cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5125339
title: Supplementary Material for: How Nervous Systems Evolve in Relation to Their Embodiment: What We Can Learn from Octopuses and Other Molluscs

description: Cephalopods such as the octopus show the most advanced behavior among invertebrates, which they accomplish with an exceptionally flexible body plan. In this review I propose that the embodied organization approach, developed by roboticists to design efficient autonomous robots, is useful for understanding the evolution and development of the efficient adaptive interaction of animals with their environment, using the octopus as the leading example. The embodied organization approach explains adaptive behavior as emerging from the continuous dynamical and reciprocal physical and informational interactions between four elements: the controller, the mechanical and the sensory systems and the environment. In contrast to hierarchical organization, in embodied organization, self-organization processes can take part in the emergence of the adaptive properties. I first discuss how the embodiment concept explains covariation of body form, nervous system organization, and level of behavioral complexity using the Mollusca as an example. This is an ideal phylum to test such a qualitative correlation between body/brain/behavior, because they show the greatest variations of body plan within a single phylum. In some cases the covariation of nervous system and body structure seems to arise independently of close phylogenetic relationships. Next, I dwell on the octopus as an ideal model to test the embodiment concept within a single biological system. Here, the unusual body morphology of the octopus exposes the uniqueness of the four components comprising the octopus' embodiment. Considering together the results from behavioral, physiological, anatomical, and motor control research suggests that these four elements mutually influence each other. It is this mutual interactions and self-organization which have led to their unique evolution and development to create the unique and highly efficient octopus embodiment.
DOI: 10.6084/m9.figshare.5125342
title: Supplementary Material for: Baseline IGF-I Levels Determine Insulin Secretion and Insulin Sensitivity during the First Year on Growth Hormone Therapy in Children Born Small for Gestational Age. Results from a North European Multicentre Study (NESGAS)

description: <b><i>Objective:</i></b> Developmental programming alters growth and metabolic outcome in children born small for gestational age (SGA). We explored insulin and glucose metabolism in SGA children treated with a fixed GH dose over 1 year. <b><i>Methods:</i></b> In the North European Small for Gestational Age Study (NESGAS), 110 short SGA children received GH at 67 µg/kg/day for 1 year. Insulin secretion was assessed by acute insulin response (AIR), insulin sensitivity (IS) by HOMA and disposition index (DI) by insulin secretion adjusted for IS. <b><i>Results:</i></b> First-year GH therapy led to increases in height and IGF-I standard deviation score (SDS), and reductions in IS (p &lt; 0.0001). Compensatory increases in AIR (p &lt; 0.0001) were insufficient and resulted in reduced DI (p = 0.032). Children in the highest IGF-I SDS tertile at baseline were the least insulin sensitive at baseline (p = 0.024) and 1 year (p = 0.006). IGF-I responses after 1 year were positively related to AIR (r = 0.30, p = 0.007) and DI (r = 0.29, p = 0.005). <b><i>Conclusion:</i></b> In SGA children treated with a high GH dose for 1 year, baseline IGF-I levels were related to IS whilst gains in height and IGF-I responses were associated with insulin secretion. Defining heterogeneity in IGF-I in SGA children may be useful in predicting growth and metabolic response.
DOI: 10.6084/m9.figshare.5125336
title: Supplementary Material for: High-Frequency Oscillatory Ventilation with Low Oscillatory Frequency in Pulmonary Interstitial Emphysema

description: <b><i>Background:</i></b> Pulmonary interstitial emphysema (PIE) is a common respiratory illness in preterm infants associated with significant morbidity and mortality for which the ventilatory management is imperfect. <b><i>Objectives:</i></b> To evaluate the impact of high-frequency oscillatory ventilation (HFOV) with a low oscillatory frequency and thus prolonged expiratory time in preterm infants with severe PIE. <b><i>Methods:</i></b> In a retrospective cohort study, preterm infants ≤30 weeks' gestation with radiological findings of severe PIE, and either high FiO<sub>2</sub> or persistent respiratory acidosis were studied if managed on HFOV with a low frequency (5-6 Hz, inspiratory time 30%) for &gt;24 h. Trends in physiological and ventilatory parameters were examined over the first 72 h, radiological changes noted, and in-hospital outcomes ascertained. <b><i>Results:</i></b> 19 cases were identified and analysed in two groups: 14 with bilateral and 5 with predominantly unilateral disease. After transition to low-frequency HFOV, physiological responses were seen in both groups, in particular a rapid and sustained improvement in oxygenation in the bilateral group (mean (SD) alveolar-arterial oxygen difference at baseline: 404 ± 206 mm Hg; 4 h post-transition: 262 ± 181 mm Hg; 72 h: 155 ± 74 mm Hg; p = 0.0003). This occurred following a reduction in mean airway pressure (mean (SD) baseline: 14 ± 3.9 cm H<sub>2</sub>O; 72 h: 12 ± 2.9 cm H<sub>2</sub>O; p = 0.011). In the unilateral group, radiological resolution of PIE was observed on re-inflation following collapse of the affected lung. Overall, 15 infants survived, including 10 of the bilateral cases (71%), and all of the unilateral cases. <b><i>Conclusion:</i></b> HFOV with a low oscillatory frequency may afford benefit in preterm babies with severe PIE.
DOI: 10.6084/m9.figshare.5125339.v1
title: Supplementary Material for: How Nervous Systems Evolve in Relation to Their Embodiment: What We Can Learn from Octopuses and Other Molluscs

description: Cephalopods such as the octopus show the most advanced behavior among invertebrates, which they accomplish with an exceptionally flexible body plan. In this review I propose that the embodied organization approach, developed by roboticists to design efficient autonomous robots, is useful for understanding the evolution and development of the efficient adaptive interaction of animals with their environment, using the octopus as the leading example. The embodied organization approach explains adaptive behavior as emerging from the continuous dynamical and reciprocal physical and informational interactions between four elements: the controller, the mechanical and the sensory systems and the environment. In contrast to hierarchical organization, in embodied organization, self-organization processes can take part in the emergence of the adaptive properties. I first discuss how the embodiment concept explains covariation of body form, nervous system organization, and level of behavioral complexity using the Mollusca as an example. This is an ideal phylum to test such a qualitative correlation between body/brain/behavior, because they show the greatest variations of body plan within a single phylum. In some cases the covariation of nervous system and body structure seems to arise independently of close phylogenetic relationships. Next, I dwell on the octopus as an ideal model to test the embodiment concept within a single biological system. Here, the unusual body morphology of the octopus exposes the uniqueness of the four components comprising the octopus' embodiment. Considering together the results from behavioral, physiological, anatomical, and motor control research suggests that these four elements mutually influence each other. It is this mutual interactions and self-organization which have led to their unique evolution and development to create the unique and highly efficient octopus embodiment.
DOI: 10.6084/m9.figshare.5125351.v1
title: Supplementary Material for: Influence of Cochleostomy and Cochlear Implant Insertion on Drug Gradients following Intratympanic Application in Guinea Pigs

description: Locally applied drugs can protect residual hearing following cochlear implantation. The influence of cochlear implantation on drug levels in the scala tympani (ST) after round window application was investigated in guinea pigs using the marker trimethylphenylammonium (TMPA) measured in real time with TMPA-selective microelectrodes. TMPA concentration in the upper basal turn of the ST rapidly increased during implantation and then declined due to cerebrospinal fluid entering the ST at the cochlear aqueduct and exiting at the cochleostomy. The TMPA increase was found to be caused by the cochleostomy drilling if the burr tip partially entered the ST. TMPA distribution in the second turn was less affected by implantation procedures. These findings show that basal turn drug levels may be changed during implantation and the changes may need to be considered in the interpretation of therapeutic effects of drugs in conjunction with implantation.
DOI: 10.6084/m9.figshare.5125324
title: Supplementary Material for: Genomic Constitution and Atypical Reproduction in Polyploid and Unisexual Lineages of the <b><i>Misgurnus</i></b> Loach, a Teleost Fish

description: The loach <i>(Misgurnus anguillicaudatus)</i> is an excellent animal model to elucidate biological origin and evolutionary significance of genome duplication and unisexual reproduction because artificially induced and naturally occurring polyploids and parthenogenetic (gynogenetic, androgenetic) animals can be compared. First, we summarize the chromosome manipulation techniques to induce triploids and tetraploids by inhibiting meiotic or mitotic divisions of inseminated eggs, respectively, as well as parthenogenetic animals, obtained after fertilization with genetically inactivated gametes. Then, we review the knowledge on natural polyploid and unisexual lineages found in <i>Misgurnus</i> loaches. A natural diploid-tetraploid complex occurs in wild populations in central China, and these diploid and tetraploid loaches reproduce bisexually. Chinese tetraploids are considered autotetraploid, which may have arisen by doubling of the entire genome of an ancestral diploid, based on cytogenetic results from FISH (fluorescence in situ hybridization) karyotypes and meiotic configurations. In contrast, gynogenetically reproducing clonal diploid lineages have been discovered in a few wild populations in Japan, although most wild-type individuals are bisexually reproducing diploids. Such clonal diploid loaches sometimes produce triploid progeny by accidental incorporation of a sperm nucleus into an unreduced diploid egg, and the resulting triploid generates haploid eggs by meiotic hybridogenesis. Unreduced diploid gametes of clonal loaches are generated by a cytological mechanism, premeiotic endomitosis, which likely occurs in the early (gonium stage) germ cells. Initiation of gynogenetic development is related to a failure of decondensation of the male (sperm) pronucleus in unreduced diploid eggs of a clonal loach. Clonal lineages may have arisen from a past hybrid event between genetically divergent groups, but their exact origins are unknown at present. See also the sister article focusing on plants by Hegarty et al. in this themed issue.
DOI: 10.6084/m9.figshare.5125330
title: Supplementary Material for: Retrotransposons Represent the Most Labile Fraction for Genomic Rearrangements in Polyploid Plant Species

description: Understanding how increased genome size and diversity within polyploid genomes impacts plant evolution and breeding continues to be challenging. Although historical studies by McClintock suggested the importance of transposable elements mediated by polyploidisation on genomic changes, data from plant crosses remain scarce. Despite the absence of a conclusive proof regarding autonomous retrotransposon movement in synthetic allopolyploids, the transposition of retrotransposons and their ubiquitous dispersion in all plant species might explain the positive correlation between the genome size of plants and the prevalence of retrotransposons. Here, we address polyploidisation-mediated rearrangements of retrotransposon-associated sequences and discuss a tendency for a preferential restructuring of large ancestral genomes after polyploidisation. A comparative analysis of the frequency of modifications of retrotransposon-associated sequences in synthetic polyploids with marked differences in genome sizes is presented. Such analyses suggest the absence of a significant difference in the rates of rearrangements despite vast dissimilarities in the retrotransposon copy number between species, which emphasises the high plasticity of this genomic feature. See also the sister article focusing on animals by Arkhipova and Rodriguez in this themed issue.
DOI: 10.6084/m9.figshare.5125333
title: Supplementary Material for: Genetic Polymorphisms in Calcitonin Receptor Gene and Risk for Recurrent Kidney Calcium Stone Disease

description: <b><i>Introduction:</i></b> In this study the full sequence of the calcitonin receptor gene <i>(CALCR)</i> in a group of Iranian males suffering from recurrent calcium urinary stones was compared with that of a control group. <b><i>Methods:</i></b> Serum and urinary biochemistry related to urolithiasis were evaluated in 105 males diagnosed with recurrent kidney calcium stones and 101 age-matched healthy control males. The polymerase chain reaction single-strand conformation polymorphism method was used to detect new polymorphisms in the <i>CALCR</i>. <b><i>Results:</i></b> Nine polymorphisms were detected; seven were in the non-coding and two in the coding region. The T allele associated with the <i>3</i>′<i>UTR+18C&gt;T</i> polymorphism was observed exclusively in the stone formers. The exact odds ratio for the T allele in this locus for those at risk of stone formation was 36.72 (95% CI 4.95-272.0) (p &lt; 0.001). The mean (standard deviation) urine calcium concentration was 117 (60) mg/l in patients with the C allele and 152 (72) mg/l in those with the T allele (p = 0.03). In addition, <i>IVS1-6T&gt;C</i> and <i>IVS1insA</i> polymorphisms in intron 1 were associated with kidney stone disease (p &lt; 0.001). Regarding single nucleotide polymorphism 447, mean (standard deviation) of serum calcitonin levels were 16.7 (18.7) pg/ml, 10.5 (11.0) pg/ml and 9.94 (9.7) pg/ml in subjects with TT, TC and CC genotypes, respectively (p = 0.01). <b><i>Conclusion:</i></b> Our data indicate a potential association between <i>3</i>′<i>UTR+18C&gt;T</i> and intron 1 polymorphisms in the <i>CALCR</i> and the risk of kidney stone disease.
DOI: 10.6084/m9.figshare.5125336.v1
title: Supplementary Material for: High-Frequency Oscillatory Ventilation with Low Oscillatory Frequency in Pulmonary Interstitial Emphysema

description: <b><i>Background:</i></b> Pulmonary interstitial emphysema (PIE) is a common respiratory illness in preterm infants associated with significant morbidity and mortality for which the ventilatory management is imperfect. <b><i>Objectives:</i></b> To evaluate the impact of high-frequency oscillatory ventilation (HFOV) with a low oscillatory frequency and thus prolonged expiratory time in preterm infants with severe PIE. <b><i>Methods:</i></b> In a retrospective cohort study, preterm infants ≤30 weeks' gestation with radiological findings of severe PIE, and either high FiO<sub>2</sub> or persistent respiratory acidosis were studied if managed on HFOV with a low frequency (5-6 Hz, inspiratory time 30%) for &gt;24 h. Trends in physiological and ventilatory parameters were examined over the first 72 h, radiological changes noted, and in-hospital outcomes ascertained. <b><i>Results:</i></b> 19 cases were identified and analysed in two groups: 14 with bilateral and 5 with predominantly unilateral disease. After transition to low-frequency HFOV, physiological responses were seen in both groups, in particular a rapid and sustained improvement in oxygenation in the bilateral group (mean (SD) alveolar-arterial oxygen difference at baseline: 404 ± 206 mm Hg; 4 h post-transition: 262 ± 181 mm Hg; 72 h: 155 ± 74 mm Hg; p = 0.0003). This occurred following a reduction in mean airway pressure (mean (SD) baseline: 14 ± 3.9 cm H<sub>2</sub>O; 72 h: 12 ± 2.9 cm H<sub>2</sub>O; p = 0.011). In the unilateral group, radiological resolution of PIE was observed on re-inflation following collapse of the affected lung. Overall, 15 infants survived, including 10 of the bilateral cases (71%), and all of the unilateral cases. <b><i>Conclusion:</i></b> HFOV with a low oscillatory frequency may afford benefit in preterm babies with severe PIE.
DOI: 10.6084/m9.figshare.5125321
title: Supplementary Material for: Smooth Muscle Contractile Plasticity in Rat Mesenteric Small Arteries: Sensitivity to Specific Vasoconstrictors, Distension and Inflammatory Cytokines

description: Small artery remodeling may involve a shift in the diameter-dependent force generating capacity of smooth muscle cells (SMC). We tested to what extent and under which conditions such contractile plasticity occurs. Rat mesenteric arteries were mounted on isometric myographs. Active diameter-tension relations were determined after application of several stimuli for 16 or 40 h at 40 or 110% of the passive diameter at 100 mm Hg. At 40%, 16-hour incubation with endothelin-1 (ET-1) but not U46619 shifted force capacity towards smaller diameters. Inflammatory cytokines (TNF-α, IL-1β, IFN-γ), TGF-β or serum neither induced such shift nor augmented the effect of ET-1. The ET-1-mediated change was not affected by superoxide dismutase and catalase. Inward matrix remodeling in the presence of ET-1 was slower, occurring after 40 h. Arteries maintained at 110% showed a shift of force capacity to larger diameters, which was prevented by ET-1 but not by U46619. In the active but not the passive state, SMC had altered nuclear lengths after incubation at 40%. These data demonstrate contractile plasticity in small arteries, where chronic strain is an outward drive and specifically ET-1 an inward drive, acting through mechanisms that do not seem to relate to oxidative stress, inflammatory pathways or major reorganization of the SMC.
DOI: 10.6084/m9.figshare.5125324.v1
title: Supplementary Material for: Genomic Constitution and Atypical Reproduction in Polyploid and Unisexual Lineages of the <b><i>Misgurnus</i></b> Loach, a Teleost Fish

description: The loach <i>(Misgurnus anguillicaudatus)</i> is an excellent animal model to elucidate biological origin and evolutionary significance of genome duplication and unisexual reproduction because artificially induced and naturally occurring polyploids and parthenogenetic (gynogenetic, androgenetic) animals can be compared. First, we summarize the chromosome manipulation techniques to induce triploids and tetraploids by inhibiting meiotic or mitotic divisions of inseminated eggs, respectively, as well as parthenogenetic animals, obtained after fertilization with genetically inactivated gametes. Then, we review the knowledge on natural polyploid and unisexual lineages found in <i>Misgurnus</i> loaches. A natural diploid-tetraploid complex occurs in wild populations in central China, and these diploid and tetraploid loaches reproduce bisexually. Chinese tetraploids are considered autotetraploid, which may have arisen by doubling of the entire genome of an ancestral diploid, based on cytogenetic results from FISH (fluorescence in situ hybridization) karyotypes and meiotic configurations. In contrast, gynogenetically reproducing clonal diploid lineages have been discovered in a few wild populations in Japan, although most wild-type individuals are bisexually reproducing diploids. Such clonal diploid loaches sometimes produce triploid progeny by accidental incorporation of a sperm nucleus into an unreduced diploid egg, and the resulting triploid generates haploid eggs by meiotic hybridogenesis. Unreduced diploid gametes of clonal loaches are generated by a cytological mechanism, premeiotic endomitosis, which likely occurs in the early (gonium stage) germ cells. Initiation of gynogenetic development is related to a failure of decondensation of the male (sperm) pronucleus in unreduced diploid eggs of a clonal loach. Clonal lineages may have arisen from a past hybrid event between genetically divergent groups, but their exact origins are unknown at present. See also the sister article focusing on plants by Hegarty et al. in this themed issue.
DOI: 10.6084/m9.figshare.5125333.v1
title: Supplementary Material for: Genetic Polymorphisms in Calcitonin Receptor Gene and Risk for Recurrent Kidney Calcium Stone Disease

description: <b><i>Introduction:</i></b> In this study the full sequence of the calcitonin receptor gene <i>(CALCR)</i> in a group of Iranian males suffering from recurrent calcium urinary stones was compared with that of a control group. <b><i>Methods:</i></b> Serum and urinary biochemistry related to urolithiasis were evaluated in 105 males diagnosed with recurrent kidney calcium stones and 101 age-matched healthy control males. The polymerase chain reaction single-strand conformation polymorphism method was used to detect new polymorphisms in the <i>CALCR</i>. <b><i>Results:</i></b> Nine polymorphisms were detected; seven were in the non-coding and two in the coding region. The T allele associated with the <i>3</i>′<i>UTR+18C&gt;T</i> polymorphism was observed exclusively in the stone formers. The exact odds ratio for the T allele in this locus for those at risk of stone formation was 36.72 (95% CI 4.95-272.0) (p &lt; 0.001). The mean (standard deviation) urine calcium concentration was 117 (60) mg/l in patients with the C allele and 152 (72) mg/l in those with the T allele (p = 0.03). In addition, <i>IVS1-6T&gt;C</i> and <i>IVS1insA</i> polymorphisms in intron 1 were associated with kidney stone disease (p &lt; 0.001). Regarding single nucleotide polymorphism 447, mean (standard deviation) of serum calcitonin levels were 16.7 (18.7) pg/ml, 10.5 (11.0) pg/ml and 9.94 (9.7) pg/ml in subjects with TT, TC and CC genotypes, respectively (p = 0.01). <b><i>Conclusion:</i></b> Our data indicate a potential association between <i>3</i>′<i>UTR+18C&gt;T</i> and intron 1 polymorphisms in the <i>CALCR</i> and the risk of kidney stone disease.
DOI: 10.6084/m9.figshare.5125342.v1
title: Supplementary Material for: Baseline IGF-I Levels Determine Insulin Secretion and Insulin Sensitivity during the First Year on Growth Hormone Therapy in Children Born Small for Gestational Age. Results from a North European Multicentre Study (NESGAS)

description: <b><i>Objective:</i></b> Developmental programming alters growth and metabolic outcome in children born small for gestational age (SGA). We explored insulin and glucose metabolism in SGA children treated with a fixed GH dose over 1 year. <b><i>Methods:</i></b> In the North European Small for Gestational Age Study (NESGAS), 110 short SGA children received GH at 67 µg/kg/day for 1 year. Insulin secretion was assessed by acute insulin response (AIR), insulin sensitivity (IS) by HOMA and disposition index (DI) by insulin secretion adjusted for IS. <b><i>Results:</i></b> First-year GH therapy led to increases in height and IGF-I standard deviation score (SDS), and reductions in IS (p &lt; 0.0001). Compensatory increases in AIR (p &lt; 0.0001) were insufficient and resulted in reduced DI (p = 0.032). Children in the highest IGF-I SDS tertile at baseline were the least insulin sensitive at baseline (p = 0.024) and 1 year (p = 0.006). IGF-I responses after 1 year were positively related to AIR (r = 0.30, p = 0.007) and DI (r = 0.29, p = 0.005). <b><i>Conclusion:</i></b> In SGA children treated with a high GH dose for 1 year, baseline IGF-I levels were related to IS whilst gains in height and IGF-I responses were associated with insulin secretion. Defining heterogeneity in IGF-I in SGA children may be useful in predicting growth and metabolic response.