Serpentinization in the trench-outer rise region offshore of Nicaragua: constraints from seismic refraction and wide-angle data

Recent seismic evidence suggested that most oceanic plate hydration is associated with trench-outer rise faulting prior to subduction. Hydration at trenches may have a significant impact on the subduction zone water cycle. Previous seismic experiments conducted to the northwest of Nicoya Peninsula, Northern Costa Rica, have shown that the subducting Cocos lithosphere is pervasively altered, which was interpreted to be due to both hydration (serpentinization) and fracturing of the crustal and upper-mantle rocks. New seismic wide-angle reflection and refraction data were collected along two profiles, running parallel to the Middle American trench axis offshore of central Nicaragua, revealing lateral changes of the seismic properties of the subducting lithosphere. Seismic structure along both profiles is characterized by low velocities both in the crust and upper mantle. Velocities in the uppermost mantle are found to be in the range 7.3–7.5 km s−1; thus are 8–10 per cent lower than velocities typical for unaltered peridotites and hence confirm the assumption that serpentinization is a common process at the trench-outer rise area offshore of Nicaragua. In addition, a prominent velocity anomaly occurred within the crust beneath two seamounts. Here, velocity reduction may indicate increased porosity and perhaps permeability, supporting the idea that seamounts serve as sites for water percolation and circulation

Temporal variability of gas seeps offshore New Zealand: multi-frequency geoacoustic imaging of the Wairarapa area, Hikurangi margin

Cold seeps on Opouawe Bank, situated in around 1000 m water depth on the Hikurangi Margin offshore North Island. New Zealand, were investigated using multibeam bathymetry, 75 and 410 kHz sidescan sonar imagery, and 2–8 kHz Chirp sediment echosounder data. Towed video camera observations allowed ground-truthing the various geoacoustic data. At least eleven different seep locations displaying a range of seep activity were identified in the study area. The study area consists of an elongated, northward-widening ridge that is part of the accretionary Hikurangi Margin and is well separated from direct terrigenous input by margin channels surrounding the ridge. The geoacoustic signature of individual cold-seep sites ranged from smooth areas with slightly elevated backscatter intensity resulting from high gas content or the presence of near-surface gas hydrates, to rough areas with widespread patches of carbonates at the seafloor. Five cold seeps also show indications for active gas emissions in the form of acoustic plumes in the water column. Repeated sidescan sonar imagery of the plumes indicates they are highly variable in intensity and direction in the water column, probably reflecting the control of gas emission by tides and currents. Although gas emission appears strongly focused in the Wairarapa area, the actual extents of the cold seep structures are much wider in the subsurface as is shown by sediment echosounder profiles, where large gas fronts were observed

Extent of non-publication in cohorts of studies approved by research ethics committees or included in trial registries

BACKGROUND: The synthesis of published research in systematic reviews is essential when providing evidence to inform clinical and health policy decision-making. However, the validity of systematic reviews is threatened if journal publications represent a biased selection of all studies that have been conducted (dissemination bias). To investigate the extent of dissemination bias we conducted a systematic review that determined the proportion of studies published as peer-reviewed journal articles and investigated factors associated with full publication in cohorts of studies (i) approved by research ethics committees (RECs) or (ii) included in trial registries. METHODS AND FINDINGS: Four bibliographic databases were searched for methodological research projects (MRPs) without limitations for publication year, language or study location. The searches were supplemented by handsearching the references of included MRPs. We estimated the proportion of studies published using prediction intervals (PI) and a random effects meta-analysis. Pooled odds ratios (OR) were used to express associations between study characteristics and journal publication. Seventeen MRPs (23 publications) evaluated cohorts of studies approved by RECs; the proportion of published studies had a PI between 22% and 72% and the weighted pooled proportion when combining estimates would be 46.2% (95% CI 40.2%-52.4%, I2 = 94.4%). Twenty-two MRPs (22 publications) evaluated cohorts of studies included in trial registries; the PI of the proportion published ranged from 13% to 90% and the weighted pooled proportion would be 54.2% (95% CI 42.0%-65.9%, I2 = 98.9%). REC-approved studies with statistically significant results (compared with those without statistically significant results) were more likely to be published (pooled OR 2.8; 95% CI 2.2-3.5). Phase-III trials were also more likely to be published than phase II trials (pooled OR 2.0; 95% CI 1.6-2.5). The probability of publication within two years after study completion ranged from 7% to 30%. CONCLUSIONS: A substantial part of the studies approved by RECs or included in trial registries remains unpublished. Due to the large heterogeneity a prediction of the publication probability for a future study is very uncertain. Non-publication of research is not a random process, e.g., it is associated with the direction of study findings. Our findings suggest that the dissemination of research findings is biased

Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation.

Cancer progression involves the gradual loss of a differentiated phenotype and acquisition of progenitor and stem-cell-like features. Here, we provide novel stemness indices for assessing the degree of oncogenic dedifferentiation. We used an innovative one-class logistic regression (OCLR) machine-learning algorithm to extract transcriptomic and epigenetic feature sets derived from non-transformed pluripotent stem cells and their differentiated progeny. Using OCLR, we were able to identify previously undiscovered biological mechanisms associated with the dedifferentiated oncogenic state. Analyses of the tumor microenvironment revealed unanticipated correlation of cancer stemness with immune checkpoint expression and infiltrating immune cells. We found that the dedifferentiated oncogenic phenotype was generally most prominent in metastatic tumors. Application of our stemness indices to single-cell data revealed patterns of intra-tumor molecular heterogeneity. Finally, the indices allowed for the identification of novel targets and possible targeted therapies aimed at tumor differentiation

Reducing the environmental impact of surgery on a global scale: systematic review and co-prioritization with healthcare workers in 132 countries

Abstract Background Healthcare cannot achieve net-zero carbon without addressing operating theatres. The aim of this study was to prioritize feasible interventions to reduce the environmental impact of operating theatres. Methods This study adopted a four-phase Delphi consensus co-prioritization methodology. In phase 1, a systematic review of published interventions and global consultation of perioperative healthcare professionals were used to longlist interventions. In phase 2, iterative thematic analysis consolidated comparable interventions into a shortlist. In phase 3, the shortlist was co-prioritized based on patient and clinician views on acceptability, feasibility, and safety. In phase 4, ranked lists of interventions were presented by their relevance to high-income countries and low–middle-income countries. Results In phase 1, 43 interventions were identified, which had low uptake in practice according to 3042 professionals globally. In phase 2, a shortlist of 15 intervention domains was generated. In phase 3, interventions were deemed acceptable for more than 90 per cent of patients except for reducing general anaesthesia (84 per cent) and re-sterilization of ‘single-use’ consumables (86 per cent). In phase 4, the top three shortlisted interventions for high-income countries were: introducing recycling; reducing use of anaesthetic gases; and appropriate clinical waste processing. In phase 4, the top three shortlisted interventions for low–middle-income countries were: introducing reusable surgical devices; reducing use of consumables; and reducing the use of general anaesthesia. Conclusion This is a step toward environmentally sustainable operating environments with actionable interventions applicable to both high– and low–middle–income countries

Outcome in patients with open abdomen treatment for peritonitis: a multidomain approach outperforms single domain predictions.

Numerous patient-related clinical parameters and treatment-specific variables have been identified as causing or contributing to the severity of peritonitis. We postulated that a combination of clinical and surgical markers and scoring systems would outperform each of these predictors in isolation. To investigate this hypothesis, we developed a multivariable model to examine whether survival outcome can reliably be predicted in peritonitis patients treated with open abdomen. This single-center retrospective analysis used univariable and multivariable logistic regression modeling in combination with repeated random sub-sampling validation to examine the predictive capabilities of domain-specific predictors (i.e., demography, physiology, surgery). We analyzed data of 1,351 consecutive adult patients (55.7% male) who underwent open abdominal surgery in the study period (January 1998 to December 2018). Core variables included demographics, clinical scores, surgical indices and indicators of organ dysfunction, peritonitis index, incision type, fascia closure, wound healing, and fascial dehiscence. Postoperative complications were also added when available. A multidomain peritonitis prediction model (MPPM) was constructed to bridge the mortality predictions from individual domains (demographic, physiological and surgical). The MPPM is based on data of n = 597 patients, features high predictive capabilities (area under the receiver operating curve: 0.87 (0.85 to 0.90, 95% CI)) and is well calibrated. The surgical predictor "skin closure" was found to be the most important predictor of survival in our cohort, closely followed by the two physiological predictors SAPS-II and MPI. Marginal effects plots highlight the effect of individual outcomes on the prediction of survival outcome in patients undergoing staged laparotomies for treatment of peritonitis. Although most single indices exhibited moderate performance, we observed that the predictive performance was markedly increased when an integrative prediction model was applied. Our proposed MPPM integrative prediction model may outperform the predictive power of current models

Discovery of potent SOS1 inhibitors that block RAS activation via disruption of the RAS–SOS1 interaction

Since the late 1980s, mutations in the RAS genes have been recognized as major oncogenes with a high occurrence rate in human cancers. Such mutations reduce the ability of the small GTPase RAS to hydrolyze GTP, keeping this molecular switch in a constitutively active GTP-bound form that drives, unchecked, oncogenic downstream signaling. One strategy to reduce the levels of active RAS is to target guanine nucleotide exchange factors, which allow RAS to cycle from the inactive GDP-bound state to the active GTP-bound form. Here, we describe the identification of potent and cell-active small-molecule inhibitors which efficiently disrupt the interaction between KRAS and its exchange factor SOS1, a mode of action confirmed by a series of biophysical techniques. The binding sites, mode of action, and selectivity were elucidated using crystal structures of KRAS$^{G12C}$–SOS1, SOS1, and SOS2. By preventing formation of the KRAS–SOS1 complex, these inhibitors block reloading of KRAS with GTP, leading to antiproliferative activity. The final compound 23 (BAY-293) selectively inhibits the KRAS–SOS1 interaction with an IC$_{50}$ of 21 nM and is a valuable chemical probe for future investigations