cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5683780
title: Gene networks associated with non-syndromic intellectual disability

description: Non-syndromic intellectual disability (NS-ID) is a genetically heterogeneous disorder, with more than 200 candidate genes to date. Despite the increasing number of novel mutations detected, a relatively low number of recurrently mutated genes have been identified, highlighting the complex genetic architecture of the disorder. A systematic search of PubMed and Medline identified 245 genes harbouring non-synonymous variants, insertions or deletions, which were identified as candidate NS-ID genes from case reports or from linkage or pedigree analyses. From this list, 33 genes are common to syndromic intellectual disability (S-ID) and 58 genes are common to certain neurological and neuropsychiatric disorders that often include intellectual disability as a clinical feature. We examined the evolutionary constraint and brain expression of these gene sets, and we performed gene network and protein–protein interaction analyses using GeneGO MetaCore<sup>TM</sup> and DAPPLE, respectively. The 245 NS-ID candidate genes were over-represented in axon guidance, synaptogenesis, cell adhesion and neurotransmission pathways, all of which are key neurodevelopmental processes for the establishment of mature neuronal circuitry in the brain. These 245 genes exhibit significantly elevated expression in human brain and are evolutionarily constrained, consistent with expectations for a brain disorder such as NS-ID that is associated with reduced fecundity. In addition, we report enrichment of dopaminergic and glutamatergic pathways for those candidate NS-ID genes that are common to S-ID and/or neurological and neuropsychiatric disorders that exhibit intellectual disability. Collectively, this study provides an overview and analysis of gene networks associated with NS-ID and suggests modulation of neurotransmission, particularly dopaminergic and glutamatergic systems as key contributors to synaptic dysfunction in NS-ID.
DOI: 10.6084/m9.figshare.5683780.v2
title: Gene networks associated with non-syndromic intellectual disability

description: Non-syndromic intellectual disability (NS-ID) is a genetically heterogeneous disorder, with more than 200 candidate genes to date. Despite the increasing number of novel mutations detected, a relatively low number of recurrently mutated genes have been identified, highlighting the complex genetic architecture of the disorder. A systematic search of PubMed and Medline identified 245 genes harbouring non-synonymous variants, insertions or deletions, which were identified as candidate NS-ID genes from case reports or from linkage or pedigree analyses. From this list, 33 genes are common to syndromic intellectual disability (S-ID) and 58 genes are common to certain neurological and neuropsychiatric disorders that often include intellectual disability as a clinical feature. We examined the evolutionary constraint and brain expression of these gene sets, and we performed gene network and protein–protein interaction analyses using GeneGO MetaCore<sup>TM</sup> and DAPPLE, respectively. The 245 NS-ID candidate genes were over-represented in axon guidance, synaptogenesis, cell adhesion and neurotransmission pathways, all of which are key neurodevelopmental processes for the establishment of mature neuronal circuitry in the brain. These 245 genes exhibit significantly elevated expression in human brain and are evolutionarily constrained, consistent with expectations for a brain disorder such as NS-ID that is associated with reduced fecundity. In addition, we report enrichment of dopaminergic and glutamatergic pathways for those candidate NS-ID genes that are common to S-ID and/or neurological and neuropsychiatric disorders that exhibit intellectual disability. Collectively, this study provides an overview and analysis of gene networks associated with NS-ID and suggests modulation of neurotransmission, particularly dopaminergic and glutamatergic systems as key contributors to synaptic dysfunction in NS-ID.
DOI: 10.6084/m9.figshare.5683780.v1
title: Gene networks associated with non-syndromic intellectual disability

description: Non-syndromic intellectual disability (NS-ID) is a genetically heterogeneous disorder, with more than 200 candidate genes to date. Despite the increasing number of novel mutations detected, a relatively low number of recurrently mutated genes have been identified, highlighting the complex genetic architecture of the disorder. A systematic search of PubMed and Medline identified 245 genes harbouring non-synonymous variants, insertions or deletions, which were identified as candidate NS-ID genes from case reports or from linkage or pedigree analyses. From this list, 33 genes are common to syndromic intellectual disability (S-ID) and 58 genes are common to certain neurological and neuropsychiatric disorders that often include intellectual disability as a clinical feature. We examined the evolutionary constraint and brain expression of these gene sets, and we performed gene network and protein–protein interaction analyses using GeneGO MetaCore<sup>TM</sup> and DAPPLE, respectively. The 245 NS-ID candidate genes were over-represented in axon guidance, synaptogenesis, cell adhesion and neurotransmission pathways, all of which are key neurodevelopmental processes for the establishment of mature neuronal circuitry in the brain. These 245 genes exhibit significantly elevated expression in human brain and are evolutionarily constrained, consistent with expectations for a brain disorder such as NS-ID that is associated with reduced fecundity. In addition, we report enrichment of dopaminergic and glutamatergic pathways for those candidate NS-ID genes that are common to S-ID and/or neurological and neuropsychiatric disorders that exhibit intellectual disability. Collectively, this study provides an overview and analysis of gene networks associated with NS-ID and suggests modulation of neurotransmission, particularly dopaminergic and glutamatergic systems as key contributors to synaptic dysfunction in NS-ID.
DOI: 10.6084/m9.figshare.5683774
title: Supplementary Material for: Dental Caries and Developmental Defects of Enamel in the Primary Dentition of Preterm Infants: Case-Control Observational Study

description: <b><i>Aim:</i></b> Assessment of dental health in the primary dentition of preterm infants (PTI) including investigation of mother- and infant-related risk factors in a case-control study design. <b><i>Material and Methods:</i></b> One hundred twenty-eight infants aged 3-4 years were included. Sixty-four PTI (27 males) were randomly selected from the preterm registry of the Jena University Hospital. As a control group served 64 full-term infants (FTI) recruited from the Department of Paediatric Dentistry, matched for age and sex. Dental examinations were provided by one dentist under standard clinical conditions. Caries was scored using the International Caries Detection and Assessment System (ICDAS II) and the DMFT, gingival health using the Periodontal Screening Index, and developmental defects of enamel using the DDE index. Mother- and infant-related factors were collected via a questionnaire and from medical records. <b><i>Results:</i></b> The caries prevalence was 50.0% (ICDAS II &gt;0) in PTI and 12.5% (ICDAS II &gt;0) in FTI. The caries experience was higher in PTI (DMFT 1.0 ± 3.1) than in FTI (DMFT 0.3 ± 1.0). PTI had a higher risk of caries (OR 7.0), initial lesions (OR 6.2), DDE (OR 7.5), and gingivitis (OR 6.5) than FTI. The highest risk occurred in PTI with an extremely low birth weight (&lt;1,000 g). A higher risk of DDE was present when mothers suffered from illness during pregnancy (OR 3.9). A higher risk of caries was revealed in infants with respiratory syndrome (OR 6.2) or when their mothers had a lower socioeconomic status (OR 6.3). <b><i>Conclusions:</i></b> PTI had less healthy teeth than FTI and are at a higher risk for DDE, caries, and gingivitis. The poorer dental health in PTI is associated with a low birth weight, a low socioeconomic status, and mothers' illness during pregnancy.
DOI: 10.6084/m9.figshare.5683771
title: Amplified fragment length polymorphism analysis supports the valid separate species status of <i>Lucilia caesar</i> and <i>L. illustris</i> (Diptera: Calliphoridae)

description: Common DNA-based species determination methods fail to distinguish some blow flies in the forensically and medically important genus <i>Lucilia</i> Robineau-Desvoidy. This is a practical problem, and it has also been interpreted as casting doubt on the validity of some morphologically defined species. An example is <i>Lucilia illustris</i> and <i>L. caesar</i>, which co-occur in Europe whilst only <i>L. illustris</i> has been collected in North America. Reports that these species shared both mitochondrial and nuclear gene sequences, along with claims that diagnostic morphological characters are difficult to interpret, were used to question their separate species status. We report here that amplified fragment length polymorphism profiles strongly support the validity of both species based on both assignment and phylogenetic analysis, and that traditional identification criteria based on male and female genital morphology are more reliable than has been claimed.
DOI: 10.6084/m9.figshare.5683771.v1
title: Amplified fragment length polymorphism analysis supports the valid separate species status of <i>Lucilia caesar</i> and <i>L. illustris</i> (Diptera: Calliphoridae)

description: Common DNA-based species determination methods fail to distinguish some blow flies in the forensically and medically important genus <i>Lucilia</i> Robineau-Desvoidy. This is a practical problem, and it has also been interpreted as casting doubt on the validity of some morphologically defined species. An example is <i>Lucilia illustris</i> and <i>L. caesar</i>, which co-occur in Europe whilst only <i>L. illustris</i> has been collected in North America. Reports that these species shared both mitochondrial and nuclear gene sequences, along with claims that diagnostic morphological characters are difficult to interpret, were used to question their separate species status. We report here that amplified fragment length polymorphism profiles strongly support the validity of both species based on both assignment and phylogenetic analysis, and that traditional identification criteria based on male and female genital morphology are more reliable than has been claimed.
DOI: 10.6084/m9.figshare.5683765
title: Supplementary Material for: Association between Loss of Skeletal Muscle Mass and Mortality and Tumor Recurrence in Hepatocellular Carcinoma: A Systematic Review and Meta-Analysis

description: <b><i>Background:</i></b> Hepatocellular carcinoma (HCC) has multiple prognostic factors, and there is an increase in knowledge about the body composition and physical status of patients with HCC. The present meta-analysis aimed to explore whether loss of skeletal muscle mass is associated with mortality and tumor recurrence in patients with HCC. <b><i>Method:</i></b> A systematic search was conducted for published literature using PubMed, Embase, and Scopus. We included cohort or case-control studies investigating patients with HCC. The primary and secondary outcomes were the associations of loss of skeletal muscle mass with overall survival and tumor recurrence, respectively, expressed by a summary hazard ratio (HR) and 95% confidence interval (CI). <b><i>Result:</i></b> A total of 13 studies comprising 3,111 patients were included. The summary HRs calculated by either univariate or multivariate analysis both suggested a significant association between sarcopenia and all-cause mortality (crude HR = 2.04, 95% CI: 1.74-2.38; adjusted HR = 1.95, 95% CI: 1.60-2.37). Similarly, loss of skeletal muscle mass was associated with tumor recurrence (crude HR = 1.85, 95% CI: 1.44-2.37; adjusted HR = 1.76, 95% CI: 1.27-2.45). The stratified analysis showed that treatment types and inclusion of body mass index or body weight in the Cox regression model did not modify both clinical outcomes. With an increase in cut-off values of muscle mass on computed tomography images (especially for male patients), there was an insignificant trend of stronger associations between loss of skeletal muscle mass and all-cause mortality. <b><i>Conclusion:</i></b> Loss of skeletal muscle mass is associated with increased all-cause mortality and tumor recurrence in patients with HCC. Further prospective studies incorporating measurements of muscle strength and physical function are warranted to see whether inclusion of both parameters better predicts the outcome than use of muscle mass only.
DOI: 10.6084/m9.figshare.5683741
title: Mitochondrial DNA reveals the natal origin of <i>Caretta caretta</i> (Testudines: Cheloniidae) stranded or bycaught along the Southwestern Adriatic coasts

description: The Mediterranean Sea is an important regional management unit (RMU) for the conservation of the loggerhead turtle (<i>Caretta caretta</i>) because it hosts both nesting and foraging grounds for this species. In this study, attention was focused on an important foraging ground located on the southern Italian coast of the Adriatic Sea, the Gulf of Manfredonia. In this area, <i>C. caretta</i> is threatened by a high level of anthropogenic pressure, especially caused by fishing activities. To understand the genetic composition of the Southwestern Adriatic feeding ground and to highlight which rookeries could be the most impacted by human activities in this area, the mitochondrial haplotype of 239 individuals stranded or incidentally caught in fishing gears from 2008 to 2013 was determined. A mixed stock analysis (MSA) identified the Mediterranean rookeries as the most important contributors to this feeding ground, with contributions also from Atlantic rookeries of Florida and Gulf of Mexico. Finally, the identification of two “orphan haplotypes” and the recovery of three hatchlings on the Vieste beach draw attention to the need for better identification and genetic characterisation of new nesting sites within the Mediterranean Basin.
DOI: 10.6084/m9.figshare.5683741.v1
title: Mitochondrial DNA reveals the natal origin of <i>Caretta caretta</i> (Testudines: Cheloniidae) stranded or bycaught along the Southwestern Adriatic coasts

description: The Mediterranean Sea is an important regional management unit (RMU) for the conservation of the loggerhead turtle (<i>Caretta caretta</i>) because it hosts both nesting and foraging grounds for this species. In this study, attention was focused on an important foraging ground located on the southern Italian coast of the Adriatic Sea, the Gulf of Manfredonia. In this area, <i>C. caretta</i> is threatened by a high level of anthropogenic pressure, especially caused by fishing activities. To understand the genetic composition of the Southwestern Adriatic feeding ground and to highlight which rookeries could be the most impacted by human activities in this area, the mitochondrial haplotype of 239 individuals stranded or incidentally caught in fishing gears from 2008 to 2013 was determined. A mixed stock analysis (MSA) identified the Mediterranean rookeries as the most important contributors to this feeding ground, with contributions also from Atlantic rookeries of Florida and Gulf of Mexico. Finally, the identification of two “orphan haplotypes” and the recovery of three hatchlings on the Vieste beach draw attention to the need for better identification and genetic characterisation of new nesting sites within the Mediterranean Basin.
DOI: 10.6084/m9.figshare.5683732
title: Lephoto dam site

description: 3-D model and associated photographs of the Lephoto dam site.<br><br><br>Abrahams, M., Bordy, E.M., Sciscio, L. and Knoll, F., 2017. Scampering, trotting, walking tridactyl bipedal dinosaurs in southern Africa: ichnological account of a Lower Jurassic palaeosurface (upper Elliot Formation, Roma Valley) in Lesotho. <i>Historical Biology</i>, pp.1-18.http://www.tandfonline.com/doi/figure/10.1080/08912963.2016.1267164?scroll=top&needAccess=true&<br>
DOI: 10.6084/m9.figshare.5683732.v1
title: Lephoto dam site

description: 3-D model and associated photographs of the Lephoto dam site.<br><br><br>Abrahams, M., Bordy, E.M., Sciscio, L. and Knoll, F., 2017. Scampering, trotting, walking tridactyl bipedal dinosaurs in southern Africa: ichnological account of a Lower Jurassic palaeosurface (upper Elliot Formation, Roma Valley) in Lesotho. <i>Historical Biology</i>, pp.1-18.http://www.tandfonline.com/doi/figure/10.1080/08912963.2016.1267164?scroll=top&needAccess=true&<br>
DOI: 10.6084/m9.figshare.5683711
title: Data for Aakala: 'Forest fire histories and tree age structures in Värriö and Maltio Strict Nature Reserves, northern Finland'

description: Site and fire history data used in the paper Aakala: 'Forest fire histories and tree age structures in Värriö and Maltio Strict Nature Reserves, northern Finland', published in Boreal Environment Research<br>
DOI: 10.6084/m9.figshare.5683705
title: How would Rome react to a NCBR attack?

description: https://www.researchgate.net/publication/317056840_How_would_Rome_react_to_a_CBRNe_attack?_iepl[viewId]=xII0E2id248g2Wv925MRTgsK&_iepl[profilePublicationItemVariant]=default&_iepl[contexts][0]=prfpi&_iepl[targetEntityId]=PB:317056840&_iepl[interactionType]=publicationTitle
DOI: 10.6084/m9.figshare.5683705.v1
title: How would Rome react to a NCBR attack?

description: https://www.researchgate.net/publication/317056840_How_would_Rome_react_to_a_CBRNe_attack?_iepl[viewId]=xII0E2id248g2Wv925MRTgsK&_iepl[profilePublicationItemVariant]=default&_iepl[contexts][0]=prfpi&_iepl[targetEntityId]=PB:317056840&_iepl[interactionType]=publicationTitle
DOI: 10.6084/m9.figshare.5683681
title: On the importance of homology in the age of phylogenomics

description: Homology is perhaps the most central concept of phylogenetic biology. Molecular systematists have traditionally paid due attention to the homology statements that are implied by their alignments of orthologous sequences, but some authors have suggested that manual gene-by-gene curation is not sustainable in the phylogenomics era. Here, we show that there are multiple ways to efficiently screen for and detect homology errors in phylogenomic data sets. Application of these screening approaches to two phylogenomic data sets, one for birds and another for mammals, shows that these data are replete with homology errors including alignments of different exons to each other, alignments of exons to introns, and alignments of paralogues to each other. The extent of these homology errors weakens the conclusions of studies based on these data sets. Despite advances in automated phylogenomic pipelines, we contend that much of the long, difficult, and sometimes tedious work of systematics is still required to guard against pervasive homology errors. This conclusion is underscored by recent studies that show that just a few outlier genes can impact phylogenetic results at short, tightly spaced internodes that are deep in the Tree of Life. The view that widespread DNA sequence alignment errors are not a major concern for rigorous systematic research is not tenable. If a primary goal of phylogenomics is to resolve the most challenging phylogenetic problems with the abundant data that are now available, researchers must employ effective procedures to screen for and correct homology errors prior to performing downstream phylogenetic analyses.
DOI: 10.6084/m9.figshare.5683681.v1
title: On the importance of homology in the age of phylogenomics

description: Homology is perhaps the most central concept of phylogenetic biology. Molecular systematists have traditionally paid due attention to the homology statements that are implied by their alignments of orthologous sequences, but some authors have suggested that manual gene-by-gene curation is not sustainable in the phylogenomics era. Here, we show that there are multiple ways to efficiently screen for and detect homology errors in phylogenomic data sets. Application of these screening approaches to two phylogenomic data sets, one for birds and another for mammals, shows that these data are replete with homology errors including alignments of different exons to each other, alignments of exons to introns, and alignments of paralogues to each other. The extent of these homology errors weakens the conclusions of studies based on these data sets. Despite advances in automated phylogenomic pipelines, we contend that much of the long, difficult, and sometimes tedious work of systematics is still required to guard against pervasive homology errors. This conclusion is underscored by recent studies that show that just a few outlier genes can impact phylogenetic results at short, tightly spaced internodes that are deep in the Tree of Life. The view that widespread DNA sequence alignment errors are not a major concern for rigorous systematic research is not tenable. If a primary goal of phylogenomics is to resolve the most challenging phylogenetic problems with the abundant data that are now available, researchers must employ effective procedures to screen for and correct homology errors prior to performing downstream phylogenetic analyses.
DOI: 10.6084/m9.figshare.5683678
title: Phytosociological, structural and conservation analysis of the habitats of Dupont’s lark in Europe: a phytosociological survey applied to the conservation of an endangered species

description: Based on an updated census for the endangered Dupont’s lark (<i>Chersophilus duponti</i>), we conducted a phytosociological survey of 167 sites representative of the distribution area of the species in Europe. Results were used as a starting point for conservation assessment. According to our observations, the bird selects flat deforested areas colonized by small shrubs corresponding to successional, subclimax stages that are either naturally or artificially exploited. Four groups of scrubs were occupied by the bird: (1) supramediterranean dwarf cushion scrubs dominated by <i>Genista pumila</i> ssp. <i>rigidissima</i> or <i>Erinacea anthyllis</i>; (2) gypicolous shrublands and grasslands associated with <i>Lygeum spartum</i>; (3) shrubs dominated by chamaephytes producing allelopathic substances (<i>Thymus, Lavandula, Salvia</i>) and showing different facies according to the level of disturbance; and (4) supramediterranean acidophilous scrubs dominated by <i>Cistus, Erica</i> or <i>Cytisus</i> species. As management measures, we propose reducing tree density in flat areas, promoting the growth of chamaephytes by clearing phanerophytes, and encouraging traditional low-level transhumance grazing. These measures will provide high-quality habitats and help preserve, or even expand, habitable patches to ensure the viability of the European metapopulation of this rare and sensitive songbird.