cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7987097.v1
title: Autophagy in <i>Xenopus laevis</i> rod photoreceptors is independently regulated by phototransduction and misfolded RHO<sup>P23H</sup>

description: We previously reported autophagic structures in rod photoreceptors expressing a misfolding RHO (rhodopsin) mutant (RHO<sup>P23H</sup>), suggesting that autophagy may play a role in degrading the mutant RHO and/or be involved in photoreceptor cell death. To further examine autophagy in normal and diseased rods, we generated transgenic <i>Xenopus laevis</i> tadpoles expressing the dually fluorescent autophagy marker mRFP-eGFP-LC3 in rods, which changes from green to yellow and finally red as autophagic structures develop and mature. Using transgenic lines with constitutive and inducible expression, we determined the time-course of autophagy in rod photoreceptors: autophagosomes last for 6 to 8 hours before fusing with lysosomes, and acidified autolysosomes last for about 28 hours before being degraded. Autophagy was diurnally regulated in normal rods, with more autophagic structures generated during periods of light, and this regulation was non-circadian. We also found that more autophagosomes were produced in rods expressing the misfolding RHO<sup>P23H</sup> mutant. The RHO chromophore absorbs photons to initiate phototransduction, and is consumed in this process; it also promotes RHO folding. To determine whether increased autophagy in light-exposed normal rods is caused by increased RHO misfolding or phototransduction, we used CRISPR/Cas9 to knock out the <i>RPE65</i> and <i>GNAT1</i> genes, which are essential for chromophore biosynthesis and phototransduction respectively. Both knockouts suppressed light-induced autophagy, indicating that although light and misfolded rhodopsin can both induce autophagy in rods, light-induced autophagy is not due to misfolding of RHO, but rather due to phototransduction. <b>Abbreviations</b>: CYCS: cytochrome c; bRHO<sup>P23H</sup>: bovine RHO<sup>P23H</sup>; Cas9: CRISPR associated protein 9; dpf: days post-fertilization; eGFP: enhanced green fluorescent protein; GNAT1: guanine nucleotide-binding protein G(t) subunit alpha-1 aka rod alpha-transducin; HSPA1A/hsp70: heat shock protein of 70 kilodaltons; LAMP1: lysosomal-associated membrane protein 1; LC3: microtubule-associated protein 1A/1B light chain 3; mRFP: monomeric red fluorescent protein; RHO: rhodopsin; RP: retinitis pigmentosa; RPE65: retinal pigment epithelium-specific 65 kDa protein: sfGFP: superfolding GFP; sgRNA: single guide RNA; WGA: wheat germ agglutinin; <i>RHO<sub>p</sub></i>: the <i>Xenopus laevis RHO.2.L</i> promoter.
DOI: 10.6084/m9.figshare.7987082
title: Shared gene ontology terms from Convergent evolution in human and domesticate adaptation to high-altitude environments

description: Humans and their domestic animals have lived and thrived in high-altitude environments worldwide for thousands of years. These populations have developed a number of adaptations to survive in a hypoxic environment, and several genomic studies have been conducted to identify the genes that drive these adaptations. Here, we discuss the various adaptations and genetic variants that have been identified as adaptive in human and domestic animal populations and the ways in which convergent evolution has occurred as these populations have adapted to high-altitude environments. We found that human and domesticate populations have adapted to hypoxic environments in similar ways. Specific genes and biological pathways have been involved in high-altitude adaptation for multiple populations, although the specific variants differ between populations. Additionally, we found that the gene <i>EPAS1</i> is often a target of selection in hypoxic environments and has been involved in multiple adaptive introgression events. High-altitude environments exert strong selective pressures, and human and animal populations have evolved in convergent ways to cope with a chronic lack of oxygen.This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions'.
DOI: 10.6084/m9.figshare.7987088.v1
title: Analysis of authors and museum addresses of papers on convergent evolution from Integrating natural history collections and comparative genomics to study the genetic architecture of convergent evolution

description: Evolutionary convergence has been long considered primary evidence of adaptation driven by natural selection and provides opportunities to explore evolutionary repeatability and predictability. In recent years, there has been increased interest in exploring the genetic mechanisms underlying convergent evolution, in part, due to the advent of genomic techniques. However, the current ‘genomics gold rush’ in studies of convergence has overshadowed the reality that most trait classifications are quite broadly defined, resulting in incomplete or potentially biased interpretations of results. Genomic studies of convergence would be greatly improved by integrating deep ‘vertical’, natural history knowledge with ‘horizontal’ knowledge focusing on the breadth of taxonomic diversity. Natural history collections have and continue to be best positioned for increasing our comprehensive understanding of phenotypic diversity, with modern practices of digitization and databasing of morphological traits providing exciting improvements in our ability to evaluate the degree of morphological convergence. Combining more detailed phenotypic data with the well-established field of genomics will enable scientists to make progress on an important goal in biology: to understand the degree to which genetic or molecular convergence is associated with phenotypic convergence. Although the fields of comparative biology or comparative genomics alone can separately reveal important insights into convergent evolution, here we suggest that the synergistic and complementary roles of natural history collection-derived phenomic data and comparative genomics methods can be particularly powerful in together elucidating the genomic basis of convergent evolution among higher taxa.This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions’.
DOI: 10.6084/m9.figshare.7987046
title: Supplementary Material for: A Trained Pulmonologist Can Reliably Assess Endosonography-Derived Lymph Node Samples during Rapid On-Site Evaluation

description: <b><i>Background:</i></b> The widespread use of rapid on-site evaluation is hampered by constraints related to time and resources, inadequate reimbursement, and evidence from randomized trials that show a lack of increase in diagnostic yield and specimen adequacy associated with its usage. <b><i>Objective:</i></b> We aimed to verify whether a pulmonologist can assess endosonography-derived lymph node samples after a comprehensive and reproducible training provided by a specialist pathologist. <b><i>Methods:</i></b>Prospective, observational trial structured in three phases. In the first (training) phase, a pathologist critically evaluated the smears from 150 archival endosonography cases with a pulmonologist. In the second (test) phase, the pulmonologist was asked to assess 50 archival endosonography-derived samples. In the last (real-life) phase, the pulmonologist classified the samples from 200 patients during the endosonography. The overall agreement between pulmonologist and pathologist (gold standard), assessed through κ-statistics, was the primary outcome. The agreement for the identification of specific cytological categories was the secondary outcome. <b><i>Results:</i></b> The overall<b><i></i></b>agreement between pulmonologist and pathologist was 84% (κ<i></i>0.765, 95% CI 0.732–0.826) in the test phase and 89.7% (κ 0.844, 95% CI 0.799–0.881) in the real-life phase. The agreement for specific cytological categories was 92.7% (95% CI 0.824–0.980) for inadequate samples, 90.3% (95% CI 84.5–94.5%) for reactive lymphadenopathies, 90.5% (95% CI 0.845–0.946) for malignancy, and 73% (95% CI 0.515–0.897) for granulomatous samples. <b><i>Conclusions:</i></b> A trained pulmonologist can reliably assess adequacy and malignancy for endosonography-derived samples, which could be useful in institutions where a cytopathologist/cytotechnician is not available regularly.
DOI: 10.6084/m9.figshare.7987085.v1
title: Genes in most common gene ontology terms from Convergent evolution in human and domesticate adaptation to high-altitude environments

description: Humans and their domestic animals have lived and thrived in high-altitude environments worldwide for thousands of years. These populations have developed a number of adaptations to survive in a hypoxic environment, and several genomic studies have been conducted to identify the genes that drive these adaptations. Here, we discuss the various adaptations and genetic variants that have been identified as adaptive in human and domestic animal populations and the ways in which convergent evolution has occurred as these populations have adapted to high-altitude environments. We found that human and domesticate populations have adapted to hypoxic environments in similar ways. Specific genes and biological pathways have been involved in high-altitude adaptation for multiple populations, although the specific variants differ between populations. Additionally, we found that the gene <i>EPAS1</i> is often a target of selection in hypoxic environments and has been involved in multiple adaptive introgression events. High-altitude environments exert strong selective pressures, and human and animal populations have evolved in convergent ways to cope with a chronic lack of oxygen.This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions'.
DOI: 10.6084/m9.figshare.7987019
title: Baluk cave (NW China) Holocene speleothem trace element ratios

description: The interpretation of trace element/calcium ratios of speleothems as indicators of local hydroclimatic variability in the vicinity of caves has led to controversy in reconstructing the evolution of moisture conditions in arid central Asia (ACA) during the Holocene. Here we present records of Mg/Ca, Sr/Ca, Ba/Ca, and U/Ca from precisely dated stalagmites from Baluk cave in Xinjiang (northwest China), spanning the past 9370 years. The co-variations of the trace element ratios, together with the slopes of the regression lines of the corresponding logarithmically transformed data, suggest that they are dominated by prior calcite precipitation (PCP) and thus can be used as reliable proxies of changes in moisture/precipitation. The trace element ratios are relatively high during ~9 to 5 ka and lower from 5 ka to the present, indicating a trend of increasing mid–late Holocene moisture in ACA. The long-term trend of variation of the trace element ratios is correlative with two other records of speleothem trace element ratios from caves in ACA: Kesang cave (western Xinjiang) and Ton cave (Uzbekistan). This spatial coherency of the trend of inferred moisture conditions from three caves that are separated by hundreds of kilometers demonstrates that speleothem trace element ratios are indicative of large spatial scale rather than local hydroclimatic variability in ACA during the Holocene. However, the long-term trend of variation of the trace element ratios is the inverse of the corresponding oxygen isotope (δ<sup>18</sup>O) records from the same cave sites, which implies that Holocene speleothem δ<sup>18</sup>O records do not represent changes in the precipitation amount in ACA; rather, they most likely reflect moisture sources and related water vapor transport controlled by Northern Hemisphere summer insolation (NHSI). Our findings provide new evidence for a ‘westerlies-dominated climatic regime’, which influenced hydroclimatic changes in ACA during the Holocene.
DOI: 10.6084/m9.figshare.7987082.v1
title: Shared gene ontology terms from Convergent evolution in human and domesticate adaptation to high-altitude environments

description: Humans and their domestic animals have lived and thrived in high-altitude environments worldwide for thousands of years. These populations have developed a number of adaptations to survive in a hypoxic environment, and several genomic studies have been conducted to identify the genes that drive these adaptations. Here, we discuss the various adaptations and genetic variants that have been identified as adaptive in human and domestic animal populations and the ways in which convergent evolution has occurred as these populations have adapted to high-altitude environments. We found that human and domesticate populations have adapted to hypoxic environments in similar ways. Specific genes and biological pathways have been involved in high-altitude adaptation for multiple populations, although the specific variants differ between populations. Additionally, we found that the gene <i>EPAS1</i> is often a target of selection in hypoxic environments and has been involved in multiple adaptive introgression events. High-altitude environments exert strong selective pressures, and human and animal populations have evolved in convergent ways to cope with a chronic lack of oxygen.This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions'.
DOI: 10.6084/m9.figshare.12873680.v7
title: Additional file of Expression profile analysis of the inflammatory response regulated by hepatocyte nuclear factor 4α

description: Additional file of Expression profile analysis of the inflammatory response regulated by hepatocyte nuclear factor 4α
DOI: 10.6084/m9.figshare.7987046.v1
title: Supplementary Material for: A Trained Pulmonologist Can Reliably Assess Endosonography-Derived Lymph Node Samples during Rapid On-Site Evaluation

description: <b><i>Background:</i></b> The widespread use of rapid on-site evaluation is hampered by constraints related to time and resources, inadequate reimbursement, and evidence from randomized trials that show a lack of increase in diagnostic yield and specimen adequacy associated with its usage. <b><i>Objective:</i></b> We aimed to verify whether a pulmonologist can assess endosonography-derived lymph node samples after a comprehensive and reproducible training provided by a specialist pathologist. <b><i>Methods:</i></b>Prospective, observational trial structured in three phases. In the first (training) phase, a pathologist critically evaluated the smears from 150 archival endosonography cases with a pulmonologist. In the second (test) phase, the pulmonologist was asked to assess 50 archival endosonography-derived samples. In the last (real-life) phase, the pulmonologist classified the samples from 200 patients during the endosonography. The overall agreement between pulmonologist and pathologist (gold standard), assessed through κ-statistics, was the primary outcome. The agreement for the identification of specific cytological categories was the secondary outcome. <b><i>Results:</i></b> The overall<b><i></i></b>agreement between pulmonologist and pathologist was 84% (κ<i></i>0.765, 95% CI 0.732–0.826) in the test phase and 89.7% (κ 0.844, 95% CI 0.799–0.881) in the real-life phase. The agreement for specific cytological categories was 92.7% (95% CI 0.824–0.980) for inadequate samples, 90.3% (95% CI 84.5–94.5%) for reactive lymphadenopathies, 90.5% (95% CI 0.845–0.946) for malignancy, and 73% (95% CI 0.515–0.897) for granulomatous samples. <b><i>Conclusions:</i></b> A trained pulmonologist can reliably assess adequacy and malignancy for endosonography-derived samples, which could be useful in institutions where a cytopathologist/cytotechnician is not available regularly.
DOI: 10.6084/m9.figshare.7987001
title: Supplementary Material for: Social Complexity and Brain Evolution: Comparative Analysis of Modularity and Integration in Ant Brain Organization

description: The behavioral demands of living in social groups have been linked to the evolution of brain size and structure, but how social organization shapes investment and connectivity within and among functionally specialized brain regions remains unclear. To understand the influence of sociality on brain evolution in ants, a premier clade of eusocial insects, we statistically analyzed patterns of brain region size covariation as a proxy for brain region connectivity. We investigated brain structure covariance in young and old workers of two formicine ants, the Australasian weaver ant <i>Oecophylla smaragdina</i>, a pinnacle of social complexity in insects, and its socially basic sister clade <i>Formica subsericea</i>. As previously identified in other ant species, we predicted that our analysis would recognize in both species an olfaction-related brain module underpinning social information processing in the brain, and a second neuroanatomical cluster involved in nonolfactory sensorimotor processes, thus reflecting conservation of compartmental connectivity. Furthermore, we hypothesized that covariance patterns would reflect divergence in social organization and life histories either within this species pair or compared to other ant species. Contrary to our predictions, our covariance analyses revealed a weakly defined visual, rather than olfactory, sensory processing cluster in both species. This pattern may be linked to the reliance on vision for worker behavioral performance outside of the nest and the correlated expansion of the optic lobes to meet navigational demands in both species. Additionally, we found that colony size and social organization, key measures of social complexity, were only weakly correlated with brain modularity in these formicine ants. Worker age also contributed to variance in brain organization, though in different ways in each species. These findings suggest that brain organization may be shaped by the divergent life histories of the two study species. We compare our findings with patterns of brain organization of other eusocial insects.
DOI: 10.6084/m9.figshare.7987001.v1
title: Supplementary Material for: Social Complexity and Brain Evolution: Comparative Analysis of Modularity and Integration in Ant Brain Organization

description: The behavioral demands of living in social groups have been linked to the evolution of brain size and structure, but how social organization shapes investment and connectivity within and among functionally specialized brain regions remains unclear. To understand the influence of sociality on brain evolution in ants, a premier clade of eusocial insects, we statistically analyzed patterns of brain region size covariation as a proxy for brain region connectivity. We investigated brain structure covariance in young and old workers of two formicine ants, the Australasian weaver ant <i>Oecophylla smaragdina</i>, a pinnacle of social complexity in insects, and its socially basic sister clade <i>Formica subsericea</i>. As previously identified in other ant species, we predicted that our analysis would recognize in both species an olfaction-related brain module underpinning social information processing in the brain, and a second neuroanatomical cluster involved in nonolfactory sensorimotor processes, thus reflecting conservation of compartmental connectivity. Furthermore, we hypothesized that covariance patterns would reflect divergence in social organization and life histories either within this species pair or compared to other ant species. Contrary to our predictions, our covariance analyses revealed a weakly defined visual, rather than olfactory, sensory processing cluster in both species. This pattern may be linked to the reliance on vision for worker behavioral performance outside of the nest and the correlated expansion of the optic lobes to meet navigational demands in both species. Additionally, we found that colony size and social organization, key measures of social complexity, were only weakly correlated with brain modularity in these formicine ants. Worker age also contributed to variance in brain organization, though in different ways in each species. These findings suggest that brain organization may be shaped by the divergent life histories of the two study species. We compare our findings with patterns of brain organization of other eusocial insects.
DOI: 10.6084/m9.figshare.12873680.v10
title: Additional file of Expression profile analysis of the inflammatory response regulated by hepatocyte nuclear factor 4α

description: Additional file of Expression profile analysis of the inflammatory response regulated by hepatocyte nuclear factor 4α
DOI: 10.6084/m9.figshare.7987019.v1
title: Baluk cave (NW China) Holocene speleothem trace element ratios

description: The interpretation of trace element/calcium ratios of speleothems as indicators of local hydroclimatic variability in the vicinity of caves has led to controversy in reconstructing the evolution of moisture conditions in arid central Asia (ACA) during the Holocene. Here we present records of Mg/Ca, Sr/Ca, Ba/Ca, and U/Ca from precisely dated stalagmites from Baluk cave in Xinjiang (northwest China), spanning the past 9370 years. The co-variations of the trace element ratios, together with the slopes of the regression lines of the corresponding logarithmically transformed data, suggest that they are dominated by prior calcite precipitation (PCP) and thus can be used as reliable proxies of changes in moisture/precipitation. The trace element ratios are relatively high during ~9 to 5 ka and lower from 5 ka to the present, indicating a trend of increasing mid–late Holocene moisture in ACA. The long-term trend of variation of the trace element ratios is correlative with two other records of speleothem trace element ratios from caves in ACA: Kesang cave (western Xinjiang) and Ton cave (Uzbekistan). This spatial coherency of the trend of inferred moisture conditions from three caves that are separated by hundreds of kilometers demonstrates that speleothem trace element ratios are indicative of large spatial scale rather than local hydroclimatic variability in ACA during the Holocene. However, the long-term trend of variation of the trace element ratios is the inverse of the corresponding oxygen isotope (δ<sup>18</sup>O) records from the same cave sites, which implies that Holocene speleothem δ<sup>18</sup>O records do not represent changes in the precipitation amount in ACA; rather, they most likely reflect moisture sources and related water vapor transport controlled by Northern Hemisphere summer insolation (NHSI). Our findings provide new evidence for a ‘westerlies-dominated climatic regime’, which influenced hydroclimatic changes in ACA during the Holocene.