Additional file 11. 850,096 map file. Plain text file containing the map position (cM) of all loci on the 850,096 linkage map, in the format required for analysis using MAPQTL 6.0.

Additional file 11. 850,096 map file. Plain text file containing the map position (cM) of all loci on the 850,096 linkage map, in the format required for analysis using MAPQTL 6.0.

Additional file 10. 850,055 map file. Plain text file containing the map position (cM) of all loci on the 850,055 linkage map, in the format required for analysis using MAPQTL 6.0.

Abstract Background Mouse is probably the most important model organism to study mammal biology and human diseases. A better understanding of the mouse genome will help understand the human genome, biology and diseases. However, despite the recent progress, the characterization of the regulatory sequences in the mouse genome is still far from complete, limiting its use to understand the regulatory sequences in the human genome. Results Here, by integrating binding peaks in ~ 9,000 transcription...

Additional file 1: Figure S1. Odds ratio for the association between mortality (1A–C), intensive care unit admission (2A–C) and use of invasive mechanical ventilation during the hospitalization (3A–C) and ischemic heart disease in each of the four cohorts and overall. I2 indicates heterogeneity in the estimates. Odds ratio estimates adjusted for: model 1: age and sex (B); model 2: model 1 + type of diabetes, arterial hypertension, and the presence of microvascular disease (C).

Additional file 2: Figure S2. Odds ratio for the association between mortality (1A–C), intensive care unit admission (2A–C) and and stroke in each of the four cohorts and overall. I2 indicates heterogeneity in the estimates. Odds ratio estimates adjusted for: model 1: age and sex (B); model 2: model 1 + type of diabetes, arterial hypertension, and the presence of microvascular disease (C).

Additional file 3: Figure S3. Odds ratio for the association between mortality (1A–C), intensive care unit admission (2A–C) and peripheral artery disease in each of the four cohorts and overall. I2 indicates heterogeneity in the estimates. Odds ratio estimates adjusted for: model 1: age and sex (B); model 2: model 1 + type of diabetes, arterial hypertension, and the presence of microvascular disease (C).

Abstract Background It is not clear whether pre-existing macrovascular complications (ischemic heart disease, stroke or peripheral artery disease) are associated with health outcomes in people with diabetes mellitus hospitalized for COVID-19. Methods We conducted cohort studies of adults with pre-existing diabetes hospitalized for COVID-19 infection in the UK, France, and Spain during the early phase of the pandemic (between March 2020—October 2020). Logistic regression models adjusted for demographic factors and other comorbidities were used to...

Climatic niche evolution during the diversification of tropical plants has received little attention in Africa. To address this, we characterized the climatic niche of >4000 tropical African woody species, distinguishing two broad bioclimatic groups (forest vs. savanna) and six subgroups. We quantified niche conservatism versus lability at the genus level and for higher clades, using a molecular phylogeny of >800 genera. Although niche stasis at speciation is prevalent, numerous clades individually cover vast climatic spaces...

Lungfish (Dipnoi) are lobe-finned fish (Sarcopterygii) that have persisted for over 400 million years from the Devonian Period to present day. They are the extant sister group to tetrapods and thus have the ability to provide unique insight into the condition of the earliest tetrapods as well as their own evolutionary history. The evolution of their dermal skull and dentition is relatively well understood, but this is not the case for the central nervous system....

Auxin-inducible degrons are a chemical genetic tool for targeted protein degradation and are widely used to study protein function in cultured mammalian cells. Here we develop CRISPR-engineered mouse lines that enable rapid and highly specific degradation of tagged endogenous proteins in vivo. Most but not all cell types are competent for degradation. By combining ligand titrations with genetic crosses to generate animals with different allelic combinations, we show that degradation kinetics depend upon the dose...

Spatial variation in plant chemical defence towards herbivores can help us understand variation in herbivore top-down control of shrubs in the Arctic and possibly also shrub responses to global warming. Less defended, non-resinous shrubs could be more influenced by herbivores than more defended, resinous shrubs. However, sparse field measurements limit our current understanding of how much of the circum-Arctic variation in defence compounds is explained by taxa or defence functional groups (resinous/non-resinous). We measured circum-Arctic...

Additional file 1: Figure S1. Distribution of N3 and CLA fatty acid indices in beef in our population. N3 index estimated as the natural logarithm of the ratio between C18:3n-3 + C20:5n-3 + C22:5n-3 + C22:6n-3 and C12:0 + C14:0 + C16:0. CLA index estimated as the natural logarithm of the ratio between cis-9, trans-11 C18:2 + trans-11 C18:1 and C12:0 + C14:0 + C16:0. Values are corrected by breed, diet and experiment combined effect....

Additional file 1: Figure S1. Distribution of N3 and CLA fatty acid indices in beef in our population. N3 index estimated as the natural logarithm of the ratio between C18:3n-3 + C20:5n-3 + C22:5n-3 + C22:6n-3 and C12:0 + C14:0 + C16:0. CLA index estimated as the natural logarithm of the ratio between cis-9, trans-11 C18:2 + trans-11 C18:1 and C12:0 + C14:0 + C16:0. Values are corrected by breed, diet and experiment combined effect....

Additional file 2: Table S1. Microbial gene abundances in rumen microbiome (analyzed after an additive log-ratio transformation) with significant host genomic effects referred to as host-specific functional core microbiome (HGFC). Table S2. Occupancy rates and heritabilities of micobial gene abundances (analyzed after an additive log-ratio transformation) involved in lipolysis and biohydrogenation processes in rumen found in our population. Table S3. Host genomic correlations between heritable additive log-ratio transformed microbial gene abundances and N3 and CLA...

Abstract Background Healthier ruminant products can be achieved by adequate manipulation of the rumen microbiota to increase the flux of beneficial fatty acids reaching host tissues. Genomic selection to modify the microbiome function provides a permanent and accumulative solution, which may have also favourable consequences in other traits of interest (e.g. methane emissions). Possibly due to a lack of data, this strategy has never been explored. Results This study provides a comprehensive identification of ruminal...

Abstract Background Healthier ruminant products can be achieved by adequate manipulation of the rumen microbiota to increase the flux of beneficial fatty acids reaching host tissues. Genomic selection to modify the microbiome function provides a permanent and accumulative solution, which may have also favourable consequences in other traits of interest (e.g. methane emissions). Possibly due to a lack of data, this strategy has never been explored. Results This study provides a comprehensive identification of ruminal...

Additional file 3: Figure S3. Effects of reduced androgen exposure via blocking of the androgen receptor in ex vivo culture of human fetal testes. Quantification of A) testosterone B) androstenedione and C) DHEAS secretion by ex vivo cultured fetal testis tissue from GW 7-12 following treatment with flutamide (10-6 M) and ketoconazole (10-6 M) for 14 days. Media were collected every 48 hours throughout the 14-day culture period and were pooled for each individual tissue...

Abstract Background The advent of low cost, high throughput DNA sequencing has led to the availability of thousands of complete genome sequences for a wide variety of bacterial species. Examining and interpreting genetic variation on this scale represents a significant challenge to existing methods of data analysis and visualisation. Results Starting with the output of standard pangenome analysis tools, we describe the generation and analysis of interactive, 3D network graphs to explore the structure of...

Abstract Background The advent of low cost, high throughput DNA sequencing has led to the availability of thousands of complete genome sequences for a wide variety of bacterial species. Examining and interpreting genetic variation on this scale represents a significant challenge to existing methods of data analysis and visualisation. Results Starting with the output of standard pangenome analysis tools, we describe the generation and analysis of interactive, 3D network graphs to explore the structure of...

Abstract Background Second-hand smoke exposure from tobacco significantly contributes to morbidity and mortality worldwide. A cluster RCT in Bangladesh compared a community-based smoke-free home (SFH) intervention delivered in mosques, with or without indoor air quality (IAQ) feedback to households to no intervention. Neither was effective nor cost-effective compared to no intervention using an objective measure of second-hand smoke. This paper presents the process evaluation embedded within the trial and seeks to understand this. Methods A...

Abstract Background Over the last decade, computational sciences have contributed immensely to characterization of phenotypes of airway diseases, but it is difficult to compare derived phenotypes across studies, perhaps as a result of the different decisions that fed into these phenotyping exercises. We aim to perform a systematic review of studies using computational approaches to phenotype obstructive airway diseases in children and adults. Methods and analysis We will search PubMed, Embase, Scopus, Web of Science,...

Additional file 1:

Additional file 7: Table S4. The information of transcriptome data of T. aestivum RING-zf genes.

Additional file 7: Table S4. The information of transcriptome data of T. aestivum RING-zf genes.