In silico prediction of physical protein interactions and characterization of interactome orphans.

Protein-protein interactions (PPIs) are useful for understanding signaling cascades, predicting protein function, associating proteins with disease and fathoming drug mechanism of action. Currently, only ∼ 10% of human PPIs may be known, and about one-third of human proteins have no known interactions. We introduce FpClass, a data mining-based method for proteome-wide PPI prediction. At an estimated false discovery rate of 60%, we predicted 250,498 PPIs among 10,531 human proteins; 10,647 PPIs involved 1,089 proteins without known interactions. We experimentally tested 233 high- and medium-confidence predictions and validated 137 interactions, including seven novel putative interactors of the tumor suppressor p53. Compared to previous PPI prediction methods, FpClass achieved better agreement with experimentally detected PPIs. We provide an online database of annotated PPI predictions (http://ophid.utoronto.ca/fpclass/) and the prediction software (http://www.cs.utoronto.ca/~juris/data/fpclass/).

Consensus on Training and Implementation of Enhanced Recovery After Surgery: A Delphi Study.

BACKGROUND: Enhanced Recovery After Surgery (ERAS) is widely accepted in current surgical practice due to its positive impact on patient outcomes. The successful implementation of ERAS is challenging and compliance with protocols varies widely. Continual staff education is essential for successful ERAS programmes. Teaching modalities exist, but there remains no agreement regarding the optimal training curriculum or how its effectiveness is assessed. We aimed to draw consensus from an expert panel regarding the successful training and implementation of ERAS. METHODS: A modified Delphi technique was used; three rounds of questionnaires were sent to 58 selected international experts from 11 countries across multiple ERAS specialities and multidisciplinary teams (MDT) between January 2016 and February 2017. We interrogated opinion regarding four topics: (1) the components of a training curriculum and the structure of training courses; (2) the optimal framework for successful implementation and audit of ERAS including a guide for data collection; (3) a framework to assess the effectiveness of training; (4) criteria to define ERAS training centres of excellence. RESULTS: An ERAS training course must cover the evidence-based principles of ERAS with team-oriented training. Successful implementation requires strong leadership, an ERAS facilitator and an effective MDT. Effectiveness of training can be measured by improved compliance. A training centre of excellence should show a willingness to teach and demonstrable team working. CONCLUSIONS: We propose an international expert consensus providing an ERAS training curriculum, a framework for successful implementation, methods for assessing effectiveness of training and a definition of ERAS training centres of excellence.

Consensus on structured training curriculum for transanal total mesorectal excision (TaTME).

BACKGROUND: The interest and adoption of transanal total mesorectal excision (TaTME) is growing amongst the colorectal surgical community, but there is no clear guidance on the optimal training framework to ensure safe practice for this novel operation. The aim of this study was to establish a consensus on a detailed structured training curriculum for TaTME. METHODS: A consensus process to agree on the framework of the TaTME training curriculum was conducted, seeking views of 207 surgeons across 18 different countries, including 52 international experts in the field of TaTME. The process consisted of surveying potential learners of this technique, an international experts workshop and a final expert's consensus to draw an agreement on essential elements of the curriculum. RESULTS: Appropriate case selection was strongly recommended, and TaTME should be offered to patients with mid and low rectal cancers, but not proximal rectal cancers. Pre-requisites to learn TaTME should include completion of training and accreditation in laparoscopic colorectal surgery, with prior experience in transanal surgery. Ideally, two surgeons should undergo training together in centres with high volume for rectal cancer surgery. Mentorship and multidisciplinary training were the two most important aspects of the curriculum, which should also include online modules and simulated training for purse-string suturing. Mentors should have performed at least 20 TaTME cases and be experienced in laparoscopic training. Reviewing the specimens' quality, clinical outcome data and entering data into a registry were recommended. Assessment should be an integral part of the curriculum using Global Assessment Scales, as formative assessment to promote learning and competency assessment tool as summative assessment. CONCLUSIONS: A detailed framework for a structured TaTME training curriculum has been proposed. It encompasses various training modalities and assessment, as well as having the potential to provide quality control and future research initiatives for this novel technique.

Elucidation of the hepatoprotective moiety of 5ß-scymnol that suppresses paracetamol toxicity in mice.

The shark bile alcohol, 5ß-scymnol, protects mice from the hepatotoxic effects of paracetamol (APAP) overdose. To elucidate the hepatoprotective structural moiety of scymnol, we compared its effect with that of its analogue and natural bile salt, sodium scymnol sulfate, in a clinically relevant model of APAP-induced toxicity. Exposure of healthy male Swiss mice to a toxic overdose of APAP (350 mg/kg, ip) significantly increased serum hepatocellular enzyme activities, decreased hepatocellular glutathione (GSH) levels, and induced severe centrilobular hepatocellular necrosis. Repeated low-dose scymnol (5 mg/kg/day for 7 days, ip) significantly reduced the extent of APAP-induced hepatotoxicity without preventing GSH depletion. Sodium scymnol sulfate, which lacks the tri-hydroxyl-substituted aliphatic side chain of scymnol, failed to reduce the APAP hepatotoxicity or prevent GSH depletion when tested under the same experimental conditions. We conclude that the tri-hydroxyl-substituted aliphatic side chain is the hepatoprotective structural moiety of 5ß-scymnol that suppresses APAP-induced cytotoxicity in mice.

The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases.

IntAct (freely available at http://www.ebi.ac.uk/intact) is an open-source, open data molecular interaction database populated by data either curated from the literature or from direct data depositions. IntAct has developed a sophisticated web-based curation tool, capable of supporting both IMEx- and MIMIx-level curation. This tool is now utilized by multiple additional curation teams, all of whom annotate data directly into the IntAct database. Members of the IntAct team supply appropriate levels of training, perform quality control on entries and take responsibility for long-term data maintenance. Recently, the MINT and IntAct databases decided to merge their separate efforts to make optimal use of limited developer resources and maximize the curation output. All data manually curated by the MINT curators have been moved into the IntAct database at EMBL-EBI and are merged with the existing IntAct dataset. Both IntAct and MINT are active contributors to the IMEx consortium (http://www.imexconsortium.org).

The IntAct molecular interaction database in 2012.

IntAct is an open-source, open data molecular interaction database populated by data either curated from the literature or from direct data depositions. Two levels of curation are now available within the database, with both IMEx-level annotation and less detailed MIMIx-compatible entries currently supported. As from September 2011, IntAct contains approximately 275,000 curated binary interaction evidences from over 5000 publications. The IntAct website has been improved to enhance the search process and in particular the graphical display of the results. New data download formats are also available, which will facilitate the inclusion of IntAct's data in the Semantic Web. IntAct is an active contributor to the IMEx consortium (http://www.imexconsortium.org). IntAct source code and data are freely available at http://www.ebi.ac.uk/intact.

Maternal undernutrition in cows impairs ovarian and cardiovascular systems in their offspring.

Severe prenatal undernutrition is usually associated with low birth weights in offspring and disorders including hypertension, obesity, and diabetes. Whether alterations in maternal nutrition insufficient to impair birth weight or prenatal growth impact the cardiovascular, stress, or metabolic systems is unknown. In addition, little is known about the effects of maternal dietary restriction on development of the reproductive system in mammals. Here, we use the bovine model, which has a gestational length and birth rate similar to humans, to show that offspring from nutritionally restricted dams (during the first trimester) were born with identical birth weights and had similar postnatal growth rates (to 95 wk of age), puberty, glucose metabolism, and responses to stress compared to offspring from control mothers. However, an increase in maternal testosterone concentrations was detected during dietary restriction, and these dams had offspring with a diminished ovarian reserve (as assessed by a reduction in antral follicle count, reduced concentrations of anti-Müllerian hormone, and increased follicle-stimulating hormone concentrations), enlarged aorta, and increased arterial blood pressure compared with controls. Our study links transient maternal undernutrition and enhanced maternal androgen production with a diminished ovarian reserve as well as potential suboptimal fertility, enlarged aortic trunk size, and enhanced blood pressure independent of alterations in birth weight, postnatal growth, or stress response and glucose tolerance. The implications are that relatively mild transient reductions in maternal nutrition during the first trimester of pregnancy (even those that do not affect gross development) should be avoided to ensure healthy development of reproductive and cardiovascular systems in offspring.

Sequential analysis of global gene expression profiles in immature and in vitro matured bovine oocytes: potential molecular markers of oocyte maturation.

BACKGROUND: Without intensive selection, the majority of bovine oocytes submitted to in vitro embryo production (IVP) fail to develop to the blastocyst stage. This is attributed partly to their maturation status and competences. Using the Affymetrix GeneChip Bovine Genome Array, global mRNA expression analysis of immature (GV) and in vitro matured (IVM) bovine oocytes was carried out to characterize the transcriptome of bovine oocytes and then use a variety of approaches to determine whether the observed transcriptional changes during IVM was real or an artifact of the techniques used during analysis. RESULTS: 8489 transcripts were detected across the two oocyte groups, of which ~25.0% (2117 transcripts) were differentially expressed (p < 0.001); corresponding to 589 over-expressed and 1528 under-expressed transcripts in the IVM oocytes compared to their immature counterparts. Over expression of transcripts by IVM oocytes is particularly interesting, therefore, a variety of approaches were employed to determine whether the observed transcriptional changes during IVM were real or an artifact of the techniques used during analysis, including the analysis of transcript abundance in oocytes in vitro matured in the presence of α-amanitin. Subsets of the differentially expressed genes were also validated by quantitative real-time PCR (qPCR) and the gene expression data was classified according to gene ontology and pathway enrichment. Numerous cell cycle linked (CDC2, CDK5, CDK8, HSPA2, MAPK14, TXNL4B), molecular transport (STX5, STX17, SEC22A, SEC22B), and differentiation (NACA) related genes were found to be among the several over-expressed transcripts in GV oocytes compared to the matured counterparts, while ANXA1, PLAU, STC1and LUM were among the over-expressed genes after oocyte maturation. CONCLUSION: Using sequential experiments, we have shown and confirmed transcriptional changes during oocyte maturation. This dataset provides a unique reference resource for studies concerned with the molecular mechanisms controlling oocyte meiotic maturation in cattle, addresses the existing conflicting issue of transcription during meiotic maturation and contributes to the global goal of improving assisted reproductive technology.

Development, validation and implementation of a monitoring tool for training in laparoscopic colorectal surgery in the English National Training Program.

INTRODUCTION: The National Training Program for laparoscopic colorectal surgery (LCS) provides supervised training to colorectal surgeons in England. The purpose of this study was to create, validate, and implement a method for monitoring training progression in laparoscopic colorectal surgery that met the requirements of a good assessment tool. METHODS: A generic scale for different tasks in LCS was created under the guidance of a national expert group. The scores were defined by the extent to which the trainees were dependent on support (1 = unable to perform, 5 = unaided (benchmark), 6 = proficient). Trainers were asked to rate their trainees after each supervised case; trainees completed a similar self-assessment form. Construct validity was evaluated comparing scores of trainees at different experience levels (1-5, 6-10, 11-15, 16+) using the Wilcoxon signed-rank test and ANOVA. Internal consistency was determined by Crohnbach's alpha, interrater reliability by comparing peer- and self-assessment (interclass correlation coefficient, ICC). Proficiency gain curves were plotted using CUSUM charts. RESULTS: Analysis included 610 assessments (333 by trainers and 277 by trainees). There was high interrater reliability (ICC = 0.867), internal consistency (α = 0.920), and construct validity [F(3,40) = 6.128, p < 0.001]. Detailed analysis of proficiency gain curves demonstrates that theater setup, exposure, and anastomosis were performed independently after 5 to 15 sessions, and the dissection of the vascular pedicle took 24 cases. Mobilization of the colon and of the splenic/hepatic flexure took more than 25 procedures. Median assessment time was 3.3 (interquartile range (IQR) 1-5) minutes and the tool was accepted as useful [median score 5 of 6 (IQR 4-5)]. DISCUSSION: A valid and reliable monitoring tool for surgical training has been implemented successfully into the National Training Program. It provides a description of an individualized proficiency gain curve in terms of both the level of support required and the competency level achieved.

European consensus on a competency-based virtual reality training program for basic endoscopic surgical psychomotor skills.

BACKGROUND: Virtual reality (VR) simulators have been demonstrated to improve basic psychomotor skills in endoscopic surgery. The exercise configuration settings used for validation in studies published so far are default settings or are based on the personal choice of the tutors. The purpose of this study was to establish consensus on exercise configurations and on a validated training program for a virtual reality simulator, based on the experience of international experts to set criterion levels to construct a proficiency-based training program. METHODS: A consensus meeting was held with eight European teams, all extensively experienced in using the VR simulator. Construct validity of the training program was tested by 20 experts and 60 novices. The data were analyzed by using the t test for equality of means. RESULTS: Consensus was achieved on training designs, exercise configuration, and examination. Almost all exercises (7/8) showed construct validity. In total, 50 of 94 parameters (53%) showed significant difference. CONCLUSIONS: A European, multicenter, validated, training program was constructed according to the general consensus of a large international team with extended experience in virtual reality simulation. Therefore, a proficiency-based training program can be offered to training centers that use this simulator for training in basic psychomotor skills in endoscopic surgery.

Relationship between virulence gene profiles of atypical enteropathogenic Escherichia coli and Shiga toxin-producing E. coli isolates from cattle and sheep in New Zealand.

Virulence gene profiles of atypical enteropathogenic Escherichia coli (aEPEC) and Shiga toxin-producing E. coli (STEC) from cattle, sheep, and humans were examined to determine the relationship between pathotypes. Shared virulence factors (intimin, EHEC hemolysin, serine protease, and a type II secretion system) were identified, suggesting a dynamic evolutionary relationship between aEPEC and STEC.

Predicting physiological imbalance in Holstein dairy cows by three different sets of milk biomarkers.

Blood biomarkers may be used to detect physiological imbalance and potential disease. However, blood sampling is difficult and expensive, and not applicable in commercial settings. Instead, individual milk samples are readily available at low cost, can be sampled easily and analysed instantly. The present observational study sampled blood and milk from 234 Holstein dairy cows from experimental herds in six European countries. The objective was to compare the use of three different sets of milk biomarkers for identification of cows in physiological imbalance and thus at risk of developing metabolic or infectious diseases. Random forests was used to predict body energy balance (EBAL), index for physiological imbalance (PI-index) and three clusters differentiating the metabolic status of cows created on basis of concentrations of plasma glucose, ß-hydroxybutyrate (BHB), non-esterified fatty acids (NEFA) and serum IGF-1. These three metabolic clusters were interpreted as cows in balance, physiological imbalance and "intermediate cows" with physiological status in between. The three sets of milk biomarkers used for prediction were: milk Fourier transform mid-IR (FT-MIR) spectra, 19 immunoglobulin G (IgG) N-glycans and 8 milk metabolites and enzymes (MME). Blood biomarkers were sampled twice; around 14 days after calving (days in milk (DIM)) and around 35 DIM. MME and FT-MIR were sampled twice weekly 1-50 DIM whereas IgG N-glycan were measured only four times. Performances of EBAL and PI-index predictions were measured by coefficient of determination (R2cv) and root mean squared error (RMSEcv) from leave-one-cow-out cross-validation (cv). For metabolic clusters, performance was measured by sensitivity, specificity and global accuracy from this cross-validation. Best prediction of PI-index was obtained by MME (R2cv = 0.40 (95 % CI: 0.29-0.50) at 14 DIM and 0.35 (0.23-0.44) at 35 DIM) while FT-MIR showed a better performance than MME for prediction of EBAL (R2cv = 0.28 (0.24-0.33) vs 0.21 (0.18-0.25)). Global accuracies of predicting metabolic clusters from MME and FT-MIR were at the same level ranging from 0.54 (95 % CI: 0.39-0.68) to 0.65 (0.55-0.75) for MME and 0.51 (0.37-0.65) to 0.68 (0.53-0.81) for FT-MIR. R2cv and accuracies were lower for IgG N-glycans. In conclusion, neither EBAL nor PI-index were sufficiently well predicted to be used as a management tool for identification of risk cows. MME and FT-MIR may be used to predict the physiological status of the cows, while the use of IgG N-glycans for prediction still needs development. Nevertheless, accuracies need to be improved and a larger training data set is warranted.

Molecular subtyping and distribution of the serine protease from shiga toxin-producing Escherichia coli among atypical enteropathogenic E. coli strains.

Atypical enteropathogenic Escherichia coli (aEPEC) and Shiga toxin-producing E. coli (STEC) were examined to determine the prevalence and sequence of espP, which encodes a serine protease. These analyses indicated shared espP sequence types between the two E. coli pathotypes and thus provide further insights into the evolution of aEPEC and STEC.

Gene expression profile of cumulus cells derived from cumulus-oocyte complexes matured either in vivo or in vitro.

Although it is well established that maturation conditions have a clear influence on oocyte developmental competence, it is not known whether this could be due to downstream effects of perturbation of the transcript profile of the oocyte's adjacent cumulus cells. Therefore, the aim of the present study was to compare the transcript profiles of cumulus cells derived from cumulus-oocyte complexes (COCs) matured in vitro or in vivo. Using a previously validated combined synchronisation and superstimulation protocol, COCs were recovered from beef heifer ovaries just before the expected time of the LH surge and matured in vitro, while in vivo-matured COCs were recovered just before ovulation (20 h after the LH surge). A custom-made cDNA microarray containing 2278 granulosa/cumulus transcripts was used for target and dye-swap hybridisations. In all, 64 genes were differentially expressed between the two groups. Transcript abundance of key genes associated with cumulus expansion (TNFAIP6) and regulation of oocyte maturation (INHBA and FST) were upregulated in in vivo-derived cumulus cells. However, cumulus cells derived from IVM COCs were enriched with genes involved in response to stress (HSPA5 and HSP90AB1). Quantitative real-time polymerase chain reaction confirmed the array results for eight of 10 genes selected for validation. The data presented here reveal that differences in oocyte developmental capacity after maturation in vitro or in vivo are accompanied by distinct differences in transcript abundance of the surrounding cumulus cells.

Exploring the fundamental aspects of the Enhanced Recovery After Surgery nurse's role.

Enhanced Recovery After Surgery (ERAS) is a multimodal, multidisciplinary programme that aims to limit surgical stress during the perioperative period. The importance of a facilitator to improve patients' compliance with the ERAS pathway and ensure its successful implementation is described in the literature. This role is commonly undertaken by a nurse, but it is unclear what their role entails in practice. AIM: To investigate the common aspects of the role of the ERAS nurse, and similar roles. METHOD: A modified Delphi technique was used to explore the opinions of ERAS nurses, facilitators and their colleagues in the UK. A series of consensus statements on the role of the ERAS nurse were produced that were voted on and agreed via an online survey, then subsequently voted on at the seventh ERAS UK conference. RESULTS: Six consensus statements were proposed and agreed in the second round of voting. In the final round of voting, consensus was reached on four of the six statements related to data collection, patient education, staff education and patient support throughout the pathway. The two statements that did not reach consensus were related to leadership and project management. CONCLUSION: It is hoped that by producing these consensus statements, the role of the ERAS nurse will be better understood by all members of multidisciplinary ERAS teams, particularly managers and decision-makers, and can be supported in the future.

Understanding the benefits and implications of Enhanced Recovery After Surgery.

Enhanced Recovery After Surgery (ERAS) programmes are an innovative approach to optimising patient outcomes in the perioperative period and have been implemented in various surgical departments across a range of specialties, with varying degrees of success. ERAS is an evidence-based, multimodal programme that has repeatedly demonstrated a reduction in post-operative complications and reduced the length of hospital stays following elective surgery. However, despite extensive evidence to support these benefits, several barriers to ERAS implementation have been identified. This article outlines the components of ERAS, focusing on the barriers to its implementation and how these could be overcome. It also discusses the implications of ERAS for patients, nurses and healthcare organisations.

Modern perioperative medicine - past, present, and future.

Modern perioperative medicine has dramatically altered the care for patients undergoing major surgery. Anaesthetic and surgical practice has been directed at mitigating the surgical stress response and reducing physiological insult. The development of standardised enhanced recovery programmes combined with minimally invasive surgical techniques has lead to reduction in length of stay, morbidity, costs, and improved outcomes. The enhanced recovery after surgery (ERAS) society and its national chapters provide a means for sharing best practice in this field and developing evidence based guidelines. Research has highlighted persisting challenges with compliance as well as ensuring the effectiveness and sustainability of ERAS. There is also a growing need for increasingly personalised care programmes as well as complex geriatric assessment of frailer patients. Continuous collection of outcome and process data combined with machine learning, offers a potentially powerful solution to delivering bespoke care pathways and optimising individual management. Long-term data from ERAS programmes remain scarce and further evaluation of functional recovery and quality of life is required.

Consensus views on the optimum training curriculum for advanced minimally invasive surgery: A delphi study.

INTRODUCTION: There has been a wide uptake in the use of Minimal Invasive Surgery (MIS) globally across different surgical specialties. Whilst evidence exists for a structured training curriculum for basic laparoscopic surgery, there is little agreement on a complete framework for an advanced MIS training curriculum, defining the essential elements of the curriculum including the optimal assessment methods. The aim of this study is to obtain a consensus on the essential elements of a training curriculum for advanced MIS. MATERIALS AND METHODS: A Delphi study was carried out involving 57 international experts in advanced MIS across different surgical specialties. A three round survey was conducted to reach consensus on the essential domains of a curriculum. This included defining the learners, trainers and training centres; curriculum content and competency based assessment. RESULTS: Unanimous agreement was reached for the completion of basic laparoscopic training before entry into advanced training. A trainer should have reached competency in advanced MIS and attended a 'Train the trainer' course. The curriculum should be delivered as modular training, including a multi-modal approach with a structured clinical proctorship programme. Formative assessment was considered as an integral part of learning and should be performed using objective work based assessment tools such as global assessment scale (GAS) forms. Accreditation in advanced MIS can be achieved by objective assessment of technical performance of unedited videos in addition to key clinical performance outcomes. CONCLUSION: A consensus on the framework of an advanced MIS training curriculum has been achieved defining the essential elements of entry criteria, selection of trainers and training units and curriculum content. Multimodal learning, clinical proctorship programme and competency based assessment are integral parts of the curriculum.

Intimin subtyping of Escherichia coli: concomitant carriage of multiple intimin subtypes from forage-fed cattle and sheep.

The outer membrane protein, intimin (eae), which mediates bacterial attachment to epithelial cells, is associated with enteropathogenic Escherichia coli and some Shiga toxin-producing E. coli. The eae subtype of E. coli strains isolated from healthy cattle and sheep was identified using a rapid PCR-restriction fragment length polymorphism (RFLP) method to produce profiles that were compared with those generated in silico. The 139 eae-positive E. coli strains were separated into 11 different PCR-RFLP profiles. The most common eae PCR-RFLP type was beta (23.7%), followed by zeta (20.1%), theta (16.5%), iota (12.2%), kappa (8.6%), epsilon (7.2%), gamma (2.9%), nu and beta2 (2.2%) and iota2 (1.4%). Four isolates did not yield a PCR-RFLP amplification product but complete sequencing of the eae gene matched subtype rho. Two different eae variants were isolated from the same swab from 18 different animals and subtype iota was the most 'promiscuous', being isolated with four other eae subtypes from seven separate animals. None of the eae-positive STEC were subtype gamma, which is associated with STEC serogroup O157. This method allowed the rapid identification of eae subtypes and indicates that forage-fed animals possessed a wide diversity of bacterial eae subtypes with a low frequency of eae subtype gamma.