Soil bacterial and fungal communities show within field heterogeneity that varies by land management and distance metric

Increasing interest in the use of microbial metrics to evaluate soil health raises the issue of how fine-scale heterogeneity can affect microbial community measurements. Here we analyse bacterial and fungal communities of over 100 soil samples across 17 pasture farms and evaluate beta diversity at different scales. We find large variation in microbial communities between different points in the same field, and if Aitchison distance is used we find that within-field variation is as high as between-farm variation. However, if Bray-Curtis or Jaccard distance are used this variation is partially explained by differences in soil pH and vegetation and is higher under mob grazing for fungi. Hence, field scale variation in microbial communities can impact the evaluation of soil health

Soil networks become more connected and take up more carbon as nature restoration progresses

Soil organisms have an important role in aboveground community dynamics and ecosystem functioning in terrestrial ecosystems. However, most studies have considered soil biota as a black box or focussed on specific groups, whereas little is known about entire soil networks. Here we show that during the course of nature restoration on abandoned arable land a compositional shift in soil biota, preceded by tightening of the belowground networks, corresponds with enhanced efficiency of carbon uptake. In mid- and long-term abandoned field soil, carbon uptake by fungi increases without an increase in fungal biomass or shift in bacterial-to-fungal ratio. The implication of our findings is that during nature restoration the efficiency of nutrient cycling and carbon uptake can increase by a shift in fungal composition and/or fungal activity. Therefore, we propose that relationships between soil food web structure and carbon cycling in soils need to be reconsidered

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio

Soil microbiomes show consistent and predictable responses to extreme events

Increasing extreme climatic events threaten the functioning of terrestrial ecosystems1, 2. Because soil microbes govern key biogeochemical processes, understanding their response to climate extremes is crucial in predicting the consequences for ecosystem functioning3, 4. Here we subjected soils from 30 grasslands across Europe to four contrasting extreme climatic events under common controlled conditions (drought, flood, freezing and heat), and compared the response of soil microbial communities and their functioning with those of undisturbed soils. Soil microbiomes exhibited a small, but highly consistent and phylogenetically conserved, response under the imposed extreme events. Heat treatment most strongly impacted soil microbiomes, enhancing dormancy and sporulation genes and decreasing metabolic versatility. Microbiome response to heat in particular could be predicted by local climatic conditions and soil properties, with soils that do not normally experience the extreme conditions being imposed being most vulnerable. Our results suggest that soil microbiomes from different climates share unified responses to extreme climatic events, but that predicting the extent of community change may require knowledge of the local microbiome. These findings advance our understanding of soil microbial responses to extreme events, and provide a first step for making general predictions about the impact of extreme climatic events on soil functioning

Serendipitous discovery of the unidentified extended TeV gamma-ray source HESS J1303-631

The serendipitous discovery of an unidentified extended TeVgamma-ray source close to the galactic plane named HESS J1303-631 at a significance of 21 standard deviations is reported. The observations were performed between February and June 2004 with the H.E.S.S. stereoscopic system of Cherenkov telescopes in Namibia. HESS J1303-631 was discovered roughly 0.6 deg north of the binary system PSR B1259-63/SS 2883, the target object of the initial observation campaign which was also detected at TeV energies in the same field of view. HESS J1303-631 is extended with a width of an assumed intrinsic Gaussian emission profile of sigma = (0.16 +- 0.02) deg and the integral flux above 380 GeV is compatible with constant emission over the entire observational period of (17 +- 3)% of the Crab Nebula flux. The measured energy spectrum can be described by a power-law dN/dE ~ E^-Gamma with a photon index of Gamma = 2.44 +- 0.05_stat +- 0.2_syst. Up to now, no counterpart at other wavelengths is identified. Various possible TeV production scenarios are discussed.Comment: 9 pages, 8 figures, accepted in Astronomy and Astrophysic

Pooled analysis of who surgical safety checklist use and mortality after emergency laparotomy

Background: The World Health Organization (WHO) Surgical Safety Checklist has fostered safe practice for 10 years, yet its place in emergency surgery has not been assessed on a global scale. The aim of this study was to evaluate reported checklist use in emergency settings and examine the relationship with perioperative mortality in patients who had emergency laparotomy. Methods: In two multinational cohort studies, adults undergoing emergency laparotomy were compared with those having elective gastrointestinal surgery. Relationships between reported checklist use and mortality were determined using multivariable logistic regression and bootstrapped simulation. Results: Of 12 296 patients included from 76 countries, 4843 underwent emergency laparotomy. After adjusting for patient and disease factors, checklist use before emergency laparotomy was more common in countries with a high Human Development Index (HDI) (2455 of 2741, 89⋅6 per cent) compared with that in countries with a middle (753 of 1242, 60⋅6 per cent; odds ratio (OR) 0⋅17, 95 per cent c.i. 0⋅14 to 0⋅21, P < 0⋅001) or low (363 of 860, 42⋅2 percent; OR 0⋅08, 0⋅07 to 0⋅10, P < 0⋅001) HDI. Checklist use was less common in elective surgery than for emergency laparotomy in high-HDI countries (risk difference −9⋅4 (95 per cent c.i. −11⋅9 to −6⋅9) per cent; P < 0⋅001), but the relationship was reversed in low-HDI countries (+12⋅1 (+7⋅0 to +17⋅3) per cent; P < 0⋅001). In multivariable models, checklist use was associated with a lower 30-day perioperative mortality (OR 0⋅60, 0⋅50 to 0⋅73; P < 0⋅001). The greatest absolute benefit was seen for emergency surgery in low-and middle-HDI countries. Conclusion: Checklist use in emergency laparotomy was associated with a significantly lower perioperative mortality rate. Checklist use in low-HDI countries was half that in high-HDI countries

Surgical site infection after gastrointestinal surgery in high-income, middle-income, and low-income countries: a prospective, international, multicentre cohort study

Background Surgical site infection (SSI) is one of the most common infections associated with health care, but its importance as a global health priority is not fully understood. We quantified the burden of SSI after gastrointestinal surgery in countries in all parts of the world. Methods This international, prospective, multicentre cohort study included consecutive patients undergoing elective or emergency gastrointestinal resection within 2-week time periods at any health-care facility in any country. Countries with participating centres were stratified into high-income, middle-income, and low-income groups according to the UN's Human Development Index (HDI). Data variables from the GlobalSurg 1 study and other studies that have been found to affect the likelihood of SSI were entered into risk adjustment models. The primary outcome measure was the 30-day SSI incidence (defined by US Centers for Disease Control and Prevention criteria for superficial and deep incisional SSI). Relationships with explanatory variables were examined using Bayesian multilevel logistic regression models. This trial is registered with ClinicalTrials.gov, number NCT02662231. Findings Between Jan 4, 2016, and July 31, 2016, 13 265 records were submitted for analysis. 12 539 patients from 343 hospitals in 66 countries were included. 7339 (58·5%) patient were from high-HDI countries (193 hospitals in 30 countries), 3918 (31·2%) patients were from middle-HDI countries (82 hospitals in 18 countries), and 1282 (10·2%) patients were from low-HDI countries (68 hospitals in 18 countries). In total, 1538 (12·3%) patients had SSI within 30 days of surgery. The incidence of SSI varied between countries with high (691 [9·4%] of 7339 patients), middle (549 [14·0%] of 3918 patients), and low (298 [23·2%] of 1282) HDI (p<0·001). The highest SSI incidence in each HDI group was after dirty surgery (102 [17·8%] of 574 patients in high-HDI countries; 74 [31·4%] of 236 patients in middle-HDI countries; 72 [39·8%] of 181 patients in low-HDI countries). Following risk factor adjustment, patients in low-HDI countries were at greatest risk of SSI (adjusted odds ratio 1·60, 95% credible interval 1·05–2·37; p=0·030). 132 (21·6%) of 610 patients with an SSI and a microbiology culture result had an infection that was resistant to the prophylactic antibiotic used. Resistant infections were detected in 49 (16·6%) of 295 patients in high-HDI countries, in 37 (19·8%) of 187 patients in middle-HDI countries, and in 46 (35·9%) of 128 patients in low-HDI countries (p<0·001). Interpretation Countries with a low HDI carry a disproportionately greater burden of SSI than countries with a middle or high HDI and might have higher rates of antibiotic resistance. In view of WHO recommendations on SSI prevention that highlight the absence of high-quality interventional research, urgent, pragmatic, randomised trials based in LMICs are needed to assess measures aiming to reduce this preventable complication. Funding DFID-MRC-Wellcome Trust Joint Global Health Trial Development Grant, National Institute of Health Research Global Health Research Unit Grant

The impact of surgical delay on resectability of colorectal cancer: An international prospective cohort study

AIM: The SARS-CoV-2 pandemic has provided a unique opportunity to explore the impact of surgical delays on cancer resectability. This study aimed to compare resectability for colorectal cancer patients undergoing delayed versus non-delayed surgery. METHODS: This was an international prospective cohort study of consecutive colorectal cancer patients with a decision for curative surgery (January-April 2020). Surgical delay was defined as an operation taking place more than 4 weeks after treatment decision, in a patient who did not receive neoadjuvant therapy. A subgroup analysis explored the effects of delay in elective patients only. The impact of longer delays was explored in a sensitivity analysis. The primary outcome was complete resection, defined as curative resection with an R0 margin. RESULTS: Overall, 5453 patients from 304 hospitals in 47 countries were included, of whom 6.6% (358/5453) did not receive their planned operation. Of the 4304 operated patients without neoadjuvant therapy, 40.5% (1744/4304) were delayed beyond 4 weeks. Delayed patients were more likely to be older, men, more comorbid, have higher body mass index and have rectal cancer and early stage disease. Delayed patients had higher unadjusted rates of complete resection (93.7% vs. 91.9%, P = 0.032) and lower rates of emergency surgery (4.5% vs. 22.5%, P < 0.001). After adjustment, delay was not associated with a lower rate of complete resection (OR 1.18, 95% CI 0.90-1.55, P = 0.224), which was consistent in elective patients only (OR 0.94, 95% CI 0.69-1.27, P = 0.672). Longer delays were not associated with poorer outcomes. CONCLUSION: One in 15 colorectal cancer patients did not receive their planned operation during the first wave of COVID-19. Surgical delay did not appear to compromise resectability, raising the hypothesis that any reduction in long-term survival attributable to delays is likely to be due to micro-metastatic disease

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

H.E.S.S. observations of PKS 2155-304

The high-frequency peaked BL Lac PKS 2155-304 at redshift z = 0.117 has been detected with high significance (∼45σ) at energies greater than 160 GeV, using the H.E.S.S. stereoscopic array of imaging air-Cherenkov telescopes in Namibia. A strong signal is found in each of the data sets corresponding to the dark periods of July and October, 2002, and June-September, 2003. The observed flux of VHE gamma rays shows variability on time scales of months, days, and hours. The monthly-averaged integral flux above 300 GeV varies between 10% and 60% of the flux observed from the Crab Nebula. Energy spectra are measured for these individual periods of data taking and are characterized by a steep power law with a time-averaged photon index of Γ = 3.32 ± 0.06. An improved x2 per degree of freedom is found when either a power law with an exponential cutoff energy or a broken power law are fit to the time-averaged energy spectrum. However, the significance of the improvement is marginal (∼2σ). The suggested presence of features in the energy spectrum may be intrinsic to the emission from the blazar, or an indication of absorption of TeV gamma rays by the extragalactic infrared background light.F. Aharonian, A. G. Akhperjanian, K.-M. Aye, A. R. Bazer-Bachi, M. Beilicke, W. Benbow, D. Berge, P. Berghaus, K. Bernlöhr, O. Bolz, C. Boisson, C. Borgmeier, F. Breitling, A. M. Brown, J. Bussons Gordo, P. M. Chadwick, V. R. Chitnis, L.-M. Chounet, R. Cornils, L. Costamante, B. Degrange, A. Djannati-Ataï, L.O'C. Drury, T. Ergin, P. Espigat, F. Feinstein, P. Fleury, G. Fontaine, S. Funk, Y. A. Gallant, B. Giebels, S. Gillessen, P. Goret, J. Guy, C. Hadjichristidis, M. Hauser, G. Heinzelmann, G. Henri, G. Hermann, J. A. Hinton, W. Hofmann, M. Holleran, D. Horns, O. C. de Jager, I. Jung, B. Khélifi, Nu. Komin, A. Konopelko, I. J. Latham, R. Le Gallou, M. Lemoine, A. Lemière, N. Leroy, T. Lohse, A. Marcowith, C. Masterson, T. J. L. McComb, M. de Naurois, S. J. Nolan, A. Noutsos, K. J. Orford, J. L. Osborne, M. Ouchrif, M. Panter, G. Pelletier, S. Pita, M. Pohl, G. Pühlhofer, M. Punch, B. C. Raubenheimer, M. Raue, J. Raux, S. M. Rayner, I. Redondo, A. Reimer, O. Reimer, J. Ripken, M. Rivoal, L. Rob, L. Rolland, G. Rowell, V. Sahakian, L. Saugé, S. Schlenker, R. Schlickeiser, C. Schuster, U. Schwanke, M. Siewert, H. Sol, R. Steenkamp, C. Stegmann, J.-P. Tavernet, C. G. Théoret, M. Tluczykont, D. J. van der Walt, G. Vasileiadis, P. Vincent, B. Visser, H. J. Völk and S. J. Wagne