cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7987313.v1
title: A new specimen of <i>Platypterygius sachicarum</i> (Reptilia, Ichthyosauria) from the Early Cretaceous of Colombia and its phylogenetic implications

description: <i>Platypterygius sachicarum</i> is one of the few Lower Cretaceous ichthyosaurian species described from the Hauterivian–Aptian-aged Paja Formation, the most complete Lower Cretaceous sedimentary sequence in northern South America. To date, <i>P. sachicarum</i> has been described only from a single skull, limiting morphological, stratigraphic, and phylogenetic comparisons. Here, we describe a new skull and associated postcranium of upper Barremian age from Villa de Leyva, Colombia, which represent the first documented postcranial remains of this species and enable detailed comparison with other Early Cretaceous ophthalmosaurid ichthyosaurs. <i>Platypterygius sachicarum</i> shares many morphological similarities with contemporaneous taxa from Europe but differs in both skull and tooth morphology from coeval South American species from northern South America and from the eastern Pacific. The additional data provide new diagnostic characters for this species and resolve the position of <i>P. sachicarum</i> as part of a polytomy of other species historically referred to <i>Platypterygius</i>. However, as with previous analyses, all recovered clades are poorly supported. The rich vertebrate fossil record of the Paja Formation provides an unparalleled opportunity to explore paleobiogeographic and paleoecological questions pertaining to Cretaceous marine reptiles; however, in most cases, a robust stratigraphic and phylogenetic framework remains elusive.
DOI: 10.6084/m9.figshare.7987190
title: Supplementary Material for: Therapeutic Challenge of Minicircle Vector Encoding Klotho in Animal Model

description: <b><i>Background:</i></b> Klotho treatment is a promising approach against kidney injury, but its clinical application is still undetermined. We developed a novel strategy to allow self-production of Klotho protein, using minicircle (MC) technology, and evaluated its feasibility in therapeutic Klotho delivery. <b><i>Methods:</i></b> We engineered MC vectors to carry cassette sequences of Klotho and verified the self-production of Klotho protein from in HEK293T cells. We evaluated the location and persistence of delivered MC in vivo, and the duration of Klotho protein production from MCs by serial measurement of Klotho protein in blood. We subsequently evaluated the therapeutic potential of Klotho-encoding MCs in experimental model of renal injury. <b><i>Results:</i></b> We confirmed the production of Klotho from MC by its significant availability in cells transfected with the MC, as well as in its conditioned medium, compared to that in cells transfected with parent vector. MCs were delivered in vivo by hydrodynamic injection via tail vein. After a single injection of MCs, red fluorescence protein was detected until 30 days in liver, and Klotho protein was maintained until 10 days in the blood, suggesting the production of Klotho protein from MCs via protein synthesis machinery in liver. Therapeutic effect of MC was confirmed by functional and histological improvement seen in mouse model of acute ischemia-reperfusion injury and unilateral ureteral obstruction. <b><i>Conclusion:</i></b> Together, these findings implied that self-generated Klotho protein, using MC technology, is functionally active and relevant as a therapeutic approach in renal injury.
DOI: 10.6084/m9.figshare.7987193
title: Supplementary Material for: Sepsis Management with a Blood Purification Membrane: European Experience

description: <b><i>Background:</i></b> Septic shock is a leading cause of acute kidney injury (AKI). Endotoxins and cytokine levels are associated with the occurrence and severity of AKI, and different blood purification devices are available to remove them from circulation. One such device, oXiris, is a hollow-fibre purification filter that clears both endotoxins and cytokines. Due to limited evidence, clinical use of this device is not currently advocated in guidelines. However, clinics do regularly use this device, and there is a critical need for guidance on the application of it in sepsis with and without AKI. <b><i>Method:</i></b> A modified Delphi-based method was used to collate ­European experts’ views on the indication(s), initiation and discontinuation criteria and success measures for oXiris. <b><i>Results:</i></b> A panel of 14 participants was selected based on known clinical expertise in the areas of critical care and sepsis management, as well as their experience of using the oXiris blood purification device. The participants used different criteria to initiate treatment with oXiris in sepsis patients with and without AKI. Septic shock with AKI was the priority patient population, with oXiris used to rapidly improve haemodynamic parameters. Achieving haemodynamic stability within 72 h was a key factor for determining treatment success. <b><i>Conclusion:</i></b> In the absence of established guidelines, users of hollow-fibre purification devices such as oXiris may benefit from standardised approaches to selecting patients and initiating and terminating treatment, as well as measuring success. Further evidence in the form of randomised clinical trials is urgently required.
DOI: 10.6084/m9.figshare.7987187
title: MSPG-DATA

description: These data are generated during the testing of MSPG method, and the CPU and memory overhead during the experiment are recorded. The frame forwarding delay in the network is recorded, and the communication overhead between the data plane and the control plane during the experiment is recorded.
DOI: 10.6084/m9.figshare.7987193.v1
title: Supplementary Material for: Sepsis Management with a Blood Purification Membrane: European Experience

description: <b><i>Background:</i></b> Septic shock is a leading cause of acute kidney injury (AKI). Endotoxins and cytokine levels are associated with the occurrence and severity of AKI, and different blood purification devices are available to remove them from circulation. One such device, oXiris, is a hollow-fibre purification filter that clears both endotoxins and cytokines. Due to limited evidence, clinical use of this device is not currently advocated in guidelines. However, clinics do regularly use this device, and there is a critical need for guidance on the application of it in sepsis with and without AKI. <b><i>Method:</i></b> A modified Delphi-based method was used to collate ­European experts’ views on the indication(s), initiation and discontinuation criteria and success measures for oXiris. <b><i>Results:</i></b> A panel of 14 participants was selected based on known clinical expertise in the areas of critical care and sepsis management, as well as their experience of using the oXiris blood purification device. The participants used different criteria to initiate treatment with oXiris in sepsis patients with and without AKI. Septic shock with AKI was the priority patient population, with oXiris used to rapidly improve haemodynamic parameters. Achieving haemodynamic stability within 72 h was a key factor for determining treatment success. <b><i>Conclusion:</i></b> In the absence of established guidelines, users of hollow-fibre purification devices such as oXiris may benefit from standardised approaches to selecting patients and initiating and terminating treatment, as well as measuring success. Further evidence in the form of randomised clinical trials is urgently required.
DOI: 10.6084/m9.figshare.7987229.v1
title: AJPEM_Omentin_Suppl Tab.1

description: List of the 92 bioamarkers of the OLINK Inflammation panel.<br>
DOI: 10.6084/m9.figshare.7987190.v1
title: Supplementary Material for: Therapeutic Challenge of Minicircle Vector Encoding Klotho in Animal Model

description: <b><i>Background:</i></b> Klotho treatment is a promising approach against kidney injury, but its clinical application is still undetermined. We developed a novel strategy to allow self-production of Klotho protein, using minicircle (MC) technology, and evaluated its feasibility in therapeutic Klotho delivery. <b><i>Methods:</i></b> We engineered MC vectors to carry cassette sequences of Klotho and verified the self-production of Klotho protein from in HEK293T cells. We evaluated the location and persistence of delivered MC in vivo, and the duration of Klotho protein production from MCs by serial measurement of Klotho protein in blood. We subsequently evaluated the therapeutic potential of Klotho-encoding MCs in experimental model of renal injury. <b><i>Results:</i></b> We confirmed the production of Klotho from MC by its significant availability in cells transfected with the MC, as well as in its conditioned medium, compared to that in cells transfected with parent vector. MCs were delivered in vivo by hydrodynamic injection via tail vein. After a single injection of MCs, red fluorescence protein was detected until 30 days in liver, and Klotho protein was maintained until 10 days in the blood, suggesting the production of Klotho protein from MCs via protein synthesis machinery in liver. Therapeutic effect of MC was confirmed by functional and histological improvement seen in mouse model of acute ischemia-reperfusion injury and unilateral ureteral obstruction. <b><i>Conclusion:</i></b> Together, these findings implied that self-generated Klotho protein, using MC technology, is functionally active and relevant as a therapeutic approach in renal injury.
DOI: 10.6084/m9.figshare.7987175
title: branch scores

description: Suspensory ligament total branch scores collected form review of images of 60 horses.
DOI: 10.6084/m9.figshare.7987169
title: data_proof_of_concept

description: To obtain a detailed picture of the dynamics of antibiotic resistance development in <i>Neisseria gonorrhoeae</i>, we built a morbidostat according to the protocol of Toprak <i>et al</i>., adjusted to the specific characteristics required for the growth of <i>N. gonorrhoeae</i>. In this article we describe the adaptations, specifications and the difficulties we encountered during the construction and optimization of the NG morbidostat. As a proof of concept, we conducted a morbidostat experiment by increasing concentrations of azithromycin in response to bacterial growth. We started the experiment with two <i>N. gonorrhoeae</i> reference strains WHO-F and WHO-X. These strains were grown in 12 mL GC Broth supplemented with IsoVitaleX™ (1%) and vancomycin, colistin, nystatin, trimethoprim (VCNT) selective supplement for 30 days in a 6% CO<sub>2</sub> environment at 36°C. Samples of the cultures were taken 2-3 times a week and minimal inhibitory concentrations (MICs) of azithromycin were determined using E-test. The initial MICs of WHO-F and WHO-X were 0,125 µg/mL and 0,25 µg/mL, respectively. In less than 30 days, we were able to induce high level azithromycin resistance in <i>N. gonorrhoeae</i>, with a 750 and 1000 fold increase in MIC for WHO-F and WHO-X, respectively.
DOI: 10.6084/m9.figshare.7987139
title: MSPG-DAD

description: These data are generated during the testing of MSPG method, and the CPU and memory overhead during the experiment are recorded. The frame forwarding delay in the network is recorded, and the communication overhead between the data plane and the control plane during the experiment is recorded.
DOI: 10.6084/m9.figshare.7987175.v1
title: branch scores

description: Suspensory ligament total branch scores collected form review of images of 60 horses.
DOI: 10.6084/m9.figshare.7987136
title: Supplementary Material for: Urinary Nephrin as a Biomarker of Glomerular Maturation and Injury Is Associated with Acute Kidney Injury and Mortality in Critically Ill Neonates

description: <b><i>Background:</i></b> Nephrin is a key component of the slit diaphragm of the glomerular podocyte, and increased urinary nephrin level may reflect glomerular injury. <b><i>Objectives:</i></b> To determine whether urinary nephrin is a useful biomarker of glomerular maturation and injury and whether it is associated with acute kidney injury (AKI) and neonatal intensive care unit (NICU) mortality in critically ill neonates. <b><i>Methods:</i></b> Urinary samples were serially collected in 234 neonates during NICU stay for measurements of nephrin, cystatin C (CysC), and albumin. AKI diagnosis was based on neonatal Kidney Disease: Improving Global Outcome (KDIGO) criteria. <b><i>Results:</i></b> Of the neonates, 26 developed AKI and 24 died during NICU stay. The independent contributors to the initial urinary nephrin level obtained on the first 24 h admitted to NICU were gestational age (<i>p</i> = 0.004) and initial urinary CysC level (<i>p</i> &lt; 0.001). Both initial (<i>p</i> = 0.037) and peak (<i>p</i> = 0.039) urinary nephrin were significantly associated with AKI, even after controlling for significant covariates, and had an area under the receiver-operating characteristic curve (AUC) of 0.71 and 0.70, respectively, for predicting AKI. At the optimal cutoff value of 0.375 μg/mg urinary creatinine, the initial urinary nephrin displayed sensitivity of 61.5% and specificity of 76.9% for predicting AKI. The AUCs for initial and peak urinary nephrin to predict NICU mortality were 0.81 and 0.83, respectively. <b><i>Conclusions:</i></b> Urinary nephrin, which may decrease with increasing glomerular maturity, is significantly associated with increased risk for AKI and NICU mortality even after adjustment for potential confounders. A higher level of urinary nephrin may be independently predictive of AKI and NICU mortality in critically ill neonates.
DOI: 10.6084/m9.figshare.7987169.v2
title: data_proof_of_concept

description: To obtain a detailed picture of the dynamics of antibiotic resistance development in <i>Neisseria gonorrhoeae</i>, we built a morbidostat according to the protocol of Toprak <i>et al</i>., adjusted to the specific characteristics required for the growth of <i>N. gonorrhoeae</i>. In this article we describe the adaptations, specifications and the difficulties we encountered during the construction and optimization of the NG morbidostat. As a proof of concept, we conducted a morbidostat experiment by increasing concentrations of azithromycin in response to bacterial growth. We started the experiment with two <i>N. gonorrhoeae</i> reference strains WHO-F and WHO-X. These strains were grown in 12 mL GC Broth supplemented with IsoVitaleX™ (1%) and vancomycin, colistin, nystatin, trimethoprim (VCNT) selective supplement for 30 days in a 6% CO<sub>2</sub> environment at 36°C. Samples of the cultures were taken 2-3 times a week and minimal inhibitory concentrations (MICs) of azithromycin were determined using E-test. The initial MICs of WHO-F and WHO-X were 0,125 µg/mL and 0,25 µg/mL, respectively. In less than 30 days, we were able to induce high level azithromycin resistance in <i>N. gonorrhoeae</i>, with a 750 and 1000 fold increase in MIC for WHO-F and WHO-X, respectively.
DOI: 10.6084/m9.figshare.7987100
title: Codes and Data - Correa et al. JNeuro 2018

description: This folder contains all codes and data necessary to reproduce the behavioral analyses and results reported in Correa, et al. (2018) J.Neuro. <br><br>[Correa CMC, Noorman S, Jiang J, Palminteri S, Cohen MX, Lebreton M*, van Gaal S* (2018).How the level of reward awareness changes the computational and electrophysiological signatures of reinforcement learning. <br>Journal of Neuroscience 8(48):10338 –10348 <br>https://doi.org/10.1523/JNEUROSCI.0457-18.2018]<br>Please note that the codes needs Matlab R2014b or a more resent version, with the Statistics and Machine Learning toolbox.
DOI: 10.6084/m9.figshare.7987169.v1
title: data_proof_of_concept

description: To obtain a detailed picture of the dynamics of antibiotic resistance development in <i>Neisseria gonorrhoeae</i>, we built a morbidostat according to the protocol of Toprak <i>et al</i>., adjusted to the specific characteristics required for the growth of <i>N. gonorrhoeae</i>. In this article we describe the adaptations, specifications and the difficulties we encountered during the construction and optimization of the NG morbidostat. As a proof of concept, we conducted a morbidostat experiment by increasing concentrations of azithromycin in response to bacterial growth. We started the experiment with two <i>N. gonorrhoeae</i> reference strains WHO-F and WHO-X. These strains were grown in 12 mL GC Broth supplemented with IsoVitaleX™ (1%) and vancomycin, colistin, nystatin, trimethoprim (VCNT) selective supplement for 30 days in a 6% CO<sub>2</sub> environment at 36°C. Samples of the cultures were taken 2-3 times a week and minimal inhibitory concentrations (MICs) of azithromycin were determined using E-test. The initial MICs of WHO-F and WHO-X were 0,125 µg/mL and 0,25 µg/mL, respectively. In less than 30 days, we were able to induce high level azithromycin resistance in <i>N. gonorrhoeae</i>, with a 750 and 1000 fold increase in MIC for WHO-F and WHO-X, respectively.
DOI: 10.6084/m9.figshare.7987097
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.7987088
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.7987100.v1
title: Codes and Data - Correa et al. JNeuro 2018

description: This folder contains all codes and data necessary to reproduce the behavioral analyses and results reported in Correa, et al. (2018) J.Neuro. <br><br>[Correa CMC, Noorman S, Jiang J, Palminteri S, Cohen MX, Lebreton M*, van Gaal S* (2018).How the level of reward awareness changes the computational and electrophysiological signatures of reinforcement learning. <br>Journal of Neuroscience 8(48):10338 –10348 <br>https://doi.org/10.1523/JNEUROSCI.0457-18.2018]<br>Please note that the codes needs Matlab R2014b or a more resent version, with the Statistics and Machine Learning toolbox.
DOI: 10.6084/m9.figshare.7987085
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'.