cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7862072.v1
title: <i>Tupelocetus palmeri</i>, a new species of protocetid whale (Mammalia, Cetacea) from the middle Eocene of South Carolina

description: We describe <i>Tupelocetus palmeri</i>, a new genus and species of archaeocete whale, based on a single specimen from the Cross Member of the middle Eocene Tupelo Bay Formation (Bartonian). The holotype consists of a partial cranium with complete petrosals, posterior processes of tympanics, the posterior ends of the nasals, a part of the right orbit, and what are interpreted as the right and left P2s. The incomplete skull was collected from the Martin Marietta Cross Quarry (Berkeley County, South Carolina), which has also furnished the holotype of <i>Carolinacetus gingerichi</i>. The new species differs from all other protocetids in having a deep cavity on the occiput, as well as having the following combination of features: large nasal processes of frontals, single-cusped P2, and premaxilla terminates at level of P2 or P3. A phylogenetic analysis places <i>T. palmeri</i> in a large polytomy along the cetacean stem, more closely related to crown Cetacea than <i>Maiacetus</i>, <i>Artiocetus</i>, and <i>Rodhocetus</i>, but more basal than <i>Georgiacetus</i>, <i>Babiacetus</i>, and <i>Eocetus</i>. Another member of this polytomy is <i>Natchitochia jonesi</i>, and although specimens of <i>Natchitochia</i> and <i>T. palmeri</i> do not share any elements, what is preserved suggests that they are similar in size and among the largest of all protocetids. Although we are unable to differentiate these two species, we outline future data that could resolve this question.
DOI: 10.6084/m9.figshare.7862081.v1
title: Scripts used in modelling DMTA data from Incorporating intraspecific variation into dental microwear texture analysis

description: R scripts used in this manuscript. Specifically the sections on subsampling and Linear Mixed-Effect Modelling
DOI: 10.6084/m9.figshare.7862045
title: Low bone mineral density and renal malformation in Mexican patients with Turner syndrome are associated with single nucleotide variants in vitamin D-metabolism genes

description: Turner syndrome (TS) is a common genetic disorder. TS-phenotype includes short stature, gonadal dysgenesis, cardiac and kidney malformations, low bone mineral density (low-BMD) and thyroiditis. TS-phenotype varies from patient to patient and the cause is not clear, the genomic background may be an important contributor for this variability. Our aim was to identify the association of specific single nucleotide variants in the <i>PTPN22, VDR</i>, <i>KL</i>, and <i>CYP27B1</i> genes and vitamin D-metabolism, heart malformation, renal malformation, thyroiditis, and low-BMD in 61 Mexican TS-patients. DNA samples were genotyped for SNVs: rs7975232 (<i>VDR</i>), rs9536282 (<i>KL</i>), rs4646536 (<i>CYP27B1</i>), and rs1599971 (<i>PTPN22</i>) using the KASP assay. Chi-square test under a recessive model and multifactorial dimensionality reduction method were used for analysis. We found a significant association between renal malformation and the rs9536282 (<i>KL</i>) variant and between rs4646536 (<i>CYP27B1</i>) and low-BMD, these variants may have modest effects on these characteristics but contribute to the variability of the TS phenotype. In addition, we identified gene–gene interactions between variants in genes <i>KL</i>, <i>CYP27B1</i> and <i>VDR</i> related to vitamin D-metabolism and low-BMD in TS-patients. Our results support the idea that the genetic background of TS-patients contributes to the clinical variability seen in them.
DOI: 10.6084/m9.figshare.7862045.v1
title: Low bone mineral density and renal malformation in Mexican patients with Turner syndrome are associated with single nucleotide variants in vitamin D-metabolism genes

description: Turner syndrome (TS) is a common genetic disorder. TS-phenotype includes short stature, gonadal dysgenesis, cardiac and kidney malformations, low bone mineral density (low-BMD) and thyroiditis. TS-phenotype varies from patient to patient and the cause is not clear, the genomic background may be an important contributor for this variability. Our aim was to identify the association of specific single nucleotide variants in the <i>PTPN22, VDR</i>, <i>KL</i>, and <i>CYP27B1</i> genes and vitamin D-metabolism, heart malformation, renal malformation, thyroiditis, and low-BMD in 61 Mexican TS-patients. DNA samples were genotyped for SNVs: rs7975232 (<i>VDR</i>), rs9536282 (<i>KL</i>), rs4646536 (<i>CYP27B1</i>), and rs1599971 (<i>PTPN22</i>) using the KASP assay. Chi-square test under a recessive model and multifactorial dimensionality reduction method were used for analysis. We found a significant association between renal malformation and the rs9536282 (<i>KL</i>) variant and between rs4646536 (<i>CYP27B1</i>) and low-BMD, these variants may have modest effects on these characteristics but contribute to the variability of the TS phenotype. In addition, we identified gene–gene interactions between variants in genes <i>KL</i>, <i>CYP27B1</i> and <i>VDR</i> related to vitamin D-metabolism and low-BMD in TS-patients. Our results support the idea that the genetic background of TS-patients contributes to the clinical variability seen in them.
DOI: 10.6084/m9.figshare.7862009
title: Cognitive Impairments in Depressed Patients with Suicidal Ideation: a Magnetic Source Imaging Study

description: This is the first study using Magnetic Source Image to explore the correlations cognitive dysfunction and functional connectivity between IFG and thalamus in major depressive disorder patients with suicidal ideation. We aimed to establish reliable predicative indicators of suicide ideation and to understand the cognitive impairment in MDD more thoroughly, in this way, promoting accurate treatment to cognitive dysfunction, reducing global suicide rates and enables depressed patients to return to society faster and better.
DOI: 10.6084/m9.figshare.7862009.v1
title: Cognitive Impairments in Depressed Patients with Suicidal Ideation: a Magnetic Source Imaging Study

description: This is the first study using Magnetic Source Image to explore the correlations cognitive dysfunction and functional connectivity between IFG and thalamus in major depressive disorder patients with suicidal ideation. We aimed to establish reliable predicative indicators of suicide ideation and to understand the cognitive impairment in MDD more thoroughly, in this way, promoting accurate treatment to cognitive dysfunction, reducing global suicide rates and enables depressed patients to return to society faster and better.
DOI: 10.6084/m9.figshare.7861985
title: Supplementary Material for: The Study of Psychopathology from the Network Analysis Perspective: A Systematic Review

description: <b><i>Background:</i></b> Network analysis (NA) is an analytical tool that allows one to explore the map of connections and eventual dynamic influences among symptoms and other elements of mental disorders. In recent years, the use of NA in psychopathology has rapidly grown, which calls for a systematic and critical analysis of its clinical utility. <b><i>Methods:</i></b> Following PRISMA guidelines, a systematic review of published empirical studies applying NA in psychopathology, between 2010 and 2017, was conducted. We included the literature published in PubMed and PsycINFO using as keywords any combination of “network analysis” with the terms “anxiety,” “affective disorders,” “depression,” “schizophrenia,” “psychosis,” “personality disorders,” “substance abuse” and “psychopathology.” <b><i>Results:</i></b> The review showed that NA has been applied in a plethora of mental disorders in adults (i.e., 13 studies on anxiety disorders; 19 on mood disorders; 7 on psychosis; 1 on substance abuse; 1 on borderline personality disorder; 18 on the association of symptoms between disorders), and 6 on childhood and adolescence. <b><i>Conclusions:</i></b> A critical examination of the results of each study suggests that NA helps to identify, in an innovative way, important aspects of psychopathology like the centrality of the symptoms in a given disorder as well as the mutual dynamics among symptoms. Yet, despite these promising results, the clinical utility of NA is still uncertain as there are important limitations on the analytic procedures (e.g., reliability of indices), the type of data included (e.g., typically restricted to secondary analysis of already published data), and ultimately, the psychometric and clinical validity of the results.
DOI: 10.6084/m9.figshare.7861985.v1
title: Supplementary Material for: The Study of Psychopathology from the Network Analysis Perspective: A Systematic Review

description: <b><i>Background:</i></b> Network analysis (NA) is an analytical tool that allows one to explore the map of connections and eventual dynamic influences among symptoms and other elements of mental disorders. In recent years, the use of NA in psychopathology has rapidly grown, which calls for a systematic and critical analysis of its clinical utility. <b><i>Methods:</i></b> Following PRISMA guidelines, a systematic review of published empirical studies applying NA in psychopathology, between 2010 and 2017, was conducted. We included the literature published in PubMed and PsycINFO using as keywords any combination of “network analysis” with the terms “anxiety,” “affective disorders,” “depression,” “schizophrenia,” “psychosis,” “personality disorders,” “substance abuse” and “psychopathology.” <b><i>Results:</i></b> The review showed that NA has been applied in a plethora of mental disorders in adults (i.e., 13 studies on anxiety disorders; 19 on mood disorders; 7 on psychosis; 1 on substance abuse; 1 on borderline personality disorder; 18 on the association of symptoms between disorders), and 6 on childhood and adolescence. <b><i>Conclusions:</i></b> A critical examination of the results of each study suggests that NA helps to identify, in an innovative way, important aspects of psychopathology like the centrality of the symptoms in a given disorder as well as the mutual dynamics among symptoms. Yet, despite these promising results, the clinical utility of NA is still uncertain as there are important limitations on the analytic procedures (e.g., reliability of indices), the type of data included (e.g., typically restricted to secondary analysis of already published data), and ultimately, the psychometric and clinical validity of the results.
DOI: 10.6084/m9.figshare.7861964
title: Supplementary Material for: Hemolytic Uremic Syndrome in an Infant with Primary Hyperoxaluria Type II: An Unreported Clinical Association

description: A 6-month-old boy presented with acute renal failure, thrombocytopenia, and severe non-immune hemolytic anemia. Infection by Shiga-like toxin-producing <i>Escherichia coli</i> and other causes of microangiopathic hemolysis were ruled out, leading to a diagnosis of atypical hemolytic uremic syndrome (aHUS). Neither pathogenic variants in HUS-associated genes nor anti-factor H antibodies were identified. Copy number variation analysis uncovered 4 copies of complement factor H related genes, <i>CFHR1</i>-<i>CFHR4</i>, conceivably leading to higher than normal levels of the corresponding proteins. However, this abnormality was also found in the healthy relatives, neither explaining the disease nor the excessive complement deposition on endothelial cells detected by an ex-vivo test. Whole-exome sequencing revealed a pathogenic homozygous variant in <i>GRHPR</i> encoding the glyoxylate and hydroxypyruvate reductase. Recessive <i>GRHPR</i> mutations cause primary hyperoxaluria type 2 (PH2). The presence of renal calculi in the patient and elevated oxalate levels in the urine were consistent with the genetic diagnosis of PH2. We hypothesize that, in this patient, hyperoxaluria caused by the <i>GRHPR</i> genetic defect triggered endothelial perturbation and complement activation, which was amplified by impaired factor H regulatory activity due to the increased ­<i>CFHR1-CFHR4</i> copy numbers, resulting in aHUS.
DOI: 10.6084/m9.figshare.7861967
title: Supplementary Material for: Use of a Simple in vitro Test to Assess Loss of Chemical due to Volatility during an in vitro Human Skin Absorption Study

description: <b><i>Background:</i></b> We tested the cutaneous distribution of 50 chemicals in frozen human skin. The mass balance (MB) values for 48% of the chemicals were &lt; 90%, possibly due to evaporation. <b><i>Methods:</i></b> We confirmed the reduction in MB was due to evaporation for two chemicals tested in skin penetration experiments using a carbon filter above the skin to trap airborne chemical. An in vitro assay was used to predict the reduction in MB due to evaporation by comparing the recovery of chemicals after 4 h of incubation at room temperature in open and closed vials. <b><i>Results:</i></b> Evaporative losses in vitro correlated well with measured MBs (i.e., &lt; 90%) in skin penetration experiments (<i>R</i><sup>2</sup> = 0.81). There was a correlation of the MB with the vapour pressure (VP) which could be used to group chemicals according to their likelihood to evaporate during the course of a skin penetration study. There was also a correlation of MB with Henry’s law constants, melting and boiling points. <b><i>Conclusion:</i></b> Our data support the use of a quick and simple test for volatility to account for the loss of MB in skin penetration experiment due to volatility. The best parameter to indicate the potential of a chemical to evaporate is the VP.
DOI: 10.6084/m9.figshare.7861928
title: Dataset of University League Tables and Teaching Qualification in UK.xlsx

description: <i>The data article presents the relationship between university league tables and teaching qualification in the UK. Data were collected from the university and subject league tables (Complete University Guide) and teaching qualification (The Higher Education Academy - HEA), and Higher Education Funding Council for England - Hefce), UK. </i>
DOI: 10.6084/m9.figshare.7861964.v1
title: Supplementary Material for: Hemolytic Uremic Syndrome in an Infant with Primary Hyperoxaluria Type II: An Unreported Clinical Association

description: A 6-month-old boy presented with acute renal failure, thrombocytopenia, and severe non-immune hemolytic anemia. Infection by Shiga-like toxin-producing <i>Escherichia coli</i> and other causes of microangiopathic hemolysis were ruled out, leading to a diagnosis of atypical hemolytic uremic syndrome (aHUS). Neither pathogenic variants in HUS-associated genes nor anti-factor H antibodies were identified. Copy number variation analysis uncovered 4 copies of complement factor H related genes, <i>CFHR1</i>-<i>CFHR4</i>, conceivably leading to higher than normal levels of the corresponding proteins. However, this abnormality was also found in the healthy relatives, neither explaining the disease nor the excessive complement deposition on endothelial cells detected by an ex-vivo test. Whole-exome sequencing revealed a pathogenic homozygous variant in <i>GRHPR</i> encoding the glyoxylate and hydroxypyruvate reductase. Recessive <i>GRHPR</i> mutations cause primary hyperoxaluria type 2 (PH2). The presence of renal calculi in the patient and elevated oxalate levels in the urine were consistent with the genetic diagnosis of PH2. We hypothesize that, in this patient, hyperoxaluria caused by the <i>GRHPR</i> genetic defect triggered endothelial perturbation and complement activation, which was amplified by impaired factor H regulatory activity due to the increased ­<i>CFHR1-CFHR4</i> copy numbers, resulting in aHUS.
DOI: 10.6084/m9.figshare.7861916
title: Torbjørn Raugstad - Crayfish datasets for master's thesis 2019

description: My datasets contain information about crayfish activity (arrivals_df), size (size_df), fighting (fight_df) and sex & length (field_df). The "size" variable in size_df is different from the "length" variable in field_df. Size in "size_df" was measured digitally from screenshots of my videos using a computer program called Fiji. Crayfish length was measured directly by catching crayfish and measuring them out in the field. I aslo include the data from my three temperature loggers (Temperature&LightLoggers) as well as the environmental variable used in my analyses (env). The text and xlsx versions of the dataset are the same. The only difference is the format (.txt vs .xlsx). For more information about my datasets, read my master's thesis.
DOI: 10.6084/m9.figshare.7861916.v1
title: Torbjørn Raugstad - Crayfish datasets for master's thesis 2019

description: My datasets contain information about crayfish activity (arrivals_df), size (size_df), fighting (fight_df) and sex & length (field_df). The "size" variable in size_df is different from the "length" variable in field_df. Size in "size_df" was measured digitally from screenshots of my videos using a computer program called Fiji. Crayfish length was measured directly by catching crayfish and measuring them out in the field. I aslo include the data from my three temperature loggers (Temperature&LightLoggers) as well as the environmental variable used in my analyses (env). The text and xlsx versions of the dataset are the same. The only difference is the format (.txt vs .xlsx). For more information about my datasets, read my master's thesis.
DOI: 10.6084/m9.figshare.7861928.v1
title: Dataset of University League Tables and Teaching Qualification in UK.xlsx

description: <i>The data article presents the relationship between university league tables and teaching qualification in the UK. Data were collected from the university and subject league tables (Complete University Guide) and teaching qualification (The Higher Education Academy - HEA), and Higher Education Funding Council for England - Hefce), UK. </i>
DOI: 10.6084/m9.figshare.7861901
title: A natural hybrid of Impatiens, in the introduced range, demonstrated by sequence analysis of the nuclear ribosomal DNA-gene repeat

description: In a nature reserve, in Ticino canton in Switzerland amidst a mixed population of non-native <i>Impatiens parviflora</i> and <i>I. glandulifera</i> aberrant plants of <i>I. parviflora</i> were observed. A herbarium voucher and seeds were collected and seedlings subsequently raised in a greenhouse. Molecular analysis for ITS region and chloroplast markers revealed the plants to be a hybrid between <i>I. parviflora</i> and <i>I. balfourii</i>, another non-native <i>Impatiens</i> species occurring in the Ticino canton. No crossing out nor reduced fertility was observed in F2 and F3 generations, raised in a greenhouse. Sizeable populations of the hybrid have been observed in 2014 in the Ticino canton in the absence of the parental species. Nuclear genome size as measured by flow cytometry with propidium iodide did not indicate polyploidy and the ITS region remained 100% uniform. Therefore a homoploid hybrid speciation event is assumed.
DOI: 10.6084/m9.figshare.7861784
title: Prediction and integration of semantics during L2 and L1 listening

description: Using the visual world paradigm, we tested whether Dutch-English bilinguals predict upcoming semantic information in auditory sentence comprehension to the same extent in their native (L1) and second language (L2). Participants listened to sentences in L1 and L2 while their eye-movements were measured. A display containing a picture of either a target word or a semantic competitor, and three unrelated objects was shown before the onset of the auditory target word in the sentence. There were more fixations on the target and competitor pictures relative to the unrelated pictures in both languages, before hearing the target word could affect fixations. Also, semantically stronger related competitors attracted more fixations. This relatedness effect was stronger, and it started earlier in the L1 than in the L2. These results suggest that bilinguals predict semantics in the L2, but the spread of semantic activation during prediction is slower and weaker than in the L1.
DOI: 10.6084/m9.figshare.7861901.v2
title: A natural hybrid of Impatiens, in the introduced range, demonstrated by sequence analysis of the nuclear ribosomal DNA-gene repeat

description: In a nature reserve, in Ticino canton in Switzerland amidst a mixed population of non-native <i>Impatiens parviflora</i> and <i>I. glandulifera</i> aberrant plants of <i>I. parviflora</i> were observed. A herbarium voucher and seeds were collected and seedlings subsequently raised in a greenhouse. Molecular analysis for ITS region and chloroplast markers revealed the plants to be a hybrid between <i>I. parviflora</i> and <i>I. balfourii</i>, another non-native <i>Impatiens</i> species occurring in the Ticino canton. No crossing out nor reduced fertility was observed in F2 and F3 generations, raised in a greenhouse. Sizeable populations of the hybrid have been observed in 2014 in the Ticino canton in the absence of the parental species. Nuclear genome size as measured by flow cytometry with propidium iodide did not indicate polyploidy and the ITS region remained 100% uniform. Therefore a homoploid hybrid speciation event is assumed.
DOI: 10.6084/m9.figshare.7861784.v2
title: Prediction and integration of semantics during L2 and L1 listening

description: Using the visual world paradigm, we tested whether Dutch-English bilinguals predict upcoming semantic information in auditory sentence comprehension to the same extent in their native (L1) and second language (L2). Participants listened to sentences in L1 and L2 while their eye-movements were measured. A display containing a picture of either a target word or a semantic competitor, and three unrelated objects was shown before the onset of the auditory target word in the sentence. There were more fixations on the target and competitor pictures relative to the unrelated pictures in both languages, before hearing the target word could affect fixations. Also, semantically stronger related competitors attracted more fixations. This relatedness effect was stronger, and it started earlier in the L1 than in the L2. These results suggest that bilinguals predict semantics in the L2, but the spread of semantic activation during prediction is slower and weaker than in the L1.
DOI: 10.6084/m9.figshare.7861901.v1
title: A natural hybrid of Impatiens, in the introduced range, demonstrated by sequence analysis of the nuclear ribosomal DNA-gene repeat

description: In a nature reserve, in Ticino canton in Switzerland amidst a mixed population of non-native <i>Impatiens parviflora</i> and <i>I. glandulifera</i> aberrant plants of <i>I. parviflora</i> were observed. A herbarium voucher and seeds were collected and seedlings subsequently raised in a greenhouse. Molecular analysis for ITS region and chloroplast markers revealed the plants to be a hybrid between <i>I. parviflora</i> and <i>I. balfourii</i>, another non-native <i>Impatiens</i> species occurring in the Ticino canton. No crossing out nor reduced fertility was observed in F2 and F3 generations, raised in a greenhouse. Sizeable populations of the hybrid have been observed in 2014 in the Ticino canton in the absence of the parental species. Nuclear genome size as measured by flow cytometry with propidium iodide did not indicate polyploidy and the ITS region remained 100% uniform. Therefore a homoploid hybrid speciation event is assumed.