. The concentrations of the other metabolites in root exudates were affected differently by plant N or P status. These results suggest that rice roots actively release many metabolites in response to N and P deficiency.
DOI: 10.6084/m9.figshare.6324491
title: Données Milieu Intérieur

description: Données Milieu Intérieur"<br>Challenge PREDICT<br><br><br>Description du projet et des données<br><br>Le premier jeu de données provient du LabeX « Milieu Intérieur » de l’Institut Pasteur [1]. Dans le cadre de ce LabeX, une étude a été menée sur 803 donneurs sains à qui on a prélevé -entre autres- des échantillons de sang total. Ces échantillons ont par la suite été utilisés pour mesurer l'expression d'un sous-ensemble de gènes dans différentes conditions de stimulation du système immunitaire [2] et pour mesurer des phénotypes de répartition en sous-populations de cellules du système immunitaire [3]. Les deux questions majeures posées sur ce jeu de données sont les suivantes : (i) peut on prédire la distribution des sous-populations cellulaires en fonctions des données d'expression et (ii) peut on identifier les sous-populations cellulaires qui vont répondre à un stimulus donné ?<br><br>Répartition des données<br><br>Données transcriptomiques : 803 individus x 560 transcrits x 7 conditions d'activation.<br>Données de répartition en populations cellulaires : 803 individus x 166 variables de quantification cellulaire (MFI ou nombre de cellules).<br><br>Chaque tableau de données est sauvegardé au format csv. La première colonne de ces fichiers contient le numéro des individus.<br><br>Références<br><br> 1. Piasecka, B., Duffy, D., Urrutia, A., Quach, H., Patin, E., Posseme, C., … Milieu Intérieur Consortium, the M. I. (2018). Distinctive roles of age, sex, and genetics in shaping transcriptional variation of human immune responses to microbial challenges. Proceedings of the National Academy of Sciences of the United States of America, 115(3), E488–E497. https://doi.org/10.1073/pnas.1714765115<br> 2. Thomas, S., Rouilly, V., Patin, E., Alanio, C., Dubois, A., Delval, C., … Albert, M. L. (2015). The Milieu Intérieur study — An integrative approach for study of human immunological variance. Clinical Immunology, 157(2), 277–293. https://doi.org/10.1016/J.CLIM.2014.12.004<br> 3. Patin, E., Hasan, M., Bergstedt, J., Rouilly, V., Libri, V., Urrutia, A., … Albert, M. L. (2018). Natural variation in the parameters of innate immune cells is preferentially driven by genetic factors. Nature Immunology, 19(3), 302–314. https://doi.org/10.1038/s41590-018-0049-7<br><br>
DOI: 10.6084/m9.figshare.6324152
title: Speech and language pathologists’ perceptions and practises of communication partner training to support children’s communication with high-tech speech generating devices

description: <b>Purpose:</b> This study examined speech and language pathologists’ (SLPs’) perceptions and practices of communication partner training with high-tech speech generating devices (SGDs). <b>Method:</b> Fifteen SLPs were recruited throughout Sweden. The SLPs answered a study-specific questionnaire on communication partner training in relation to communication partners to children with severe cerebral palsy and intellectual disability. The results were analysed with descriptive statistics (closed-ended questions, responses on Likert scales) and content analysis (open-ended question) using ICF-CY. <b>Results</b>: Twelve SLPs completed the survey. Half had no or one training session with communication partners in the last year. One-third never used documents for goal-setting. Half seldom or never taught communication partner strategies. Three quarters only used verbal instructions. The main obstacles were environmental factors. <b>Conclusions:</b> This study contributes valuable knowledge about high-tech SGD interventions targeting communication partners. The high-tech SGD intervention may benefit from goal-setting, extended number of training sessions and a range of instructional approaches.Implications for RehabilitationSpeech and language pathologist (SLPs) reported that children with severe cerebral palsy and intellectual disability (SSPI) can benefit from speech generating device (SGD) communication.Communication partner strategies and goal-setting supports the development of communication with SGD. SLPs seldom taught stakeholder communication partner strategies and instruments for goal-setting.Because stakeholders may vary in their way of learning SLPs need to use a variety of instructional approaches. SLPs used few instructional approaches, typically verbal information. Speech and language pathologist (SLPs) reported that children with severe cerebral palsy and intellectual disability (SSPI) can benefit from speech generating device (SGD) communication. Communication partner strategies and goal-setting supports the development of communication with SGD. SLPs seldom taught stakeholder communication partner strategies and instruments for goal-setting. Because stakeholders may vary in their way of learning SLPs need to use a variety of instructional approaches. SLPs used few instructional approaches, typically verbal information.
DOI: 10.6084/m9.figshare.6324152.v1
title: Speech and language pathologists’ perceptions and practises of communication partner training to support children’s communication with high-tech speech generating devices

description: <b>Purpose:</b> This study examined speech and language pathologists’ (SLPs’) perceptions and practices of communication partner training with high-tech speech generating devices (SGDs). <b>Method:</b> Fifteen SLPs were recruited throughout Sweden. The SLPs answered a study-specific questionnaire on communication partner training in relation to communication partners to children with severe cerebral palsy and intellectual disability. The results were analysed with descriptive statistics (closed-ended questions, responses on Likert scales) and content analysis (open-ended question) using ICF-CY. <b>Results</b>: Twelve SLPs completed the survey. Half had no or one training session with communication partners in the last year. One-third never used documents for goal-setting. Half seldom or never taught communication partner strategies. Three quarters only used verbal instructions. The main obstacles were environmental factors. <b>Conclusions:</b> This study contributes valuable knowledge about high-tech SGD interventions targeting communication partners. The high-tech SGD intervention may benefit from goal-setting, extended number of training sessions and a range of instructional approaches.Implications for RehabilitationSpeech and language pathologist (SLPs) reported that children with severe cerebral palsy and intellectual disability (SSPI) can benefit from speech generating device (SGD) communication.Communication partner strategies and goal-setting supports the development of communication with SGD. SLPs seldom taught stakeholder communication partner strategies and instruments for goal-setting.Because stakeholders may vary in their way of learning SLPs need to use a variety of instructional approaches. SLPs used few instructional approaches, typically verbal information. Speech and language pathologist (SLPs) reported that children with severe cerebral palsy and intellectual disability (SSPI) can benefit from speech generating device (SGD) communication. Communication partner strategies and goal-setting supports the development of communication with SGD. SLPs seldom taught stakeholder communication partner strategies and instruments for goal-setting. Because stakeholders may vary in their way of learning SLPs need to use a variety of instructional approaches. SLPs used few instructional approaches, typically verbal information.
DOI: 10.6084/m9.figshare.6324128
title: raisd_data_1_70

description: Simulated datasets 1 - 70 with non-equilibrium demography (bottlenecks and migrations)<br>
DOI: 10.6084/m9.figshare.6324128.v1
title: raisd_data_1_70

description: Simulated datasets 1 - 70 with non-equilibrium demography (bottlenecks and migrations)<br>
DOI: 10.6084/m9.figshare.12782426
title: Codex Marianus: Egda-clauses (Raw)

description: The project gathers all datasets used for the study 'Early Slavic dative absolutes in discourse: the value of deeply versus strategically annotated treebanks'.<br><br>- egda_raw.csv: Dataset containing all egda-clauses in the Codex Marianus. The only part which has been manipulated is where two subjects were coordinated by *i* 'and'. In these cases, an extra row was created, allowing both subjects to appear in the ocs_sub_lemma column. The row containing the second subject was left empty under all but the subject lemma variable. This allows to observe frequencies regarding lexical variation among egda-clauses' subjects, but at the same time to discard those rows when dealing with other variables.<br>DA_Marianus_raw.csv: Codex Marianus dataset, containing all dative absolutes, as well as genitive absolutes for which there is an OCS parallel. It lists as separate entries both multiple dative participles with one dative subjects, and multiple dative subjects with one dative participle.<br>E.g.: 1) бꙑвъши же печали и гонению словесе ради абье съблажнѣатъ сѧ2) и въшедъши дъштери еѩ иродиѣдѣ. i плѧсавъши и оугождъши иродови<br>Both 1) and 2) are listed as multiple entries, although only 2) has technically more than one dative absolute.DA_Marianus_abridged.csv: This is the same as DA_Marianus_raw.csv, but lists as one dative absolute instances with multiple dative subjects and one dative participle. The criterion chosen was to only retain the entry for the subject which was the closest to the participle (the choice can make a difference should one want to consider the properties of a dative absolute with respect to its subjects).<br><br>DA_Marianus_manipulated.csv: Starting from DA_Marianus_abridged.csv, this dataset treats all dative absolutes in bystъ-clauses as preceding the main clause.<br>The reader interested in reproducing the results of the paper should refer to the 'manipulated' versions of both the egda-clause and the dative absolute datasets.<br>
DOI: 10.6084/m9.figshare.12782426.v2
title: Codex Marianus: Egda-clauses (Raw)

description: The project gathers all datasets used for the study 'Early Slavic dative absolutes in discourse: the value of deeply versus strategically annotated treebanks'.<br><br>- egda_raw.csv: Dataset containing all egda-clauses in the Codex Marianus. The only part which has been manipulated is where two subjects were coordinated by *i* 'and'. In these cases, an extra row was created, allowing both subjects to appear in the ocs_sub_lemma column. The row containing the second subject was left empty under all but the subject lemma variable. This allows to observe frequencies regarding lexical variation among egda-clauses' subjects, but at the same time to discard those rows when dealing with other variables.<br>DA_Marianus_raw.csv: Codex Marianus dataset, containing all dative absolutes, as well as genitive absolutes for which there is an OCS parallel. It lists as separate entries both multiple dative participles with one dative subjects, and multiple dative subjects with one dative participle.<br>E.g.: 1) бꙑвъши же печали и гонению словесе ради абье съблажнѣатъ сѧ2) и въшедъши дъштери еѩ иродиѣдѣ. i плѧсавъши и оугождъши иродови<br>Both 1) and 2) are listed as multiple entries, although only 2) has technically more than one dative absolute.DA_Marianus_abridged.csv: This is the same as DA_Marianus_raw.csv, but lists as one dative absolute instances with multiple dative subjects and one dative participle. The criterion chosen was to only retain the entry for the subject which was the closest to the participle (the choice can make a difference should one want to consider the properties of a dative absolute with respect to its subjects).<br><br>DA_Marianus_manipulated.csv: Starting from DA_Marianus_abridged.csv, this dataset treats all dative absolutes in bystъ-clauses as preceding the main clause.<br>The reader interested in reproducing the results of the paper should refer to the 'manipulated' versions of both the egda-clause and the dative absolute datasets.<br>
DOI: 10.6084/m9.figshare.12782426.v1
title: Codex Marianus: Egda-clauses (Raw)

description: Dataset containing all egda-clauses in the Codex Marianus.<br>The only part which has been manipulated is where two subjects were coordinated by *i* 'and'. In these cases, an extra row was created, allowing both subjects to appear in the ocs_sub_lemma column. The row containing the second subject was left empty under all but the subject lemma variable. This allows to observe frequencies regarding lexical variation among egda-clauses' subjects, but at the same time to discard those rows when dealing with other variables.
DOI: 10.6084/m9.figshare.6323837
title: d25.tar.gz

description: bottleneck simulations<br>
DOI: 10.6084/m9.figshare.6323837.v1
title: d25.tar.gz

description: bottleneck simulations<br>
DOI: 10.6084/m9.figshare.6323729
title: Infrared Ellipsometry Analysis of Heritage Photographic Prints

description: Focusing on the photographic archive of Julian Carrillo (Mexico), we study and characterize the photographic processes of a set of 13 photographs dated between 1884 and 1925. By using infrared spectroscopic ellipsometry, we classified a selected set of photographs according to its kind of binder. Thus, we recognized for each photograph, the presence of proteins, and therefore, the particular photographic process. Furthermore, we have identified the presence of baryta layer, the use of plasticizer, and the eventual coating utilized to protect the photograph, whose composition was based in natural organic components, mainly shellac, beeswax, or camphor.
DOI: 10.6084/m9.figshare.6323729.v1
title: Infrared Ellipsometry Analysis of Heritage Photographic Prints

description: Focusing on the photographic archive of Julian Carrillo (Mexico), we study and characterize the photographic processes of a set of 13 photographs dated between 1884 and 1925. By using infrared spectroscopic ellipsometry, we classified a selected set of photographs according to its kind of binder. Thus, we recognized for each photograph, the presence of proteins, and therefore, the particular photographic process. Furthermore, we have identified the presence of baryta layer, the use of plasticizer, and the eventual coating utilized to protect the photograph, whose composition was based in natural organic components, mainly shellac, beeswax, or camphor.
DOI: 10.6084/m9.figshare.6323240
title: Data for Fig. 3 in Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory

description: Data for Fig. 3 in Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory and the related Mathematica notebooks used for producing the plots.
DOI: 10.6084/m9.figshare.6323099
title: MinKNOW + Porechop nanopore reads

description: These files contain the nanopore long reads produced by R9.4 MinION, basecalled during sequencing by MinKNOW (v.Jun17) and demultiplexed by Porechop v0.2.1.<br>Half of each strain's sample underwent FFPE repair, and half did not - these were sequenced under different barcodes. The samples here have had the reads from both barcodes pooled (see "Albacore + Porechop nanopore reads" for the individual readsets).<br><br>These reads were superseded by those from the more accurate basecaller, Albacore (see "Albacore only nanopore reads" for like-for-like equivalents).
DOI: 10.6084/m9.figshare.6323096
title: Table S6

description: Supplementary Table S6: Putative glycosylations of truncated SIPC (Settlement-Inducing protein complex) fragments<br>
DOI: 10.6084/m9.figshare.6323096.v1
title: Table S6

description: Supplementary Table S6: Putative glycosylations of truncated SIPC (Settlement-Inducing protein complex) fragments<br>
DOI: 10.6084/m9.figshare.6323093
title: Table S5

description: Supplementary Table S5: Bioinformatic analysis of putative post-translational modifications of Settlement-Inducing protein complex<br>
DOI: 10.6084/m9.figshare.6323093.v1
title: Table S5

description: Supplementary Table S5: Bioinformatic analysis of putative post-translational modifications of Settlement-Inducing protein complex<br>
DOI: 10.6084/m9.figshare.6323090
title: Table S4

description: <b>Supplementary Table S4:</b> List of primers used in this study.
DOI: 10.6084/m9.figshare.6323090.v1
title: Table S4

description: <b>Supplementary Table S4:</b> List of primers used in this study.
DOI: 10.6084/m9.figshare.6323084
title: Table S3

description: <b>Supplementary Table S3:</b> Differences in the nucleotide and amino acid sequences between the 2 published sequences of SIPC (GenBank: AAR33079.1 and GenBank: AMR58954.1) and the recombinant SIPC described in this study. *:The nucleotide and amino acid sequences deposited by Zhang et al. in GenBank: AMR58954.1 lacks the signal peptide sequence.
DOI: 10.6084/m9.figshare.6323084.v1
title: Table S3

description: <b>Supplementary Table S3:</b> Differences in the nucleotide and amino acid sequences between the 2 published sequences of SIPC (GenBank: AAR33079.1 and GenBank: AMR58954.1) and the recombinant SIPC described in this study. *:The nucleotide and amino acid sequences deposited by Zhang et al. in GenBank: AMR58954.1 lacks the signal peptide sequence.
DOI: 10.6084/m9.figshare.6323081
title: Table S2

description: <b>Supplementary Table S2:</b> Alignment of the amino acid sequences from 3 A. amphitrite SIPC proteins using the multiple sequence alignment software MAFFT at http://www.ebi.ac.uk/Tools/msa/mafft/. Bold letters in red indicate the differences between the amino acid sequences.
DOI: 10.6084/m9.figshare.6323081.v1
title: Table S2

description: <b>Supplementary Table S2:</b> Alignment of the amino acid sequences from 3 A. amphitrite SIPC proteins using the multiple sequence alignment software MAFFT at http://www.ebi.ac.uk/Tools/msa/mafft/. Bold letters in red indicate the differences between the amino acid sequences.
DOI: 10.6084/m9.figshare.6323072
title: Table S1

description: <b>Supplementary Table S1:</b> Alignment of the open reading frame from 3 cDNA sequences of A. amphitrite SIPC using the multiple sequence alignment software MAFFT at http://www.ebi.ac.uk/Tools/msa/mafft/. Bold letters in red indicate the differences between the nucleotide sequences.
DOI: 10.6084/m9.figshare.6323072.v1
title: Table S1

description: <b>Supplementary Table S1:</b> Alignment of the open reading frame from 3 cDNA sequences of A. amphitrite SIPC using the multiple sequence alignment software MAFFT at http://www.ebi.ac.uk/Tools/msa/mafft/. Bold letters in red indicate the differences between the nucleotide sequences.
DOI: 10.6084/m9.figshare.6323069
title: Hilfield Pk Res 09052018 TQ 15886 95516 pt 1

description: Hilfield Pk Res 09052018 TQ 15886 95516 pt 1
DOI: 10.6084/m9.figshare.6323039
title: Supplementary Material for: The cGAS/STING Pathway Is Important for Dendritic Cell Activation but Is Not Essential to Induce Protective Immunity against <b><i>Mycobacterium tuberculosis</i></b> Infection

description: <i>Mycobacterium tuberculosis</i> (Mtb) infection remains a major public health concern. The STING (stimulator of interferon genes) pathway contributes to the cytosolic surveillance of host cells. Most studies on the role of STING activation in Mtb infection have focused on macrophages. Moreover, a detailed investigation of the role of STING during Mtb infection in vivo is required. Here, we deciphered the involvement of STING in the activation of dendritic cells (DCs) and the host response to Mtb infection in vivo. In DCs, this adaptor molecule was important for <i>Ifn-β</i> expression and IL-12 production as well as for the surface expression of the activation markers CD40 and CD86. We also documented that Mtb DNA induces STING activation in murine fibroblasts. In vivo Mtb aerogenic infection induced the upregulation of the <i>STING</i> and <i>cGAS</i> (cyclic GMP-AMP synthase) genes, and <i>Ifn-β</i> pulmonary expression was dependent on both sensors. However, mice deficient for STING or cGAS presented a similar outcome to wild-type controls, with no major alterations in body weight gain, bacterial burden, or survival. Lung inflammation, proinflammatory cytokine production, and inflammatory cell recruitment were similar in STING- and cGAS-deficient mice compared to wild-type controls. In summary, although the STING pathway seems to be crucial for DC activation during Mtb infection, it is dispensable for host protection in vivo.
DOI: 10.6084/m9.figshare.6323069.v1
title: Hilfield Pk Res 09052018 TQ 15886 95516 pt 1

description: Hilfield Pk Res 09052018 TQ 15886 95516 pt 1