cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6755138
title: Identifying and assessing the efficiency of different networks of a fine-scale hierarchy of biodiversity hotspots

description: <b>Background</b>: For prioritising practical conservation measures in areas of high endemic plant diversity, a fine-scale hierarchy of sites needs to be established. In this context, conservation sites designed at local and regional levels are considered a network of interconnected areas. <b>Aims</b>: The main aim was to identify two hierarchical levels of a network of conservation sites, called ‘micro hotspots’ and ‘nano hotspots’, and test their efficiency for achieving conservation objectives across the island of Sardinia, Mediterranean Basin. <b>Methods</b>: We analysed the spatial distribution of endemic vascular plant species (EVPS) richness. Additionally, the area, perimeter, connectivity and surplus costs for the protection of all endemic plant populations were used as ranking criteria for a hierarchical classification. <b>Results</b>: We identified eight micro hotspots and 82 nano hotspots. Amongst the three possible solutions compared, the integrated network of micro and nano hotspots resulted in more effective conservation than any of the single-level network solutions with only micro or nano hotspots, and it included 89% of all EVPS in a relatively small areal extent. <b>Conclusions</b>: The identification of hotspot networks at the regional level allowed determining priority areas to implement conservation efforts for EVPS. The integration of micro hotspots with nano hotspots resulted in the most effective network from both conservation and economic perspectives. We suggest that our model may provide an effective tool for integrated and effective conservation actions in the Mediterranean Basin.
DOI: 10.6084/m9.figshare.6755138.v1
title: Identifying and assessing the efficiency of different networks of a fine-scale hierarchy of biodiversity hotspots

description: <b>Background</b>: For prioritising practical conservation measures in areas of high endemic plant diversity, a fine-scale hierarchy of sites needs to be established. In this context, conservation sites designed at local and regional levels are considered a network of interconnected areas. <b>Aims</b>: The main aim was to identify two hierarchical levels of a network of conservation sites, called ‘micro hotspots’ and ‘nano hotspots’, and test their efficiency for achieving conservation objectives across the island of Sardinia, Mediterranean Basin. <b>Methods</b>: We analysed the spatial distribution of endemic vascular plant species (EVPS) richness. Additionally, the area, perimeter, connectivity and surplus costs for the protection of all endemic plant populations were used as ranking criteria for a hierarchical classification. <b>Results</b>: We identified eight micro hotspots and 82 nano hotspots. Amongst the three possible solutions compared, the integrated network of micro and nano hotspots resulted in more effective conservation than any of the single-level network solutions with only micro or nano hotspots, and it included 89% of all EVPS in a relatively small areal extent. <b>Conclusions</b>: The identification of hotspot networks at the regional level allowed determining priority areas to implement conservation efforts for EVPS. The integration of micro hotspots with nano hotspots resulted in the most effective network from both conservation and economic perspectives. We suggest that our model may provide an effective tool for integrated and effective conservation actions in the Mediterranean Basin.
DOI: 10.6084/m9.figshare.6754880
title: Shaw-et-al-Analysis.zip

description: Zipped archive allowing reproduction of the results in the associated paper, in which we fit different models of microbiome recovery to experimental data from individuals receiving antibiotics. <br>This archive contains all the analysis code (R and Stan); data files of reanalyzed datasets; and an Rmarkdown file (with associated cache) reproducing all main results figures in the paper. <br><br>N.B. The original experimental dataset was made available through Zaura et al. (2015) doi: 10.1128/mBio.01693-15. SRA accession: SRP057504.<br><br>
DOI: 10.6084/m9.figshare.6754232
title: Supplementary Material for: The Expression of MAS1, an Angiotensin (1–7) Receptor, in the Eutopic Proliferative Endometria of Endometriosis Patients

description: <b><i>Background/Aim:</i></b> We demonstrated that AT1 and AT2 are expressed and both pathways balance the renin-angiotensin system in endometriosis. MAS1, a specific receptor of angiotensin (1–7), opposes AT1 pathway-associated tissue remodelling. It is not known whether MAS1 has an effect on the pathogenesis of endometriosis or not. <b><i>Materials and Methods:</i></b> Ovarian endometriotic tissues (endo-Ov) and eutopic endometrial tissues (endo-Em) were obtained from 29 patients with endometrial cysts. Normal endometrial tissues (cont-Em) were obtained from patients without endometriosis. Immunohistochemical staining was performed for MAS1, AT1 and AT2 in the endometriosis-associated tissues. The mRNA levels of these receptors were examined by quantitative reverse transcription PCR. <b><i>Results:</i></b> MAS1 was immune-positive at the apical side of the glandular epithelium in the endometriotic lesions. The MAS1 mRNA levels in endo-Ov were increased significantly, irrespective of the menstrual cycle phase. The MAS1 mRNA levels were significantly higher in the proliferative-tissues of the endometriosis patients than in those of the controls. The ratio of the MAS1 to the AT1 mRNA in the proliferative tissues was increased predominantly in the endometriosis patients compared with that in the controls. <b><i>Conclusion:</i></b> High MAS1 expression in the endometrium might promote the initiation of endometriosis via migration of proliferative tissue.
DOI: 10.6084/m9.figshare.6754232.v1
title: Supplementary Material for: The Expression of MAS1, an Angiotensin (1–7) Receptor, in the Eutopic Proliferative Endometria of Endometriosis Patients

description: <b><i>Background/Aim:</i></b> We demonstrated that AT1 and AT2 are expressed and both pathways balance the renin-angiotensin system in endometriosis. MAS1, a specific receptor of angiotensin (1–7), opposes AT1 pathway-associated tissue remodelling. It is not known whether MAS1 has an effect on the pathogenesis of endometriosis or not. <b><i>Materials and Methods:</i></b> Ovarian endometriotic tissues (endo-Ov) and eutopic endometrial tissues (endo-Em) were obtained from 29 patients with endometrial cysts. Normal endometrial tissues (cont-Em) were obtained from patients without endometriosis. Immunohistochemical staining was performed for MAS1, AT1 and AT2 in the endometriosis-associated tissues. The mRNA levels of these receptors were examined by quantitative reverse transcription PCR. <b><i>Results:</i></b> MAS1 was immune-positive at the apical side of the glandular epithelium in the endometriotic lesions. The MAS1 mRNA levels in endo-Ov were increased significantly, irrespective of the menstrual cycle phase. The MAS1 mRNA levels were significantly higher in the proliferative-tissues of the endometriosis patients than in those of the controls. The ratio of the MAS1 to the AT1 mRNA in the proliferative tissues was increased predominantly in the endometriosis patients compared with that in the controls. <b><i>Conclusion:</i></b> High MAS1 expression in the endometrium might promote the initiation of endometriosis via migration of proliferative tissue.
DOI: 10.6084/m9.figshare.6754205
title: Endotoxin - House characteristic analysis database

description: Endotoxin levels in five house typesThe house characteristics
DOI: 10.6084/m9.figshare.6754205.v1
title: Endotoxin - House characteristic analysis database

description: Endotoxin levels in five house typesThe house characteristics
DOI: 10.6084/m9.figshare.6754181
title: EUBAR

description: The EUBAR database includes 1785 <sup>14</sup>C dates and the associated information from more than 650 archaeological sites located in Central-Southern Europe, in a wide territory between the Ebro and Danube rivers. The geographic area under study encompasses the Eastern Iberian Peninsula with the Autonomous Communities of Catalonia, Aragon (Provinces of Huesca and Zaragoza), Navarre and the Basque Country; southern France including from west to east the regions of Aquitaine, Midi-Pyrénées, Languedoc-Roussillon, Limousin, Auvergne, Burgundy (only the departments of Côte-d'Or, Nièvre and Saône-et-Loire), Rhône-Alpes, Provence-Alpes-Côte d’Azur, Franche-Comté, Alsace; northern Italy (regions of Aosta Valley, Piedmont, Lombardy, Trentino/Alto Adige-Südtirol, Veneto, Friuli Venezia Giulia, Liguria, Emilia Romagna and Tuscany; the entire territory of Switzerland, as well of Austria, and the southern part of Germany with the states of Baden-Württemberg and Bavaria (Lower Franconia, Upper Franconia and Middle Franconia not included). The time span of the EUBAR database is one millennium, from 1800 to 750 BC, with that end date determined by the Hallstatt plateau: a plane on the IntCal13 calibration curve, caused by variations in solar activity records.The references of the database are reported at https://www.tdx.cat/handle/10803/283401
DOI: 10.6084/m9.figshare.6754169
title: Supplementary Material for: Structural Genome Variations Related to Craniosynostosis

description: Craniosynostosis refers to a condition during early development in which one or more of the fibrous sutures of the skull prematurely fuse by turning into bone, which produces recognizable patterns of cranial shape malformations depending on which suture(s) are affected. In addition to cases with isolated cranial dysmorphologies, craniosynostosis appears in syndromes that include skeletal features of the eyes, nose, palate, hands, and feet as well as impairment of vision, hearing, and intellectual development. Approximately 85% of the cases are nonsyndromic sporadic and emerge after de novo structural genome rearrangements or single nucleotide variation, while the remainders consist of syndromic cases following mendelian inheritance. By karyotyping, genome wide linkage, and CNV analyses as well as by whole exome and whole genome sequencing, numerous candidate genes for craniosynostosis belonging to the FGF, Wnt, BMP, Ras/ERK, ephrin, hedgehog, STAT, and retinoic acid signaling pathways have been identified. Many of the craniosynostosis-related candidate genes form a functional network based upon protein-protein or protein-DNA interactions. Depending on which node of this craniosynostosis-related network is affected by a gene mutation or a change in gene expression pattern, a distinct craniosynostosis syndrome or set of phenotypes ensues. Structural variations may alter the dosage of one or several genes or disrupt the genomic architecture of genes and their regulatory elements within topologically associated chromatin domains. These may exert dominant effects by either haploinsufficiency, dominant negative partial loss of function, gain of function, epistatic interaction, or alteration of levels and patterns of gene expression during development. Molecular mechanisms of dominant modes of action of these mutations may include loss of one or several binding sites for cognate protein partners or transcription factor binding sequences. Such losses affect interactions within functional networks governing development and consequently result in phenotypes such as craniosynostosis. Many of the novel variants identified by genome wide CNV analyses, whole exome and whole genome sequencing are incorporated in recently developed diagnostic algorithms for craniosynostosis.
DOI: 10.6084/m9.figshare.6754181.v1
title: EUBAR.xlsx

description: The EUBAR database includes more than 1700 <sup>14</sup>C dates and the associated information from more than 650 archaeological sites located in a wide territory between the Ebro and Danube rivers. The geographic area under study encompasses the Eastern Iberian Peninsula with the Autonomous Communities of Catalonia, Aragon (Provinces of Huesca and Zaragoza), Navarre and the Basque Country; southern France including from west to east the regions of Aquitaine, Midi-Pyrénées, Languedoc-Roussillon, Limousin, Auvergne, Burgundy (only the departments of Côte-d'Or, Nièvre and Saône-et-Loire), Rhône-Alpes, Provence-Alpes-Côte d’Azur, Franche-Comté, Alsace; northern Italy (regions of Aosta Valley, Piedmont, Lombardy, Trentino/Alto Adige-Südtirol, Veneto, Friuli Venezia Giulia, Liguria, Emilia Romagna and Tuscany; the entire territory of Switzerland, as well of Austria, and the southern part of Germany with the states of Baden-Württemberg and Bavaria (Lower Franconia, Upper Franconia and Middle Franconia not included). The time span of the EUBAR database is one millennium, from 1800 to 750 BC, with that end date determined by the Hallstatt plateau: a plane on the calibration curve, caused by variations in solar activity records.
DOI: 10.6084/m9.figshare.6754169.v1
title: Supplementary Material for: Structural Genome Variations Related to Craniosynostosis

description: Craniosynostosis refers to a condition during early development in which one or more of the fibrous sutures of the skull prematurely fuse by turning into bone, which produces recognizable patterns of cranial shape malformations depending on which suture(s) are affected. In addition to cases with isolated cranial dysmorphologies, craniosynostosis appears in syndromes that include skeletal features of the eyes, nose, palate, hands, and feet as well as impairment of vision, hearing, and intellectual development. Approximately 85% of the cases are nonsyndromic sporadic and emerge after de novo structural genome rearrangements or single nucleotide variation, while the remainders consist of syndromic cases following mendelian inheritance. By karyotyping, genome wide linkage, and CNV analyses as well as by whole exome and whole genome sequencing, numerous candidate genes for craniosynostosis belonging to the FGF, Wnt, BMP, Ras/ERK, ephrin, hedgehog, STAT, and retinoic acid signaling pathways have been identified. Many of the craniosynostosis-related candidate genes form a functional network based upon protein-protein or protein-DNA interactions. Depending on which node of this craniosynostosis-related network is affected by a gene mutation or a change in gene expression pattern, a distinct craniosynostosis syndrome or set of phenotypes ensues. Structural variations may alter the dosage of one or several genes or disrupt the genomic architecture of genes and their regulatory elements within topologically associated chromatin domains. These may exert dominant effects by either haploinsufficiency, dominant negative partial loss of function, gain of function, epistatic interaction, or alteration of levels and patterns of gene expression during development. Molecular mechanisms of dominant modes of action of these mutations may include loss of one or several binding sites for cognate protein partners or transcription factor binding sequences. Such losses affect interactions within functional networks governing development and consequently result in phenotypes such as craniosynostosis. Many of the novel variants identified by genome wide CNV analyses, whole exome and whole genome sequencing are incorporated in recently developed diagnostic algorithms for craniosynostosis.
DOI: 10.6084/m9.figshare.6754148
title: Supplementary Material for: Patientenerwartungen optimieren: Beschreibung einer präoperativen Kurzintervention am Beispiel von Patienten vor einer Bypass-Operation

description: Hintergrund: Patientenerwartungen gelten als wichtige Wirkmechanismen bei psychotherapeutischen und medizinischen Behandlungen und spielen für die Genesung eine große Rolle. Vor diesem Hintergrund wurde eine psychologische präoperative Kurzintervention zur Erwartungsoptimierung entwickelt, um den Genesungsprozess nach Herzoperationen positiv zu beeinflussen. Dieser Artikel beschreibt die psychologische Kurzintervention (EXPECT) und stellt Evaluationsergebnisse der Intervention aus Patientensicht dar. Patienten und Methoden: 124 herzchirurgische Patienten wurden randomisiert und einer von drei Interventionen zugeteilt: a) Erwartungsoptimierung, b) supportive Therapie oder c) ausschließlich medizinische Standardbehandlung. In der Erwartungsintervention, die 2 Sitzungen und 2 Telefonate vor der Operation umfasst, wurden systematisch verhaltens- und behandlungsbezogene Ergebniserwartungen optimiert. Die Patienten wurden mithilfe von Fragebögen zu ihrer Zufriedenheit mit der Intervention befragt. Mittelwerte wurden berechnet. Ergebnisse: Die Zufriedenheit der Patienten mit beiden psychologischen Interventionen war im Mittel hoch bis sehr hoch. In der Erwartungsinterventionsgruppe fühlten sich die Patienten noch besser informiert und erwarteten einen positiveren Heilungsverlauf als die Patienten, die eine supportive Therapie erhielten. Ein Großteil der Patienten erlebte die Interventionen als hilfreich und erwartete durch diese positivere Ergebnisse, was sich auch im längsschnittlichen Verlauf bestätigte. Somit können präoperative Interventionen bei herzchirurgischen Eingriffen das bestehende Behandlungsangebot sinnvoll erweitern. Schlussfolgerungen: Die Optimierung von verhaltens- und ergebnisbezogenen Patientenerwartungen vor der eigentlichen Intervention kann zu einer Verbesserung von Behandlungsergebnissen beitragen. Eine solche psychologische Intervention wird gut angenommen und ist im Rahmen eines herzchirurgischen Settings durchführbar. Die Förderung positiver Erwartungen und die Veränderung ungünstiger Ausgangserwartungen von <br> Patienten sollten sowohl bei psychotherapeutischen als auch bei herzchirurgischen Behandlungen stärker berücksichtigt werden.
DOI: 10.6084/m9.figshare.6754163
title: Supplementary Material for: Craniofrontonasal Syndrome Caused by Introduction of a Novel uATG in the 5′UTR of EFNB1

description: Craniofrontonasal syndrome (CFNS) is an X-linked disorder caused by <i>EFNB1</i> mutations in which females are more severely affected than males. Severe male phenotypes are associated with mosaicism, supporting cellular interference for sex bias in this disease. Although many variants have been found in the coding region of <i>EFNB1</i>, only 2 pathogenic variants have been identified in the same nucleotide in 5′UTR, disrupting the stop codon of an upstream open reading frame (uORF). uORFs are known to be part of a wide range of post-transcriptional regulation processes, and just recently, their association with human diseases has come to light. In the present study, we analyzed <i>EFNB1 </i>in a female patient with typical features of CFNS. We identified a variant, located at c.-411, creating a new upstream ATG (uATG) in the 5′UTR of <i>EFNB1,</i> which is predicted to alter an existing uORF. Dual-luciferase reporter assays showed significant reduction in protein translation, but no difference in the mRNA levels. Our study demonstrates, for the first time, the regulatory impact of uATG formation on EFNB1 levels and suggests that this should be the target region in molecular diagnosis of CFNS cases without pathogenic variants in the coding and splice sites regions of <i>EFNB1</i>.
DOI: 10.6084/m9.figshare.6754148.v1
title: Supplementary Material for: Patientenerwartungen optimieren: Beschreibung einer präoperativen Kurzintervention am Beispiel von Patienten vor einer Bypass-Operation

description: Hintergrund: Patientenerwartungen gelten als wichtige Wirkmechanismen bei psychotherapeutischen und medizinischen Behandlungen und spielen für die Genesung eine große Rolle. Vor diesem Hintergrund wurde eine psychologische präoperative Kurzintervention zur Erwartungsoptimierung entwickelt, um den Genesungsprozess nach Herzoperationen positiv zu beeinflussen. Dieser Artikel beschreibt die psychologische Kurzintervention (EXPECT) und stellt Evaluationsergebnisse der Intervention aus Patientensicht dar. Patienten und Methoden: 124 herzchirurgische Patienten wurden randomisiert und einer von drei Interventionen zugeteilt: a) Erwartungsoptimierung, b) supportive Therapie oder c) ausschließlich medizinische Standardbehandlung. In der Erwartungsintervention, die 2 Sitzungen und 2 Telefonate vor der Operation umfasst, wurden systematisch verhaltens- und behandlungsbezogene Ergebniserwartungen optimiert. Die Patienten wurden mithilfe von Fragebögen zu ihrer Zufriedenheit mit der Intervention befragt. Mittelwerte wurden berechnet. Ergebnisse: Die Zufriedenheit der Patienten mit beiden psychologischen Interventionen war im Mittel hoch bis sehr hoch. In der Erwartungsinterventionsgruppe fühlten sich die Patienten noch besser informiert und erwarteten einen positiveren Heilungsverlauf als die Patienten, die eine supportive Therapie erhielten. Ein Großteil der Patienten erlebte die Interventionen als hilfreich und erwartete durch diese positivere Ergebnisse, was sich auch im längsschnittlichen Verlauf bestätigte. Somit können präoperative Interventionen bei herzchirurgischen Eingriffen das bestehende Behandlungsangebot sinnvoll erweitern. Schlussfolgerungen: Die Optimierung von verhaltens- und ergebnisbezogenen Patientenerwartungen vor der eigentlichen Intervention kann zu einer Verbesserung von Behandlungsergebnissen beitragen. Eine solche psychologische Intervention wird gut angenommen und ist im Rahmen eines herzchirurgischen Settings durchführbar. Die Förderung positiver Erwartungen und die Veränderung ungünstiger Ausgangserwartungen von <br> Patienten sollten sowohl bei psychotherapeutischen als auch bei herzchirurgischen Behandlungen stärker berücksichtigt werden.
DOI: 10.6084/m9.figshare.6754163.v1
title: Supplementary Material for: Craniofrontonasal Syndrome Caused by Introduction of a Novel uATG in the 5′UTR of EFNB1

description: Craniofrontonasal syndrome (CFNS) is an X-linked disorder caused by <i>EFNB1</i> mutations in which females are more severely affected than males. Severe male phenotypes are associated with mosaicism, supporting cellular interference for sex bias in this disease. Although many variants have been found in the coding region of <i>EFNB1</i>, only 2 pathogenic variants have been identified in the same nucleotide in 5′UTR, disrupting the stop codon of an upstream open reading frame (uORF). uORFs are known to be part of a wide range of post-transcriptional regulation processes, and just recently, their association with human diseases has come to light. In the present study, we analyzed <i>EFNB1 </i>in a female patient with typical features of CFNS. We identified a variant, located at c.-411, creating a new upstream ATG (uATG) in the 5′UTR of <i>EFNB1,</i> which is predicted to alter an existing uORF. Dual-luciferase reporter assays showed significant reduction in protein translation, but no difference in the mRNA levels. Our study demonstrates, for the first time, the regulatory impact of uATG formation on EFNB1 levels and suggests that this should be the target region in molecular diagnosis of CFNS cases without pathogenic variants in the coding and splice sites regions of <i>EFNB1</i>.
DOI: 10.6084/m9.figshare.6754127
title: Subject 5_csv

description: CSV files of S5
DOI: 10.6084/m9.figshare.6754127.v1
title: Subject 5_csv

description: CSV files of S5