cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5918908
title: 3D outline files for the chimpanzee bones (uuencoded tgz file) from Quadrupedal locomotor simulation: producing more realistic gaits using dual-objective optimization

description: In evolutionary biomechanics it is often considered that gaits should evolve to minimize the energetic cost of travelling a given distance. In gait simulation this goal often leads to convincing gait generation. However, as the musculoskeletal models used get increasingly sophisticated, it becomes apparent that such a single goal can lead to extremely unrealistic gait patterns. In this paper, we explore the effects of requiring adequate lateral stability and show how this both increases energetic cost and the realism of the generated walking gait in a high biofidelity chimpanzee musculoskeletal model. We also explore the effects of changing the footfall sequences in the simulation so it mimics both the diagonal sequence walking gaits that primates typically use and also the lateral sequence walking gaits that are much more widespread among mammals. It is apparent that adding a lateral stability criterion has an important effect on the footfall phase relationship suggesting that lateral stability may be one of the key drivers behind the observed footfall sequences in quadrupedal gaits. The observation that single optimization goals are no longer adequate for generating gait in current models has important implications for the use of biomimetic virtual robots to predict the locomotor patterns in fossil animals.
DOI: 10.6084/m9.figshare.5918908.v1
title: 3D outline files for the chimpanzee bones (uuencoded tgz file) from Quadrupedal locomotor simulation: producing more realistic gaits using dual-objective optimization

description: In evolutionary biomechanics it is often considered that gaits should evolve to minimize the energetic cost of travelling a given distance. In gait simulation this goal often leads to convincing gait generation. However, as the musculoskeletal models used get increasingly sophisticated, it becomes apparent that such a single goal can lead to extremely unrealistic gait patterns. In this paper, we explore the effects of requiring adequate lateral stability and show how this both increases energetic cost and the realism of the generated walking gait in a high biofidelity chimpanzee musculoskeletal model. We also explore the effects of changing the footfall sequences in the simulation so it mimics both the diagonal sequence walking gaits that primates typically use and also the lateral sequence walking gaits that are much more widespread among mammals. It is apparent that adding a lateral stability criterion has an important effect on the footfall phase relationship suggesting that lateral stability may be one of the key drivers behind the observed footfall sequences in quadrupedal gaits. The observation that single optimization goals are no longer adequate for generating gait in current models has important implications for the use of biomimetic virtual robots to predict the locomotor patterns in fossil animals.
DOI: 10.6084/m9.figshare.5918893
title: Supplementary material S5 from Palaeoecological inferences for the fossil Australian snakes <i>Yurlunggur</i> and <i>Wonambi</i> (Serpentes, Madtsoiidae)

description: Scripts used to run the analyses in R.
DOI: 10.6084/m9.figshare.5918893.v1
title: Supplementary material S5 from Palaeoecological inferences for the fossil Australian snakes <i>Yurlunggur</i> and <i>Wonambi</i> (Serpentes, Madtsoiidae)

description: Scripts used to run the analyses in R.
DOI: 10.6084/m9.figshare.5918878
title: Supplementary material S1 - Table S1 from Palaeoecological inferences for the fossil Australian snakes <i>Yurlunggur</i> and <i>Wonambi</i> (Serpentes, Madtsoiidae)

description: Specimen numbers, taxonomic authorities, and institutional abbreviations.
DOI: 10.6084/m9.figshare.5918878.v1
title: Supplementary material S1 - Table S1 from Palaeoecological inferences for the fossil Australian snakes <i>Yurlunggur</i> and <i>Wonambi</i> (Serpentes, Madtsoiidae)

description: Specimen numbers, taxonomic authorities, and institutional abbreviations.
DOI: 10.6084/m9.figshare.5918872
title: SI_tables (Additional Supplementary Tables) from Rewilding the world's large carnivores

description: Photo credits for large carnivore images; data on largest protected areas by species; data on largest low footprint regions by species; table describing the variables in Tables S2 and S3.
DOI: 10.6084/m9.figshare.5918872.v1
title: SI_tables (Additional Supplementary Tables) from Rewilding the world's large carnivores

description: Photo credits for large carnivore images; data on largest protected areas by species; data on largest low footprint regions by species; table describing the variables in Tables S2 and S3.
DOI: 10.6084/m9.figshare.5918869
title: GaitSym config files for all the individual run conditions (uuencoded tgz file) from Quadrupedal locomotor simulation: producing more realistic gaits using dual-objective optimization

description: In evolutionary biomechanics it is often considered that gaits should evolve to minimize the energetic cost of travelling a given distance. In gait simulation this goal often leads to convincing gait generation. However, as the musculoskeletal models used get increasingly sophisticated, it becomes apparent that such a single goal can lead to extremely unrealistic gait patterns. In this paper, we explore the effects of requiring adequate lateral stability and show how this both increases energetic cost and the realism of the generated walking gait in a high biofidelity chimpanzee musculoskeletal model. We also explore the effects of changing the footfall sequences in the simulation so it mimics both the diagonal sequence walking gaits that primates typically use and also the lateral sequence walking gaits that are much more widespread among mammals. It is apparent that adding a lateral stability criterion has an important effect on the footfall phase relationship suggesting that lateral stability may be one of the key drivers behind the observed footfall sequences in quadrupedal gaits. The observation that single optimization goals are no longer adequate for generating gait in current models has important implications for the use of biomimetic virtual robots to predict the locomotor patterns in fossil animals.
DOI: 10.6084/m9.figshare.5918869.v1
title: GaitSym config files for all the individual run conditions (uuencoded tgz file) from Quadrupedal locomotor simulation: producing more realistic gaits using dual-objective optimization

description: In evolutionary biomechanics it is often considered that gaits should evolve to minimize the energetic cost of travelling a given distance. In gait simulation this goal often leads to convincing gait generation. However, as the musculoskeletal models used get increasingly sophisticated, it becomes apparent that such a single goal can lead to extremely unrealistic gait patterns. In this paper, we explore the effects of requiring adequate lateral stability and show how this both increases energetic cost and the realism of the generated walking gait in a high biofidelity chimpanzee musculoskeletal model. We also explore the effects of changing the footfall sequences in the simulation so it mimics both the diagonal sequence walking gaits that primates typically use and also the lateral sequence walking gaits that are much more widespread among mammals. It is apparent that adding a lateral stability criterion has an important effect on the footfall phase relationship suggesting that lateral stability may be one of the key drivers behind the observed footfall sequences in quadrupedal gaits. The observation that single optimization goals are no longer adequate for generating gait in current models has important implications for the use of biomimetic virtual robots to predict the locomotor patterns in fossil animals.
DOI: 10.6084/m9.figshare.5918866
title: Supplementary material S3 from Palaeoecological inferences for the fossil Australian snakes <i>Yurlunggur</i> and <i>Wonambi</i> (Serpentes, Madtsoiidae)

description: Landmark coordinates of all taxa included in the study (.tps format).
DOI: 10.6084/m9.figshare.5918866.v1
title: Supplementary material S3 from Palaeoecological inferences for the fossil Australian snakes <i>Yurlunggur</i> and <i>Wonambi</i> (Serpentes, Madtsoiidae)

description: Landmark coordinates of all taxa included in the study (.tps format).
DOI: 10.6084/m9.figshare.5918857
title: Supplementary material S4 - Table S2 from Palaeoecological inferences for the fossil Australian snakes <i>Yurlunggur</i> and <i>Wonambi</i> (Serpentes, Madtsoiidae)

description: Ecology of all the taxa included in the study and literature sources.
DOI: 10.6084/m9.figshare.5918857.v1
title: Supplementary material S4 - Table S2 from Palaeoecological inferences for the fossil Australian snakes <i>Yurlunggur</i> and <i>Wonambi</i> (Serpentes, Madtsoiidae)

description: Ecology of all the taxa included in the study and literature sources.
DOI: 10.6084/m9.figshare.5918761
title: 3D-Scanner_Database_De-ID.dta

description: Replication data for: Delgado et al. Unconventional 3D torso anthropometry in children and adolescents. F1000Research, 2018.
DOI: 10.6084/m9.figshare.5918761.v1
title: 3D-Scanner_Database_De-ID.dta

description: Replication data for: Delgado et al. Unconventional 3D torso anthropometry in children and adolescents. F1000Research, 2018.
DOI: 10.6084/m9.figshare.5918701
title: Binary Artifact for TACAS-2018 paper "Optimal DPOR with Observers"

description: This is a binary artifact related to the TACAS-2018 paper "Optimal Dynamic Partial Order Reduction with Observers". The paper describes an extension to the Optimal DPOR (Dynamic Partical Order Reduction) algorithm that enables use of observers, and demonstrates its utility through two implementations: one in an SMC tool for C/C++ programs with pthreads and one in an SMC tool for Erlang programs.<br>This artifact contains the code and benchmarks used to generate the results in the paper, as well as instructions on how to do so. The artifact is designed to be used with https://doi.org/10.6084/m9.figshare.5896615.<br>Within the artifact there are two subdirectories ("Concuerror" and "Nidhugg"), which each contain a README.md file, describing how the experimental results of the relevant sections can be replicated.
DOI: 10.6084/m9.figshare.5918701.v1
title: Binary Artifact for TACAS-2018 paper "Optimal DPOR with Observers"

description: This is a binary artifact related to the TACAS-2018 paper "Optimal Dynamic Partial Order Reduction with Observers". The paper describes an extension to the Optimal DPOR (Dynamic Partical Order Reduction) algorithm that enables use of observers, and demonstrates its utility through two implementations: one in an SMC tool for C/C++ programs with pthreads and one in an SMC tool for Erlang programs.<br>This artifact contains the code and benchmarks used to generate the results in the paper, as well as instructions on how to do so. The artifact is designed to be used with https://doi.org/10.6084/m9.figshare.5896615.<br>Within the artifact there are two subdirectories ("Concuerror" and "Nidhugg"), which each contain a README.md file, describing how the experimental results of the relevant sections can be replicated.
DOI: 10.6084/m9.figshare.5918620
title: Supplementary Material for: The Long Intergenic Noncoding RNA 00707 Promotes Lung Adenocarcinoma Cell Proliferation and Migration by Regulating Cdc42

description: <b><i>Background/Aims:</i></b> Lung cancer (LC) is a serious disease with high morbidity and mortality. Long noncoding RNAs (lncRNAs) have garnered attention because they participate in diverse human disorders, including cancer. Our study examined the long intergenic noncoding RNA 00707 (LINC00707). The effects of LINC00707 on lung adenocarcinoma (LAD) and molecular mechanisms are unclear. This study is aimed to investigate the role of LINC00707 in the malignant processes of LAD. <b><i>Methods:</i></b> Quantitative reverse transcription PCR (qRT-PCR) was used to examine the expression level of LINC00707 in tissues and cell lines. The association of LINC00707 expression and postoperative prognosis was analyzed by the Kaplan-Meier method and log-rank test. Cell proliferation was evaluated <i>in vitro</i> and <i>in vivo</i>. Transwell assays were performed to examine cell migration. Cell cycle and apoptosis was determined by flow -cytometric and western blot analyses. Microarray analysis was conducted to screen for the downstream target gene Cdc42 of LINC00707, which was identified by qRT-PCR, functional analysis, and rescue experiment. <b><i>Results:</i></b> The expression level of LINC00707 was clearly upregulated in LAD tissues compared to that in corresponding normal tissues. Its overexpression was related to advanced TNM stage, larger tumor size, lymphatic metastasis, and poor prognosis. Functional assays revealed that LINC00707 knockdown repressed LAD cell proliferation both <i>in vitro</i> and <i>in vivo</i>. This process may involve the inducing of G1 arrest and apoptosis. Moreover, cell migration was impaired after LINC00707 inhibition. Microarray analysis and rescue assays suggested that Cdc42 is an important target gene involved in the carcinogenesis of LINC00707. <b><i>Conclusions:</i></b> In summary, LINC00707 is a noncoding oncogene that exerts important regulatory functions in LAD, suggesting its potential as a biomarker in the prognosis and treatment of LAD.
DOI: 10.6084/m9.figshare.5918620.v1
title: Supplementary Material for: The Long Intergenic Noncoding RNA 00707 Promotes Lung Adenocarcinoma Cell Proliferation and Migration by Regulating Cdc42

description: <b><i>Background/Aims:</i></b> Lung cancer (LC) is a serious disease with high morbidity and mortality. Long noncoding RNAs (lncRNAs) have garnered attention because they participate in diverse human disorders, including cancer. Our study examined the long intergenic noncoding RNA 00707 (LINC00707). The effects of LINC00707 on lung adenocarcinoma (LAD) and molecular mechanisms are unclear. This study is aimed to investigate the role of LINC00707 in the malignant processes of LAD. <b><i>Methods:</i></b> Quantitative reverse transcription PCR (qRT-PCR) was used to examine the expression level of LINC00707 in tissues and cell lines. The association of LINC00707 expression and postoperative prognosis was analyzed by the Kaplan-Meier method and log-rank test. Cell proliferation was evaluated <i>in vitro</i> and <i>in vivo</i>. Transwell assays were performed to examine cell migration. Cell cycle and apoptosis was determined by flow -cytometric and western blot analyses. Microarray analysis was conducted to screen for the downstream target gene Cdc42 of LINC00707, which was identified by qRT-PCR, functional analysis, and rescue experiment. <b><i>Results:</i></b> The expression level of LINC00707 was clearly upregulated in LAD tissues compared to that in corresponding normal tissues. Its overexpression was related to advanced TNM stage, larger tumor size, lymphatic metastasis, and poor prognosis. Functional assays revealed that LINC00707 knockdown repressed LAD cell proliferation both <i>in vitro</i> and <i>in vivo</i>. This process may involve the inducing of G1 arrest and apoptosis. Moreover, cell migration was impaired after LINC00707 inhibition. Microarray analysis and rescue assays suggested that Cdc42 is an important target gene involved in the carcinogenesis of LINC00707. <b><i>Conclusions:</i></b> In summary, LINC00707 is a noncoding oncogene that exerts important regulatory functions in LAD, suggesting its potential as a biomarker in the prognosis and treatment of LAD.
DOI: 10.5517/ccdc.csd.cc20cfhb
title: CCDC 1858031: Experimental Crystal Structure Determination

description: Related Article: Palas Baran Pati, Eunji Jin, Yohan Kim, Yongchul Kim, Jinhong Mun, So Jung Kim, Seok Ju Kang, Wonyoung Choe, Geunsik Lee, Hyung-Joon Shin, Young S. Park|2020|Angew.Chem.,Int.Ed.|59|14891|doi:10.1002/anie.202004049
DOI: 10.6084/m9.figshare.5918617
title: Supplementary Material for: Downregulation of the Cl<sup>-</sup>/HCO<sub>3</sub><sup>-</sup>Exchanger Pendrin in Kidneys of Mice with Cystic Fibrosis: Role in the Pathogenesis of Metabolic Alkalosis

description: <b><i>Background/Aims:</i></b> Patients with cystic fibrosis (CF) are prone to the development of metabolic alkalosis; however, the pathogenesis of this life threatening derangement remains unknown. We hypothesized that altered acid base transport machinery in the kidney collecting duct underlies the mechanism of impaired bicarbonate elimination in the CF kidney. <b><i>Methods:</i></b> Balance studies in metabolic cages were performed in WT and CFTR knockout (CF) mice with the intestinal rescue in response to bicarbonate loading or salt restriction, and the expression levels and cellular distribution of acid base and electrolyte transporters in the proximal tubule, collecting duct and small intestine were examined by western blots, northern blots and/or immunofluorescence labeling. <b><i>Results:</i></b> Baseline parameters, including acid-base and systemic vascular volume status were comparable in WT and CF mice, as determined by blood gas, kidney renin expression and urine chloride excretion. Compared with WT animals, CF mice demonstrated a significantly higher serum HCO<sub>3</sub><sup>-</sup> concentration (22.63 in WT vs. 26.83 mEq/l in CF mice; n=4, p=0.013) and serum pH (7.33 in WT vs. 7.42 in CF mice; n=4, p=0.00792) and exhibited impaired kidney HCO<sub>3</sub><sup>-</sup> excretion (urine pH 8.10 in WT vs. 7.35 in CF mice; n=7, p=0.00990) following a 3-day oral bicarbonate load. When subjected to salt restriction, CF mice developed a significantly higher serum HCO<sub>3</sub><sup>-</sup> concentration vs. WT animals (29.26 mEq/L in CF mice vs. 26.72 in WT; n=5, p=0.0291). Immunofluorescence labeling demonstrated a profound reduction in the apical expression of the Cl<sup>-</sup>/HCO<sub>3</sub><sup>-</sup> exchanger pendrin in cortical collecting duct cells and western and northern blots indicated diminished plasma membrane abundance and mRNA expression of pendrin in CF kidneys. <b><i>Conclusions:</i></b> We propose that patients with cystic fibrosis are prone to the development of metabolic alkalosis secondary to the inactivation of the bicarbonate secreting transporter pendrin, specifically during volume depletion, which is a common occurrence in CF patients.
DOI: 10.6084/m9.figshare.5918608
title: Growth data of the E. coli strains carrying the reduced genomes

description: This dataset contains growth curve data of a series of E. coli cells carrying reduced genomes, in the media of LB (rich medium), MAA (M63 supplied with 20 amino acids) and M63 (minimal medium).<br>The dataset consists of three <b>.xlsx </b>files accessible via MS Excel and open office formats. Each file contains experimental growth curve data by time in a series of tabs, each representing one strain with the tab name bearing <b>n</b>. Individual columns in a tab represent individual wells per strain. Each separate file corresponds to one of the growth media above: LB, MAA, and M63, which represent the rich, supplementary, and poor growth conditions, respectively.<br>Measurement data are provided at 30 minute or one hour intervals for all growth media and groupings.<br><b>KHK growth curves_LB.xlsx</b> - <i>E. coli </i>growth curve data by strain for LB (rich medium)<b>KHK growth curves_M63.xlsx</b> - <i>E. coli </i>growth curve data by strain for M63 (minimal medium)<b>KHK growth curves_MAA.xlsx</b> - <i>E. coli </i>growth curve data by strain for MAA (M63 supplied with 20 amino acids)<br><b>Methodology (see related publication for full details)</b><b><br></b>E. coli culture cell growth was detected at an absorbance of 600 nm, with readings obtained at 30-min or 1-h intervals for 24 to 48 h. The growth curves were obtained for each well. Repeated tests were performed, which resulted in 11 to 30 growth curves used for further calculations of growth rate and population density for each strain at each growth condition (medium). Growth curves were acquired in three different media: LB, M63 and MAA.<br><b><br></b><b>Background</b><br>Genome reduction by removing dispensable genomic sequences in bacteria is commonly used in both fundamental and applied studies to determine the minimal genetic requirements for a living system or to develop highly efficient bioreactors. Nevertheless, whether and how the accumulative loss of dispensable genomic sequences disturbs bacterial growth remains unclear. To investigate the relationship between genome reduction and growth, a series of Escherichia coli strains carrying genomes reduced in a stepwise manner were used. Intensive growth analyses revealed that the accumulation of multiple genomic deletions caused decreases in the exponential growth rate and the saturated cell density in a deletion-length-dependent manner as well as gradual changes in the patterns of growth dynamics, regardless of the growth media. Accordingly, a perspective growth model linking genome evolution to genome engineering was proposed. This study provides the first demonstration of a quantitative connection between genomic sequence and bacterial growth, indicating that growth rate is potentially associated with dispensable genomic sequences.<br>
DOI: 10.6084/m9.figshare.5918599
title: Quality of life in pregnancy

description: datos sin procesar de la investigación en calidad de vida relacionada con la salud durante el embarazo
DOI: 10.6084/m9.figshare.5918599.v1
title: Quality of life in pregnancy

description: datos sin procesar de la investigación en calidad de vida relacionada con la salud durante el embarazo
DOI: 10.6084/m9.figshare.5918590
title: Supplementary Material for: Neuroinflammation in Response to Intracerebral Injections of Different HMGB1 Redox Isoforms

description: <b><i>Background:</i></b> Neuroinflammation triggered by infection or trauma is the cause of central nervous system dysfunction. High-mobility group box 1 protein (HMGB1), released from stressed and dying brain cells, is a potent neuroinflammatory mediator. The proinflammatory functions of HMGB1 are tightly regulated by post-translational redox modifications, and we here investigated detailed neuroinflammatory responses induced by the individual redox isoforms. <b><i>Methods:</i></b> Male Dark Agouti rats received a stereotactic injection of saline, lipopolysaccharide, disulfide HMGB1, or fully reduced HMGB1, and were accessed for blood-brain barrier modifications using magnetic resonance imaging (MRI) and inflammatory responses by immunohistochemistry. <b><i>Results and Conclusions:</i></b> Significant blood-brain barrier disruption appeared 24 h after injection of lipopolysaccharide, disulfide HMGB1, or fully reduced HMGB1 compared to controls, as assessed in post-gadolinium T1-weighted MRI images and confirmed by increased uptake of FITC-conjugated dextran. Immunohistochemistry revealed that both HMGB1 isoforms also induced a local production of IL-1β. Additionally, disulfide HMGB1 increased major histocompatibility complex class II expression and apoptosis. Together, the results demonstrate that extracellular, cerebral HMGB1 causes significant blood-brain barrier disruption in a redox-independent manner and activates several components of neuroinflammation. Blocking HMGB1 might potentially improve clinical outcome in conditions such as stroke and traumatic brain injury.