PSAMM: A Portable System for the Analysis of Metabolic Models

The genome-scale models of metabolic networks have been broadly applied in phenotype prediction, evolutionary reconstruction, community functional analysis, and metabolic engineering. Despite the development of tools that support individual steps along the modeling procedure, it is still difficult to associate mathematical simulation results with the annotation and biological interpretation of metabolic models. In order to solve this problem, here we developed a Portable System for the Analysis of Metabolic Models (PSAMM), a new open-source software package that supports the integration of heterogeneous metadata in model annotations and provides a user-friendly interface for the analysis of metabolic models. PSAMM is independent of paid software environments like MATLAB, and all its dependencies are freely available for academic users. Compared to existing tools, PSAMM significantly reduced the running time of constraint-based analysis and enabled flexible settings of simulation parameters using simple one-line commands. The integration of heterogeneous, model-specific annotation information in PSAMM is achieved with a novel format of YAML-based model representation, which has several advantages, such as providing a modular organization of model components and simulation settings, enabling model version tracking, and permitting the integration of multiple simulation problems. PSAMM also includes a number of quality checking procedures to examine stoichiometric balance and to identify blocked reactions. Applying PSAMM to 57 models collected from current literature, we demonstrated how the software can be used for managing and simulating metabolic models. We identified a number of common inconsistencies in existing models and constructed an updated model repository to document the resolution of these inconsistencies

Factors Associated with Attrition and Performance Throughout Surgical Training:A Systematic Review and Meta-Analysis

Background Attrition within surgical training is a challenge. In the USA, attrition rates are as high as 20-26%. The factors predicting attrition are not well known. The aim of this systematic review is to identify factors that influence attrition or performance during surgical training. Method The review was performed in line with PRISMA guidelines and registered with the Open Science Framework (OSF). Medline, EMBASE, PubMed and the Cochrane Central Register of Controlled Trials were searched for articles. Risk of bias was assessed using the Newcastle-Ottawa scale. Pooled estimates were calculated using random effects meta-analyses in STATA version 15 (Stata Corp Ltd). A sensitivity analysis was performed including only multi-institutional studies. Results The searches identified 3486 articles, of which 31 were included, comprising 17,407 residents. Fifteen studies were based on multi-institutional data and 16 on single-institutional data. Twenty-nine of the studies are based on US residents. The pooled estimate for overall attrition was 17% (95% CI 14-20%). Women had a significantly higher pooled attrition than men (24% vs 16%, p \ 0.001). Some studies reported Hispanic residents had a higher attrition rate than non-Hispanic residents. There was no increased risk of attrition with age, marital or parental status. Factors reported to affect performance were non-white ethnicity and faculty assessment of clinical performance. Childrearing was not associated with performance. Conclusion Female gender is associated with higher attrition in general surgical residency. Longitudinal studies of contemporary surgical cohorts are needed to investigate the complex multi-factorial reasons for failing to complete surgical residency

‘Blood in pee’ campaign: Increased demand on secondary care with no change in cancers diagnosed

Objective:As part of the national Be Clear on Cancer campaign, the ‘blood in pee’ campaign was launched in 2013. We aimed to evaluate the impact of the campaign on 2-week wait (2WW) referrals and the resulting diagnoses of malignancy at a single trust, and secondly, to evaluate the socio-economic background of patients referred.Patients and methods:Suspected cancer 2WW patients in the 3 months pre- and post-campaign were included. Demographics, investigations and diagnoses were recorded. A Kolmogorov–Smirnov test demonstrated a normal distribution. The data were treated as parametric and analysed with the unpaired Student’s t-test.Results:Referrals for visible haematuria significantly increased by 52% from 135 pre-campaign to 205 post-campaign (p = 0.03). There was a fall in the proportion of patients diagnosed with malignancy from 20.27% pre-campaign to 15.36% post-campaign. The mean index of multiple deprivation score of referrals did not change: p = 0.43.Conclusion:This campaign has increased referrals without increasing the proportion of malignancies diagnosed, placing large demand on services without benefit or extra funding. Nor has the campaign effectively reached deprived socio-economic groups. There is little evidence as to the efficacy of untargeted cancer awareness campaigns and further work is needed to improve their pick-up of malignancies

Analysis of Sharing Economy Services : Initial Findings from Sharing Cities Sweden

In this paper, we analyze different types of sharing economy services. The sharing economy is a wide concept where many types of activities and services can be included. Overall we aim to identify recurrent patterns but also similarities and differences between different types of sharing services. We discuss a multitude of different services, e.g. car pools, bike pools, sharing of tools and equipment, sharing of land for farming, sharing of parking and homes, and co-working spaces. It is a mix of different set ups regarding if it is commercial or community driven, type of service provider, usage fee or for free, open or closed access

Event-based, 6-DOF Camera Tracking from Photometric Depth Maps

Event cameras are bio-inspired vision sensors that output pixel-level brightness changes instead of standard intensity frames. These cameras do not suffer from motion blur and have a very high dynamic range, which enables them to provide reliable visual information during high-speed motions or in scenes characterized by high dynamic range. These features, along with a very low power consumption, make event cameras an ideal complement to standard cameras for VR/AR and video game applications. With these applications in mind, this paper tackles the problem of accurate, low-latency tracking of an event camera from an existing photometric depth map (i.e., intensity plus depth information) built via classic dense reconstruction pipelines. Our approach tracks the 6-DOF pose of the event camera upon the arrival of each event, thus virtually eliminating latency. We successfully evaluate the method in both indoor and outdoor scenes and show that—because of the technological advantages of the event camera—our pipeline works in scenes characterized by high-speed motion, which are still unaccessible to standard cameras

Pre‐emptive and preventive opioids for postoperative pain in adults undergoing all types of surgery

Background: Postoperative pain is a common consequence of surgery and can have deleterious effects. It has been suggested that the administration of opioid analgesia before a painful stimulus may improve pain control. This can be done in two ways. We defined 'preventive opioids' as opioids administered before incision and continued postoperatively, and 'pre‐emptive opioids' as opioids given before incision but not continued postoperatively. Both pre‐emptive and preventive analgesia involve the initiation of an analgesic agent prior to surgical incision with the aim of reducing intraoperative nociception and therefore postoperative pain.Objectives: To assess the efficacy of preventive and pre‐emptive opioids for reducing postoperative pain in adults undergoing all types of surgery.Search methods: We searched the following electronic databases: CENTRAL, MEDLINE, Embase, AMED, and CINAHL (up to 18 March 2018). In addition, we searched for unpublished studies in three clinical trial databases, conference proceedings, grey literature databases, and reference lists of retrieved articles. We did not apply any restrictions on language or date of publication.Selection criteria: We included parallel‐group randomized controlled trials (RCTs) only. We included participants aged over 15 years old undergoing any type of surgery. We defined postincision opioids as the same intervention administered after incision whether single dose (as comparator with pre‐emptive analgesia) or continued postoperatively (as comparator with preventive analgesia) (control group). We considered studies that did and did not use a double‐dummy placebo (e.g. intervention group received active drug before incision and placebo after incision; control group received placebo before incision and active drug after incision).Data collection and analysis: We used the standard methodological procedures expected by Cochrane. Our primary outcomes were: early acute postoperative pain (measured within six hours and reported on a 0‐to‐10 scale) and respiratory depression. Our secondary outcomes included: late acute postoperative pain (24 to 48 hours and reported on a 0‐to‐10 scale), 24‐hour morphine consumption, and adverse events (intraoperative bradycardia and hypotension). We used GRADE to assess the quality of the evidence for each outcome.Main results: We included 20 RCTs, including one unpublished study with 1343 participants. Two studies were awaiting classification as the full text for these studies was not available. One study evaluated pre‐emptive opioids, and 19 studies evaluated preventive opioids. We considered only one study to be at low risk of bias for most domains. The surgeries and opioids used varied, although roughly half of the included studies were conducted in abdominal hysterectomy, and around a quarter used morphine as the intervention. All studies were conducted in secondary care.Pre‐emptive opioids compared to postincision opioidsFor pre‐emptive opioids in dental surgery, there may be a reduction in early acute postoperative pain (mean difference (MD) ‐1.20, 95% confidence interval (CI) ‐1.75 to ‐0.65; 40 participants; 1 study; low‐quality evidence). This study did not report on adverse events (respiratory depression, bradycardia, or hypotension). There may be a reduction in late acute postoperative pain (MD ‐2.10, 95% CI ‐2.57 to ‐1.63; 40 participants; 1 study; low‐quality evidence). This study did not report 24‐hour morphine consumption.Preventive opioids compared to postincision opioidsFor preventive opioids, there was probably no reduction in early acute postoperative pain (MD 0.11, 95% CI ‐0.32 to 0.53; 706 participants; 10 studies; I2 = 61%; moderate‐quality evidence). There were no events of respiratory depression in four studies (433 participants). There was no important reduction in late acute postoperative pain (MD ‐0.06, 95% CI ‐0.13 to 0.01; 668 participants; 9 studies; I2 = 0%; moderate‐quality evidence). There may be a small reduction in 24‐hour morphine consumption (MD ‐4.91 mg, 95% CI ‐9.39 mg to ‐0.44 mg; 526 participants; 11 studies; I2 = 82%; very low‐quality evidence). There may be similar rates of bradycardia (risk ratio (RR) 0.33, 95% CI 0.01 to 7.88; 112 participants; 2 studies; I2 = 0%; low‐quality evidence) and hypotension (RR 1.08, 95% CI 0.25 to 4.73; 88 participants; 2 studies; I2 = 0%; low‐quality evidence).Authors' conclusions: Due to the low quality of the evidence, we are uncertain whether pre‐emptive opioids reduce postoperative pain. Based on the trials conducted thus far, there was no clear evidence that preventive opioids result in reductions in pain scores. It was unclear if there was a reduction in morphine consumption due to very low‐quality of evidence. Too few studies reported adverse events to be able to draw any definitive conclusions. Once assessed, the two studies awaiting classification may alter the conclusions of the review