11,260 research outputs found

    A compendium of genetic regulatory effects across pig tissues

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    The Farm Animal Genotype-Tissue Expression (FarmGTEx) project has been established to develop a public resource of genetic regulatory variants in livestock, which is essential for linking genetic polymorphisms to variation in phenotypes, helping fundamental biological discovery and exploitation in animal breeding and human biomedicine. Here we show results from the pilot phase of PigGTEx by processing 5,457 RNA-sequencing and 1,602 whole-genome sequencing samples passing quality control from pigs. We build a pig genotype imputation panel and associate millions of genetic variants with five types of transcriptomic phenotypes in 34 tissues. We evaluate tissue specificity of regulatory effects and elucidate molecular mechanisms of their action using multi-omics data. Leveraging this resource, we decipher regulatory mechanisms underlying 207 pig complex phenotypes and demonstrate the similarity of pigs to humans in gene expression and the genetic regulation behind complex phenotypes, supporting the importance of pigs as a human biomedical model.</p

    Global fine-resolution data on springtail abundance and community structure

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    Springtails (Collembola) inhabit soils from the Arctic to the Antarctic and comprise an estimated ~32% of all terrestrial arthropods on Earth. Here, we present a global, spatially-explicit database on springtail communities that includes 249,912 occurrences from 44,999 samples and 2,990 sites. These data are mainly raw sample-level records at the species level collected predominantly from private archives of the authors that were quality-controlled and taxonomically-standardised. Despite covering all continents, most of the sample-level data come from the European continent (82.5% of all samples) and represent four habitats: woodlands (57.4%), grasslands (14.0%), agrosystems (13.7%) and scrublands (9.0%). We included sampling by soil layers, and across seasons and years, representing temporal and spatial within-site variation in springtail communities. We also provided data use and sharing guidelines and R code to facilitate the use of the database by other researchers. This data paper describes a static version of the database at the publication date, but the database will be further expanded to include underrepresented regions and linked with trait data

    Effect of centre volume on pathological outcomes and postoperative complications after surgery for colorectal cancer: results of a multicentre national study

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    Background: The association between volume, complications and pathological outcomes is still under debate regarding colorectal cancer surgery. The aim of the study was to assess the association between centre volume and severe complications, mortality, less-than-radical oncologic surgery, and indications for neoadjuvant therapy.Methods: Retrospective analysis of 16,883 colorectal cancer cases from 80 centres (2018-2021). Outcomes: 30-day mortality; Clavien-Dindo grade >2 complications; removal of >= 12 lymph nodes; non-radical resection; neoadjuvant therapy. Quartiles of hospital volumes were classified as LOW, MEDIUM, HIGH, and VERY HIGH. Independent predictors, both overall and for rectal cancer, were evaluated using logistic regression including age, gender, AJCC stage and cancer site.Results: LOW-volume centres reported a higher rate of severe postoperative complications (OR 1.50, 95% c.i. 1.15-1.096, P = 0.003). The rate of >= 12 lymph nodes removed in LOW-volume (OR 0.68, 95% c.i. 0.56-0.85, P = 12 lymph nodes removed was lower in LOW-volume than in VERY HIGH-volume centres (OR 0.57, 95% c.i. 0.41-0.80, P = 0.001). A lower rate of neoadjuvant chemoradiation was associated with HIGH (OR 0.66, 95% c.i. 0.56-0.77, P < 0.001), MEDIUM (OR 0.75, 95% c.i. 0.60-0.92, P = 0.006), and LOW (OR 0.70, 95% c.i. 0.52-0.94, P = 0.019) volume centres (vs. VERY HIGH).Conclusion: Colorectal cancer surgery in low-volume centres is at higher risk of suboptimal management, poor postoperative outcomes, and less-than-adequate oncologic resections. Centralisation of rectal cancer cases should be taken into consideration to optimise the outcomes

    Additional file 1 of Systematic evaluation of B-cell clonal family inference approaches

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    Additional file 1: Supplementary Figure 1. Data simulation pipeline. Simulation approach is an integration of ImmuneSim, Alakazam and SHazaM tools and equally use the data of CF groupings obtained from each of the 10 CF inference approaches. Supplementary Figure 2. Determination of the number of TP, TN, FP, and FN. Three simulated CFs (2 singletons) and two inferred CFs are shown. Supplementary Figure 3. Overall correlation between the log10(number of CFs) and the standardized sequence depth for all combinations of approach (except SCOPer; A7, A8) and dataset. Supplementary Figure 4. Overall trend between the log10(number of CFs) and the standardized mutation load for all combinations of approach (except SCOPer; A7, A8) and dataset. Supplementary Figure 5. Summary of significant pairwise comparisons between Approaches. Supplementary Figure 6. Number of TP, TN, FP, and FN cases produced by the ten approaches when applied to six samples from three simulated datasets (D10, D11, D12). Supplementary Figure 7. Normalized number of TP, TN, FP, and FN cases produced by the ten approaches when applied to six samples from three simulated datasets (D10, D11, D12)

    Treatment-limiting decisions in patients with severe traumatic brain injury in the Netherlands

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    Introduction: Treatment-limiting decisions (TLDs) can be inevitable severe traumatic brain injury (s-TBI) patients, but data on their use remain scarce. Research question: To investigate the prevalence, timing and considerations of TLDs in s-TBI patients. Material and methods: s-TBI patients between 2008 and 2017 were analysed retrospecively. Patient data, timing, location, involvement of proxies, and reasons for TLDs were collected. Baseline characteristics and in-hospital outcomes were compared between s-TBI patients with and without TLDs. Results: TLDs were reported in 117 of 270 s-TBI patients (43.3%) and 95.9% of deaths after s-TBI were preceded by a TLD. The majority of TLDs (68.4%) were categorized as withdrawal of therapy, of which withdrawal of organ-support in 64.1%. Neurosurgical intervention was withheld in 29.9%. The median time from admission to TLD was 2 days [IQR, 0–8] and 50.4% of TLDs were made within 3 days of admission. The main reason for a TLD was that the patients were perceived as unsalvageable (66.7%). Nearly all decisions were made multidisciplinary (99.1%) with proxies involvement (75.2%). The predicted mortality (CRASH-score) between patients with and without TLDs were 72.6 vs. 70.6%. The percentage of TLDs in s-TBI patients increased from 20.0% in 2008 to 42.9% in 2012 and 64.3% in 2017. Discussion and conclusion: TLDs occurred in almost half of s-TBI patients and were instituted more frequently over time. Half of TLDs were made within 3 days of admission in spite of baseline prognosis between groups being similar. Future research should address whether prognostic nihilism contributes to self-fulfilling prophecies

    Understanding the complex dynamics of zebra mussel invasions over several decades in European rivers: drivers, impacts and predictions

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    The zebra mussel Dreissena polymorpha is one of the most successful, notorious, and detrimental aquatic invasive non-native species worldwide, having invaded Europe and North America while causing substantial ecological and socio-economic impacts. Here, we investigated the spatiotemporal trends in this species' invasion success using 178 macroinvertebrate abundance time series, containing 1451 records of D. polymorpha collected across nine European countries between 1972–2019. Using these raw (absolute) abundance data, we examined trends and drivers of occurrences and relative abundances of D. polymorpha within invaded communities. Meta-regression models revealed non-significant trends both at the European level and for the majority of the invaded countries, except for France (significant decreasing trend) and Hungary (marginally positive trend). At the European level, the number of D. polymorpha occurrences over time followed a flat-top bell-shaped distribution, with a steep increase between 1973–1989 followed by a plateau phase prior to significantly declining post-1998. Using a series of climatic and hydromorphological site-specific characteristics of invaded and uninvaded sites from two periods (1998–2002; 2011–2015), we found that native richness, non-native abundance, distance to the next barrier, and elevation were associated with the occurrence of D. polymorpha. We also found that higher native richness and lower latitude were related to lower relative abundances. Using Cohen's D as a measure of D. polymorpha impact, we found that biodiversity within the invaded sites was initially higher than in uninvaded ones, but then declined, suggesting differences in biodiversity trends across invaded and uninvaded sites. While our results emphasise the high invasion success of D. polymorpha, increasing stressors within the context of global change – particularly ongoing climate change – are likely to enhance invasion rates and the impact of D. polymorpha in the near future, exacerbated by the lack of timely and effective management actions

    Impact of liver cirrhosis, severity of cirrhosis and portal hypertension on the difficulty of laparoscopic and robotic minor liver resections for primary liver malignancies in the anterolateral segments

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    SEAwise Report on improved predictive models of growth, production and stock quality.

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    The SEAwise project works to deliver a fully operational tool that will allow fishers, managers, and policy makers to easily apply Ecosystem Based Fisheries Management (EBFM) in their fisheries and understanding how ecological drivers impact stock productivity through growth, condition and maturity is essential to this proces. In this SEAwise report, we present the predictive models of fish growth, condition and maturity obtained so far in each of the four regional case studies.The biological processes (fish growth, condition and maturity) were studied in terms of body size (weight-at-age, length-at-age), condition factor, otolith increments and size at first maturity. Underlying data were available at different levels, ranging from individual fish, to sampling haul or stock level. Accordingly, the methods employed varied across case studies to adapt to the specific features of the process under study and the available data.The methodology encompassed statistical models (linear models, generalised additive models, mixed models, Bayesian nested hierarchical models, changepoint models), otolith growth increment analyses and mechanistic models (DEB-IBM model coupled to the environment and mizer model). Some of these models were focused on detecting overall trends, including potential changepoints along the time series or identification of the main intrinsic factors. Other models explored the impact of ecological drivers such as temperature, salinity, food availability or density dependence.In the Baltic Sea, two regimes were identified in the weight-at-age time series of herring in the Gulf of Riga (1961-1988 and 1989-2020). During the first period the main driver of the individual annual growth of the fish was the abundance of the copepod L. macrurus macrurus, while the abundance of the adult stages of E. affinis affinis was the dominating explanatory variable affecting herring growth during the second period. Neither SSB nor summer temperature during the main feeding period were significant drivers of the individual growth in the two distinct ecosystem regimes.In the Mediterranean Sea, the analysis of the impact of the environmental variables on biological parameters like size at first maturity, condition factor and growth in South Adriatic Sea and North-West Ionian Sea showed some significant effects in relation to the different species/area. In most of the cases, the environmental driver was bottom temperature, although some relationships with bottom salinity and primary production were also found. The model outcomes suggested that temperatures prevailing in deeper waters were the most significant factor affecting gonad maturity of hakes, while those in the shallow zone had the main impact on the L50 of red mullets. Condition factor of hake and red mullet in the Eastern Ionian Sea were affected not only by temperature, but also by zooplankton abundance.In the North Sea, mediated length-based growth models, linear mixed models and state-space linear mixed models were applied to four gadoids, two flatfishes and one pelagic stock and their performances were assessed in terms of model fit and predictive capability. For the mediated length-based growth model approach, the best model differed across stocks, but density dependent mediation effects were significant for five out of the seven stocks. Regarding the linear mixed models, the two types of models and the different penalisation procedures led to different models across stocks. Among the additional ecological variables, surface temperature was the most frequently included in the final model, closely followed closely by SSB and to a lesser extent by NAO. Detailed otolith increment analysis was used in the development of multidecadal biochronologies of average annual growth of sole in the North Sea and in the Irish Sea. In the North Sea, the best extrinsic model of sole growth included sea bottom temperature, fishing mortality at age, and stock biomass at maturity stage, and their interactions with age and maturity stage, while in the Irish Sea, the best extrinsic model included sea bottom temperature and fishing mortality at maturity stage and its interaction with maturity stage. These results confirmed the expected positive effect of temperature on adult growth. However, in the North Sea, temperature showed unexpected negative effect on juvenile growth, which might be linked to changes in food availability and/or intraspecific competition and need to be further studied. The mizer model (package for size-spectrum ecological modelling) with environmental forcing was used to study whether warming in the North Sea is responsible for the failure of the cod stock. The simulated fish community response when recruitment and carrying capacity depended on surface temperature fitted better with the assessment data than when the environment was fixed. However, the qualitative differences remain, suggesting that temperature effects were not the main cause of the model-assessment disparity.In the Western Waters, the mediated length-based growth models developed for the North Sea case study were applied to 14 stocks in the Celtic Sea. The best model differed across stocks, but again SSB mediation was significant for most of the stocks. From visual inspection of the plots, however, it was noted that the raw data from certain stock objects showed a reduced growth compared to the model fits, requiring further analyses. The analysis on biological measurements of individuals collected at fish markets, observers at sea or during scientific cruises allowed to study temporal variations in body size and condition factor of benthic, pelagic and demersal species in the Celtic Sea and the Bay of Biscay. The linear models indicated a significant negative monotonic relationship of sizes at all ages for anchovy and pilchard, but variations in size at age were less clear and significant for benthic and demersal species. In contrast, the results of the body condition indices showed a moderate but significant decrease for all the studied 19 species over time. The in-depth analysis for anchovy in the Bay of Biscay based on research surveys confirmed the decline in the length and weight of anchovy in the Bay of Biscay and pointed to a decline in body condition toward slender body shapes. Detected associations between temperature and size became more apparent for adult age classes than for juveniles, whereas the association between anchovy size and the biomass of spawners was more important for juvenile than for adult age classes. Associations between anchovy size and chlorophyll-a concentration were in general weak. Finally, the DEB-IBM model coupled to the environment that is under development for the two main seabass stocks of the North East Atlantic will provide further insights on how growth, condition and maturation can affect the future dynamics and productivity of these stocks.Read more about the project at www.seawiseproject.org</p
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