Statin therapy is regarded as an effective medication to reduce cardiovascular events in patients at higher risk for future incidence of coronary artery disease. However, very few studies have been conducted to examine its implementation in non-Western real-world practice. In this study, we sought to describe statin prescription patterns in relation to patient characteristics in a Japanese multicenter percutaneous coronary intervention (PCI) registry as a foundation for quality improvement. We studied 15,024 patients that were prospectively enrolled in the Japan Cardiovascular Database-Keio interhospital Cardiovascular Study Registry from January 2009 to August 2014. The overall discharge statin non-prescription rate was 15.2%, without significant interhospital (MOR = 1.01) or annual differences (MOR = 1.13) observed. Hierarchical multivariable logistic regression analysis accounting for regional differences revealed that the presence of chronic kidney disease was associated with higher rates of statin non-prescription , and higher age (per 1-year increase) showed a trend for prescription of low-intensity statin  within the subset of PCI patients  enrolled after the year 2011. Our study indicates that patients with chronic kidney disease and elderlies may be the primary targets for maximizing the beneficial effect of statin therapy in post PCI patients. Statin therapy is regarded as an essential medication to reduce cardiovascular events through its blood cholesterol lowering and anti-inflammatory effects.  2–4] Wh–4 Wh2–4]In this study, we sought to describe prescription patterns of statin therapy after PCI and identify patient risk factors for statin non-prescription or low-intensity statin prescription in a contemporary Japanese percutaneous coronary intervention (PCI) registry as a foundation for quality improvement.We studied 15,024 patients undergoing PCI in the Japan Cardiovascular Database-Keio interhospital Cardiovascular Studies (JCD-KiCS) registry from January 2009 to August 2014. The JCD-KiCS is a multicenter registry designed to collect clinical variables and outcome data from patients undergoing PCI. Dedicated clinical research coordinators assigned at each site enrolled the PCI patients consecutively. The clinical variables and in-hospital outcomes for the JCD-KiCS were defined in accordance with those specified for CathPCI Registry v4.1  in order to enable a direct comparison with the NCDR CathPCI Registry program.  Fifteen The participating hospitals were instructed to record and register data from consecutive hospital visits for PCI using an internet-based data collection system. Written informed consent was routinely obtained from patients before undergoing PCI. PCI with any commercially available coronary device was included. The quality of the data entered in the web-based data capture system were assured by an automatic validation system and reporting for data completeness, and through standardized education and training for the dedicated clinical research coordinators at each site (I.U.). Finally, the collected data were checked for completeness and internal consistency .http://www.umin.ac.jp/english/whatisumin.htm).The Institutional Review Board of Keio University School of Medicine as well as each participating hospital approved the JCD-KiCS registry study protocol. The study was carried out in accordance with the approved guidelines. Before the launch of the registry, the objectives of the present study, its social significance, and an abstract were provided for clinical trial registration with the University hospital Medical Information Network (UMIN), which is recognized by the International Committee of Medical Journal Editors as an “acceptable registry” according to a statement issued in September 2004 (UMIN R000004736). UMIN is the largest and most versatile academic network information center for biomedical sciences in the world, and it is now considered as an indispensable information infrastructure for the Japanese medical community  was calculated using the Modification of Diet in Renal Disease (MDRD) Study equation . PresencFirst, we compared the baseline demographics of patients discharged with and without statins  . PatientSecond, within the subgroup of patients with complete statin intensity status   that begp value below 0.05 was considered to be statistically significant, unless mentioned otherwise in our analysis. All statistical analysis was performed using STATA version 13.1 (http://www.stata.com).The Student’s t-test or the Wilcoxon rank-sum test was used to compare continuous variables of those with or without discharge statin at PCI discharge. The Chi-square test or Fisher’s exact test was used to compare categorical variables, as appropriate. To examine the extent of practice-level variation in statin use multivariable hierarchical logistic regression models were constructed to determine the median rate ratio (RR). These were two-level hierarchical models with the practice modeled as a random effect and patient covariates as fixed effects.  26] The The26] TP value <0.001), clopidogrel , renin angiotensin aldosterone system inhibitors  and beta-blockers  were significantly lower in the statin non-prescription group while a greater proportion of patients were on warfarin in the same group . Statin non-prescription rate ranged from a minimum of 11.9% to a maximum of 18.0% among participating hospitals (MOR = 1.01)   and a miThe second part of our analysis was performed within the subgroup of patients with full description of statin type and dosing ; 41.5%  of the patients were on low-intensity statins and 58.4% were on moderate to high-intensity statins at the timing of discharge . Merely Finally, hierarchical multivariable logistic regression analysis accounting for practice variability revealed that the presence of chronic kidney disease was associated with higher rates of statin non-prescription  after adjusting for age, previous history of PCI , whereasOur current study showed that more than 15% of PCI patients were discharged without statin therapy despite a strong recommendation from various practice guidelines. Moreover, low-intensity statins was frequently observed in those who did receive statins at the timing of discharge. The proportion of statin non-prescription and low-intensity statin prescription were similar across the participating sites and throughout patient enrollment year. These results suggest that patient characteristics such as the presence of CKD and higher age can be potential targets to enhance the quality of care for PCI patients in Japan through maximizing statin therapy.In our dataset, the overall discharge statin non-prescription rate was comparable or higher than that reported in previous Western/non-Western databases. Recently, Pokharel et al reported the current trend of moderate-intensity to high-intensity statin therapy usage in the United States, before and after the publication of the 2013 ACC/AHA guideline from the American College of Cardiology National Cardiovascular Data Registry’s Practice Innovation and Clinical Excellence (PINNACLE) Registry.  The authNotably, an exceptionally high statin non-prescription rate was observed in CKD patients of our registry. In fact, the odds of receiving a statin at the timing of discharge were halved when CKD was present in the current Japanese study. Prescribing a fixed dose of statins in CKD patient has been controversial since these patients are perceived to be the most vulnerable to experience statin adverse effects especially when receiving higher intensity statins. The 2013 ACC/AHA Guideline on the Treatment of Blood Cholesterol to Reduce Atherosclerotic Cardiovascular Risk in Adults  support Suboptimal dosing of discharge statins is also a problem along with statin non-prescription. In our study, only 3 (0.1%) patients were prescribed with high-intensity statins while 41.6% were on low-intensity statins that may lead to cardiovascular events if not titrated up to higher dosing. Importantly, Rodriguez et al. described that high-intensity statins are indeed associated with a small but significant survival advantage compared with moderate-intensity statins, even among older adults.  In the cRecently, two new classes of non-statin blood-lowering medications have been shown to improve clinical outcomes in addition to maximally tolerated dose of statins; ezetimibe and proprotein convertase subtilisin/kexin type 9 (PCSK9) inhibitors.–44 TheseThere are several limitations to our current study. First, our study had the inherent limitations of any nonrandomized observational research. These results are derived from a multicenter cohort registry that cannot indefinitely clarify the cause and effect relationship between the exposure of interest and outcomes even after rigorous adjustment for possible confounders. Second, key factors that may have affected statin non-prescription such as medication status prior to PCI admission, previous intolerance to statins, statin allergy, patient preferences, socioeconomic and education level were not collected in this registry although the impact of socioeconomic status may be smaller compared to other countries with much disparity since Japan is known to have a relatively large proportion of middle-class income households reinforced with a universal health care system. Third, the current registry did not collect details of post-discharge follow-up clinic, especially data on post-discharge statin initiation or titrations, however, we believe that the number of these patients are small and do not affect the overall results shown in our current analysis. Fourth, long-term outcome data on cardiovascular death or unplanned hospitalization for revascularization were not available in this current database. Further follow-up data is necessary to evaluate the relationship of discharge statin non-prescription, dose-intensity and subsequent clinical hard endpoints. Fifth, although evaluated within a large prospective multicenter registry, our current data represents the real-world prescription of statins in Japanese PCI patients and may not be generalizable in Western countries where the incidence and demographics of coronary artery disease patients differ largely. However, given the fact that we are still at the dawn of implementing high-intensity statins after PCI when looking at a global scale, our results may be of value in countries struggling to improve quality of care by targeting patients with high-risk characteristics based on current/previous cardiology practice.The findings of this study suggest that discharge statin non-prescription rates following PCI in a Japanese context are considerably high, especially in those with chronic kidney disease. In addition, in contrast to the recommendation of using high-intensity statins in established CAD patients, low-intensity statins prescription was frequently observed in a subgroup of post PCI patients with complete statin intensity status. Long-term data on the subsequent incidence of recurrent coronary events as a function of these observed treatment practices is warranted.S1 Table(DOCX)Click here for additional data file.S2 Table(DOCX)Click here for additional data file.S3 Table(DOCX)Click here for additional data file.


The causes of insulin resistance are not well-understood in either type 1 or type 2 diabetes. Insulin (INS) is known to undergo rapid non-enzymatic covalent conjugation to glucose or other sugars (glycation). Because the insulin receptor (IR) has INS-like regions associated with both glucose and INS binding, we hypothesize that hyperglycemic conditions may rapidly glycate the IR, chronically interfering with INS binding. IR peptides were synthesized spanning IR- associated INS-binding regions. Glycation rates of peptides under hyperglycemic conditions were followed over six days using matrix assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry. INS conjugated to horse-radish peroxidase was used to determine INS binding to IR peptides in glycated and non-glycated forms. Several IR peptides were glycated up to 14% within days of exposure to 20–60 mM glucose. Rates of IR-peptide glycation were comparable to those of insulin. Glycation of four IR peptides significantly inhibits INS binding to them. Glycation of intact IR also decreases INS binding by about a third, although it was not possible to confirm the glycation sites on the intact IR. Glycation of the IR may therefore provide a mechanism by which INS resistance develops in diabetes. Demonstration of glycation of intact IR in vivo is needed. We propose a novel mechanism by which insulin (INS) resistance might arise in both type 1 (T1DM) and type 2 (T2DM) diabetes: Rapid glycation of the insulin receptor (IR) may result in decreased INS binding and subsequent impairment of IR activity. We test the plausibility of this hypothesis in vitro using mass spectrometry to follow the glycation of IR-derived peptides, an enzyme-linked-insulin binding assay to measure INS binding to these peptides, and ultraviolet spectroscopy to measure binding of INS to intact, glycated IR.While development of insulin resistance is an important concomitant of the development and progression of both T1DM and T2DM, its causes are still mysterious. Insulin resistance is characterized by the presence of normal numbers of insulin receptors (IR), significantly increased levels of insulin (INS), but decreased INS activity. Various mechanisms have been proposed to explain insulin resistance. In T1DM, insulin resistance is thought to be due to hyperglycemia producing down-regulation of glucose transporters and the disruption of fatty acid regulation producing post-transport regulation of insulin activity . The posWhile non-enzymatic glycation of some proteins such as insulin (INS) and hemoglobin A1C is a well-known phenomenon accompanying hyperglycemia in both type 1 and type 2 diabetes ,15, the We hypothesize that glycation of the IR provides a logical mechanism for producing INS resistance. Our hypothesis is an extrapolation from the work of several groups that have previously demonstrated that INS itself undergoes rapid glycation under hyperglycemic conditions combined with the facts that the IR shares sequence homologies with INS and that the IR itself binds glucose.INS glycation is well-characterized. Glycation is defined as the non-enzymatic covalent conjugation of glucose (or other sugars) to a peptide or protein. In solution, hexoses exist in equilibrium as two primary isomeric forms: the open-chain aldohexose and cyclic hemiacetal. In the presence of dissolved peptide, the aldohexose is usually susceptible to nucleophilic attack by terminal α- or lysine residue ε- amino groups. This reaction results in condensation of an unstable glycosylamine adduct, which rearranges over time into the Amadori aminodeoxyketose. The Amadori product becomes the basis for the development of advanced glycation end products (AGEs) that are highly associated with diabetic complications . It is gd-galactose, d-mannose and 2-deoxy-d-glucose bind with lower affinity to these glucose binding sites   was added to each well, incubated for thirty minutes, and the plate was then read on a SpectraMax Plus scanning microplate spectrophotometer at 405 nm. Controls wells lacking peptide but with PVA, INS-HRP and ABTS measured non-specific binding that was subtracted from the absorbance values of the rest of the wells. All experiments were run in triplicate and the averages of the corrected absorbances were then plotted against the concentration of the INS–HRP for each peptide to yield binding curves. Because binding curves are calculated by plotting differences, it was not possible to incorporate error bars into these curves.The same technique just described in Intact recombinant IR was obtained from Sigma-Aldrich  and utilized at 42.9 units/mL in phosphate buffered saline, pH 7.4 (PBS) or in PBS with 20 mM glucose added. PBS and 20 mM glucose solutions of IR were incubated for six days at 37 °C. An aliquot of each preparation was then subjected to centrifugal filtration and washing through Ultrafree-MC 5 kda or Ultracel 3 kda filter units. The resulting retentates were resuspended in PBS. In this way, identical preparations of unglycated IR and glycated IR were made in both PBS and in 20 mM gucose PBS. Microliter quantities of PBS buffer, or 20 mM glucose PBS, or human recombinant INS  in PBS or 20 mM glucose PBS were then added serially to 100 µL of each of the four preparations of IR and to control wells containing only PBS or 20 mM glucose PBS. Experiments were carried out in a crystal 96-well plate and the serial combinations subjected to UV spectrophotometry to obtain their spectra. The spectra of the control wells were subtracted from the spectra of the experimental wells to yield expected values at each UV wavelength and differences between the controls and experimental values determined. These differences were plotted according to the concentration of INS added to the IR to yield binding curves. Binding constants were determined from the concentration at which the binding curves inverted. Because of the small amount of retentates, the various conditions were not run in duplicate; instead, the experiment was run independently, twice. Each run yielded similar binding constants, but because the data from each run had different baseline values, it was not possible to average the results, so only one of the sets of results is presented here.The IR rapidly glycates under hyperglycemic conditions resulting in significantly decreased INS binding under in vitro conditions. If this effect also occurs in vivo, the clinical implications of rapid glycation under hyperglycemic conditions may be to cause interference with binding of INS, IGF, and related hormones to their receptors that would last for the lifetime of the ligands and their receptors. Direct measurement of IR, IGFR, and glucagon receptor-glycation might provide more accurate and sensitive means for evaluating the effects of hyperglycemic episodes in diabetes than does hemoglobin A1C.Understanding glycation mechanisms of INS-related proteins such as the IR and IGFR may provide new means for pharmacologically or nutritionally mitigating some adverse effects of hyperglycemic episodes. Since glycation of IR peptides is not complete at six days under hyperglycemic conditions, and the initial steps are reversible, various interventions may be possible to block glycation. Various investigators have reported that vitamin C, aspirin, lysine, and other natural compounds can inhibit INS or human serum albumin glycation in vitro or in vivo ,51,52. IIn summary, IR glycation due to hyperglycemia may broaden the significance of protein glycation for understanding insulin resistance well beyond the existing literature on INS, hemoglobin, and serum albumin by providing a direct mechanism for lasting effects of acute hyperglycemic episodes on IR function. These results may extend to other INS-related proteins such as IGF and the IGFR. Better understanding of rapid non-enzymatic glycation of such proteins may provide better clinical diagnostic measures as well as lead to specific treatment interventions.


Epigenetics regulations have an important role in fertilization and proper embryonic development, and several human diseases are associated with epigenetic modification disorders, such as Rett syndrome, Beckwith-Wiedemann syndrome and Angelman syndrome. However, the dynamics and functions of long non-coding RNAs (lncRNAs), one type of epigenetic regulators, in human pre-implantation development have not yet been demonstrated. In this study, a comprehensive analysis of human and mouse early-stage embryonic lncRNAs was performed based on public single-cell RNA sequencing data. Expression profile analysis revealed that lncRNAs are expressed in a developmental stage–specific manner during human early-stage embryonic development, whereas a more temporal-specific expression pattern was identified in mouse embryos. Weighted gene co-expression network analysis suggested that lncRNAs involved in human early-stage embryonic development are associated with several important functions and processes, such as oocyte maturation, zygotic genome activation and mitochondrial functions. We also found that the network of lncRNAs involved in zygotic genome activation was highly preservative between human and mouse embryos, whereas in other stages no strong correlation between human and mouse embryo was observed. This study provides insight into the molecular mechanism underlying lncRNA involvement in human pre-implantation embryonic development. Understanding human pre-implantation development can not only provides insight into common human birth defects but also improve our understanding of the pathogenic mechanisms of many complex diseases such as Rett syndrome, Beckwith-Wiedemann syndrome and Angelman syndrome , 2. ThusMembers of numerous non-coding RNA classes are expressed in the oocyte and pre-implantation embryo, and they have have an important role in fertilization and proper embryonic development , includicis-inactivation of the X chromosome during the 4-cell stage, and another lncRNA; Fendrr, mediates long-term epigenetic marks to define expression levels of its target genes in mammalian embryogenesis  and specificities[i] respectively denote the sensitivities and specificities of the ith coverage threshold. The value for i is enumerated in I, ranging from 1 to the size of the coverage threshold set T. Then the optimum coverage threshold can be obtained with formula A coverage threshold set nscripts . The indThe novel lncRNAs were obtained by the following steps: (1) Cuffcompare in Cufflinks was run using default parameters (and ‘-M discard (ignore) single-exon transfrags and reference transcripts’) to combine our transcripts with annotations from five well-established databases, Refseq (ref_GRCh37.p13_top_level.gtf), Ensembl (Ensembl_Homo_sapiens.GRCh37.75.gtf), UCSC (hg19), Gencode (gencode.v19.annotation.gtf) and the lncRNA database NONCODE 4.0 (NONCODEv4u1_human_lncRNA.gtf) –49; (2) A matrix of gene expression levels across all samples was obtained by computing the expression levels of Refseq coding genes and lncRNAs (both novel lncRNAs and the annotated lncRNAs) with Cuffquant and Cuffnorm . The ann2 fold change was >1 and the false discovery rate–adjusted P-value indicated statistical significance  after the Benjamini-Hochberg correction for multiple testing [The R package Monocle was used to conduct differential expression tests between any two consecutive stages. Differential expression of a specific gene between any two consecutive stages was noted if the log testing , 55.10(FPKM+1). Then this expression vector was normalized to a density vector by formula V =  is the original raw FPKM abundance estimation of each gene and V' is the new normalized density vector [To calculate the temporal specificity scores of genes, the expression vector needed to be converted to an abundance density. First, the raw FPKM (fragments per kilobase of exons per million fragments mapped) of each gene was converted to logy vector .To calculate the temporal specificity score, we used an entropy-based measure to quantify the similarity between a gene's expression pattern and another predefined pattern that represents an extreme case in which a gene was expressed during only one stage . The entJSdist dist was the Jensen-Shannon distance (JSD) between two stage expression patterns and e was the gene expression pattern across n stages  between their density-normalized expression vectors [Two genes were defined as neighbors if the distance between the gene bodies was < 10 kb. Correlation between the expression pattern of an lncRNA and its neighbor coding gene was estimated by calculating the Pearson correlation coefficient . To minimize effects of noise and spurious associations, the adjacency matrix was transformed into a Topological Overlap Matrix (TOM). Genes with highly similar co-expression relationships were grouped together by performing average linkage hierarchical clustering on the topological overlap. Dynamic Hybrid Tree Cut algorithm was used to cut the hierarchal clustering tree and define modules as branches from the tree cutting. The expression profile of each module was represented by its first principal component (module eigengene), which could explain the most variation in the module expression levels. Modules with highly correlated module eigengenes (correlation > 0.85) were merged together.The R package WGCNA was used to construct an lncRNA co-expression network . The staix is the gene expression profile of gene i and qME is the module eigengene of the module q [The module membership  of each gene was calculated by correlating the gene expression profile with module eigengenes with formula module q .P-value < 10−22). Intramodular hub genes, which were centrally located inside the module, represent the expression profiles of the entire module and reflect the core functions of the module [Genes with the highest module membership values were referred to as intramodular hub genes  database . The funP-value cut-off of 0.05 and minimum gene count of 5. Each module was tested for GO enrichment in terms of the Biological Process categories [Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of modules was carried out with the R packages GOstats and org.Hs.eg.db. Hypergeometric tests were applied with a tegories , 63.


Workplaces today demand graduates who are prepared with field-specific knowledge, advanced social skills, problem-solving skills, and integration capabilities. Meeting these goals with didactic learning (DL) is becoming increasingly difficult. Enhanced training methods that would better prepare tomorrow’s graduates must be more engaging and game-like, such as feedback based e-learning or simulation-based training, while saving time. Empirical evidence regarding the effectiveness of advanced learning methods is lacking. Objective quantitative research comparing advanced training methods with DL is sparse.This quantitative study assessed the effectiveness of a computerized interactive simulator coupled with an instructor who monitored students’ progress and provided Web-based immediate feedback.P<.001. Two independent experiments involving obstetrics and gynecology (Ob-Gyn) physicians and senior ultrasound sonographers, with 32 subjects, were conducted using a new interactive concept of the WOZ (Wizard of OZ) simulator platform. The contribution of an instructor to learning outcomes was evaluated by comparing students’ knowledge before and after each interactive instructor-led session as well as after fully automated e-learning in the field of Ob-Gyn. Results from objective knowledge tests were analyzed using hypothesis testing and model fitting.A low-cost, globally accessible, telemedicine simulator, developed at the Technion—Israel Institute of Technology, Haifa, Israel—was used. A previous study in the field of interventional cardiology, evaluating the efficacy of the simulator to enhanced learning via knowledge exams, presented promising results of average scores varying from 94% after training and 54% before training (n=20) with P=.01) was found in favor of the WOZ training approach. Content type and training audience were not significant.A significant advantage (This study evaluated the contribution of an integrated teaching environment using a computerized interactive simulator, with an instructor providing immediate Web-based immediate feedback to trainees. Involvement of an instructor in the simulation-based training process provided better learning outcomes that varied training content and trainee populations did not affect the overall learning gains. Medical education is becoming increasingly challenging. Physicians must master an ever-expanding knowledge base; yet, they are constrained by a limited educational time frame. Didactic learning (DL) is no longer sufficient, hence interactive methods are needed. Thus, and in part due to the Internet, an alternative—Web-based educational—content has emerged . ExampleIn addition to increase our knowledge base, cognitive learning can change our beliefs and the way we see and understand events. A major step in understanding the way people learn evolved in the late 1950s when the field of cognitive science emerged . Cognitie-learning is a powerful, cost-effective training tool. Although some have described it as boring and monotonous  when comTo improve medical education and training, we developed a novel, low-cost, low-fidelity, accessible telemedicine simulator at the Technion—Israel Institute of Technology, Haifa, Israel—using a Wizard of Oz (WOZ) simulator. The WOZ is a well-established method for simulating the functionality and user experience in which a human operator, the Wizard, mediates the interaction. Using a human wizard to mimic certain operations of a potential system is particularly useful in situations where extensive engineering effort would otherwise be needed to explore the design possibilities offered by such operations .The WOZ simulator features a remote instructor (the Wizard) in the training loop, controlling students’ learning. This approach enables trainers to effectively detect learners’ flawed mental models (misconceptions) and supply corrective immediate feedback during the training sessions . Web-BasP<.001 [The WOZ simulator is a novel form of a low-fidelity, semiautomatic simulator designed to enhance medical education. It has been used to remotely train physicians in fields of emergency medicine, pediatrics, and interventional cardiology ,4. PromiP<.001 .The field of Obstetrics and Gynecology (Ob-Gyn) was chosen for this study due to its focus on knowledge-related tasks and diagnostic skills, such as US imagery interpretation. Fields that rely on knowledge-specific tasks and diagnostic skills better match the remote training, low-fidelity, instructor-led WOZ simulator platform.This prospective study was performed at the Simultech Center for Simulation in Medicine. The Center specializes in Ob-Gyn training. The WOZ simulator was accessed through a weblink . TraininIn the automated e-learning mode, the follow-up question would immediately appear. In the WOZ mode, the instructor could proceed to the follow-up question or ask additional questions, send clarifying information, or skip some questions depending on the trainee’s progress. After answering the final question, automated feedback would be presented to the trainee in the e-learning format, whereas in the WOZ format, the instructor would provide feedback in an open conversation.The design of our experiment required that there be a number of medical trainees sharing a similar medical knowledge background as well as qualified medical trainers. The Simultech Simulation Center satisfied these requirements. Integrating our WOZ simulator experiments into Simultech’s training schedule was done in two different courses and included a total of 32 Ob-Gyn ultrasonography specialists.The first experiment group consisted of 18 (12 men and 6 women) physicians who were participating in an Ob-Gyn ultrasound imaging fellowship program. The second experiment group included 14 women, who were senior ultrasound technicians with 5-20 years of experience.In the first experiment group, 8 random subjects went through the WOZ training session, whereas in the second experiment group 7 subjects (4 from the ovary subgroup and 3 from the uterus subgroup) were trained using the WOZ format. The interactive WOZ training session used the same case as the e-learning session, yet subjects received interactive, remote (sitting in a different room) Web-based immediate feedback from an instructor monitoring their progress . Case prIn the first experiment group, 10 random subjects went through the e-learning training session, whereas in the second experiment group, 7 subjects (3 from the ovary subgroup and 4 from the uterus subgroup) were trained using the e-learning format. e-learning sessions included self-paced training on the simulator and a post-session knowledge test. The self-paced training (a new question appeared immediately after the previous question was answered) included a set of questions, their supporting media and a self-assessment feedback table  received at the end of the session. Case questions, their detailed answers and the knowledge test were developed and validated by Simultech instructors and the medical professionals supporting them. The validated medical case was uploaded to a local server, accessed by a local network at Simultech.All evaluators were tested by a post-training, objective knowledge exam. All knowledge exams  were validated by medical professionals from the Simultech Simulation Center and included 10 open questions that were evaluated and scored by professional medical supervisors.Control groups (e-learning) from both experiments received an automated, self-assessment computerized case, where trainees answered a set of questions . Each e-The outcome measure evaluated in both experiments was knowledge gain based on the training received. Knowledge gain was evaluated using knowledge exams that were given to all subjects upon completion of their computerized training. According to the magnitude of difference between knowledge exam scores, the significance of instructors’ contribution to the learning process can be deduced.Before all training sessions, students were informed that the training was part of a research project. Due to a current change in Simultech’s policy toward minimizing e-learning trainings, the experiment was divided into two sections: Training of Ob-Gyn physicians as part of a full-day training event and training senior US technicians as part of a continuing education program.Training sessions for the first experiment (Ob-Gyn physicians) were conducted by professional instructors (Simultech’s instructor team). They focused on supplying new techniques, knowledge reinforcement, and skill acquisition. Simultech’s instructors are certified teachers with no medical background. Instructors study specific medical cases built by Simultech’s medical professionals. The WOZ simulator training was scheduled to run once a week or every 2 weeks, depending on instructors’ availability. Participants were randomly chosen to use the e-learning mode (control group) or the interactive WOZ mode (intervention group).The second experiment included 14 of 23  senior ultrasound technicians who attended a senior technicians’ ultrasound course. The course included four meetings in 1 month. The course was attended by 23 senior ultrasound technicians . A month after the course ended, a half-day training was added for students to practice and train with the WOZ simulator on cases designed by students during the course. Contrary to previous ultrasound senior technician courses that used DL during class time, this course included a homework assignment . The homework required students to study a specific medical topic, whereas some of the class time was used to train, instruct, and facilitate team learning, using Simultech instructors as medical consultants.The WOZ simulator and the new exercise were presented to the ultrasound technicians at the first-class meeting. Students were divided into a uterus and an ovary subgroup and were asked to build a training case for the WOZ simulator that would include the following:A minimum of 10 training knowledge questions (multiple choice and open questions);Media to support the questions ;Detailed best practice answers with additional supporting media;A set of 10 open questions for an objective knowledge exam to be administered to each group after simulator training.Additionally, students were informed that they would assume the role of instructors while training their peers on the WOZ simulator using their prebuilt training case. During the course, each student was responsible for developing one training question, its answer, and all supporting media, per his or her assigned topic of uterus or ovary. This assignment required each student to study a specific topic using written information, consult with the course staff and his or her medical coworkers. A team leader was chosen for each group to integrate all the questions into one training case that was validated by the Simultech training staff. Each group wrote a knowledge test of 10 open questions for each case. Several selected topics (questions built by students) that were not integrated into the simulator cases were presented as lectures at the end of the fourth meeting of the course.The second experiment was held at Simultech a month after the first course ended. Fourteen students participated in the final simulator training (7 from each group). As illustrated in The simulator used for training by the two groups, is a low-fidelity, Web-based application that was developed using Microsoft SharePoint 2010 technology. The simulator was used in previous studies and its efficacy as a training tool in various fields of medicine was evaluated ,4. For tThe JMP statistical package was used to compare the results of the knowledge tests taken after the completion of each training mode: e-learning and the interactive WOZ. The results for both experiments of 32 participants are displayed in The first experiment included 18 medical, fellowship physicians who were randomly divided into two subgroups. The first subgroup included 10 e-learning trainees who scored an average of 64% (SD 13), and the second subgroup included 8 interactive (trainer-led) WOZ trainees who scored an average of 79% (SD 24).The second experiment included 14 females, senior ultrasound technicians. They were randomly divided into 7 e-learning trainees who scored an average of 63% (SD 11) and 7 interactive trainees who scored an average of 83% (SD 7). Each training method was also subdivided based on the selected topic . The topic and its interaction with the training method were not significant relative to the grades scored.The first sessions included Simultech instructors training Ob-Gyn physicians as part of a full-day training at Simultech. Trainees were randomly selected to perform the e-learning or the instructor-led WOZ session. The WOZ training included summarized verbal feedback at the end of the interactive case. Most of the WOZ training was done by one dedicated instructor. The knowledge test included general Ob-Gyn and US-related questions taken from previous cases built by Simultech’s professional staff. This part of the training included 18 sessions, spanning more than 6 months.The second training session lasted 1 day and took place a month after the four meetings of the course. Both training cases were built by course students, supported by Simultech’s medical professionals and were uploaded to the WOZ Web server at the Technion. Training cases and their knowledge tests were divided into 2 knowledge areas (ovary and uterus). The WOZ training for all 7 trainees occurred in the same room with a trainer from the other group sitting behind each trainee. A knowledge exam consisting of 10 open questions was given after the computerized training and scored by an Ob-Gyn, physician an hour after all exams were submitted.Training sessions lasted from 40 to 60 minutes. All participating students in both experiments completed 10 open questions in a written knowledge exam post-simulator training. All interactive WOZ sessions included 1 instructor training 1 trainee; yet, in previous studies we showed that 1 trainer can train 2 trainees or a small team [Before running the full model based on both experiments, a homogeneity of variance test was conducted  and 2. RP value of .01  compared with the e-learning alternative. The impact of the training method on test grades was reinforced by the lack of statistical significance of the medical subject (area) and its interaction with the training method. Moreover, the experiment factor (operator type) and its interaction with the training method were not significant. This indicates that most of the variability in students’ grades was due to the training method (WOZ vs e-learning).The experiments were integrated to evaluate the overall contribution of the instructor (man in the loop) to the training process. The joint analysis indicated that the interactive WOZ training presented a significant advantage  to research a specific topic (uterus or ovary), build a WOZ simulator training case based on their research, and assume the role of the instructor and train their fellow classmates.This exercise had very positive outcomes. Students and the management team described it as the most educational course Simultech had ever provided. Students training on the simulator described their experience as fun and educational, as was previously described by trainees using the WOZ simulator ,4. DurinThe study presented interesting insights regarding the contribution of instructors to a computerized training process, although there were several limitations. The study was conducted with limited access to trainees’ personal and background data. It had a small sample size because ongoing courses at Simultech are constrained to a short timeframe with little flexibility to apply additional content. This study can contribute to the developing field of enhanced learning and can support continued research in this area.The added value of Web-based immediate feedback and integrating an instructor to simulation-based training were introduced in the literature review ,7,14,16 quantitatively the contribution of an instructor to learning with a computer-based WOZ simulator training. The results indicate the WOZ training was superior to automated e-learning. In one experiment, students were responsible for developing training materials and for training their peers. Researching and developing an educational unit contributed immensely to the overall student satisfaction. Additionally, this exercise initiated new discussions among students, improved team building, increased motivation, and created new work relations between technicians from various organizations. The results of this study present interesting insights in favor of interactive, instructor WOZ simulator training as compared with automated e-learning.We conducted two independent experiments using a WOZ simulator to evaluate


Native sub-Saharan African black men (SSBM) are disproportionately impacted by higher stage and incurable forms of prostate cancer (PCa). This study evaluates the natural history and survival of a cohort of SSBM with castration-resistant prostate cancer (CRPC).A retrospective study of patients with CRPC as defined by the Prostate Cancer Working Group 2 managed at a centre in sub-Saharan Africa between January 2011 and December 2015 was conducted. The principal endpoint was overall survival (OS). Potential prognostic variables were evaluated using Cox proportional hazard regression models.A total of 48 patients were identified. Median (IQR) age and prostate-specific antigen (PSA) at diagnosis were 70 (64–74.5) years and 42 (8.0–123.6) ng/mL, respectively. Only 15 (31.3%) patients received docetaxel and one patient each received the novel drugs enzalutamide and abiraterone. Twenty-eight patients (58.3%) died during follow-up with a median OS of 11 (95% CI: 8–14) months. Docetaxel chemotherapy and ECOG performance status were found to be prognostic .This study of SSBM with CRPC revealed a mainly unmodulated clinical course with poor access to active treatments and poor survival. Improving access to new active therapies would improve survival. Compared to men from other world regions, sub-Saharan African black men (SSBM) are disproportionately impacted by higher stage and incurable forms of prostate cancer (PCa) –4. This Records of patients with pathologically confirmed PCa treated at a single public tertiary-care hospital in Nigeria, western sub-Saharan Africa, from January 2011 to December 2015 were retrieved. The hospital is typical of similar public tertiary-care centres all over the country with urology departments and a similar case load of prostate diseases, including PCa. Using a strict selection algorithm , patientOf 161 patients’ records reviewed, 48 patients diagnosed with CRPC met the inclusion criteria and were subsequently analysed. Cohort characteristics are shown in Being black confers a higher risk to developing PCa compared to other racial groups. Despite this, there has been a dearth of research into the impact of the disease on the black populations of sub-Saharan Africa. Though the better studied African-American and Afro-Caribbean men derived their ancestral origins mainly from native black populations of Africa, the wide socio-cultural and economic dissimilarities that now exists between these two groups is such that no safe assumptions of similarities in PCa clinical course or survival can be made. The few reports from Africa available in the literature reveals observations of a high prevalence of advanced disease and high mortality rates –4, 12. TDespite ADT, patients with advanced disease do eventually progress to CRPC. While non-metastatic CRPC is a common early clinical manifestation following castration resistance in Western men, the native African blacks in this study all had documented metastasis at CRPC diagnosis . This fiSurgical castration was found to be the more frequent form of ADT received by patients in this study. This may be due to its lower cost compared to medical castration. Health insurance coverage rates in sub-Saharan African region are dismally low, payments for health care are mainly an out-of-pocket expenditure and cancer treatments can easily result in financial catastrophe . This siProgression-free survival from the diagnosis of advanced disease to CRPC have been previously reported to be approximately 27 months in African men ; and givSome limitations to this study to be acknowledged include the retrospective design, single-centre recruitment and a relatively small cohort; 13 patients were excluded from analysis due to missing data. Non-informative censoring was ensured by excluding patients lost to follow-up. Despite the limitations, the study is the first to describe the natural history and survival of CRPC in the high-risk but under-researched black men of sub-Saharan African origin and reveals a mainly unmodulated clinical course and poor OS.


Evidence-based mailed educational brochures about the harms of sedative-hypnotic use lead to discontinuation of chronic benzodiazepine use in older adults. It remains unknown whether patients with mild cognitive impairment (MCI) are able to understand the information in the EMPOWER brochures, and whether they achieve similar rates of benzodiazepine discontinuation.n = 139) or MCI (n = 122) was determined during baseline cognitive testing using the Montreal Cognitive Assessment questionnaire. Changes in knowledge pre- and post-intervention were assessed with a knowledge questionnaire and changes in beliefs were calculated using the Beliefs about Medicines Questionnaire. Logistic regression was used to compare knowledge gained, change in beliefs and benzodiazepine cessation rates between participants with and without MCI.Post-hoc analysis of the EMPOWER randomized, double-blind, wait-list controlled trial that assessed the effect of a direct-to-consumer educational intervention on benzodiazepine discontinuation. 303 community-dwelling chronic users of benzodiazepine medication aged 65–95 years were recruited from general community pharmacies in the original trial, 261 (86%) of which completed the trial extension phase. All participants of the control arm received the EMPOWER brochure during the trial extension. Normal cognition  participants with MCI and in 53  with normal cognition . Compared to individuals with normal cognition, MCI had no effect on the acquisition of new knowledge, change in beliefs about benzodiazepines or elicitation of cognitive dissonance.The EMPOWER brochure is effective for reducing benzodiazepines in community-dwelling older adults with mild cognitive impairment.NCT01148186, June 21st 2010.Our ClinicalTrials.gov identifier is  Sedative-hypnotic use is associated with cognitive impairment, and may contribute to mild neurocognitive disorders in older adults –3. For tThe majority of long-term benzodiazepine users aged 65 years of age and older report not being concerned about side effects, mainly because they have never been alerted to the risks . Howevern = 261) ) participants with normal cognition and 55  (Table Compared to participants with normal cognition, those with MCI exhibited the same ability to acquire new knowledge and change their beliefs following the intervention. Self-efficacy to taper and experience of withdrawal symptoms was the same in both groups. Additionally, cognitive status did not affect the participants’ decision to partake in a discussion about the intervention with their healthcare provider Table .Although previous research indicates that individuals with MCI perform significantly worse than controls in multiple aspects of medical decision-making , 8, 15, This is the first study of its kind to explore the association between MCI and the success rates of a patient-centered educational deprescribing intervention in a community-based clinical trial of older, community-dwelling adults. As the mild neurocognitive disorder diagnosis was not yet developed at the time of the study and the MoCA’s usefulness in detecting mild neurocognitive disorder is modest , we cateThis report illustrates that the EMPOWER brochure can be distributed to community-dwelling older adults with MCI and still work, whether directly through patient comprehension of the material or through the support of caregivers or family. The EMPOWER tool can and should be used in primary care or memory clinics for chronic benzodiazepine users who are candidates for deprescribing sedative-hypnotic medication.


HIV-associated tuberculosis (TB) co-infection remains an enormous burden to international public health. Post-mortem studies have highlighted the high proportion of HIV-positive adults admitted to hospital with TB. Determine TB-LAM and Xpert MTB/RIF assays can substantially increase diagnostic yield of TB within one day of hospital admission. However, it remains unclear if this approach can impact clinical outcomes. The STAMP trial aims to test the hypothesis that the implementation a urine-based screening strategy for TB can reduce all cause-mortality among HIV-positive patients admitted to hospital when compared to current, sputum-based screening.The trial is a pragmatic, individually randomised, multi-country  clinical trial with two study arms (1:1 recruitment). Unselected HIV-positive patients admitted to medical wards, irrespective of presentation, meeting the inclusion criteria and giving consent will be randomized to screening for TB using either: (i) ‘standard of care’- testing of sputum using the Xpert MTB/RIF assay (Xpert) or (ii) ‘intervention’- testing of sputum using Xpert and testing of urine using (a) Determine TB-LAM lateral-flow assay and (b) Xpert following concentration of urine by centrifugation. Patients will be excluded if they have received TB treatment in the previous 12 months, if they have received isoniazid preventive therapy in the last 6 months, if they are aged <18 years or they live outside the pre-specified geographical area. Results will be provided to the responsible medical team as soon as available to inform decisions regarding TB treatment. Both the study and routine medical team will be masked to study arm allocation. 1300 patients will be enrolled per arm . The primary endpoint is all-cause mortality at 56 days. An economic analysis will be conducted to project long-term outcomes for shorter-term trial data, including cost-effectiveness.This pragmatic trial assesses an intervention to reduce the high mortality caused by HIV-associated TB, which could feasibly be scaled up in high-burden settings if shown to be efficacious and cost-effective. We discuss the challenges of designing a trial to assess the impact on mortality of laboratory-based TB screening interventions given frequent initiation of empirical treatment and a failure of several previous clinical trials to demonstrate an impact on clinical outcomes. We also elaborate on the practical and ethical issues of ‘testing a test’ in general.ISRCTN71603869) prospectively registered 08 May 2015; the South African National Controlled Trials Registry (DOH-27-1015-5185) prospectively registered October 2015.ISRCTN Registry ( HIV-associated TB remains an enormous burden to international public health, even in regions with high coverage of antiretroviral therapy (ART). Globally, in 2014, there were an estimated 0.4 million TB related deaths in people living with HIV, which accounts for approximately one-quarter of TB deaths and one-third of HIV deaths . Al. Al32]. For the primary outcome the risk difference and odds ratio, and their associated 95 % confidence intervals for the effect of study arm on mortality risk will be calculated. The primary analysis of this endpoint will assume participants who are lost to follow-up before 56 days have not died. Sensitivity analyses will be conducted to assess assumptions made regarding missing data and patients lost to follow-up. A sub-group analysis of the primary outcome will be conducted for the following variables: study site, calendar time, baseline CD4 cell count (<100 or >100 cells/μL), presence of severe anaemia (Hb <80 g/L) and clinically suspected TB at admission. The interaction effects by subgroup will be investigated and p-values reported.Secondary outcomes (as defined above) will be compared between study arms using logistic regression for binary outcome and survival analysis with Kaplan-Meier curves and Cox proportional hazards for time to event. All analyses will be adjusted for randomisation site.A statistical analysis plan documents the analysis of all trial outcomes in detail, and was reviewed by the Data Safety and Monitoring Board (DSMB).The trial will be governed by a Trial Steering Committee (TSC), including an independent chairperson and at least three other independent members. The TSC will oversee the trial and advise the investigator team, including monitoring progress, receiving reports from the Data and Safety Monitoring Board (DSMB), and assessing the impact of new scientific evidence. The DSMB’s role is to protect the safety of trial participants, they will meet every six months to review data from the trial, as set out in the DSMB charter, and are independent to the trial sponsor . Monitoring visits will be undertaken at least three-monthly for quality assurance and to ensure adherence to the trial protocol, and auditing of the trial conduct will be undertaken by the trial sponsor.The trial has also received approval from the Research Ethics Committees of the London School of Hygiene & Tropical Medicine (ref: 9630), College of Medicine University of Malawi (ref: P.06/15/1743) and the University of KwaZulu-Natal Biomedical Research Ethics Committee (ref: BFC215/15). STAMP is registered with the ISRCTN Registry (ref: ISRCTN71603869) and the South African National Controlled Trials Registry (ref: DOH-27-1015-5185). The trial is funded by the Joint Global Health Trials scheme , and was peer reviewed as part of the funding application process.The STAMP trial aims to assess whether a novel, rapid urine-based screening strategy for TB with a high diagnostic yield can reduce early mortality in HIV-positive patients admitted to hospital in sub-Saharan Africa. The need for this trial is clear given the high mortality among HIV-positive patients admitted to hospital in these settings, and the high proportion of patients that die with undiagnosed TB disease , 30. PosOther trials have assessed empirical TB treatment in HIV-positive patients at high risk of TB, although mostly in outpatient settings. The REMEMBER trial failed to demonstrate a mortality benefit of empirical TB treatment compared to isoniazid preventive therapy . The TB A trial of adjunctive urine testing with the TB-LAM assay in a selected population of hospitalised HIV-positive patients being investigated for TB (the LAM RCT) recently demonstrated a reduction in mortality at 2-months . The STAThe rationale for a clinical trial to demonstrate impact prior to implementation is supported by the lack of demonstrable benefit upon patient outcomes of sputum screening using Xpert in HIV-positive patients, despite increases in diagnostic yield compared to sputum smear microscopy . ReasonsThese issues have been considered when designing the STAMP trial. For example, in-patient settings have a high mortality, and initiating TB treatment following positive results is more likely to occur when patients are admitted to hospital compared to community settings. Masking of clinicians, investigators and patients to the study intervention arm should reduce any ‘Hawthorne’ effect which could increase empirical TB treatment in the standard of care arm due to clinicians observing higher diagnostic yield in the intervention arm . The useThe STAMP trial sites have also been chosen to represent differing facilities, cadre of healthcare workers and resource utilisation in the region. Two studies to date, including one RCT, have demonstrated decreases in early mortality from expedited TB treatment in hospitalised HIV-positive patients, supporting the STAMP trial hypothesis that urine-based screening could reduce mortality , 31.The unique challenges of ‘testing a test’ have also been considered in the STAMP study design, in particular, regarding the ethics of conducting such a trial. If considering the diagnostic accuracy or yield of the STAMP study intervention compared to sputum screening or clinical diagnosis alone,  it couldFurthermore, the pragmatic nature of the STAMP trial, with clinical care including TB diagnostics outside the study intervention, TB treatment and ART under routine conditions for each study setting, make the findings more generalisable and applicable to scale up. The wide inclusion criteria and not restricting TB testing to patients with ‘presumptive’ TB (for which the definition often varies between settings) also makes the results more applicable. The recently published WHO guidance on the use of LAM lateral flow assays advises against its use for screening, based upon low quality evidence . The STAThe STAMP trial acknowledges the potential disadvantages of urine-based TB screening for this population, especially the cost implications. Although the intervention is relatively low-cost, health budgets in high TB and HIV settings are limited, and therefore widespread implementation of the STAMP study intervention may have substantial budgetary impact. The STAMP trial incorporates an economic analysis which will assess cost-effectiveness of the study intervention from a societal prospective and will include an analysis of budgetary impact of scale-up of this intervention. Should the intervention prove both effective and cost-effective, these analyses will assist in motivating the financial resources to promote its implementation.In summary, the STAMP trial is assessing a novel, urine-based screening strategy utilising the TB-LAM and Xpert assays in HIV-positive patients admitted to hospital in sub-Saharan Africa. We hypothesise that use of this screening algorithm will reduce all-cause mortality at 2 months compared to sputum and clinical diagnostics (using the Xpert assay) which is the standard of care as currently recommended by the WHO. The trial commenced recruitment of patients in October 2015, and is projected to complete recruitment by September 2017 and follow-up by November 2017.


Bacteroides fragilis (B. fragilis) and Escherichia coli (E. coli), secrete a remarkably complex array of pro-inflammatory neurotoxins which, when released from the confines of the healthy GI tract, are pathogenic and highly detrimental to the homeostatic function of neurons in the central nervous system (CNS). For the first time here we report the presence of bacterial lipopolysaccharide (LPS) in brain lysates from the hippocampus and superior temporal lobe neocortex of Alzheimer's disease (AD) brains. Mean LPS levels varied from two-fold increases in the neocortex to three-fold increases in the hippocampus, AD over age-matched controls, however some samples from advanced AD hippocampal cases exhibited up to a 26-fold increase in LPS over age-matched controls. This “Perspectives” paper will further highlight some very recent research on GI tract microbiome signaling to the human CNS, and will update current findings that implicate GI tract microbiome-derived LPS as an important internal contributor to inflammatory degeneration in the CNS.Although the potential contribution of the human gastrointestinal (GI) tract microbiome to human health, aging, and disease is becoming increasingly acknowledged, the molecular mechanics and signaling pathways of just how this is accomplished is not well-understood. Major bacterial species of the GI tract, such as the abundant Gram-negative bacilli  The human GI tract is fundamentally a highly vascularized and extensively innervated, columnar epithelial-cell lined tube about 9 m (30 feet) in length that consists of the stomach, small intestine  and large intestine  and Archaea (or “Archaeobacteria”) have been recently reclassified (as of 10/2016) into 35 phyla (http://www.bacterio.net/-classifphyla.html) or major bacterial divisions. Interestingly the GI tract microbiome of Homo sapiens has co-evolved with just two major phyla: Bacteriodetes, which make up ~20% of all GI tract bacteria, and Firmicutes, which make up ~80% of all GI tract bacteria; with Actinobacteria (~3%), Proteobacteria (~1%), and Verrumicrobia (~0.1%) making up significantly smaller fractions. These five bacterial groups appear to constitute the essential “core” of the human GI tract microbiome  and the facultative anaerobe Escherichia coli : (i) together constitute ~35–40 percent of all GI tract bacteria; (ii) are the most abundant Gram-negative bacilli of the middle and lower colon, respectively, of the human GI tract; and (iii) constitute about ~30–50 percent of the dry weight of fecal matter. B. fragilis or E. coli require about 20 min to divide under optimal conditions of commensal bacterial growth, and unless special biophysical processes of growth dynamics are in operation  have a life span of up to several hours , normally an abundant commensal microorganism of the middle GI tract, are known to be generally beneficial to human health through their ability to digest dietary fiber and related dietary fiber precursors containing substances such as cellulose, lignin, and pectin, which are normally resistant to the action of host digestive enzymes.Two large prokaryotic classes of Bacteria , they can induce substantial systemic inflammatory pathology with significant sickness, morbidity and mortality , volatile fatty acids and polysaccharides in part through the biosynthetic capability of this GI tract abundant bacillus  and their subsequent lysis indicate that lysed bacteria contents may be a relatively persistent source of exotoxins which may need to be either efficiently neutralized or eliminated by the GI tract. Interestingly, under some conditions in rodents certain endotoxins are so toxic that they may be lethal to the host before the innate immune system has a chance to mount immune defenses to promote their neutralization  and lipopolysaccharides (LPS) that are strongly immunogenic and highly pro-inflammatory toward human neurons  units in length. Other “lipid A” species show variability in the number, length, and composition of the attached fatty acids, as well as variability in the degree of phosphorylation and number and types of substituted phosphate ligands. For instance, BF-LPS lipid A is penta-acylated and mono-phosphorylated, and contains branched fatty acids 15–17 methyl(ene) units in length; deviations from the canonical lipid A structure are known to have a profound impact on innate-immune responses. Gram-negative bacterial exudates such as BF-LPSs are hypervariable in composition, and different Bacteroidetes species appear to generate unique temporal patterns of LPS production. These exhibit rapid and remarkably adaptive changes in LPS structure and alterations in damage- or pathogen-associated molecular patterns (DAMP/PAMP) as strategies for host immune evasion  from neural cells into the extracellular space is a commonly recognized phenomenon in neurobiology, the secretion of small non-coding RNA (sncRNA) from microbial cells into the GI tract has only been very recently characterized ; (ii) that bacterial LPS are readily detectable in the neocortex and hippocampus of the AD brain, and at significantly higher abundance in AD than controls, indicating that LPS may be able to transit physiological barriers to access CNS compartments  ts Figure ; (iv) ths Figure ; (vi) ths Figure ; and (vis Figure . While os Figure , here foYZ and VJ analyzed brains for LPS content; WL compiled and analyzed the data and wrote the paper.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


To enable the valid and reliable measurement of patient experiences we previously published a multicenter multi-center validation of the Quality of Trauma Care Patient-Reported Experience Measure (QTAC-PREM). The purpose of this study was to derive a simplified, short form version of the QTAC-PREM to further enhance the feasibility of measuring patient experiences in injury care. To identify candidate items for the short form we reviewed the results of the original multi-center long form validation cohort study, which included 400 injury care patients and their family members recruited from three trauma centers. We only included the best performing items on the revised short form. and one subscale on the post-acute measure (post-discharge information and communication). The measurement properties of the short form measure were similar to that of the validated long form. This short form assessment of patient injury care experiences offers a useful, practical, and easy tool for trauma centers to implement for service evaluation, quality improvement, and injury care research.The acute care component of the measure was shortened by 30% and the post-acute care component was shortened by 42%. We identified two subscales on the acute measure The online version of this article (10.1186/s13104-017-3031-9) contains supplementary material, which is available to authorized users. Governments, health care regulators, funders, and researchers have made clear that the processes and outcomes of care should align with patients’ needs, preferences, and values . TherefoThe value of measuring patient experiences has been demonstrated. For example, patient experiences have been used to identify gaps in care and guide quality improvement in primary care –4 and meTo enable the valid and reliable measurement of patient experiences we previously developed  and valiThe purpose of this analysis was therefore to derive a simplified, short form version of the QTAC-PREM to further enhance the feasibility of measuring patient experiences in injury care. In this article we report the derivation and key measurement properties of the new SF QTAC-PREM.The long form QTAC-PREM is a patient experience measure consisting of two parts administered separately: a 35-item acute care component to be self-completed in-hospital by patients (or patient proxy) and a 28-item post-acute care component administered via telephone interview 2–3 months after hospital discharge. The measure includes both close-ended and open-ended items. The multi-step development of the original scale included a literature review, focus groups with patients and providers, prospective single-center pilot-testing with 134 participants , and a pWe used the quantitative and qualitative data from our multi-center validation study to inform our selection of items for the short form .We flagged for deletion items: (1) that did not form part of existing subscales (2) to which 20% or more of patients selected “not-applicable” or “not able to answer” response options, (3) that did not correlate highly with the overall rating of the quality of care, (4) were shown to be redundant by measures of collinearity, (5) that were conceptually redundant, (6) with the lowest test–retest reliability coefficients, and (7) with limited response variation.We also used the qualitative responses that participants provided to open-ended questions and documented participants’ comments obtained during administration of the post-acute measure via telephone interview.To assess the operating characteristics of the new combination of items appearing on the short form we repeated the analyses using data from the original multi-center prospective cohort study . The datWe conducted factor analysis to identify subscales; assessed the internal consistency of the subscales using Cronbach’s alphas; and assessed construct validity by calculating univariate (Spearman correlations) and multivariate  associations between the subscales and global rating item to determine if the subscales were predictors of overall ratings of the quality of care.We used only complete cases for all analyses (i.e. cases with missing data or ‘not applicable’ or ‘not able to answer’ response selections were excluded).We have re-reported the test–retest reliability coefficients for the retained items and spearman correlations between individual items and the global rating item obtained during the long form validation. These properties are expected to remain stable between the long form and short form versions of the measure.The acute care measure was shortened to 24 items and the post-acute measure was shortened to 16 items. The final short form versions of the measure are available in the Additional files To derive the short form the following changes were made: 19 items were eliminated; 33 items were retained with no revision or minor revision to wording or response options; 2 items assessing general health status were replaced by 4 validated items assessing physical and mental health status separately; and 2 items assessing the provision and adequacy of discharge information were merged to create a single item. Detailed explanations of the item selections and revisions for both short form components can be found in Additional files information and communication, included items on the scope, clarity, consistency, and availability of acute care information and communication. Factor 2, clinical and ancillary care, included items assessing the clinical processes of care  and ancillary components including being treated unfairly. Spearman’s correlations between the subscales were moderate (0.48) suggesting that the subscale scores should not be combined to form an overall acute care score.The acute care factor analysis included 154 complete cases  and clinical and ancillary care (p < 0.001) were independently associated with the global rating item  with the global rating item  were independently associated with the global rating item, while the item on pain management  and perceived safety of care  were not . We shortened the measure by 23 items. The operating characteristics of the short form QTAC-PREM identified in this study are comparable with other validated and widely used measures of patient and family experiences of care –16.clinical and ancillary care, information and communication), while the post-acute care measure consists of one (post-discharge information and communication).We were able to identify subscales on the short form that will allow for simplified reporting and interpretation. The acute care short form consists of two subscales . This may be the result of merging items from two scales on the long form that assessed narrower constructs to form a single scale addressing a more generic construct; internal consistency is lower when the construct measured is more generic [The measurement properties of the short form measure are similar to those of the validated long form. The only notable differences include slightly lower internal consistency of the short form acute care subscale  generic . The scaThere are three benefits of using the short form QTAC-PREM as opposed to the long form. First, response burden will be reduced. Second, the short form may be a more efficient way to obtain informative and comparative data on quality of care. We slightly revised item wording and response options such that the content of the short form should be applicable to all injury patients that are hospitalized and discharged alive. As a result, this should increase the amount of useable and comparable data from each administered measure. Third, the results can be summarized and reported more efficiently. A greater proportion of items fit within subscales compared to the long form and therefore, the results can be summarized with fewer metrics.The QTAC-PREM and SF QTAC-PREM provide two complementary instruments for assessing patient experiences. The QTAC-PREM may be more relevant for research or detailed audits given its larger number of items, while the short-form may be suited for more frequent applications, such as routine audits. We believe both instruments are potentially important tools for measuring care and guiding quality improvement initiatives.Assessing patient experience is vital for designing and delivering high-quality injury care. To increase the feasibility of measuring patient experiences we derived a short form version of the Quality of Trauma Care Patient-Reported Experience Measure (SF QTAC-PREM). The short form tool has evidence of validity and reliability. The SF QTAC-PREM offers a useful, practical, and easy tool for trauma centers to implement for service evaluation, quality improvement, and injury care research.This study has some limitations. First, the data used in this study were obtained using the long form measure and, therefore, the characteristics of the items may vary slightly when implemented as a short form. Although this method has been utilized to derive and validate widely-used and highly cited scales, such as the short form oral health impact profile  and the Additional file 1. Quality of Trauma Care Patient-Reported Experience Measure (QTAC-PREM)—Short Form. Part 1: Acute Care, Patient Survey.Additional file 2. Quality of Trauma Care Patient-Reported Experience Measure (QTAC-PREM)—Short Form. Part 1: Acute Care, Family Member/Proxy Survey.Additional file 3. Quality of Trauma Care Patient-Reported Experience Measure (QTAC-PREM)—Short Form. Part 2: Post-Acute Care, Patient Survey.Additional file 4. Quality of Trauma Care Patient-Reported Experience Measure (QTAC-PREM)—Short Form. Part 2: Post-Acute Care, Family Member/Proxy Survey.Additional file 5. Mapping the derivation of the short form acute care QTAC-PREM from the original long form items.Additional file 6. Mapping the derivation of the short form post-acute care QTAC-PREM from the original long form items.Additional file 7. Short form acute care QTAC-PREM ordinal logistic regression results, Short form post-acute care QTAC-PREM ordinal logistic regression results.


An increasing number of precision oncology programmes are being launched world-wide. To support this development, we present the Cancer Variant Explorer (CVE), an R package with an interactive Shiny web browser interface.Leveraging Oncotator and the Drug Gene Interaction Database, CVE offers exploration of variants within single or multiple tumour exomes to identify drivers, resistance mechanisms and to assess druggability. We present example applications including the analysis of an individual patient and a cohort-wide study, and provide a first extension of CVE by adding a tumour-specific co-expression network.http://bioconductor.org/packages/CVE/).The CVE package allows interactive variant prioritisation to expedite the analysis of cancer sequencing studies. Our framework also includes the prioritisation of druggable targets, allows exploratory analysis of tissue specific networks and is extendable for specific applications by virtue of its modular design. We encourage the use of CVE within translational research studies and molecular tumour boards. The CVE package is available via Bioconductor (The online version of this article (doi:10.1186/s12920-017-0261-6) contains supplementary material, which is available to authorized users. The Cancer Genome Atlas  and them . For evm ..The CancIDH1 mutations) suggests that many drivers may yet remain undiscovered due to limited cohort sizes [Owing to the decreasing costs of sequencing for routine diagnostics in clinical oncology , an incrrt sizes . For varrt sizes ).Precision oncology seeks to leverage this molecular information to improve patient treatment. This is a highly collaborative effort and omics-driven therapeutic decisions are being made in molecular tumour boards consisting of physicians, bioinformaticians and biologists. A number of web applications have been developed to facilitate interactive prioritisation of variants –20 , as well as in a cohort study of 93 Shiny web application framework for the R programming language (shiny.rstudio.com), combining the high functionality of R with a concise visualisation of the variant prioritisation process  variant annotation using Oncotator; (ii) exploration of variant annotations; and (iii) assessment of druggability using the Drug Gene Interaction database (DGiDb). A graphical abstract of the CVE workflow is depicted in Fig. Cancer Variant Explorer (CVE) was created using the The input file for CVE is a comma-separated (csv) file of the format displayed in Additional file After launching the interactive CVE application , the interactive prioritisation begins with the exploration of the Oncotator annotation. The ’functional consequence’ annotation from GENCODE and UniProt classifies the variant into protein changing and non-protein changing as well as into single nucleotide (SNP), double nucleotide polymorphism (DNP) and deletion (DEL). The COSMIC database annotation denotes whether a variant has been found previously in human cancers, and the 1000 Genomes project data denotes whether a variant has been found in germline samples. The workflow aims to identify somatic driver variants, therefore we would have more confidence in protein changing variants that are recurrently mutated in cancer and that are unlikely to be germline variants. In addition information is provided as to whether a variant is in a known DNA repair gene. Variants affecting DNA repair genes are of particular therapeutic importance in cancer (and may predict sensitivity or resistance to a given treatment).Additional information on the predicted functional impact of each variant is also included, providing lower priority evidence to predict ’possible driver mutations’ in lower frequency variants. This additional information is collated from an increasing list of variant effect prediction algorithms. New algorithms are continuously added to the dbNSFP database, these are also included and updated in the Oncotator annotation.http://portals.broadinstitute.org/oncotator/help/.The prediction algorithms primarily exploit the reasoning that more deleterious gene regions have fewer observed substitutions across species due to tighter evolutionary constrains  or the different physico-chemical properties of amino acids and the corresponding three-dimensional protein structure . In addition, ensembl scores combining different approaches have been developed (e.g. CADD ). For moOf note, CVE does neither benchmark the scores of the functional prediction algorithms, nor tries to derive the best score. Instead, it displays the heterogeneity of predication based on the rankscores of the 18 algorithms in the current build of the dbNSFP database Table . Rankscoc for the rankscore of algorithm i in cluster j determined by consensus clustering We propose that the maximum useful information can be derived from the dbNSFP combination score xij is the rankscore of algorithm i in cluster j and j. c if there is significant evidence for the variant in algorithm cluster j, defined by a mean rankscore belonging to the upper quartile of rankscores.where The final step required to guide precision cancer medicine is the assessment of the druggability of candidate variants. The Drug-Gene Interaction database  offers BRAF and RAS hotspot mutations occur frequently in cutaneous melanomas and can be targeted with BRAF and MEK inhibitors, respectively. However, ≈ 27% of tumours do not harbour BRAF or RAS hotspot mutations and are lacking suitable targeted treatment options. To this end, we gathered a case study from TCGA data with the aim to identify drivers and putatively druggable variants in BRAF-wt/RAS-wt melanomas. 93 of the 345 patients could be classified as BRAF-wt/RAS-wt according to the TCGA definition [BRAF/RAS classification are appended in the Additional file finition . A ’maf’The Cancer Genome Atlas (TCGA) RNA-seq data using the WGCNA R package developed by Langfelder and Horvarth [A tutorial describing the generation of a weighted gene co-expression network analysis (WGCNA) from Horvarth  is incluHorvarth . The stueigengenes  measures can be defined as the statistical significance  between the i-th node profile (gene) xi and the sample trait T: GSi=−logpi.To identify co-expression modules in the 472 melanoma patients, genes were next clustered based on the dissimilarity measure, where branches of the dendrogram correspond to modules. The gene dendrogram obtained by average linkage hierarchical clustering is depicted in Fig. nes Fig. b. The mectivity . An advaModule significance in turn can be determined as the average absolute gene significance measure. This conceptual framework can be adapted to any research question. For the exploration of variants in a melanoma-specific pathway context, five GS measures were used: (i) lymphocyte score; (ii) survival association; (iii) UV signature; (iv) comparative analysis of primary and metastatic tumours; and (v) vemurafenib resistance. The first 4 GS measures were derived from clinical metadata of the TCGA samples. The samples were dichotomized according to lymphocyte score , the presence of a UV signature as defined by Brash and coworkers [oworkers , or primoworkers .R package [module membership is defined as Kq=|cor| where xi is the profile of gene i and Eq is the eigengene of module q. Based on this definition, K describes how closely related gene i is to module q. Figure To enable a high-level interpretation of the dendrogram of module eigengenes, gene ontology (GO) enrichment analysis was performed for the module genes using the GOstats package . ModulesTogether these data provide a framework for the tumour-specific annotation of novel ’putative events’ in melanoma.The core implementation of the CVE Shiny app comprises four interactive tabs (i) Annotation, (ii) Prioritisation, (iii) Top table and (iv) Druggability. In the following sections we describe the settings and results for a cohort case study in 93 BRAF-wt/RAS-wt melanomas, as an example implementation for variant exploration using CVE. In addition, we present a first extension of CVE functionality for the exploration of variants in melanoma using a tumour-type specific co-expression network  from the 93-patient melanoma cohort. The Annotation tab also displays the variant classification  as well as a heatmap of the clusters of prediction algorithms for the dataset. As shown in Additional file The proritisation tab is central to the interactive process of identifying variants of interest. Firstly, common germline variants identified by the 1000 Genomes project can be filtered from further analysis. In the melanoma case study, 67 of the 1084 protein changing SNVs were possible germline variants . To exclude all possible germline variants a filter ’check-box’ located on the left side panel can be applied, alternatively a threshold can be set to include variants present at low frequencies in germline data sets (e.g. DNMT3A R882 ), dependgene: gene symbolprotein change: location of amino acid change in proteintype: SNV, dinucleotide substitution (DNP), deletion (DEL) or insertion (INS)classification: functional consequence annotation from GENCODEscore: (rank)score of the mutational effect prediction algorithm selectedCOSMIC entity: number of mutations identified per tumour entity in the COSMIC databaseA table of the prioritised variants shortlisted up to this point can be accessed in the next tab of the CVE application. For streamlined data handling, this top table can also be downloaded as a tab-separated file using the download button in the sidebar . The columns of the top table summarize: BRAF-wt/RAS-wt melanoma patients, with 6 patients having two possible drug-gene combinations. The largest drug class identified for this cohort are tyrosine kinase inhibitors that could be potentially used in ≈ 15% of cases (14 of 93).Using annotations from the Drug-Gene Interaction database (DGIdb) CVE also allows exploration of potentially druggable targets within a given dataset. To show the full spectrum of evidence for or against a druggable variant in the melanoma case study, no dbNSFP combination score cutoff was initially set. Table R package, we developed a first extension to explore the variant genes in a melanoma-specific co-expression network. A vignette describing the generation of the co-expression network using the WGCNA R package [The four tabs in the core implementation of CVE can be applied to all tumor entities. To illustrate the functionality and flexibility of an open-source  package  can be fp-value of the respective gene significance measure  help to unveil this increasing list, mainly through retrospective comparisons. As more and more data are generated, clinical utility increases, but so does the complexity in data analysis.In recent years, R will be needed to effectively translate new information for specific diagnostic or research questions.A number of web applications have been developed to facilitate interactive prioritisation of variants . We developed a Shiny web application based on the R statistical environment enabling end users (such as biologists and physicians) to interactively apply different cutoffs and filters.Arguably the most challenging part of any tool for The data sources implemented in this version of CVE include the comprehensive cancer variant annotation tool Oncotator, germline annotations from the 1000 Genomes Project, known cancer-associated variants (COSMIC database), known DNA repair genes and known cancer driver genes. Ultimately, genomics-driven oncology aims at identifying druggable variants, therefore we also include functionality to explore expert-curated sources of drug-gene interactions . Due to the simple programming framework of the application, additional filters and datasets can be implemented in a very short time. This flexibility in adding parameters or data sources to the prioritisation workflow is very valuable and not offered by commercial tools for variant prioritisation . To ensure reproducibility, a spread-sheet with the prioritised variants can be downloaded from the side panel of CVE (including a list of the filters and thresholds applied).BRAF V600 mutant colorectal cancers [The aforementioned framework for variant prioritisation has the advantage to work independently of the tumour entity. However, this variant-centric annotation focuses on already known cancer drivers and variants, limiting the potential to identify less well characterised variants. A variant prioritisation workflow in the context of clinical trials or translational research should also highlight potentially functional variants that have not been extensively characterized before. In addition, some mutated genes are druggable targets in one tumour entity but not in other tumour types (e.g. vemurafenib is ineffective in  cancers ). Theref cancers , in whicCancer Variant Explorer, is an interactive, iterative and flexible application based on the R programming environment. Using the comprehensive data from the Oncotator Cancer Variant Annotation tool, CVE enables project-tailored variant prioritisation using cancer-relevant databases. Extending current workflows by adding another level of biology it offers the exploration of variant genes in tumour-specific co-expression modules. CVE was applied in a case study of melanoma patients, revealing potentially druggable targets and highlighting genes that have not previously been linked to melanoma and were associated with clinically relevant melanoma gene expression networks.The Precision Cancer Medicine has great promise to improve the treatment of cancer patients, but several obstacles have to be overcome to increase the success rates of personalised treatments. It will be crucial to more comprehensively identify mechanisms of treatment resistance, especially within the context of the clonal make-up of a tumour. Likewise, robust pharmacogenomic analysis are needed to validate the druggability of candidate variants. In addition, while targeting specific SNVs has been proven successful in some cancers, pan-cancer analysis revealed that not all tumour entities are primarily driven by point mutations, with copy number changes dominating in many cancer types . Hence,Project name: Cancer Variant Explorer (CVE)Project home page:http://bioconductor.org/packages/CVE. CVE will be continuously updated. To work with the latest version, please refer to the development branch in Bioconductor.Operating system(s): Platform independentProgramming language: ROther requirements: R 3.3 or higher, R packages: shiny, ConsensusClusterPlus, RColorBrewer, gplots, plyr, ggplot2, jsonlite, ape, WGCNA, RTCGAToolboxLicense: GNU GPL-3Additional file 1Table S1. Comparison of tools for interactive variant prioritisation applicable to cancer exomes. (PDF 72 kb)Additional file 2Table S2. Showing the input variant format of CVE. (PDF 69 kb)Additional file 3Figure S1. Consensus clustering of dbNSFP rankscores for 1084 protein-changing variants revealed in the case study. Consensus clustering of dbNSFP rankscores for 1084 protein-changing variants identified in the case study. To determine the most meaningful number of clusters of prediction scores, we first assess the consensus CDFs  and the relative change in the area under the CDF curve (Δ(k), Fig. S1B). Here, Δ(k) did not increase markedly at more than 5 clusters. Next, using the heatmap of the hierarchical clustering of consensus indexes for the different cluster numbers , we can question the plausibility of clusters in light of the different prediction score categories. This approach revealed that a fifth cluster created another subcluster in the conservation scores only, indicating that 4 clusters could be a more systematic choice. (A) Plot of cumulative distribution functions (CDFs) corresponding to the consensus matrices in the range between 2 and 6 clusters. (B) Relative change in the area under the CDF curve (Δk). (C) Heatmap illustrating the hierarchical clustering of consensus index for 4 clusters of prediction algorithms based on 100 permutations and resampling of 80% of the algorithms and 80% of the variants. Functions provided by the ConsensusClusterPlus R package were used to perform the analysis [analysis . Additional file 5Table S4. Csv table listing the 472 TCGA barcodes of melanoma RNA-seq cohort used for co-expression network analysis. (CSV 50 kb)Additional file 6Figure S2. Exploration of prioritised variant genes within co-expression modules from the case study. Exploration of prioritised variant genes within co-expression module 3 (leukocyte activation involved in immune response) for the 5 Gene Significance measures. Module membership is defined as the correlation between the gene profile and the eigengene of module 3. Dots are weighted according to effect size. A p-value cutoff of <0.05 is indicated by the vertical dashed line. A short description of the gene function is given. (PDF 20 kb)