cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7964279.v1
title: Origin of prehistoric cattle excavated from four archaeological sites in central and northeastern Thailand

description: Cattle have been domesticated in Southeast Asia, including Thailand, for thousands of years, but the history of cattle domestication in the region remains unclear. To date, only genetic studies of modern Thai cattle DNA have been reported. To gain some insight into cattle domestication in the country, a total of 56 cattle remains excavated from four archaeological sites (dated to between 3550 and 1700 years before present (YBP)) in northeastern and central Thailand were analysed in this study. Of 56, the 157-bp D-loop fragment was successfully generated from 26 samples, all of which belonged to <i>Bos taurus</i> in haplogroup T/T3. One haplotype contained 19 members from all four archaeological sites and clustered with the ancient <i>B. taurus</i> from Iran, Turkey and China. Other haplotypes have not shared haplotype with <i>B. taurus</i> from other countries but they showed close relationship to those from China. This represents the first genetic evidence that <i>B.</i> <i>taurus</i> was domesticated in Thailand between 3550 and 1700 YBP. In addition, the close relationship among ancient Thai, Iranian and Chinese taurines suggests that cattle from the Near East were introduced into North China, and were subsequently brought into Thailand thousands of years ago.
DOI: 10.6084/m9.figshare.7964252
title: Comparson to Cook et. al. from Perfect counterfactuals for epidemic simulations

description: R code containing an example where our method outperforms the construction of Cook et. al.
DOI: 10.6084/m9.figshare.7964252.v1
title: Comparson to Cook et. al. from Perfect counterfactuals for epidemic simulations

description: R code containing an example where our method outperforms the construction of Cook et. al.
DOI: 10.6084/m9.figshare.7964228
title: Kinematic data Indiv3 from Channel catfish use higher coordination to capture prey than to swallow

description: When animals move they must coordinate motion among multiple parts of the musculoskeletal system. Different behaviours exhibit different patterns of coordination, however, it remains unclear what general principles determine the coordination pattern for a particular behaviour. One hypothesis is that speed determines coordination patterns as a result of differences in voluntary versus involuntary control. An alternative hypothesis is that the nature of the behavioural task determines patterns of coordination. Suction-feeding fishes have highly kinetic skulls and must coordinate the motions of over a dozen skeletal elements to draw fluid and prey into the mouth. We used a dataset of intracranial motions at five cranial joints in channel catfish (<i>Ictalurus punctatus</i>), collected using X-ray reconstruction of moving morphology, to test whether speed or task best-explained patterns of coordination. We found that motions were significantly more coordinated (by 20–29%) during prey capture than during prey transport, supporting the hypothesis that the nature of the task determines coordination patterns. We found no significant difference in coordination between low- and high-speed motions. We speculate that capture is more coordinated to create a single fluid flow into the mouth while transport is less coordinated so that the cranial elements can independently generate multiple flows to reposition prey. Our results demonstrate the benefits of both higher and lower coordination in animal behaviours and the potential of motion analysis to elucidate motor tasks.
DOI: 10.6084/m9.figshare.7964228.v1
title: Kinematic data Indiv3 from Channel catfish use higher coordination to capture prey than to swallow

description: When animals move they must coordinate motion among multiple parts of the musculoskeletal system. Different behaviours exhibit different patterns of coordination, however, it remains unclear what general principles determine the coordination pattern for a particular behaviour. One hypothesis is that speed determines coordination patterns as a result of differences in voluntary versus involuntary control. An alternative hypothesis is that the nature of the behavioural task determines patterns of coordination. Suction-feeding fishes have highly kinetic skulls and must coordinate the motions of over a dozen skeletal elements to draw fluid and prey into the mouth. We used a dataset of intracranial motions at five cranial joints in channel catfish (<i>Ictalurus punctatus</i>), collected using X-ray reconstruction of moving morphology, to test whether speed or task best-explained patterns of coordination. We found that motions were significantly more coordinated (by 20–29%) during prey capture than during prey transport, supporting the hypothesis that the nature of the task determines coordination patterns. We found no significant difference in coordination between low- and high-speed motions. We speculate that capture is more coordinated to create a single fluid flow into the mouth while transport is less coordinated so that the cranial elements can independently generate multiple flows to reposition prey. Our results demonstrate the benefits of both higher and lower coordination in animal behaviours and the potential of motion analysis to elucidate motor tasks.
DOI: 10.6084/m9.figshare.7964210
title: Kinematic data Indiv2 from Channel catfish use higher coordination to capture prey than to swallow

description: When animals move they must coordinate motion among multiple parts of the musculoskeletal system. Different behaviours exhibit different patterns of coordination, however, it remains unclear what general principles determine the coordination pattern for a particular behaviour. One hypothesis is that speed determines coordination patterns as a result of differences in voluntary versus involuntary control. An alternative hypothesis is that the nature of the behavioural task determines patterns of coordination. Suction-feeding fishes have highly kinetic skulls and must coordinate the motions of over a dozen skeletal elements to draw fluid and prey into the mouth. We used a dataset of intracranial motions at five cranial joints in channel catfish (<i>Ictalurus punctatus</i>), collected using X-ray reconstruction of moving morphology, to test whether speed or task best-explained patterns of coordination. We found that motions were significantly more coordinated (by 20–29%) during prey capture than during prey transport, supporting the hypothesis that the nature of the task determines coordination patterns. We found no significant difference in coordination between low- and high-speed motions. We speculate that capture is more coordinated to create a single fluid flow into the mouth while transport is less coordinated so that the cranial elements can independently generate multiple flows to reposition prey. Our results demonstrate the benefits of both higher and lower coordination in animal behaviours and the potential of motion analysis to elucidate motor tasks.
DOI: 10.6084/m9.figshare.7964213
title: Kinematic data Indiv1 from Channel catfish use higher coordination to capture prey than to swallow

description: When animals move they must coordinate motion among multiple parts of the musculoskeletal system. Different behaviours exhibit different patterns of coordination, however, it remains unclear what general principles determine the coordination pattern for a particular behaviour. One hypothesis is that speed determines coordination patterns as a result of differences in voluntary versus involuntary control. An alternative hypothesis is that the nature of the behavioural task determines patterns of coordination. Suction-feeding fishes have highly kinetic skulls and must coordinate the motions of over a dozen skeletal elements to draw fluid and prey into the mouth. We used a dataset of intracranial motions at five cranial joints in channel catfish (<i>Ictalurus punctatus</i>), collected using X-ray reconstruction of moving morphology, to test whether speed or task best-explained patterns of coordination. We found that motions were significantly more coordinated (by 20–29%) during prey capture than during prey transport, supporting the hypothesis that the nature of the task determines coordination patterns. We found no significant difference in coordination between low- and high-speed motions. We speculate that capture is more coordinated to create a single fluid flow into the mouth while transport is less coordinated so that the cranial elements can independently generate multiple flows to reposition prey. Our results demonstrate the benefits of both higher and lower coordination in animal behaviours and the potential of motion analysis to elucidate motor tasks.
DOI: 10.6084/m9.figshare.7964210.v1
title: Kinematic data Indiv2 from Channel catfish use higher coordination to capture prey than to swallow

description: When animals move they must coordinate motion among multiple parts of the musculoskeletal system. Different behaviours exhibit different patterns of coordination, however, it remains unclear what general principles determine the coordination pattern for a particular behaviour. One hypothesis is that speed determines coordination patterns as a result of differences in voluntary versus involuntary control. An alternative hypothesis is that the nature of the behavioural task determines patterns of coordination. Suction-feeding fishes have highly kinetic skulls and must coordinate the motions of over a dozen skeletal elements to draw fluid and prey into the mouth. We used a dataset of intracranial motions at five cranial joints in channel catfish (<i>Ictalurus punctatus</i>), collected using X-ray reconstruction of moving morphology, to test whether speed or task best-explained patterns of coordination. We found that motions were significantly more coordinated (by 20–29%) during prey capture than during prey transport, supporting the hypothesis that the nature of the task determines coordination patterns. We found no significant difference in coordination between low- and high-speed motions. We speculate that capture is more coordinated to create a single fluid flow into the mouth while transport is less coordinated so that the cranial elements can independently generate multiple flows to reposition prey. Our results demonstrate the benefits of both higher and lower coordination in animal behaviours and the potential of motion analysis to elucidate motor tasks.
DOI: 10.6084/m9.figshare.7964213.v1
title: Kinematic data Indiv1 from Channel catfish use higher coordination to capture prey than to swallow

description: When animals move they must coordinate motion among multiple parts of the musculoskeletal system. Different behaviours exhibit different patterns of coordination, however, it remains unclear what general principles determine the coordination pattern for a particular behaviour. One hypothesis is that speed determines coordination patterns as a result of differences in voluntary versus involuntary control. An alternative hypothesis is that the nature of the behavioural task determines patterns of coordination. Suction-feeding fishes have highly kinetic skulls and must coordinate the motions of over a dozen skeletal elements to draw fluid and prey into the mouth. We used a dataset of intracranial motions at five cranial joints in channel catfish (<i>Ictalurus punctatus</i>), collected using X-ray reconstruction of moving morphology, to test whether speed or task best-explained patterns of coordination. We found that motions were significantly more coordinated (by 20–29%) during prey capture than during prey transport, supporting the hypothesis that the nature of the task determines coordination patterns. We found no significant difference in coordination between low- and high-speed motions. We speculate that capture is more coordinated to create a single fluid flow into the mouth while transport is less coordinated so that the cranial elements can independently generate multiple flows to reposition prey. Our results demonstrate the benefits of both higher and lower coordination in animal behaviours and the potential of motion analysis to elucidate motor tasks.
DOI: 10.6084/m9.figshare.7964168
title: Billion Triple Challenge 2019 (BTC 2019): Unique Triples Dataset

description: A dump of all the unique triples (256,059,548) in the BTC 2019 dataset. The data are serialised in N-Triples format and compressed with GZip.
DOI: 10.6084/m9.figshare.7964159
title: Patterns of genetic structure and adaptive positive selection in the Lithuanian population from high-density SNP data

description: The PED ans MAP files contain SNP data used in Urnikyte A et al. (<b>Patterns of genetic structure and adaptive positive selection in the Lithuanian population from high-density SNP data)</b>. The data set consists of 424 samples and 532,836 SNPs after filtering. Genotyping was performed at the Department of Human and Medical Genetics, Biomedical Science Institute, Faculty of Medicine, Vilnius University, Lithuania with the Illumina HumanOmniExpress-12v1.1 (296 samples) and the Infinium OmniExpress-24 (129 samples) arrays (Illumina, San Diego, CA, USA).
DOI: 10.6084/m9.figshare.7964141
title: Evaluation of remote pulmonary function testing in motor neuron disease

description: <i>Introduction</i>: Motor neuron disease (MND) causes respiratory insufficiency, which is managed in part through use of noninvasive ventilation (NIV). Guidelines for the initiation of NIV are based on pulmonary function tests (PFTs), usually performed once every three months. In the setting of MND telemedicine, remote monitoring of respiratory health may permit earlier intervention, but proof of equivalence to conventional PFTs is lacking. <i>Methods</i>: We implemented delivery of remote PFTs (rPFTs), based on our institution’s telemedicine platform, with the goals of validating measurement equivalence to conventional forced vital capacity (FVC) and maximal inspiratory pressure (MIP) assessments, and assessing process acceptability from both patients and therapists. <i>Results</i>: When remotely guided by a respiratory therapist, 40 patient/caregiver teams produced respiratory parameters that were tightly correlated with those acquired through the standard evaluation. Both patients and therapists generally rated the setup and use of the devices positively, with patient ratings higher than those of the therapists. <i>Discussion</i>: This study suggests that rPFTs are accurate and acceptable, and thus may be incorporated into MND telemedicine for clinical and research use.
DOI: 10.6084/m9.figshare.7964126
title: Antennal Literature

description: Literature relating to antennal physiology collected in early 2016 using Scopus and Google Scholar for the PhD of Isobel Roberts - including search terms; scanning electron microscopy, SEM, transmission electron microscopy, TEM, sensilla, antenna, physiology and insect(s). A total of 141 full text documents were included within this table. Articles ranged from 1973 to 2015.
DOI: 10.6084/m9.figshare.7964102
title: <i>In vivo</i> transcriptomes of <i>Streptococcus suis</i> reveal genes required for niche-specific adaptation and pathogenesis

description: <i>Streptococcus suis</i> is a Gram-positive bacterium and a zoonotic pathogen residing in the nasopharynx or the gastrointestinal tract of pigs with a potential of causing life-threatening invasive disease. It is endemic in the porcine production industry worldwide, and it is also an emerging human pathogen. After invasion, the pathogen adapts to cause bacteremia and disseminates to different organs including the brain. To gain insights in this process, we infected piglets with a highly virulent strain of <i>S. suis</i>, and bacterial transcriptomes were obtained from blood and different organs (brain, joints, and heart) when animals had severe clinical symptoms of infection. Microarrays were used to determine the genome-wide transcriptional profile at different infection sites and during growth in standard growth medium <i>in vitro</i>. We observed differential expression of around 30% of the Open Reading Frames (ORFs) and infection-site specific patterns of gene expression. Genes with major changes in expression were involved in transcriptional regulation, metabolism, nutrient acquisition, stress defenses, and virulence, amongst others, and results were confirmed for a subset of selected genes using RT-qPCR. Mutants were generated in two selected genes, and the encoded proteins, i.e., NADH oxidase and MetQ, were shown to be important virulence factors in coinfection experiments and <i>in vitro</i> assays. The knowledge derived from this study regarding <i>S. suis</i> gene expression <i>in vivo</i> and identification of virulence factors is important for the development of novel diagnostic and therapeutic strategies to control <i>S. suis</i> disease.
DOI: 10.6084/m9.figshare.7964117
title: 1H NMR-Based Metabolomics Reveals Metabolic Changes in the Hippocampus of MPTP-induced Mice

description: Cognitive impairment is a crucial non-motor symptom in patients with Parkinson’s disease (PD). Research carried out in recent years has indicated an association between hippocampus and cognitive deficits in PD patients with or without dementia. However, the molecular mechanism is still unclear. Metabolites including neurotransmitters modulated lots of biological functions in central nervous system. The influence of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP), which could lead to Parkinsonism in non-human primate and mice, on hippocampal metabolites is still unclear. In this study, HE staining and <sup>1</sup>H NMR were used to assess the neuronal morphology and metabolite levels in the hippocampus of MPTP-injected mice on the 1, 7, 21, and 35. Our data revealed that MPTP cannot result in any influence on the neuronal morphology in the hippocampus of mice injected with MPTP. Concentrations of Lactate (Lac), Alanine (Ala), Glutamate (Glu), Glycine (Gly), Creatine (Cr), Taurine (Tau), Choline (Cho) and Phosphocholine (P-Cho) were detected in the hippocampus using <sup>1</sup>H NMR. On the day 1, increases of all these metabolite levels were induced by MPTP-treatment, and concentrations of Lac, Cr, Glu, Cho, and P-Cho were increased in the hippocampus in the day 7. However, only P-Cho level was boosted in the hippocampus of MPTP-injected mice in the day 21. At last, a higher level of Cr was detected in the MPTP group in the day 35. Our results indicated that metabolic changes appeared in the day 1 after the last injection of MPTP prior to other symptoms of rodent model. These data suggested that metabolic dysfunction might be a good marker for the diagnosis of PD.
DOI: 10.6084/m9.figshare.7964126.v2
title: Antennal Literature

description: Literature relating to antennal physiology collected in early 2016 using Scopus and Google Scholar for the PhD of Isobel Roberts - including search terms; scanning electron microscopy, SEM, transmission electron microscopy, TEM, sensilla, antenna, physiology and insect(s). A total of 141 full text documents were included within this table. Articles ranged from 1973 to 2015.
DOI: 10.6084/m9.figshare.7964090
title: Open_CaseStudy2013_v12.R

description: Code for case study <br>
DOI: 10.6084/m9.figshare.7964102.v2
title: <i>In vivo</i> transcriptomes of <i>Streptococcus suis</i> reveal genes required for niche-specific adaptation and pathogenesis

description: <i>Streptococcus suis</i> is a Gram-positive bacterium and a zoonotic pathogen residing in the nasopharynx or the gastrointestinal tract of pigs with a potential of causing life-threatening invasive disease. It is endemic in the porcine production industry worldwide, and it is also an emerging human pathogen. After invasion, the pathogen adapts to cause bacteremia and disseminates to different organs including the brain. To gain insights in this process, we infected piglets with a highly virulent strain of <i>S. suis</i>, and bacterial transcriptomes were obtained from blood and different organs (brain, joints, and heart) when animals had severe clinical symptoms of infection. Microarrays were used to determine the genome-wide transcriptional profile at different infection sites and during growth in standard growth medium <i>in vitro</i>. We observed differential expression of around 30% of the Open Reading Frames (ORFs) and infection-site specific patterns of gene expression. Genes with major changes in expression were involved in transcriptional regulation, metabolism, nutrient acquisition, stress defenses, and virulence, amongst others, and results were confirmed for a subset of selected genes using RT-qPCR. Mutants were generated in two selected genes, and the encoded proteins, i.e., NADH oxidase and MetQ, were shown to be important virulence factors in coinfection experiments and <i>in vitro</i> assays. The knowledge derived from this study regarding <i>S. suis</i> gene expression <i>in vivo</i> and identification of virulence factors is important for the development of novel diagnostic and therapeutic strategies to control <i>S. suis</i> disease.
DOI: 10.6084/m9.figshare.7964126.v1
title: Antennal Literature

description: Literature relating to antennal physiology collected in early 2016 using Scopus and Google Scholar for the PhD of Isobel Roberts - including search terms; scanning electron microscopy, SEM, transmission electron microscopy, TEM, sensilla, antenna, physiology and insect(s). A total of 141 full text documents were included within this table. Articles ranged from 1973 to 2015.
DOI: 10.6084/m9.figshare.7964117.v2
title: 1H NMR-Based Metabolomics Reveals Metabolic Changes in the Hippocampus of MPTP-induced Mice

description: Cognitive impairment is a crucial non-motor symptom in patients with Parkinson’s disease (PD). Research carried out in recent years has indicated an association between hippocampus and cognitive deficits in PD patients with or without dementia. However, the molecular mechanism is still unclear. Metabolites including neurotransmitters modulated lots of biological functions in central nervous system. The influence of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP), which could lead to Parkinsonism in non-human primate and mice, on hippocampal metabolites is still unclear. In this study, HE staining and <sup>1</sup>H NMR were used to assess the neuronal morphology and metabolite levels in the hippocampus of MPTP-injected mice on the 1, 7, 21, and 35. Our data revealed that MPTP cannot result in any influence on the neuronal morphology in the hippocampus of mice injected with MPTP. Concentrations of Lactate (Lac), Alanine (Ala), Glutamate (Glu), Glycine (Gly), Creatine (Cr), Taurine (Tau), Choline (Cho) and Phosphocholine (P-Cho) were detected in the hippocampus using <sup>1</sup>H NMR. On the day 1, increases of all these metabolite levels were induced by MPTP-treatment, and concentrations of Lac, Cr, Glu, Cho, and P-Cho were increased in the hippocampus in the day 7. However, only P-Cho level was boosted in the hippocampus of MPTP-injected mice in the day 21. At last, a higher level of Cr was detected in the MPTP group in the day 35. Our results indicated that metabolic changes appeared in the day 1 after the last injection of MPTP prior to other symptoms of rodent model. These data suggested that metabolic dysfunction might be a good marker for the diagnosis of PD.