Data from: Circadian mood variations in Twitter content

Background: Circadian regulation of sleep, cognition, and metabolic state is driven by a central clock, which is in turn entrained by environmental signals. Understanding the circadian regulation of mood, which is vital for coping with day-to-day needs, requires large datasets and has classically utilised subjective reporting. Methods: In this study, we use a massive dataset of over 800 million Twitter messages collected over 4 years in the United Kingdom. We extract robust signals of the changes that happened during the course of the day in the collective expression of emotions and fatigue. We use methods of statistical analysis and Fourier analysis to identify periodic structures, extrema, change-points, and compare the stability of these events across seasons and weekends. Results: We reveal strong, but different, circadian patterns for positive and negative moods. The cycles of fatigue and anger appear remarkably stable across seasons and weekend/weekday boundaries. Positive mood and sadness interact more in response to these changing conditions. Anger and, to a lower extent, fatigue show a pattern that inversely mirrors the known circadian variation of plasma cortisol concentrations. Most quantities show a strong inflexion in the morning. Conclusion: Since circadian rhythm and sleep disorders have been reported across the whole spectrum of mood disorders, we suggest that analysis of social media could provide a valuable resource to the understanding of mental disorder.,Twitter Hourly WordsTime series of hourly frequencies for 9,096 psychometric words sampled between 1st January 2010 and 31st October 2014 in a represensative set of Twitter Content across the United Kingdom.data_CircadianMoodVariationsInTwitterContent.zip

Additional file 3 of The effectiveness of non-pharmacological sleep interventions for people with chronic pain: a systematic review and meta-analysis

Additional file 3

Data from: Improving Illumina assemblies with Hi-C and long reads: an example with the North African dromedary

Researchers have assembled thousands of eukaryotic genomes using Illumina reads, but traditional mate-pair libraries cannot span all repetitive elements, resulting in highly fragmented assemblies. However, both chromosome conformation capture techniques, such as Hi-C and Dovetail Genomics Chicago libraries and long-read sequencing, such as Pacific Biosciences and Oxford Nanopore, help span and resolve repetitive regions and therefore improve genome assemblies. One important livestock species of arid regions that does not have a high-quality contiguous reference genome is the dromedary (Camelus dromedarius). Draft genomes exist but are highly fragmented, and a high-quality reference genome is needed to understand adaptation to desert environments and artificial selection during domestication. Dromedaries are among the last livestock species to have been domesticated, and together with wild and domestic Bactrian camels, they are the only representatives of the Camelini tribe, which highlights their evolutionary significance. Here we describe our efforts to improve the North African dromedary genome. We used Chicago and Hi-C sequencing libraries from Dovetail Genomics to resolve the order of previously assembled contigs, producing almost chromosome-level scaffolds. Remaining gaps were filled with Pacific Biosciences long reads, and then scaffolds were comparatively mapped to chromosomes. Long reads added 99.32 Mbp to the total length of the new assembly. Dovetail Chicago and Hi-C libraries increased the longest scaffold over 12-fold, from 9.71 Mbp to 124.99 Mbp and the scaffold N50 over 50-fold, from 1.48 Mbp to 75.02 Mbp. We demonstrate that Illumina de novo assemblies can be substantially upgraded by combining chromosome conformation capture and long-read sequencing.,CamDro2 predicted proteinsCamDro2 genome predicted proteins produced by a single round of MAKER (Holt and Yandell: MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinformatics 2011 12:491).dromedary.pbjelly.pilon.abyss.pilon.all.fasta.all.maker.proteins.renamed.annotated.fasta.zipCamDro2 predicted mRNACamDro2 genome predicted mRNA transcripts produced by a single round of MAKER (Holt and Yandell: MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinformatics 2011 12:491).dromedary.pbjelly.pilon.abyss.pilon.all.fasta.all.maker.transcripts.renamed.annotated.fasta.zipCamDro1 assembly (GCA_000803125.1) improved by Dovetail Genomics Chicago and Hi-C libraries gzipped (www.gzip.org) FASTA fileDovetail Genomics created Chicago and Dovetail Hi-C libraries from a low passage cell culture line (Perelman et al. 2018) derived from ear fibroblasts of the same dromedary used in CamDro1 (GCA_000803125.1). Dovetail Genomics created both Chicago and Hi-C libraries with the DpnII restriction enzyme, sequenced these libraries on six lanes of an Illumina HiSeq sequencer, and then scaffolded the CamDro1 assembly using the HiRise pipeline (Putnam et al. 2016). First, the CamDro1 assembly was split at gaps and scaffolded using Dovetail Chicago data. Then, the Chicago assembly was improved by scaffolding with Hi-C data creating a Hi-C assembly. Assembly is a gzipped (www.gzip.org) FASTA file.dromedary.fasta.gzCamDro2 genome gzipped FASTA fileCamDro2 genome gzipped (www.gzip.org/ ) FASTA file, chromosomes are identified by >1,>2,...,>36,>X (for chromosomes 1,2,...,36,X). There is no Y chromosome as the sequenced dromedary was female.dromedary.pbjelly.pilon.abyss.pilon.chromosomes.fasta.gzCamDro2 gene annotations in GFF format (zipped)dromedary.pbjelly.pilon.abyss.pilon.all.renamed.annotated.maker.qualityfilter.gff.zipcDNA transcripts used to train Augustus for the second round of MAKERcDNA transcripts used to train Augustus for the second round of MAKERdromedary.pbjelly.pilon.abyss.pilon.all.maker.transcripts.cdna.for.augustus.training.zipanalysis-steps-for-manuscriptThese are the are the rough analysis steps for the manuscript. If you find these steps helpful, please cite the manuscript!RH-alpaca-probe-sequencesRH alpaca probe sequences for Steps 20, 28, and 33 of analysis-steps-for-manuscript.txt. RH probe sequences are in 37 different files contained in the master zip file (chromosome 1,2,...,36,and X). Even though files are named with .txt format, they are FASTA formatted files.

Data from: Improving Illumina assemblies with Hi-C and long reads: an example with the North African dromedary

Researchers have assembled thousands of eukaryotic genomes using Illumina reads, but traditional mate-pair libraries cannot span all repetitive elements, resulting in highly fragmented assemblies. However, both chromosome conformation capture techniques, such as Hi-C and Dovetail Genomics Chicago libraries and long-read sequencing, such as Pacific Biosciences and Oxford Nanopore, help span and resolve repetitive regions and therefore improve genome assemblies. One important livestock species of arid regions that does not have a high-quality contiguous reference genome is the dromedary (Camelus dromedarius). Draft genomes exist but are highly fragmented, and a high-quality reference genome is needed to understand adaptation to desert environments and artificial selection during domestication. Dromedaries are among the last livestock species to have been domesticated, and together with wild and domestic Bactrian camels, they are the only representatives of the Camelini tribe, which highlights their evolutionary significance. Here we describe our efforts to improve the North African dromedary genome. We used Chicago and Hi-C sequencing libraries from Dovetail Genomics to resolve the order of previously assembled contigs, producing almost chromosome-level scaffolds. Remaining gaps were filled with Pacific Biosciences long reads, and then scaffolds were comparatively mapped to chromosomes. Long reads added 99.32 Mbp to the total length of the new assembly. Dovetail Chicago and Hi-C libraries increased the longest scaffold over 12-fold, from 9.71 Mbp to 124.99 Mbp and the scaffold N50 over 50-fold, from 1.48 Mbp to 75.02 Mbp. We demonstrate that Illumina de novo assemblies can be substantially upgraded by combining chromosome conformation capture and long-read sequencing.,CamDro2 predicted proteinsCamDro2 genome predicted proteins produced by a single round of MAKER (Holt and Yandell: MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinformatics 2011 12:491).dromedary.pbjelly.pilon.abyss.pilon.all.fasta.all.maker.proteins.renamed.annotated.fasta.zipCamDro2 predicted mRNACamDro2 genome predicted mRNA transcripts produced by a single round of MAKER (Holt and Yandell: MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinformatics 2011 12:491).dromedary.pbjelly.pilon.abyss.pilon.all.fasta.all.maker.transcripts.renamed.annotated.fasta.zipCamDro1 assembly (GCA_000803125.1) improved by Dovetail Genomics Chicago and Hi-C libraries gzipped (www.gzip.org) FASTA fileDovetail Genomics created Chicago and Dovetail Hi-C libraries from a low passage cell culture line (Perelman et al. 2018) derived from ear fibroblasts of the same dromedary used in CamDro1 (GCA_000803125.1). Dovetail Genomics created both Chicago and Hi-C libraries with the DpnII restriction enzyme, sequenced these libraries on six lanes of an Illumina HiSeq sequencer, and then scaffolded the CamDro1 assembly using the HiRise pipeline (Putnam et al. 2016). First, the CamDro1 assembly was split at gaps and scaffolded using Dovetail Chicago data. Then, the Chicago assembly was improved by scaffolding with Hi-C data creating a Hi-C assembly. Assembly is a gzipped (www.gzip.org) FASTA file.dromedary.fasta.gzCamDro2 genome gzipped FASTA fileCamDro2 genome gzipped (www.gzip.org/ ) FASTA file, chromosomes are identified by >1,>2,...,>36,>X (for chromosomes 1,2,...,36,X). There is no Y chromosome as the sequenced dromedary was female.dromedary.pbjelly.pilon.abyss.pilon.chromosomes.fasta.gzCamDro2 gene annotations in GFF format (zipped)dromedary.pbjelly.pilon.abyss.pilon.all.renamed.annotated.maker.qualityfilter.gff.zipcDNA transcripts used to train Augustus for the second round of MAKERcDNA transcripts used to train Augustus for the second round of MAKERdromedary.pbjelly.pilon.abyss.pilon.all.maker.transcripts.cdna.for.augustus.training.zipanalysis-steps-for-manuscriptThese are the are the rough analysis steps for the manuscript. If you find these steps helpful, please cite the manuscript!RH-alpaca-probe-sequencesRH alpaca probe sequences for Steps 20, 28, and 33 of analysis-steps-for-manuscript.txt. RH probe sequences are in 37 different files contained in the master zip file (chromosome 1,2,...,36,and X). Even though files are named with .txt format, they are FASTA formatted files.

Optogenetic stimulation of kisspeptin neurones within the posterodorsal medial amygdala increases LH pulse frequency in female mice

Kisspeptin within the arcuate nucleus of the hypothalamus is a critical neuropeptide in the regulation of reproduction. Together with neurokinin B and dynorphin A, arcuate kisspeptin provides the oscillatory activity that drives the pulsatile secretion of GnRH, and therefore LH pulses, and is believed to be a central component of the GnRH pulse generator. It is well established that the amygdala also exerts an influence over gonadotrophic hormone secretion and reproductive physiology. The discovery of kisspeptin and its receptor within the posterodorsal medial amygdala (MePD), and our recent finding showing that intra-MePD administration of kisspeptin or a kisspeptin receptor antagonist results in increased LH secretion and decreased LH pulse frequency, respectively, suggests an important role for amygdala kisspeptin signalling in the regulation of the GnRH pulse generator. To further investigate the function of amygdala kisspeptin, the present study used an optogenetic approach to selectively stimulate MePD kisspeptin neurones and examine the effect on pulsatile LH secretion. MePD kisspeptin neurones in conscious Kiss1-Cre mice were virally infected to express the channelrhodopsin 2 protein and selectively stimulated by light via a chronically implanted fibre optic cannula. Continuous stimulation using 5 Hz resulted in an increased LH pulse frequency, which was not observed at the lower stimulation frequencies of 0.5 and 2 Hz. In wild-type animals, continuous stimulation at 5 Hz did not affect LH pulse frequency. These results demonstrate that selective activation of MePD Kiss1 neurons can modulate hypothalamic GnRH pulse generator frequency