cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5840706.v2
title: Molecular dynamics of DSB in nucleosome

description: These files contain the coordinate files (.gro) and compact trajectory files (.xtc) from the GROMACS runs of the nucleosome models O (experimental 1kx5), M1-M4 (model O with double strand breaks at various positions). Trajectories are compacted from the .trr files, by excluding water molecules and ions. Frames are stored each 40 ps for 1 microsecond trajectories (25,000 frames per .xtc file, about 2 Gb each).<br>PLOS submitted manuscript "Mechanical evolution of DNA double strand breaks in the nucleosome", by F. Cleri, F. Landuzzi and R. Blossey<br><br>
DOI: 10.6084/m9.figshare.5840706.v3
title: Molecular dynamics of DSB in nucleosome

description: These files contain the coordinate files (.gro) and compact trajectory files (.xtc) from the GROMACS runs of the nucleosome models O (experimental 1kx5), M1-M4 (model O with double strand breaks at various positions). Trajectories are compacted from the .trr files, by excluding water molecules and ions. Frames are stored each 40 ps for ~1 microsecond trajectories (~25,000 frames per .xtc file, ~2 Gb each).<br>PLOS submitted manuscript "Mechanical evolution of DNA double strand breaks in the nucleosome", by F. Cleri, F. Landuzzi and R. Blossey<br><br>
DOI: 10.6084/m9.figshare.5840697
title: spectra data of tea plantation

description: Collected with Cubert UHD185 hyperspectral imager mounted on a flying UAV
DOI: 10.6084/m9.figshare.5840601
title: Retention of the flight-adapted avian finger-joint complex in the Ostrich helps identify when wings began evolving in dinosaurs

description: The functional anatomies of avian finger joints have never been compared with those of the basal avian <i>Archaeopteryx lithographica</i> or maniraptoran theropod dinosaurs. These startling oversights are due to unfamiliarity of the joints outside of highly specialised studies of bird-wing biomechanics. Here fleshed to skeletonised repeated-measures analyses of finger-joint ranges of motion (ROMs) in a basal palaeognath, the Ostrich <i>Struthio camelus</i>, were utilised as a model to begin filling in these knowledge gaps. Results verified that all of the flight-adapted, avian-specific finger joints are retained in the flightless, yet large and well-differentiated fingers of the Ostrich. Moreover, Ostrich finger joints still possess flight-restricted ROMs within the semi-pronated plane of the manus. The osteological markers of these highly conserved flight-adapted characters in Ostrich show that prior descriptions have unknowingly demonstrated that the main avian finger-joint complex began evolving at the base of Pennaraptora (Oviraptorosauria + Paraves). This detailed functional analysis provides non-embryological support for the hypothesis that maniraptoran theropods shared digital homologies with birds, and supports recent pronation studies indicating that pennaraptoran theropods had evolved avian distal wing joints stiffened for aerial locomotion.
DOI: 10.6084/m9.figshare.5840601.v2
title: Retention of the flight-adapted avian finger-joint complex in the Ostrich helps identify when wings began evolving in dinosaurs

description: The functional anatomies of avian finger joints have never been compared with those of the basal avian <i>Archaeopteryx lithographica</i> or maniraptoran theropod dinosaurs. These startling oversights are due to unfamiliarity of the joints outside of highly specialised studies of bird-wing biomechanics. Here fleshed to skeletonised repeated-measures analyses of finger-joint ranges of motion (ROMs) in a basal palaeognath, the Ostrich <i>Struthio camelus</i>, were utilised as a model to begin filling in these knowledge gaps. Results verified that all of the flight-adapted, avian-specific finger joints are retained in the flightless, yet large and well-differentiated fingers of the Ostrich. Moreover, Ostrich finger joints still possess flight-restricted ROMs within the semi-pronated plane of the manus. The osteological markers of these highly conserved flight-adapted characters in Ostrich show that prior descriptions have unknowingly demonstrated that the main avian finger-joint complex began evolving at the base of Pennaraptora (Oviraptorosauria + Paraves). This detailed functional analysis provides non-embryological support for the hypothesis that maniraptoran theropods shared digital homologies with birds, and supports recent pronation studies indicating that pennaraptoran theropods had evolved avian distal wing joints stiffened for aerial locomotion.
DOI: 10.6084/m9.figshare.5840553
title: Promoting innovation: Enhancing transdisciplinary opportunities for medical and engineering students

description: <b>Purpose:</b> Addressing current healthcare challenges requires innovation and collaboration. Current literature provides limited guidance in promoting these skills in medical school. One approach involves transdisciplinary training in which students from different disciplines work together toward a shared goal. We assessed the need for such a curriculum at Dartmouth College. <b>Methods:</b> We surveyed medical and engineering students’ educational values; learning experiences; professional goals; and interest in transdisciplinary education and innovation. Data were analyzed using descriptive statistics. <b>Results:</b> Shared values among student groups included leadership development, innovation, collaboration, and resource sharing. Medical students felt their curriculum inadequately addressed creativity and innovation relative to their engineering counterparts (<i>p</i> p <b>Conclusions:</b> Medical and engineering students share an interest in the innovation process and need a shared curriculum to facilitate collaboration. A transdisciplinary course that familiarizes students with this process has the potential to promote physicians and engineers as leaders and innovators who can effectively work across industry lines. A transdisciplinary course was piloted in Spring 2017.
DOI: 10.6084/m9.figshare.5840553.v1
title: Promoting innovation: Enhancing transdisciplinary opportunities for medical and engineering students

description: <b>Purpose:</b> Addressing current healthcare challenges requires innovation and collaboration. Current literature provides limited guidance in promoting these skills in medical school. One approach involves transdisciplinary training in which students from different disciplines work together toward a shared goal. We assessed the need for such a curriculum at Dartmouth College. <b>Methods:</b> We surveyed medical and engineering students’ educational values; learning experiences; professional goals; and interest in transdisciplinary education and innovation. Data were analyzed using descriptive statistics. <b>Results:</b> Shared values among student groups included leadership development, innovation, collaboration, and resource sharing. Medical students felt their curriculum inadequately addressed creativity and innovation relative to their engineering counterparts (<i>p</i> p <b>Conclusions:</b> Medical and engineering students share an interest in the innovation process and need a shared curriculum to facilitate collaboration. A transdisciplinary course that familiarizes students with this process has the potential to promote physicians and engineers as leaders and innovators who can effectively work across industry lines. A transdisciplinary course was piloted in Spring 2017.
DOI: 10.6084/m9.figshare.5840451.v1
title: Aporte bibliográfico para el desarrollo de tesis en formación Ciudadana

description: Aporte bibliográfico para el desarrollo de tesis en formación ciudadana.<br>
DOI: 10.6084/m9.figshare.5840433
title: The genetic landscape of Mediterranean North African populations through complete mtDNA sequences

description: <b>Background:</b> The genetic composition of human North African populations is an amalgam of different ancestral components coming from the Middle East, Europe, south-Saharan Africa and autochthonous to North Africa. This complex genetic pattern is the result of migrations and admixtures in the region since Palaeolithic times. <b>Aims:</b> The objective of the present study is to refine knowledge of the population history of North African populations through the analysis of complete mitochondrial sequences. <b>Subjects and methods:</b> This study has sequenced complete mitochondrial DNAs (mtDNAs) in several North African and neighbouring individuals. <b>Results:</b> The mtDNA haplogroup classification and phylogeny shows a high genetic diversity in the region as a result of continuous admixture. The phylogenetic analysis allowed us to identify a new haplogroup characterised by positions 10 101 C and 146 C (H1v2), a sub-branch of H1v, which is restricted to North Africa and whose origins are estimated as ∼4000 years ago. <b>Conclusions:</b> The analysis of the complete mtDNA genome has allowed for the identification of a North African sub-lineage that might be ignored by the analysis of partial mtDNA control region sequences, highlighting the phylogeographic relevance of mtDNA complete sequence analysis.
DOI: 10.6084/m9.figshare.5840433.v1
title: The genetic landscape of Mediterranean North African populations through complete mtDNA sequences

description: <b>Background:</b> The genetic composition of human North African populations is an amalgam of different ancestral components coming from the Middle East, Europe, south-Saharan Africa and autochthonous to North Africa. This complex genetic pattern is the result of migrations and admixtures in the region since Palaeolithic times. <b>Aims:</b> The objective of the present study is to refine knowledge of the population history of North African populations through the analysis of complete mitochondrial sequences. <b>Subjects and methods:</b> This study has sequenced complete mitochondrial DNAs (mtDNAs) in several North African and neighbouring individuals. <b>Results:</b> The mtDNA haplogroup classification and phylogeny shows a high genetic diversity in the region as a result of continuous admixture. The phylogenetic analysis allowed us to identify a new haplogroup characterised by positions 10 101 C and 146 C (H1v2), a sub-branch of H1v, which is restricted to North Africa and whose origins are estimated as ∼4000 years ago. <b>Conclusions:</b> The analysis of the complete mtDNA genome has allowed for the identification of a North African sub-lineage that might be ignored by the analysis of partial mtDNA control region sequences, highlighting the phylogeographic relevance of mtDNA complete sequence analysis.
DOI: 10.6084/m9.figshare.5840430
title: Mitochondrial variability in the Mediterranean area: a complex stage for human migrations

description: <b>Context:</b> The Mediterranean area has always played a significant role in human dispersal due to the large number of migratory events contributing to shape the cultural features and the genetic pool of its populations. <b>Objective:</b> This paper aims to review and diachronically describe the mitogenome variability in the Mediterranean population and the main demic diffusions that occurred in this area over time. <b>Methods:</b> Frequency distributions of the leading mitochondrial haplogroups have been geographically and chronologically evaluated. The variability of U5b and K lineages has been focussed to broaden the knowledge of their genetic histories. <b>Results:</b> The mitochondrial genetic makeup of Palaeolithic hunter-gatherers is poorly defined within the extant Mediterranean populations, since only a few traces of their genetic contribution are still detectable. The Neolithic lineages are more represented, suggesting that the Neolithic revolution had a marked effect on the peopling of the Mediterranean area. The largest effect, however, was provided by historical migrations. <b>Conclusion:</b> Although the mitogenome variability has been widely used to try and clarify the evolution of the Mediterranean genetic makeup throughout almost 50 000 years, it is necessary to collect whole genome data on both extinct and extant populations from this area to fully reconstruct and interpret the impact of multiple migratory waves and their cultural and genetic consequences on the structure of the Mediterranean populations.
DOI: 10.6084/m9.figshare.5840430.v1
title: Mitochondrial variability in the Mediterranean area: a complex stage for human migrations

description: <b>Context:</b> The Mediterranean area has always played a significant role in human dispersal due to the large number of migratory events contributing to shape the cultural features and the genetic pool of its populations. <b>Objective:</b> This paper aims to review and diachronically describe the mitogenome variability in the Mediterranean population and the main demic diffusions that occurred in this area over time. <b>Methods:</b> Frequency distributions of the leading mitochondrial haplogroups have been geographically and chronologically evaluated. The variability of U5b and K lineages has been focussed to broaden the knowledge of their genetic histories. <b>Results:</b> The mitochondrial genetic makeup of Palaeolithic hunter-gatherers is poorly defined within the extant Mediterranean populations, since only a few traces of their genetic contribution are still detectable. The Neolithic lineages are more represented, suggesting that the Neolithic revolution had a marked effect on the peopling of the Mediterranean area. The largest effect, however, was provided by historical migrations. <b>Conclusion:</b> Although the mitogenome variability has been widely used to try and clarify the evolution of the Mediterranean genetic makeup throughout almost 50 000 years, it is necessary to collect whole genome data on both extinct and extant populations from this area to fully reconstruct and interpret the impact of multiple migratory waves and their cultural and genetic consequences on the structure of the Mediterranean populations.
DOI: 10.6084/m9.figshare.5840427
title: Dinucleotide (CA)n tandem repeats on the human X-chromosome and the history of the Mediterranean populations

description: <b>Background:</b> Tandem repeats (STRs) are genomic markers of particular interest in forensic and population genetics. Most of the population data currently available correspond to the variation of STRs of forensic panels, which barely include dinucleotide tandem repeats. <b>Aims:</b> The aim of the study is to test the usefulness of a battery of dinucleotide STRs on the X chromosome for population and forensic studies. <b>Subjects and methods:</b> A total of 672 individuals from 12 Mediterranean populations and two external references were analysed for 15 X-STR following the instructions of the commercial company and using control DNA from the CEPH centre whose sequences are published in GenBank. Genotypic results were analysed using standard population genetics methods including estimates of linkage disequilibrium, population structure and gene flow. Common forensic efficiency parameters were calculated. <b>Results:</b> The analysed X-STRs show high values of genetic diversity, comparable to other STRs of more common use. No significant associations between markers were found. A slight population structure was detected between the two shores of the Mediterranean. The X-STRs studied here present a similar degree of variability to that of other X-STRs used in forensics. <b>Conclusion:</b> Tandem-repeated dinucleotides are a good tool for evidencing population differences here. Forensic parameters indicate that the dinucleotide X-STRs are suitable for forensic use.
DOI: 10.6084/m9.figshare.5840427.v1
title: Dinucleotide (CA)n tandem repeats on the human X-chromosome and the history of the Mediterranean populations

description: <b>Background:</b> Tandem repeats (STRs) are genomic markers of particular interest in forensic and population genetics. Most of the population data currently available correspond to the variation of STRs of forensic panels, which barely include dinucleotide tandem repeats. <b>Aims:</b> The aim of the study is to test the usefulness of a battery of dinucleotide STRs on the X chromosome for population and forensic studies. <b>Subjects and methods:</b> A total of 672 individuals from 12 Mediterranean populations and two external references were analysed for 15 X-STR following the instructions of the commercial company and using control DNA from the CEPH centre whose sequences are published in GenBank. Genotypic results were analysed using standard population genetics methods including estimates of linkage disequilibrium, population structure and gene flow. Common forensic efficiency parameters were calculated. <b>Results:</b> The analysed X-STRs show high values of genetic diversity, comparable to other STRs of more common use. No significant associations between markers were found. A slight population structure was detected between the two shores of the Mediterranean. The X-STRs studied here present a similar degree of variability to that of other X-STRs used in forensics. <b>Conclusion:</b> Tandem-repeated dinucleotides are a good tool for evidencing population differences here. Forensic parameters indicate that the dinucleotide X-STRs are suitable for forensic use.
DOI: 10.6084/m9.figshare.5840421
title: Ripples on the surface. Surnames and genes in Sicily and Southern Italy

description: <b>Background:</b> Southern Italy and Sicily played a key role in the peopling history of the Mediterranean. While genetic research showed the remarkable homogeneity of these regions, surname-based studies instead suggested low population mobility, hence potential structuring. <b>Aim:</b> In order to better understand these different patterns, this study (1) thoroughly analysed the surname structure of Sicily and Southern Italy and (2) tested its relationships with a wide set of molecular markers. <b>Subjects and methods:</b> Surname data were collected from 1213 municipalities and compared to uniparental and autosomal genetic markers typed in ∼300 individuals from 8–10 populations. Surname analyses were performed using different multivariate methods, while comparisons with genetic data relied on correlation tests. <b>Results:</b> Surnames were clearly structured according to regional geographic patterns, which likely emerged because of recent isolation-by-distance-like population dynamics. In general, genetic markers, hinting at a pervasive homogeneity, did not correlate with surname distribution. However, long autosomal haplotypes (&gt;5 cM) that compared to genotypic (SNPs) data identify more “recent” relatedness, showing a clear association with surname patterns. <b>Conclusion:</b> The apparent contradiction between surname structure and genetic homogeneity was resolved by figuring surnames as recent “ripples” deposited on a vast and ancient homogeneous genetic “surface”.
DOI: 10.6084/m9.figshare.5840421.v1
title: Ripples on the surface. Surnames and genes in Sicily and Southern Italy

description: <b>Background:</b> Southern Italy and Sicily played a key role in the peopling history of the Mediterranean. While genetic research showed the remarkable homogeneity of these regions, surname-based studies instead suggested low population mobility, hence potential structuring. <b>Aim:</b> In order to better understand these different patterns, this study (1) thoroughly analysed the surname structure of Sicily and Southern Italy and (2) tested its relationships with a wide set of molecular markers. <b>Subjects and methods:</b> Surname data were collected from 1213 municipalities and compared to uniparental and autosomal genetic markers typed in ∼300 individuals from 8–10 populations. Surname analyses were performed using different multivariate methods, while comparisons with genetic data relied on correlation tests. <b>Results:</b> Surnames were clearly structured according to regional geographic patterns, which likely emerged because of recent isolation-by-distance-like population dynamics. In general, genetic markers, hinting at a pervasive homogeneity, did not correlate with surname distribution. However, long autosomal haplotypes (&gt;5 cM) that compared to genotypic (SNPs) data identify more “recent” relatedness, showing a clear association with surname patterns. <b>Conclusion:</b> The apparent contradiction between surname structure and genetic homogeneity was resolved by figuring surnames as recent “ripples” deposited on a vast and ancient homogeneous genetic “surface”.
DOI: 10.6084/m9.figshare.5840409
title: Additional file 1: of Clinical management and outcome of patients with advanced NSCLC carrying EGFR mutations in Spain

description: Datasets supporting the study findings. (XLSX 269 kb)
DOI: 10.6084/m9.figshare.5840409.v1
title: Additional file 1: of Clinical management and outcome of patients with advanced NSCLC carrying EGFR mutations in Spain

description: Datasets supporting the study findings. (XLSX 269 kb)
DOI: 10.6084/m9.figshare.5840403
title: Reconstructing the genetic history of Italians: new insights from a male (Y-chromosome) perspective

description: <b>Background:</b> Due to its central and strategic position in Europe and in the Mediterranean Basin, the Italian Peninsula played a pivotal role in the first peopling of the European continent and has been a crossroad of peoples and cultures since then. <b>Aim:</b> This study aims to gain more information on the genetic structure of modern Italian populations and to shed light on the migration/expansion events that led to their formation. <b>Subjects and methods:</b> High resolution Y-chromosome variation analysis in 817 unrelated males from 10 informative areas of Italy was performed. Haplogroup frequencies and microsatellite haplotypes were used, together with available data from the literature, to evaluate Mediterranean and European inputs and date their arrivals. <b>Results:</b> Fifty-three distinct Y-chromosome lineages were identified. Their distribution is in general agreement with geography, southern populations being more differentiated than northern ones. <b>Conclusions:</b> A complex genetic structure reflecting the multifaceted peopling pattern of the Peninsula emerged: southern populations show high similarity with those from the Middle East and Southern Balkans, while those from Northern Italy are close to populations of North-Western Europe and the Northern Balkans. Interestingly, the population of Volterra, an ancient town of Etruscan origin in Tuscany, displays a unique Y-chromosomal genetic structure.
DOI: 10.6084/m9.figshare.5840403.v1
title: Reconstructing the genetic history of Italians: new insights from a male (Y-chromosome) perspective

description: <b>Background:</b> Due to its central and strategic position in Europe and in the Mediterranean Basin, the Italian Peninsula played a pivotal role in the first peopling of the European continent and has been a crossroad of peoples and cultures since then. <b>Aim:</b> This study aims to gain more information on the genetic structure of modern Italian populations and to shed light on the migration/expansion events that led to their formation. <b>Subjects and methods:</b> High resolution Y-chromosome variation analysis in 817 unrelated males from 10 informative areas of Italy was performed. Haplogroup frequencies and microsatellite haplotypes were used, together with available data from the literature, to evaluate Mediterranean and European inputs and date their arrivals. <b>Results:</b> Fifty-three distinct Y-chromosome lineages were identified. Their distribution is in general agreement with geography, southern populations being more differentiated than northern ones. <b>Conclusions:</b> A complex genetic structure reflecting the multifaceted peopling pattern of the Peninsula emerged: southern populations show high similarity with those from the Middle East and Southern Balkans, while those from Northern Italy are close to populations of North-Western Europe and the Northern Balkans. Interestingly, the population of Volterra, an ancient town of Etruscan origin in Tuscany, displays a unique Y-chromosomal genetic structure.